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Sample records for phosphatidylcholine molecular species

  1. Influence of different molecular species of phosphatidylcholine on cholesterol transport from lipoprotein recombinants in the rat

    SciTech Connect

    Leduc, R.; Patton, G.M.; Atkinson, D.; Robins, S.J.

    1987-06-05

    Studies were performed to determine to what extent phosphatidylcholines (PCs) of different composition influence the turnover of lipoprotein cholesterol. Lipoprotein recombinants with the composition and structure of spherical high density lipoproteins (HDL-R) were prepared with apoproteins, /sup 14/C-labeled unesterified cholesterol (UC), a (3H)cholesteryl ester (CE), and one of four single molecular species of PC. PCs were selected to include relatively hydrophilic species (16:1-16:1 and 16:0-18:2 PCs) and relatively hydrophobic species (18:0-18:2 and 20:1-20:1 PCs). PCs were also selected to include molecules with novel acyl group pairs (16:1-16:1 and 20:1-20:1 PCs) that would permit the whole molecule to be traced during its clearance from the serum. Rats were injected with HDL-R as an intravenous bolus, and serum, liver, and bile samples were obtained for up to 2 h. The clearance from the serum of each PC was monoexponential with the two most hydrophilic species much more rapidly cleared than either of the two less hydrophilic species. Clearance of specific PCs was not accompanied by PC remodeling (i.e. transacylations), and in the main could not be attributed to the action of lecithin-cholesterol acyltransferase (LCAT). In incubations designed to simulate in vivo conditions, no more than 15% of the disappearance of 16:1-16:1 PC, one of the most rapidly cleared PCs, was due to the action of LCAT. With 20:1-20:1 PC, one of the least rapidly cleared PCs, no LCAT activity could be detected. The clearance of radiolabeled UC was multiexponential and closely corresponded to the rate of disappearance of each PC. The clearance of radiolabeled CE was linear and, in contrast to UC, was the same with the administration of different PCs. Uptake of radiolabeled UC by the liver and excretion of radiolabeled UC into bile took place in parallel and corresponded to the rapidity of turnover of UC (and PCs) in the serum.

  2. Investigation of natural phosphatidylcholine sources: separation and identification by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS2) of molecular species.

    PubMed

    Le Grandois, Julie; Marchioni, Eric; Zhao, Minjie; Giuffrida, Francesca; Ennahar, Saïd; Bindler, Françoise

    2009-07-22

    This study is a contribution to the exploration of natural phospholipid (PL) sources rich in long-chain polyunsaturated fatty acids (LC-PUFAs) with nutritional interest. Phosphatidylcholines (PCs) were purified from total lipid extracts of different food matrices, and their molecular species were separated and identified by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS(2)). Fragmentation of lithiated adducts allowed for the identification of fatty acids linked to the glycerol backbone. Soy PC was particularly rich in species containing essential fatty acids, such as (18:2-18:2)PC (34.0%), (16:0-18:2)PC (20.8%), and (18:1-18:2)PC (16.3%). PC from animal sources (ox liver and egg yolk) contained major molecular species, such as (16:0-18:2)PC, (16:0-18:1)PC, (18:0-18:2)PC, or (18:0-18:1)PC. Finally, marine source (krill oil), which was particularly rich in (16:0-20:5)PC and (16:0-22:6)PC, appeared to be an interesting potential source for food supplementation with LC-PUFA-PLs, particularly eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). PMID:19545117

  3. Molecular species of phosphatidylcholine and phosphatidylglycerol in rat lung surfactant and different pools of pneumocytes type II.

    PubMed Central

    Schlame, M; Casals, C; Rüstow, B; Rabe, H; Kunze, D

    1988-01-01

    It is not yet completely understood how a cell is able to export specific phospholipids, like dipalmitoylphosphatidylcholine (dipalmitoyl-PC), which is secreted by pneumocytes type II, into pulmonary surfactant. The acyl species composition of [3H]PC which was synthesized in type II cells in the presence of [2-3H]glycerol resembled the species composition of PC localized in intracellular pneumocyte membranes. This species pattern was different from the pattern of PC of lamellar bodies, i.e., intracellularly stored surfactant, by a higher proportion of dipalmitoyl-PC mainly at expense of 1-palmitoyl-2-oleoyl-PC. Lamellar body PC in turn showed the same species distribution as surfactant PC. The data suggest that subcellular compartmentation and/or intracellular transfer of PC destined to storage in lamellar bodies, but not secretion of lamellar bodies, involves an enrichment of dipalmitoyl-PC and a depletion of 1-palmitoyl-2-oleoyl-PC. In contrast, the acyl species pattern of phosphatidylglycerol does not seem to undergo gross changes on the path from synthesis to secretion. PMID:3421943

  4. Increased levels of a particular phosphatidylcholine species in senescent human dermal fibroblasts in vitro.

    PubMed

    Naru, Eiji; Takanezawa, Yasukazu; Kobayashi, Misako; Misaki, Yuko; Kaji, Kazuhiko; Arakane, Kumi

    2008-08-01

    Plasma membranes are essential components of living cells, and phospholipids are major components of cellular membranes. Here, we used liquid chromatography/mass spectrometry to investigate changes in the membrane phospholipid content that occur in association with aging. Our results indicate that the levels of a particular species of phosphatidylcholine comprised of stearic acid and arachidonic acid increased with age. To determine the reason for the increased levels of this particular phosphatidylcholine, we examined the effect of highly unsaturated fatty acids, such as arachidonic acid and eicosapentaenoic acid, on cellular aging. Applied arachidonic acid was incorporated into phosphatidylcholine molecules, but neither arachidonic acid nor other related unsaturated fatty acids had any effect. We conclude that increased levels of this distinctive phosphatidylcholine are a result of in vitro senescence. PMID:18667023

  5. Diacylglycerol kinase δ phosphorylates phosphatidylcholine-specific phospholipase C-dependent, palmitic acid-containing diacylglycerol species in response to high glucose levels.

    PubMed

    Sakai, Hiromichi; Kado, Sayaka; Taketomi, Akinobu; Sakane, Fumio

    2014-09-19

    Decreased expression of diacylglycerol (DG) kinase (DGK) δ in skeletal muscles is closely related to the pathogenesis of type 2 diabetes. To identify DG species that are phosphorylated by DGKδ in response to high glucose stimulation, we investigated high glucose-dependent changes in phosphatidic acid (PA) molecular species in mouse C2C12 myoblasts using a newly established liquid chromatography/MS method. We found that the suppression of DGKδ2 expression by DGKδ-specific siRNAs significantly inhibited glucose-dependent increases in 30:0-, 32:0-, and 34:0-PA and moderately attenuated 30:1-, 32:1-, and 34:1-PA. Moreover, overexpression of DGKδ2 also enhanced the production of these PA species. MS/MS analysis revealed that these PA species commonly contain palmitic acid (16:0). D609, an inhibitor of phosphatidylcholine-specific phospholipase C (PC-PLC), significantly inhibited the glucose-stimulated production of the palmitic acid-containing PA species. Moreover, PC-PLC was co-immunoprecipitated with DGKδ2. These results strongly suggest that DGKδ preferably metabolizes palmitic acid-containing DG species supplied from the PC-PLC pathway, but not arachidonic acid (20:4)-containing DG species derived from the phosphatidylinositol turnover, in response to high glucose levels. PMID:25112873

  6. Phosphatidylcholine Synthesis

    PubMed Central

    Datko, Anne H.; Mudd, S. Harvey

    1988-01-01

    The methylation steps in the biosynthesis of phosphatidylcholine by tissue culture preparations of carrot (Daucus carota L.) and soybean (Glycine max), and by soybean leaf discs, have been studied. Preparations were incubated with tracer concentrations of l-[3H3C]methionine and the kinetics of appearance of radioactivity in phosphomethylethanolamine, phosphodimethylethanolamine, phosphocholine, phosphatidylmethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, methylethanolamine, dimethylethanolamine, and choline followed at short incubation times. With soybean (tissue culture or leaves), an initial methylation utilizes phosphoethanolamine as substrate, forming phosphomethylethanolamine. The latter is converted to phosphatidylmethylethanolamine, which is successively methylated to phosphatidyldimethyethanolamine and to phosphatidylcholine. With carrot, again, an initial methylation is of phosphoethanolamine. Subsequent methylations occur at both the phospho-base and phosphatidyl-base levels. Both of these patterns differ qualitatively from that previously demonstrated in Lemna (SH Mudd, AH Datko 1986 Plant Physiol 82: 126-135) in which all three methylations occur at the phospho-base level. For soybean and carrot, some added contribution from initial methylation of phosphatidylethanolamine has not been excluded. These results, together with those from similar experiments carried out with water-stressed barley leaves (WD Hitz, D Rhodes, AD Hanson 1981 Plant Physiol 68: 814-822) and salinized sugarbeet leaves (AD Hanson, D Rhodes 1983 Plant Physiol 71: 692-700) suggest that in higher plants some, perhaps all, phosphatidylcholine synthesis occurs via a common committing step (conversion of phosphoethanolamine to phosphomethylethanolamine) followed by a methylation pattern which differs from plant to plant. PMID:16666397

  7. Oxidized phosphatidylcholines in membrane-level cellular signaling: from biophysics to physiology and molecular pathology.

    PubMed

    Volinsky, Roman; Kinnunen, Paavo K J

    2013-06-01

    The oxidation of lipids has been shown to impact virtually all cellular processes. The paradigm has been that this involvement is due to interference with the functions of membrane-associated proteins. It is only recently that methodological advances in molecular-level detection and identification have begun to provide insights into oxidative lipid modification and its involvement in cell signaling as well as in major diseases and inflammation. Extensive evidence suggests a correlation between lipid peroxidation and degenerative neurological diseases such as Parkinson's and Alzheimer's, as well as type 2 diabetes and cancer. Despite the obvious relevance of understanding the molecular basis of the above ailments, the exact modes of action of oxidized lipids have remained elusive. In this minireview, we summarize recent findings on the biophysical characteristics of biomembranes following oxidative derivatization of their lipids, and how these altered properties are involved in both physiological processes and major pathological conditions. Lipid-bearing, oxidatively truncated and functionalized acyl chains are known to modify membrane bulk physical properties, such as thermal phase behavior, bilayer thickness, hydration and polarity profiles, as manifest in the altered structural dynamics of lipid bilayers, leading to augmented membrane permeability, fast lipid transbilayer diffusion (flip-flop), loss of lipid asymmetry (scrambling) and phase segregation (the formation of 'rafts'). These changes, together with the generated reactive lipid derivatives, can be further expected to interfere with lipid-protein interactions, influencing metabolic pathways, causing inflammation, the execution phase in apoptosis and initiating pathological processes. PMID:23506295

  8. Cis and trans unsaturated phosphatidylcholine bilayers: A molecular dynamics simulation study.

    PubMed

    Kulig, Waldemar; Pasenkiewicz-Gierula, Marta; Róg, T

    2016-02-01

    Trans unsaturated lipids are uncommon in nature. In the human diet, they occur as natural products of ruminal bacteria or from industrial food processing like hydrogenation of vegetable oils. Consumption of trans unsaturated lipids has been shown to have a negative influence on human health; in particular, the risk of cardiovascular disease is higher when the amount of trans unsaturated lipids in the diet is elevated. In this study, we first performed quantum mechanical calculations to specifically and accurately parameterize cis and trans mono-unsaturated lipids and subsequently validated the newly derived parameter set. Then, we carried out molecular dynamics (MD) simulations of lipid bilayers composed of cis or trans unsaturated lipids with and without cholesterol. Our results show that trans mono-unsaturated chains are more flexible than cis mono-unsaturated chains due to lower barriers for rotation around the single bonds next to the trans double bond than those next to the cis double bond. In effect, interactions between cholesterol and trans unsaturated chains are stronger than cis unsaturated chains, which results in a higher ordering effect of cholesterol in trans unsaturated bilayers. PMID:26187855

  9. Molecular organization in striated domains induced by transmembrane alpha-helical peptides in dipalmitoyl phosphatidylcholine bilayers.

    PubMed

    Sparr, Emma; Ganchev, Dragomir N; Snel, Margot M E; Ridder, Anja N J A; Kroon-Batenburg, Loes M J; Chupin, Vladimir; Rijkers, Dirk T S; Killian, J Antoinette; de Kruijff, Ben

    2005-01-11

    Transmembrane (TM) alpha-helical peptides with neutral flanking residues such as tryptophan form highly ordered striated domains when incorporated in gel-state 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayers and inspected by atomic force microscopy (AFM) (1). In this study, we analyze the molecular organization of these striated domains using AFM, photo-cross-linking, fluorescence spectroscopy, nuclear magnetic resonance (NMR), and X-ray diffraction techniques on different functionalized TM peptides. The results demonstrate that the striated domains consist of linear arrays of single TM peptides with a dominantly antiparallel organization in which the peptides interact with each other and with lipids. The peptide arrays are regularly spaced by +/-8.5 nm and are separated by somewhat perturbed gel-state lipids with hexagonally organized acyl chains, which have lost their tilt. This system provides an example of how domains of peptides and lipids can be formed in membranes as a result of a combination of specific peptide-peptide and peptide-lipid interactions. PMID:15628840

  10. Determination of Oxidized Phosphatidylcholines by Hydrophilic Interaction Liquid Chromatography Coupled to Fourier Transform Mass Spectrometry

    PubMed Central

    Sala, Pia; Pötz, Sandra; Brunner, Martina; Trötzmüller, Martin; Fauland, Alexander; Triebl, Alexander; Hartler, Jürgen; Lankmayr, Ernst; Köfeler, Harald C.

    2015-01-01

    A novel liquid chromatography-mass spectrometry (LC-MS) approach for analysis of oxidized phosphatidylcholines by an Orbitrap Fourier Transform mass spectrometer in positive electrospray ionization (ESI) coupled to hydrophilic interaction liquid chromatography (HILIC) was developed. This method depends on three selectivity criteria for separation and identification: retention time, exact mass at a resolution of 100,000 and collision induced dissociation (CID) fragment spectra in a linear ion trap. The process of chromatography development showed the best separation properties with a silica-based Kinetex column. This type of chromatography was able to separate all major lipid classes expected in mammalian samples, yielding increased sensitivity of oxidized phosphatidylcholines over reversed phase chromatography. Identification of molecular species was achieved by exact mass on intact molecular ions and CID tandem mass spectra containing characteristic fragments. Due to a lack of commercially available standards, method development was performed with copper induced oxidation products of palmitoyl-arachidonoyl-phosphatidylcholine, which resulted in a plethora of lipid species oxidized at the arachidonoyl moiety. Validation of the method was done with copper oxidized human low-density lipoprotein (LDL) prepared by ultracentrifugation. In these LDL samples we could identify 46 oxidized molecular phosphatidylcholine species out of 99 possible candidates. PMID:25874761

  11. Docosahexaenoic acid-containing phospholipid molecular species in brains of vertebrates

    PubMed Central

    Farkas, Tibor; Kitajka, Klara; Fodor, Elfrieda; Csengeri, István; Lahdes, Eila; Yeo, Young K.; Krasznai, Zoltán; Halver, John E.

    2000-01-01

    The fatty acid composition of phospholipids and the contents of docosahexaenoic acid (DHA)-containing diacyl phosphatidylcholine and diacyl phosphatidylethanolamine molecular species were determined from brains of five fresh-water fish species from a boreal region adapted to 5°C, five fresh-water fish species from a temperate region acclimated to 5°C, five fresh-water fish species from a temperate region acclimated to 20°C, and three fresh water fish species from a subtropic region adapted to 25–26°C, as well as six mammalian species and seven bird species. There was little difference in DHA levels of fish brains from the different thermal environments; mammalian and bird brain phospholipids contained a few percentage points less DHA than those of the fish investigated. Molecular species of 22:6/22:6, 22:6/20:5, 22:6/20:4, 16:0/22:6, 18:0/22:6, and 18:1/22:6 were identified from all brain probes, and 16:0/22:6, 18:0/22:6, and 18:1/22:6 were the dominating species. Cold-water fish brains were rich in 18:1/22:6 diacyl phosphatidylethanolamine (and, to a lesser degree, in diacyl phosphatidylcholine), and its level decreased with increasing environmental/body temperature. The ratio of 18:0/22:6 to 16:0/22:6 phosphatidylcholine and phosphatidylethanolamine was inversely related to body temperature. Phospholipid vesicles from brains of cold-acclimated fish were more fluid, as assessed by using a 1,6-diphenyl-1,3,5-hexatriene fluorescent probe, than those from bird brains, but the fluidities were almost equal at the respective body temperatures. It is concluded that the relative amounts of these molecular species and their ratios to each other are the major factors contributing to the maintenance of proper fluidity relationships throughout the evolutionary chain as well as helping to maintain important brain functions such as signal transduction and membrane permeability. PMID:10823917

  12. Biosynthesis of glycerolipid molecular species in photoreceptor membranes of frog retina

    SciTech Connect

    Wiegand, R.D.; Louie, K.; Anderson, R.E. )

    1987-05-01

    Phospholipid (PL) molecular species of vertebrate retinal photoreceptor cells are unique in that they contain two polyunsaturated fatty acids per molecule. Docosahexaenoic acid (22:6 {omega}3) is the major component of these dipolyunsaturate species (DPS), which also contain 20:4{omega}6, 22:4{omega}6, 22:5{omega}6, and 22:5{omega}3. We have studied the de novo synthesis and metabolism of the (DPS) and other PL molecular species in frog rod outer segments (ROS) following intravitreal injection of 2-({sup 3}H)-glycerol. At 1, 2, 4, and 8 days after injection, ROS were prepared, PL extracted, and phosphatidylcholine (PC), phosphatidylethanolamine (PE), and phosphatidylserine (PS) isolated. PC, PE, and PS were converted to diglycerides (DG's) with phospholipase C. DG's were derivatized, fractionated into molecular species by HPLC, quantitated, and counted for radioactivity. The following were observed: (1) Specific activities (SA) of the PC DPS were 3-5 times higher than the same species in either PE or PS. (2) SA of the PC monopolyunsaturate species (MPS) (species which contain 22:6{omega}3 and/or 16:0 or 18:0) were 3-5 times lower than the SA of the PC DPS. In contrast, SA of PE MPS were 2-5 times higher than the SA of the PE DPS. (3) The major PS MPS synthesized contained 18:0 and 22:6{omega}3. SA of that species were similar to SA of the PS DPS. The data support the suggestion that PC DPS are synthesized and/or incorporated in ROS at a greater rate than the same species in either PE or PS. Our study thus provides evidence for different rates of synthesis and/or incorporation of the various molecular species of PC, PE, and PS in ROS.

  13. Molecular Genetic Analysis of Chlamydia Species.

    PubMed

    Sixt, Barbara S; Valdivia, Raphael H

    2016-09-01

    Species of Chlamydia are the etiologic agent of endemic blinding trachoma, the leading cause of bacterial sexually transmitted diseases, significant respiratory pathogens, and a zoonotic threat. Their dependence on an intracellular growth niche and their peculiar developmental cycle are major challenges to elucidating their biology and virulence traits. The last decade has seen tremendous advances in our ability to perform a molecular genetic analysis of Chlamydia species. Major achievements include the generation of large collections of mutant strains, now available for forward- and reverse-genetic applications, and the introduction of a system for plasmid-based transformation enabling complementation of mutations; expression of foreign, modified, or reporter genes; and even targeted gene disruptions. This review summarizes the current status of the molecular genetic toolbox for Chlamydia species and highlights new insights into their biology and new challenges in the nascent field of Chlamydia genetics. PMID:27607551

  14. How to Predict Molecular Interactions between Species?

    PubMed Central

    Schulze, Sylvie; Schleicher, Jana; Guthke, Reinhard; Linde, Jörg

    2016-01-01

    Organisms constantly interact with other species through physical contact which leads to changes on the molecular level, for example the transcriptome. These changes can be monitored for all genes, with the help of high-throughput experiments such as RNA-seq or microarrays. The adaptation of the gene expression to environmental changes within cells is mediated through complex gene regulatory networks. Often, our knowledge of these networks is incomplete. Network inference predicts gene regulatory interactions based on transcriptome data. An emerging application of high-throughput transcriptome studies are dual transcriptomics experiments. Here, the transcriptome of two or more interacting species is measured simultaneously. Based on a dual RNA-seq data set of murine dendritic cells infected with the fungal pathogen Candida albicans, the software tool NetGenerator was applied to predict an inter-species gene regulatory network. To promote further investigations of molecular inter-species interactions, we recently discussed dual RNA-seq experiments for host-pathogen interactions and extended the applied tool NetGenerator (Schulze et al., 2015). The updated version of NetGenerator makes use of measurement variances in the algorithmic procedure and accepts gene expression time series data with missing values. Additionally, we tested multiple modeling scenarios regarding the stimuli functions of the gene regulatory network. Here, we summarize the work by Schulze et al. (2015) and put it into a broader context. We review various studies making use of the dual transcriptomics approach to investigate the molecular basis of interacting species. Besides the application to host-pathogen interactions, dual transcriptomics data are also utilized to study mutualistic and commensalistic interactions. Furthermore, we give a short introduction into additional approaches for the prediction of gene regulatory networks and discuss their application to dual transcriptomics data. We

  15. 2H nuclear magnetic resonance order parameter profiles suggest a change of molecular shape for phosphatidylcholines containing a polyunsaturated acyl chain.

    PubMed Central

    Holte, L. L.; Peter, S. A.; Sinnwell, T. M.; Gawrisch, K.

    1995-01-01

    Solid-state 2H nuclear magnetic resonance spectroscopy was used to determine the orientational order parameter profiles for a series of phosphatidylcholines with perdeuterated stearic acid, 18:0d35, in position sn-1 and 18:1 omega 9, 18:2 omega 6, 18:3 omega 3, 20:4 omega 6, 20:5 omega 3, or 22:6 omega 3 in position sn-2. The main phase transition temperatures were derived from a first moment analysis, and order parameter profiles of sn-1 chains were calculated from dePaked nuclear magnetic resonance powder patterns. Comparison of the profiles at 37 degrees C showed that unsaturation causes an inhomogenous disordering along the sn-1 chain. Increasing sn-2 chain unsaturation from one to six double bonds resulted in a 1.6-kHz decrease in quadrupolar splittings of the sn-1 chain in the upper half of the chain (or plateau region) and maximum splitting difference of 4.4 kHz at methylene carbon 14. The change in chain order corresponds to a decrease in the 18:0 chain length of 0.4 +/- 0.2 A with 18:2 omega 6 versus 18:1 omega 9 in position sn-2. Fatty acids containing three or more double bonds in sn-2 showed a decrease in sn-1 chain length of 0.7 +/- 0.2 A compared with 18:1 omega 9. The chain length of all lipids decreased with increasing temperature. Highly unsaturated phosphatidylcholines (three or more double bonds in sn-2) had shorter sn-1 chains, but the chain length was somewhat less sensitive to temperature. The profiles reveal that the sn-1 chain exhibits a selective increase in motional freedom in a region located toward the bottom half of the chain as sn-2 unsaturation is increased. This corresponds to an area increase around carbon atom number 14 that is three to four times greater than the increase for the top part of the chain. A similar asymmetric decrease in order, largest toward the methyl end of the chain, was observed when 1 -palmitoyl-2-oleoylphosphatidylethanolamine goes from a lamellar to an inverse hexagonal (H,,) phase. This is consistent with a

  16. Differentiation of Lactobacillus Species by Molecular Typing

    PubMed Central

    Zhong, Wei; Millsap, Kevin; Bialkowska-Hobrzanska, Hanna; Reid, Gregor

    1998-01-01

    A total of 64 type, reference, clinical, health food, and stock isolates of microaerophilic Lactobacillus species were examined by restriction fragment length polymorphisms. Of particular interest were members of six of the eight species most commonly recovered from the vaginas of healthy premenopausal women, namely, Lactobacillus jensenii, L. casei, L. rhamnosus, L. acidophilus, L. plantarum, and L. fermentum. Six main groupings were identified on the basis of ribotyping. This technique was able to classify fresh isolates to the species level. In the case of the ribotype A grouping for L. rhamnosus, differences between strains were evident by chromosome typing (chromotyping). Many isolates did not possess plasmids. Six L. rhamnosus strains isolated from four different health food products appeared to be identical to L. rhamnosus ATCC 21052. The molecular typing system is useful for identifying and differentiating Lactobacillus isolates. Studies of strains of potential importance to the urogenital flora should include molecular characterization as a means of comparing genetic traits with those of strains whose characteristics associated with colonization and antagonism against pathogens have been defined. PMID:9647809

  17. Docosahexaenoate-containing molecular species of glycerophospholipids from frog retinal rod outer segments show different rates of biosynthesis and turnover

    SciTech Connect

    Louie, K.; Wiegand, R.D.; Anderson, R.E.

    1988-12-13

    The authors have studied the de novo synthesis and subsequent turnover of major docosahexaenoate-containing molecular species in frog rod outer segment (ROS) phospholipids following intravitreal injection of (2-/sup 3/H)glycerol. On selected days after injection, ROS were prepared and phospholipids extracted. Phosphatidylcholine (PC), phosphatidylethanolamine (PE), and phosphatidylserine (PS) were isolated and converted to diradylglycerols with phospholipase C. Diradylglycerols were derivatized with benzoic anhydride and resolve into diacylglycerobenzoates and ether-linked glycerobenzoates. The diacylglycerobenzoates were fractionated into molecular species by HPLC, quantitated, and counted for radioactivity. Label was incorporated into ROS phospholipids by day 1 and was followed up through the eighth day. The dipolyenoic species 22:6-22:6 from PC showed 1 3-5 times higher radiospecific activity than the same species from either PE or PS. The rate of decline was determined by calculating the half-life of each molecular species, which was used as a measure of the turnover of the species. The percent distribution of radioactivity in the molecular species of PC and PE was quite different from the relative mass distribution at day 1. However, percent dpm approached the mole percent by 31 days. In PS, percent dpm and mole percent were the same at all time points. These results indicate that the molecular species composition of PC and PE in frog retinal ROS is determined by a combination of factors, which include rate of synthesis, rate of degradation, and selective interconversions. In contrast, PS composition appears to be determined at the time of synthesis.

  18. Oxidized phosphatidylcholine formation and action in oligodendrocytes

    PubMed Central

    Qin, Jingdong; Testai, Fernando D; Dawson, Sylvia; Kilkus, John; Dawson, Glyn

    2010-01-01

    Reactive oxygen species play a major role in neurodegeneration. Increasing concentrations of peroxide induce neural cell death through activation of pro-apoptotic pathways. We now report that hydrogen peroxide generated sn-2 oxidized phosphatidylcholine (OxPC) in neonatal rat oligodendrocytes and that synthetic oxidized phosphatidylcholine (1-palmitoyl-2-(5′-oxo)valeryl-sn-glycero-3 phosphorylcholine, POVPC) also induced apoptosis in neonatal rat oligodendrocytes. POVPC activated caspases 3 and 8, and neutral sphingomyelinase (NSMase), but not acid sphingomyelinase. Downstream pro-apoptotic pathways activated by POVPC treatment included the Jun N-terminal kinase (JNK) proapoptotic cascade and the degradation of phospho-Akt. Activation of NSMase occurred within 1h, was blocked by inhibitors of caspase 8, increased mainly C18 and C24:1-ceramides, and appeared to be concentrated in detergent-resistant microdomains (Rafts). We conclude that OxPC initially activates NSMase and converts sphingomyelin into ceramide, to mediate a series of downstream pro-apoptotic events in oligodendrocytes. PMID:19545281

  19. Activity of phosphatidylcholine-transfer protein from spinach (Spinacia oleracea) leaves with mitochondria and chloroplasts.

    PubMed

    Julienne, M; Vergnolle, C; Kader, J C

    1981-09-01

    A low-molecular-weight protein catalysing the transfer of phosphatidylcholine from liposomes to mitochondria and chloroplasts has been isolated from spinach (Spinacia oleracea) by chromatography on Sephadex G-75. PMID:7325986

  20. Imaging Mass Spectrometry of Diversified Cardiolipin Molecular Species in the Brain

    PubMed Central

    2015-01-01

    MALDI imaging mass spectrometry (MALDI-IMS) has been used successfully in mapping different lipids in tissue sections, yet existing protocols fail to detect the diverse species of mitochondria-unique cardiolipins (CLs) in the brain which are essential for cellular and mitochondrial physiology. We have developed methods enabling the imaging of individual CLs in brain tissue. This was achieved by eliminating ion suppressive effects by (i) cross-linking carboxyl/amino containing molecules on tissue with 1-ethyl-3-[3-(dimethylamino)propyl]-carbodiimide hydrochloride and (ii) removing highly abundant phosphatidylcholine head groups via phospholipase C treatment. These treatments allowed the detection of CL species at 100 μm resolution and did not affect the amount or molecular species distribution of brain tissue CLs. When combined with augmented matrix application, these modifications allowed the visualization and mapping of multiple CL species in various regions of the brain including the thalamus, hippocampus, and cortex. Areas such as the dentate and stratum radiatum exhibited higher CL signals than other areas within the hippocampal formation. The habenular nuclear (Hb)/dorsal third ventricle (D3 V) and lateral ventricle (LV) areas were identified as CL “hot spots”. Our method also allowed structural MS/MS fragmentation and mapping of CLs with identified fatty acid residues and demonstrated a nonrandom distribution of individual oxidizable (polyunsaturated fatty acid containing) and nonoxidizable (nonpolyunsaturated containing) CLs in different anatomical areas of the brain. To our knowledge, this method is the first label-free approach for molecular mapping of diversified CLs in brain tissue. PMID:24949523

  1. Imaging mass spectrometry of diversified cardiolipin molecular species in the brain.

    PubMed

    Amoscato, A A; Sparvero, L J; He, R R; Watkins, S; Bayir, H; Kagan, V E

    2014-07-01

    MALDI imaging mass spectrometry (MALDI-IMS) has been used successfully in mapping different lipids in tissue sections, yet existing protocols fail to detect the diverse species of mitochondria-unique cardiolipins (CLs) in the brain which are essential for cellular and mitochondrial physiology. We have developed methods enabling the imaging of individual CLs in brain tissue. This was achieved by eliminating ion suppressive effects by (i) cross-linking carboxyl/amino containing molecules on tissue with 1-ethyl-3-[3-(dimethylamino)propyl]-carbodiimide hydrochloride and (ii) removing highly abundant phosphatidylcholine head groups via phospholipase C treatment. These treatments allowed the detection of CL species at 100 μm resolution and did not affect the amount or molecular species distribution of brain tissue CLs. When combined with augmented matrix application, these modifications allowed the visualization and mapping of multiple CL species in various regions of the brain including the thalamus, hippocampus, and cortex. Areas such as the dentate and stratum radiatum exhibited higher CL signals than other areas within the hippocampal formation. The habenular nuclear (Hb)/dorsal third ventricle (D3 V) and lateral ventricle (LV) areas were identified as CL "hot spots". Our method also allowed structural MS/MS fragmentation and mapping of CLs with identified fatty acid residues and demonstrated a nonrandom distribution of individual oxidizable (polyunsaturated fatty acid containing) and nonoxidizable (nonpolyunsaturated containing) CLs in different anatomical areas of the brain. To our knowledge, this method is the first label-free approach for molecular mapping of diversified CLs in brain tissue. PMID:24949523

  2. Method for coupling a hydrocarbon containing molecular species

    SciTech Connect

    Lingwood, C.A.

    1986-07-01

    A method is described of covalently coupling two molecular species comprising: (a) combining (i) a first molecular species having a functionality reactive with hydrocarbon when photo-activated; and (ii) a solution of at least one, hydrocarbon containing, molecular species in the absence of photo-radiation to which the functionality is sensitive; (b) removing the solvent; (c) irradiating the mixture with photo-radiation to which the functionality is photosensitive.

  3. Very high frequency electron paramagnetic resonance of 2,2,6,6-tetramethyl-1-piperidinyloxy in 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine liposomes: partitioning and molecular dynamics.

    PubMed Central

    Smirnov, A I; Smirnova, T I; Morse, P D

    1995-01-01

    Partitioning and molecular dynamics of 2,2,6,6,-tetramethylpiperedine-1-oxyl (TEMPO) nitroxide radicals in large unilamellar liposomes (LUV) composed from 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine were investigated by using very high frequency electron paramagnetic resonance (EPR) spectroscopy. Experiments carried out at a microwave frequency of 94.3 GHz completely resolved the TEMPO EPR spectrum in the aqueous and hydrocarbon phases. An accurate computer simulation method combined with Levenberg-Marquardt optimization was used to analyze the TEMPO EPR spectra in both phases. Spectral parameters extracted from the simulations gave the actual partitioning of the TEMPO probe between the LUV hydrocarbon and aqueous phases and allowed analysis of picosecond rotational dynamics of the probe in the LUV hydrocarbon phase. In very high frequency EPR experiments, phase transitions in the LUV-TEMPO system were observed as sharp changes in both partitioning and rotational correlation times of the TEMPO probe. The phase transition temperatures (40.5 +/- 0.2 and 32.7 +/- 0.5 degrees C) are in agreement with previously reported differential scanning microcalorimetry data. Spectral line widths were analyzed by using existing theoretical expressions for motionally narrowed nitroxide spectra. It was found that the motion of the small, nearly spherical, TEMPO probe can be well described by anisotropic Brownian diffusion in isotropic media and is not restricted by the much larger hydrocarbon chains existing in ripple structure (P beta') or fluid bilayer structure (L alpha) phases. PMID:7647239

  4. Lipid Classes, Fatty Acid Composition, and Glycerolipid Molecular Species of the Red Alga Gracilaria vermiculophylla, a Prostaglandin-Producing Seaweed.

    PubMed

    Honda, Masaki; Ishimaru, Takashi; Itabashi, Yutaka

    2016-01-01

    The red alga Gracilaria vermiculophylla is a well-known producer of prostaglandins, such as PGE2 and PGF2α. In this study, the characteristics of glycerolipids as substrates of prostaglandin production were clarified, and the lipid classes, fatty acid composition, and glycerolipid molecular species were investigated in detail. The major lipid classes were monogalactosyldiacylglycerol (MGDG), digalactosyldiacylglycerol (DGDG), and sulfoquinovosyldiacylglycerol (SQDG), as well as phosphatidylcholine (PC), which accounted for 43.0% of the total lipid profile. Arachidonic acid (20:4n-6), a prostaglandin precursor, and palmitic acid (16:0) were the predominant fatty acids in the total lipid profile. The 20:4n-6 content was significantly high in MGDG and PC (more than 60%), and the 16:0 content was significantly high in DGDG and SQDG (more than 50%). Chiral-phase high-performance liquid chromatography determined that fatty acids were esterified at the sn-1 and sn-2 positions of those lipids. The main glycerolipid molecular species were 20:4n-6/20:4n-6 (sn-1/sn-2) for MGDG (56.5%) and PC (40.0%), and 20:4n-6/16:0 for DGDG (75.4%) and SQDG (58.4%). Thus, it was considered that the glycerolipid molecular species containing one or two 20:4n-6 were the major substrates for prostaglandin production in G. vermiculophylla. PMID:27581490

  5. Production of 1,2-didocosahexaenoyl phosphatidylcholine by bonito muscle lysophosphatidylcholine/transacylase.

    PubMed

    Hirano, Kaoru; Matsui, Hidetoshi; Tanaka, Tamotsu; Matsuura, Fumito; Satouchi, Kiyoshi; Koike, Tohru

    2004-10-01

    1,2-Didocosahexaenoyl phosphatidylcholine (PC), which has highly unsaturated fatty acid at both sn-1 and sn-2 positions of glycerol, is a characteristic molecular species of bonito muscle. To examine the involvement of a de novo route in its synthesis, the molecular species of phosphatidic acid (PA) were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using a 1,3-bis[bis(pyridin-2-ylmethyl)amino]propan-2-olato dizinc(II) complex, a novel phosphate-capture molecule. However, 1,2-didocosahexaenoyl species could not be detected. Next, 1,2-didocosahexaenoyl PC synthesis by the cytosolic lysophosphatidylcholine (LPC)/transacylase was examined using endogenous LPC from bonito muscle, in which the 2-docosahexaenoyl species is abundant. The LPC/transacylase synthesized 1,2-didocosahexaenoyl PC as the most abundant molecular species. For further characterization, the LPC/transacylase was purified to homogeneity from the 100,000 x g supernatant of bonito muscle. The isolated LPC/transacylase is a labile glycoprotein with molecular mass of 52 kDa including a 5-kDa sugar moiety. The LPC/transacylase showed a PC synthesis (transacylase activity) below and above the critical micelle concentration of substrate LPC, and fatty acid release (lysophospholipase activity) was always smaller than the transacylase activity, even with a monomeric substrate. These results suggest that the LPC/transacylase is responsible for the synthesis of 1,2-didocosahexaenoyl PC. PMID:15625317

  6. Heterogeneous catalytic transesterification of phosphatidylcholine.

    PubMed

    Balasubramanian, Rajesh Kumar; Obbard, Jeffrey Philip

    2011-01-01

    The transesterification of phosphatidylcholine (PC) via homogeneous and heterogeneous catalysis was investigated for the production of fatty acid methyl esters (FAME) i.e. biodiesel. Calcium methoxide and calcium oxide were used as heterogeneous catalysts, and KOH as a homogeneous catalyst for the transesterification of phosphatidylcholine (PC)--a polar phospholipid prevalent in eukaryotic organisms. The initial reaction rate was higher for KOH (24.23 g of FAME/g of catalyst.min) than for calcium methoxide (17.06 g of FAME/g of catalyst.min) and calcium oxide (1.06 g of FAME/g of catalyst.min). PC was then mixed with soybean oil at different proportions (i.e. 10%, 30% and 50%, PC10, PC30 and PC50, respectively) which was then used as the feedstock for transesterification using calcium methoxide. When the mass fraction of PC was increased in the feedstock reaction rate also increased. Phosphorus content of the FAME layer of PC100, PC50, PC30 and PC10 was 0.081, 0.041, 0.035 and 0.028% (w/w), respectively. PMID:20832299

  7. Molecular dynamics simulation of the evolution of hydrophobic defects in one monolayer of a phosphatidylcholine bilayer: relevance for membrane fusion mechanisms.

    PubMed Central

    Tieleman, D Peter; Bentz, Joe

    2002-01-01

    The spontaneous formation of the phospholipid bilayer underlies the permeability barrier function of the biological membrane. Tears or defects that expose water to the acyl chains are spontaneously healed by lipid lateral diffusion. However, mechanical barriers, e.g., protein aggregates held in place, could sustain hydrophobic defects. Such defects have been postulated to occur in processes such as membrane fusion. This gives rise to a new question in bilayer structure: What do the lipids do in the absence of lipid lateral diffusion to minimize the free energy of a hydrophobic defect? As a first step to understand this rather fundamental question about bilayer structure, we performed molecular dynamic simulations of up to 10 ns of a planar bilayer from which lipids have been deleted randomly from one monolayer. In one set of simulations, approximately one-half of the lipids in the defect monolayer were restrained to form a mechanical barrier. In the second set, lipids were free to diffuse around. The question was simply whether the defects caused by removing a lipid would aggregate together, forming a large hydrophobic cavity, or whether the membrane would adjust in another way. When there are no mechanical barriers, the lipids in the defect monolayer simply spread out and thin with little effect on the other intact monolayer. In the presence of a mechanical barrier, the behavior of the lipids depends on the size of the defect. When 3 of 64 lipids are removed, the remaining lipids adjust the lower one-half of their chains, but the headgroup structure changes little and the intact monolayer is unaffected. When 6 to 12 lipids are removed, the defect monolayer thins, lipid disorder increases, and lipids from the intact monolayer move toward the defect monolayer. Whereas this is a highly simplified model of a fusion site, this engagement of the intact monolayer into the fusion defect is strikingly consistent with recent results for influenza hemagglutinin mediated

  8. Molecular Diagnosis of Pathogenic Sporothrix Species

    PubMed Central

    Rodrigues, Anderson Messias; de Hoog, G. Sybren; de Camargo, Zoilo Pires

    2015-01-01

    Background Sporotrichosis is a chronic (sub)cutaneous infection caused by thermodimorphic fungi in the order, Ophiostomatales. These fungi are characterized by major differences in routes of transmission, host predilections, species virulence, and susceptibilities to antifungals. Sporothrix species emerge in the form of outbreaks. Large zoonoses and sapronoses are ongoing in Brazil and China, respectively. Current diagnostic methods based on morphology and physiology are inaccurate due to closely related phenotypes with overlapping components between pathogenic and non-pathogenic Sporothrix. There is a critical need for new diagnostic tools that are specific, sensitive, and cost-effective. Methodology We developed a panel of novel markers, based on calmodulin (CAL) gene sequences, for the large-scale diagnosis and epidemiology of clinically relevant members of the Sporothrix genus, and its relative, Ophiostoma. We identified specific PCR-based markers for S. brasiliensis, S. schenckii, S. globosa, S. mexicana, S. pallida, and O. stenoceras. We employed a murine model of disseminated sporotrichosis to optimize a PCR assay for detecting Sporothrix in clinical specimens. Results Primer-BLAST searches revealed candidate sequences that were conserved within a single species. Species-specific primers showed no significant homology with human, mouse, or microorganisms outside the Sporothrix genus. The detection limit was 10–100 fg of DNA in a single round of PCR for identifying S. brasiliensis, S. schenckii, S. globosa, S. mexicana, and S. pallida. A simple, direct PCR assay, with conidia as a source of DNA, was effective for rapid, low-cost genotyping. Samples from a murine model of disseminated sporotrichosis confirmed the feasibility of detecting S. brasiliensis and S. schenckii DNA in spleen, liver, lungs, heart, brain, kidney, tail, and feces of infected animals. Conclusions This PCR-based method could successfully detect and identify a single species in samples

  9. Legionella bozemanae synthesizes phosphatidylcholine from exogenous choline.

    PubMed

    Palusinska-Szysz, Marta; Janczarek, Monika; Kalitynski, Rafal; Dawidowicz, Andrzej L; Russa, Ryszard

    2011-02-20

    The phospholipid class and fatty acid composition of Legionella bozemanae were determined using thin-layer chromatography, gas-liquid chromatography, and matrix-assisted laser desorption ionization-time of flight mass spectrometry. Phosphatidylcholine, phosphatidylethanolamine, and diphosphatidylglycerol were the predominant phospholipids, while phosphatidyl-N-monomethylethanolamine, phosphatidylglycerol, and phosphatidyl-N,N-dimethylethanolamine were present at low concentrations. With the use of the LC/MS technique, PC16:0/15:0, PC17:/15:0, and PE16:1/15:0 were shown to be the dominant phospholipid constituents, which may be taxonomically significant. Two independent phosphatidylcholine synthesis pathways (the three-step methylation and the one-step CDP-choline pathway) were present and functional in L. bozemanae. In the genome of L. bozemanae, genes encoding two potential phosphatidylcholine forming enzymes, phospholipid N-methyl transferase (PmtA) and phosphatidylcholine synthase (Pcs), homologous to L. longbeachae, L. drancourtii, and L. pneumophila pmtA and pcs genes were identified. Genes pmtA and pcs from L. bozemanae were sequenced and analyzed on nucleotide and amino acid levels. Bacteria grown on an artificial medium with labelled choline synthesized phosphatidylcholine predominantly via the phosphatidylcholine synthase pathway, which indicates that L. bozemanae phosphatidylcholine, similarly as in other bacteria associated with eukaryotes, is an important determinant of host-microbe interactions. PMID:20338739

  10. DNA barcode-based molecular identification system for fish species.

    PubMed

    Kim, Sungmin; Eo, Hae-Seok; Koo, Hyeyoung; Choi, Jun-Kil; Kim, Won

    2010-12-01

    In this study, we applied DNA barcoding to identify species using short DNA sequence analysis. We examined the utility of DNA barcoding by identifying 53 Korean freshwater fish species, 233 other freshwater fish species, and 1339 saltwater fish species. We successfully developed a web-based molecular identification system for fish (MISF) using a profile hidden Markov model. MISF facilitates efficient and reliable species identification, overcoming the limitations of conventional taxonomic approaches. MISF is freely accessible at http://bioinfosys.snu.ac.kr:8080/MISF/misf.jsp . PMID:21110132

  11. Characterization of Capsicum species using anatomical and molecular data.

    PubMed

    Dias, G B; Gomes, V M; Moraes, T M S; Zottich, U P; Rabelo, G R; Carvalho, A O; Moulin, M; Gonçalves, L S A; Rodrigues, R; Da Cunha, M

    2013-01-01

    Capsicum species are frequently described in terms of genetic divergence, considering morphological, agronomic, and molecular databases. However, descriptions of genetic differences based on anatomical characters are rare. We examined the anatomy and the micromorphology of vegetative and reproductive organs of several Capsicum species. Four Capsicum accessions representing the species C. annuum var. annuum, C. baccatum var. pendulum, C. chinense, and C. frutescens were cultivated in a greenhouse; leaves, fruits and seeds were sampled and their organ structure analyzed by light and scanning electronic microscopy. Molecular accession characterization was made using ISSR markers. Polymorphism was observed among tector trichomes and also in fruit color and shape. High variability among accessions was detected by ISSR markers. Despite the species studied present a wide morphological and molecular variability that was not reflected by anatomical features. PMID:23479174

  12. Changes in the Fatty Acid Profile and Phospholipid Molecular Species Composition of Human Erythrocyte Membranes after Hybrid Palm and Extra Virgin Olive Oil Supplementation.

    PubMed

    Pacetti, D; Gagliardi, R; Balzano, M; Frega, N G; Ojeda, M L; Borrero, M; Ruiz, A; Lucci, P

    2016-07-13

    This work aims to evaluate and compare, for the first time, the effects of extra virgin olive oil (EVOO) and hybrid palm oil (HPO) supplementation on the fatty acid profile and phospholipid (PL) molecular species composition of human erythrocyte membranes. Results supported the effectiveness of both HPO and EVOO supplementation (3 months, 25 mL/day) in decreasing the lipophilic index of erythrocytes with no significant differences between HPO and EVOO groups at month 3. On the other hand, the novel and rapid ultraperformance liquid chromatography-tandem mass spectrometry method used for PL analysis reveals an increase in the levels of phosphatidylcholine and phosphatidylethanolamine species esterified with polyunsaturated fatty acids. This work demonstrates the ability of both EVOO and HPO to increase the degree of unsaturation of erythrocyte membrane lipids with an improvement in membrane fluidity that could be associated with a lower risk of developing cardiovascular diseases. PMID:27315139

  13. Quadrupole time-of-flight mass spectrometry analysis of glycerophospholipid molecular species in the two halophyte seed oils: Eryngium maritimum and Cakile maritima.

    PubMed

    Zitouni, Manel; Wewer, Vera; Dörmann, Peter; Abdelly, Chedly; Ben Youssef, Nabil

    2016-12-15

    Future applications of lipids in clinical cohort studies demand detailed glycerophospholipid molecule information and the application of high-throughput lipidomics platforms. In the present work, a novel sensitive technique with high mass resolution and accuracy was applied to accomplish phospholipid analysis. Nanospray ionization quadrupole time-of-flight mass spectrometry was used to separate and quantify the glycerophospholipid classes as well as molecular species in two halophyte seed oils from Cakile maritima and Eryngium maritimum. Precursor or neutral loss scans of their polar head groups allowed the detection of molecular species within particular glycerophospholipid classes. Phosphatidylcholine was found to be the most abundant glycerophospholipid in both seed oils whereas phosphatidylethanolamine and phosphatidic acid were less abundant. Phosphatidylinositol, phosphatidylserine and phosphatidylglycerol were minor glycerophospholipids. Several molecular species within each class were detected and the main molecular species (C36:4, C36:3, C36:2, 34:2 and C34:1) were quantitatively different between the two halophytes and the different glycerophospholipids. PMID:27451187

  14. Elucidation of phosphatidylcholine composition in krill oil extracted from Euphausia superba.

    PubMed

    Winther, Bjørn; Hoem, Nils; Berge, Kjetil; Reubsaet, Léon

    2011-01-01

    High performance liquid chromatography-electrospray tandem mass spectrometry was used to elucidate the phospholipids in krill oil extracted from Euphausia superba, an emerging source for human nutritional supplements. The study was carried out in order to map the species of the choline-containing phospholipid classes: phosphatidylcholine and lyso-phosphatidylcholine. In addition, the prevalent phosphatidylcholine class was quantified and the results compared with prior analysis. The qualification was performed with separation on a reverse phase chromatography column, while the quantification was obtained with class separation on a normal phase chromatography column. An Orbitrap system was used for the detection, and pulsed-Q dissociation fragmentation was utilized for the identification of the species. An asymmetrical exclusion list was applied for detection of phospholipid species of lower concentration, significantly improving the number of species observed. A total of 69 choline-containing phospholipids were detected, whereof 60 phosphatidylcholine substances, among others seven with probable omega-3 fatty acids in both sn-1 and sn-2. The phosphatidylcholine concentration was estimated to be 34 ± 5 g/100 g oil (n = 5). These results confirm the complexity of the phospholipid composition of krill oil, and the presence of long chained, heavily unsaturated fatty acids. PMID:20848234

  15. Low molecular weight species in humic and fulvic fractions

    USGS Publications Warehouse

    Wilson, M.A.; Collin, P.J.; Malcolm, R.L.; Perdue, E.M.; Cresswell, P.

    1988-01-01

    Fourier transform solution 1H nuclear magnetic resonance (NMR) spectrometry with homogated water peak irradiation is a useful method for detecting low molecular weight substances in humic extracts. Succinate, acetate, methanol, formate, lactate and some aryl methoxyl compounds have been detected in extracts from a wide range of sources. In view of the controversy over whether low molecular weight substances are contaminants in humic extracts introduced by the concentration procedure, we report that some of these materials are not contaminants since 1H-NMR can be used to follow their formation from higher molecular weight species. ?? 1988.

  16. Analysis of phospholipid molecular species in brains from patients with infantile and juvenile neuronal-ceroid lipofuscinosis using liquid chromatography-electrospray ionization mass spectrometry.

    PubMed

    Käkelä, Reijo; Somerharju, Pentti; Tyynelä, Jaana

    2003-03-01

    Phospholipids (PL) in cerebral cortex from patients with infantile (INCL or CLN1) and juvenile (JNCL or CLN3) forms of neuronal ceroid-lipofuscinosis (NCL) and controls were analysed by normal phase HPLC and on-line electrospray ionization ion-trap mass spectrometric detection (LC-ESI-MS). The method provided quantitative data on numerous molecular species of different PL classes, which are not achieved by using the conventional chromatographic methods. Compared with the controls, the INCL brains contained proportionally more phosphatidylcholine (PC), and less phosphatidylethanolamine (PE) and phosphatidylserine (PS). Different molecular species of PC, PE, PS, phosphatidylinositol and sphingomyelin were quantified using multiple internal PL standards that differed in fatty acyl chain length and thus allowed correction for chain length dependency of instrument response. In INCL cortex, which had lost 65% of the normal PL content, the proportions of polyunsaturated molecular species, especially the PS and PE that contained docosahexaenoic acid (22:6n-3), were dramatically decreased. The membranes may have adapted to this alteration by increasing the proportions of PL molecules substituted with monounsaturated and short-chain fatty acids. Lysobisphosphatidic acid was highly elevated in the INCL brain and consisted mostly of polyunsaturated species. It is possible that changes in the composition of PL membranes accelerate progression of INCL by altering signalling and membrane trafficking in neurons. PMID:12603829

  17. Molecular Systematic Comparison of North American Lygus Species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genus Lygus is widely distributed in North America and Eurasia. The tarnished plant bug, Lygus lineolaris (Palisot de Beauvois), is one of the most serious pest species within this genus. This pest has over 300 known host plants. We employed various molecular markers to investigate both inter- a...

  18. Improved Molecular Technique for the Differentiation of Neotropical Anopheline Species

    PubMed Central

    Matson, Ryan; Rios, Carlos Tong; Chavez, Cesar Banda; Gilman, Robert H.; Florin, David; Sifuentes, Victor Lopez; Greffa, Roldan Cardenas; Yori, Pablo Peñataro; Fernandez, Roberto; Portocarrero, Daniel Velasquez; Vinetz, Joseph M.; Kosek, Margaret

    2008-01-01

    We evaluated a PCR-RFLP of the ribosomal internal transcribed spacer 2 region (ITS2) to distinguish species of Anopheles commonly reported in the Amazon and validated this method using reared F1 offspring. The following species of Anopheles were used for molecular analysis: An. (Nys.) benarrochi, An. (Nys.) darlingi, An. (Nys.) nuneztovari, An. (Nys.) konderi, An. (Nys.) rangeli, and An. (Nys.) triannulatus sensu lato (s.l.). In addition, three species of the subgenus Anopheles, An. (Ano.) forattini, An. (Ano.) mattogrossensis, and An. (Ano.) peryassui were included for testing. Each of the nine species tested yielded diagnostic banding patterns. The PCR-RFLP method was successful in identifying all life stages including exuviae with small fractions of the sample. The assay is rapid and can be applied as an unbiased confirmatory method for identification of morphologic variants, disputed samples, imperfectly preserved specimens, and life stages from which taxonomic keys do not allow for definitive species determination. PMID:18337348

  19. Unsaturated phosphatidylcholines lining on the surface of cartilage and its possible physiological roles

    PubMed Central

    Chen, Yi; Crawford, Ross W; Oloyede, Adekunle

    2007-01-01

    Background Evidence has strongly indicated that surface-active phospholipid (SAPL), or surfactant, lines the surface of cartilage and serves as a lubricating agent. Previous clinical study showed that a saturated phosphatidylcholine (SPC), dipalmitoyl-phosphatidylcholine (DPPC), was effective in the treatment of osteoarthritis, however recent studies suggested that the dominant SAPL species at some sites outside the lung are not SPC, rather, are unsaturated phosphatidylcholine (USPC). Some of these USPC have been proven to be good boundary lubricants by our previous study, implicating their possible important physiological roles in joint if their existence can be confirmed. So far, no study has been conducted to identify the whole molecule species of different phosphatidylcholine (PC) classes on the surface of cartilage. In this study we identified the dominant PC molecule species on the surface of cartilage. We also confirmed that some of these PC species possess a property of semipermeability. Methods HPLC was used to analyse the PC profile of bovine cartilage samples and comparisons of DPPC and USPC were carried out through semipermeability tests. Results It was confirmed that USPC are the dominant SAPL species on the surface of cartilage. In particular, they are Dilinoleoyl-phosphatidylcholine (DLPC), Palmitoyl-linoleoyl-phosphatidylcholine, (PLPC), Palmitoyl-oleoyl-phosphatidylcholine (POPC) and Stearoyl-linoleoyl-phosphatidylcholine (SLPC). The relative content of DPPC (a SPC) was only 8%. Two USPC, PLPC and POPC, were capable of generating osmotic pressure that is equivalent to that by DPPC. Conclusion The results from the current study confirm vigorously that USPC is the endogenous species inside the joint as against DPPC thereby confirming once again that USPC, and not SPC, characterizes the PC species distribution at non-lung sites of the body. USPC not only has better anti-friction and lubrication properties than DPPC, they also possess a level of

  20. Identification of Cryptic Anopheles Mosquito Species by Molecular Protein Profiling

    PubMed Central

    Müller, Pie; Pflüger, Valentin; Wittwer, Matthias; Ziegler, Dominik; Chandre, Fabrice; Simard, Frédéric; Lengeler, Christian

    2013-01-01

    Vector control is the mainstay of malaria control programmes. Successful vector control profoundly relies on accurate information on the target mosquito populations in order to choose the most appropriate intervention for a given mosquito species and to monitor its impact. An impediment to identify mosquito species is the existence of morphologically identical sibling species that play different roles in the transmission of pathogens and parasites. Currently PCR diagnostics are used to distinguish between sibling species. PCR based methods are, however, expensive, time-consuming and their development requires a priori DNA sequence information. Here, we evaluated an inexpensive molecular proteomics approach for Anopheles species: matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). MALDI-TOF MS is a well developed protein profiling tool for the identification of microorganisms but so far has received little attention as a diagnostic tool in entomology. We measured MS spectra from specimens of 32 laboratory colonies and 2 field populations representing 12 Anopheles species including the A. gambiae species complex. An important step in the study was the advancement and implementation of a bioinformatics approach improving the resolution over previously applied cluster analysis. Borrowing tools for linear discriminant analysis from genomics, MALDI-TOF MS accurately identified taxonomically closely related mosquito species, including the separation between the M and S molecular forms of A. gambiae sensu stricto. The approach also classifies specimens from different laboratory colonies; hence proving also very promising for its use in colony authentication as part of quality assurance in laboratory studies. While being exceptionally accurate and robust, MALDI-TOF MS has several advantages over other typing methods, including simple sample preparation and short processing time. As the method does not require DNA sequence information

  1. Anther smuts of Caryophyllaceae: molecular analyses reveal further new species.

    PubMed

    Lutz, Matthias; Piatek, Marcin; Kemler, Martin; Chlebicki, Andrzej; Oberwinkler, Franz

    2008-11-01

    Recent collections of Microbotryum (Pucciniomycotina, Basidiomycota) specimens inhabiting anthers of different caryophyllaceous host plants were analysed using LM and electron microscopy, as well as molecular phylogenetic analyses using rDNA (ITS and LSU) sequences. The phylogenetic relationships of caryophyllaceous anther parasites are discussed. Three new species, Microbotryum adenopetalae, M. minuartiae, and M. silenes-acaulis, are described based on morphological, ecological, and molecular characteristics. New host plants are reported for Microbotryum dianthorum (Dianthus jacquemontii and Petrorhagia saxifraga) and M. lychnidis-dioicae (Cucubalus baccifer and Silene zawadskii). For Microbotryum violaceum, a neotype is selected. PMID:18951773

  2. Identification of Pseudallescheria and Scedosporium Species by Three Molecular Methods▿

    PubMed Central

    Lu, Qiaoyun; Gerrits van den Ende, A. H. G.; Bakkers, J. M. J. E.; Sun, Jiufeng; Lackner, M.; Najafzadeh, M. J.; Melchers, W. J. G.; Li, Ruoyu; de Hoog, G. S.

    2011-01-01

    The major clinically relevant species in Scedosporium (teleomorph Pseudallescheria) are Pseudallescheria boydii, Scedosporium aurantiacum, Scedosporium apiospermum, and Scedosporium prolificans, while Pseudallescheria minutispora, Petriellopsis desertorum, and Scedosporium dehoogii are exceptional agents of disease. Three molecular methods targeting the partial β-tubulin gene were developed and evaluated to identify six closely related species of the S. apiospermum complex using quantitative real-time PCR (qPCR), PCR-based reverse line blot (PCR-RLB), and loop-mediated isothermal amplification (LAMP). qPCR was not specific enough for the identification of all species but had the highest sensitivity. The PCR-RLB assay was efficient for the identification of five species. LAMP distinguished all six species unambiguously. The analytical sensitivities of qPCR, PCR-RLB, and LAMP combined with MagNAPure, CTAB (cetyltrimethylammonium bromide), and FTA filter (Whatman) extraction were 50, 5 × 103, and 5 × 102 cells/μl, respectively. When LAMP was combined with a simplified DNA extraction method using an FTA filter, identification to the species level was achieved within 2 h, including DNA extraction. The FTA-LAMP assay is therefore recommended as a cost-effective, simple, and rapid method for the identification of Scedosporium species. PMID:21177887

  3. Genetic introgression and species boundary of two geographically overlapping pine species revealed by molecular markers.

    PubMed

    Zhang, Defang; Xia, Tao; Yan, Maomao; Dai, Xiaogang; Xu, Jin; Li, Shuxian; Yin, Tongming

    2014-01-01

    Gene introgression and hybrid barriers have long been a major focus of studies of geographically overlapping species. Two pine species, Pinus massoniana and P. hwangshanensis, are frequently observed growing adjacent to each other, where they overlap in a narrow hybrid zone. As a consequence, these species constitute an ideal system for studying genetic introgression and reproductive barriers between naturally hybridizing, adjacently distributed species. In this study, we sampled 270 pine trees along an elevation gradient in Anhui Province, China and analyzed these samples using EST-SSR markers. The molecular data revealed that direct gene flow between the two species was fairly low, and that the majority of gene introgression was intermediated by backcrossing. On the basis of empirical observation, the on-site distribution of pines was divided into a P. massoniana zone, a hybrid zone, and a P. hwangshanensis zone. STRUCTURE analysis revealed the existence of a distinct species boundary between the two pine species. The genetic boundary of the hybrid zone, on the other hand, was indistinct owing to intensive backcrossing with parental species. Compared with P. massoniana, P. hwangshanensis was found to backcross with the hybrids more intensively, consistent with the observation that morphological and anatomical characteristics of trees in the contact zone were biased towards P. hwangshanensis. The introgression ability of amplified alleles varied across species, with some being completely blocked from interspecific introgression. Our study has provided a living example to help explain the persistence of adjacently distributed species coexisting with their interfertile hybrids. PMID:24977711

  4. Arsenic-Containing Phosphatidylcholines: A New Group of Arsenolipids Discovered in Herring Caviar.

    PubMed

    Viczek, Sandra A; Jensen, Kenneth B; Francesconi, Kevin A

    2016-04-18

    A new group of arsenolipids based on cell-membrane phosphatidylcholines has been discovered in herring caviar (fish roe). A combination of HPLC with elemental and molecular mass spectrometry was used to identify five arsenic-containing phosphatidylcholines; the same technique applied to salmon caviar identified an arsenic-containing phosphatidylethanolamine. The arsenic group in these membrane lipids might impart particular properties to the molecules not displayed by their non-arsenic analogues. Additionally, the new compounds have human health implications according to recent results showing high cytotoxicity for some arsenolipids. PMID:26996517

  5. Arsenic‐Containing Phosphatidylcholines: A New Group of Arsenolipids Discovered in Herring Caviar

    PubMed Central

    Viczek, Sandra A.; Francesconi, Kevin A.

    2016-01-01

    Abstract A new group of arsenolipids based on cell‐membrane phosphatidylcholines has been discovered in herring caviar (fish roe). A combination of HPLC with elemental and molecular mass spectrometry was used to identify five arsenic‐containing phosphatidylcholines; the same technique applied to salmon caviar identified an arsenic‐containing phosphatidylethanolamine. The arsenic group in these membrane lipids might impart particular properties to the molecules not displayed by their non‐arsenic analogues. Additionally, the new compounds have human health implications according to recent results showing high cytotoxicity for some arsenolipids.

  6. Arsenic‐Containing Phosphatidylcholines: A New Group of Arsenolipids Discovered in Herring Caviar

    PubMed Central

    Viczek, Sandra A.; Francesconi, Kevin A.

    2016-01-01

    Abstract A new group of arsenolipids based on cell‐membrane phosphatidylcholines has been discovered in herring caviar (fish roe). A combination of HPLC with elemental and molecular mass spectrometry was used to identify five arsenic‐containing phosphatidylcholines; the same technique applied to salmon caviar identified an arsenic‐containing phosphatidylethanolamine. The arsenic group in these membrane lipids might impart particular properties to the molecules not displayed by their non‐arsenic analogues. Additionally, the new compounds have human health implications according to recent results showing high cytotoxicity for some arsenolipids. PMID:26996517

  7. Molecular classification and phylogenetic relationships of selected edible Basidiomycetes species.

    PubMed

    Avin, Farhat Ahmadi; Bhassu, Subha; Shin, Tan Yee; Sabaratnam, Vikineswary

    2012-07-01

    Morphological identification of edible mushrooms can sometimes prove troublesome, because phenotypic variation in fungi can be affected by substrate and environmental factors. One of the most important problems for mushroom breeders is the lack of a systematic consensus tool to distinguish different species, which are sometimes morphologically identical. Basidiomycetes as one of the largest groups of edible mushrooms have become more important in recent times for their medicinal and nutritional properties. Partial rDNA sequences, including the Internal Transcribed Spacer I-5.8SrDNA-Internal Transcribed Spacer II, were used in this study for molecular identification and assessment of phylogenetic relationships between selected edible species of the Basidiomycetes. Phylogenetic trees showed five distinct clades; each clade belonging to a separate family group. The first clade included all the species belonging to the Pleurotaceae (Pleurotus spp.) family; similarly, the second, third, fourth, and fifth clades consist of species from the Agaricaceae (Agaricus sp.), Lyophllaceae (Hypsigygus sp.), Marasmiaceae (Lentinula edodes sp.) and Physalacriaceae (Flammulina velutipes sp.) families, respectively. Moreover, different species of each family were clearly placed in a distinct sub-cluster and a total of 13 species were taken for analysis. Species differentiation was re-confirmed by AMOVA analysis (among the populations: 99.67%; within: 0.33%), nucleotide divergence, haplotyping and P value. Polymorphism occurred throughout the ITS regions due to insertion-deletion and point mutations, and can be clearly differentiated within the families as well as genera. Moreover, this study proves that the sequence of the ITS region is a superior molecular DNA barcode for taxonomic identification of Basidiomycetes. PMID:22327649

  8. A Congenital Muscular Dystrophy with Mitochondrial Structural Abnormalities Caused by Defective De Novo Phosphatidylcholine Biosynthesis

    PubMed Central

    Mitsuhashi, Satomi; Ohkuma, Aya; Talim, Beril; Karahashi, Minako; Koumura, Tomoko; Aoyama, Chieko; Kurihara, Mana; Quinlivan, Ros; Sewry, Caroline; Mitsuhashi, Hiroaki; Goto, Kanako; Koksal, Burcu; Kale, Gulsev; Ikeda, Kazutaka; Taguchi, Ryo; Noguchi, Satoru; Hayashi, Yukiko K.; Nonaka, Ikuya; Sher, Roger B.; Sugimoto, Hiroyuki; Nakagawa, Yasuhito; Cox, Gregory A.; Topaloglu, Haluk; Nishino, Ichizo

    2011-01-01

    Congenital muscular dystrophy is a heterogeneous group of inherited muscle diseases characterized clinically by muscle weakness and hypotonia in early infancy. A number of genes harboring causative mutations have been identified, but several cases of congenital muscular dystrophy remain molecularly unresolved. We examined 15 individuals with a congenital muscular dystrophy characterized by early-onset muscle wasting, mental retardation, and peculiar enlarged mitochondria that are prevalent toward the periphery of the fibers but are sparse in the center on muscle biopsy, and we have identified homozygous or compound heterozygous mutations in the gene encoding choline kinase beta (CHKB). This is the first enzymatic step in a biosynthetic pathway for phosphatidylcholine, the most abundant phospholipid in eukaryotes. In muscle of three affected individuals with nonsense mutations, choline kinase activities were undetectable, and phosphatidylcholine levels were decreased. We identified the human disease caused by disruption of a phospholipid de novo biosynthetic pathway, demonstrating the pivotal role of phosphatidylcholine in muscle and brain. PMID:21665002

  9. Molecular and Morphological Inference of Three Cryptic Species within the Merodon aureus Species Group (Diptera: Syrphidae).

    PubMed

    Šašić, Ljiljana; Ačanski, Jelena; Vujić, Ante; Ståhls, Gunilla; Radenković, Snežana; Milić, Dubravka; Obreht Vidaković, Dragana; Đan, Mihajla

    2016-01-01

    The Merodon aureus species group (Diptera: Syrphidae: Eristalinae) comprises a number of different sub-groups and species complexes. In this study we focus on resolving the taxonomic status of the entity previously identified as M. cinereus B, here identified as M. atratus species complex. We used an integrative approach based on morphological descriptions, combined with supporting characters that were obtained from molecular analyses of the mitochondrial cytochrome c oxidase I gene as well as from geometric morphometry of wing and surstylus shapes and environmental niche comparisons. All applied data and methods distinguished and supported three morphologically cryptic species: M. atratus stat. nov., M. virgatus sp. nov. and M. balkanicus sp. nov., which constitute the M. atratus species complex. We present an identification key for the sub-groups and species complexes of the M. aureus species group occurring in Europe, describe the taxa and discuss the utility of the applied methods for species delimitation. The estimated divergence times for the species splits of these taxa coincide with the Pleistocene Günz-Mindel interglaciation and the Great interglaciation (between the Ris and Mindel glacial periods). PMID:27532618

  10. Molecular and Morphological Inference of Three Cryptic Species within the Merodon aureus Species Group (Diptera: Syrphidae)

    PubMed Central

    Ačanski, Jelena; Vujić, Ante; Ståhls, Gunilla; Radenković, Snežana; Milić, Dubravka; Obreht Vidaković, Dragana; Đan, Mihajla

    2016-01-01

    The Merodon aureus species group (Diptera: Syrphidae: Eristalinae) comprises a number of different sub-groups and species complexes. In this study we focus on resolving the taxonomic status of the entity previously identified as M. cinereus B, here identified as M. atratus species complex. We used an integrative approach based on morphological descriptions, combined with supporting characters that were obtained from molecular analyses of the mitochondrial cytochrome c oxidase I gene as well as from geometric morphometry of wing and surstylus shapes and environmental niche comparisons. All applied data and methods distinguished and supported three morphologically cryptic species: M. atratus stat. nov., M. virgatus sp. nov. and M. balkanicus sp. nov., which constitute the M. atratus species complex. We present an identification key for the sub-groups and species complexes of the M. aureus species group occurring in Europe, describe the taxa and discuss the utility of the applied methods for species delimitation. The estimated divergence times for the species splits of these taxa coincide with the Pleistocene Günz-Mindel interglaciation and the Great interglaciation (between the Ris and Mindel glacial periods). PMID:27532618

  11. Species differences and molecular determinant of TRPA1 cold sensitivity

    PubMed Central

    Chen, Jun; Kang, Dawon; Xu, Jing; Lake, Marc; Hogan, James O.; Sun, Chaohong; Walter, Karl; Yao, Betty; Kim, Donghee

    2013-01-01

    TRPA1 is an ion channel and has been proposed as a thermosensor across species. In invertebrate and ancestral vertebrates such as fly, mosquito, frog, lizard and snakes, TRPA1 serves as a heat receptor, a sensory input utilized for heat avoidance or infrared detection. However, in mammals, whether TRPA1 is a receptor for noxious cold is highly controversial, as channel activation by cold was observed by some groups but disputed by others. Here we attribute the discrepancy to species differences. We show that cold activates rat and mouse TRPA1 but not human or rhesus monkey TRPA1. At the molecular level, a single residue within the S5 transmembrane domain (G878 in rodent but V875 in primate) accounts for the observed difference in cold sensitivity. This residue difference also underlies the species-specific effects of menthol. Together, our findings identify the species-specific cold activation of TRPA1 and reveal a molecular determinant of cold-sensitive gating. PMID:24071625

  12. Molecular diagnosis of Eimeria species affecting naturally infected Gallus gallus.

    PubMed

    Carvalho, F S; Wenceslau, A A; Teixeira, M; Albuquerque, G R

    2011-01-01

    We used PCR to test various protocols and define a technique for DNA extraction directly from chicken-shed stool samples for the identification of Eimeria species that parasitize birds. It was possible to extract and amplify DNA of seven Eimeria species from field stool samples, using both protocols tested; extractions made with phenol/chloroform protocols gave the best results. The primers were specific and sensitive, allowing amplification of samples containing as few as 20 oocysts, both in individual and in a multiplex PCR. Individualized PCR with the phenol/chloroform DNA extraction protocol detected a larger number of Eimeria species. Molecular diagnosis was found to be practical and precise, and can be used for monitoring and epidemiological studies of Eimeria. PMID:21710449

  13. Legionella dumoffii utilizes exogenous choline for phosphatidylcholine synthesis.

    PubMed

    Palusinska-Szysz, Marta; Szuster-Ciesielska, Agnieszka; Kania, Magdalena; Janczarek, Monika; Chmiel, Elżbieta; Danikiewicz, Witold

    2014-01-01

    Phosphatidycholine (PC) is the major membrane-forming phospholipid in eukaryotes but it has been found in only a limited number of prokaryotes. Bacteria synthesize PC via the phospholipid N-methylation pathway (Pmt) or via the phosphatidylcholine synthase pathway (Pcs) or both. Here, we demonstrated that Legionella dumoffii has the ability to utilize exogenous choline for phosphatidylcholine (PC) synthesis when bacteria grow in the presence of choline. The Pcs seems to be a primary pathway for synthesis of this phospholipid in L. dumoffii. Structurally different PC species were distributed in the outer and inner membranes. As shown by the LC/ESI-MS analyses, PC15:0/15:0, PC16:0/15:0, and PC17:0/17:1 were identified in the outer membrane and PC14:0/16:0, PC16:0/17:1, and PC20:0/15:0 in the inner membrane. L. dumoffii pcsA gene encoding phosphatidylcholine synthase revealed the highest sequence identity to pcsA of L. bozemanae (82%) and L. longbeachae (81%) and lower identity to pcsA of L. drancourtii (78%) and L. pneumophila (71%). The level of TNF-α in THP1-differentiated cells induced by live and temperature-killed L. dumoffii cultured on a medium supplemented with choline was assessed. Live L. dumoffii bacteria cultured on the choline-supplemented medium induced TNF-α three-fold less efficiently than cells grown on the non-supplemented medium. There is an evident effect of PC modification, which impairs the macrophage inflammatory response. PMID:24821544

  14. Legionella dumoffii Utilizes Exogenous Choline for Phosphatidylcholine Synthesis

    PubMed Central

    Palusinska-Szysz, Marta; Szuster-Ciesielska, Agnieszka; Kania, Magdalena; Janczarek, Monika; Chmiel, Elżbieta; Danikiewicz, Witold

    2014-01-01

    Phosphatidycholine (PC) is the major membrane-forming phospholipid in eukaryotes but it has been found in only a limited number of prokaryotes. Bacteria synthesize PC via the phospholipid N-methylation pathway (Pmt) or via the phosphatidylcholine synthase pathway (Pcs) or both. Here, we demonstrated that Legionella dumoffii has the ability to utilize exogenous choline for phosphatidylcholine (PC) synthesis when bacteria grow in the presence of choline. The Pcs seems to be a primary pathway for synthesis of this phospholipid in L. dumoffii. Structurally different PC species were distributed in the outer and inner membranes. As shown by the LC/ESI-MS analyses, PC15:0/15:0, PC16:0/15:0, and PC17:0/17:1 were identified in the outer membrane and PC14:0/16:0, PC16:0/17:1, and PC20:0/15:0 in the inner membrane. L. dumoffii pcsA gene encoding phosphatidylcholine synthase revealed the highest sequence identity to pcsA of L. bozemanae (82%) and L. longbeachae (81%) and lower identity to pcsA of L. drancourtii (78%) and L. pneumophila (71%). The level of TNF-α in THP1-differentiated cells induced by live and temperature-killed L. dumoffii cultured on a medium supplemented with choline was assessed. Live L. dumoffii bacteria cultured on the choline-supplemented medium induced TNF-α three-fold less efficiently than cells grown on the non-supplemented medium. There is an evident effect of PC modification, which impairs the macrophage inflammatory response. PMID:24821544

  15. Reliable molecular identification of nine tropical whitefly species

    PubMed Central

    Ovalle, Tatiana M; Parsa, Soroush; Hernández, Maria P; Becerra Lopez-Lavalle, Luis A

    2014-01-01

    The identification of whitefly species in adult stage is problematic. Morphological differentiation of pupae is one of the better methods for determining identity of species, but it may vary depending on the host plant on which they develop which can lead to misidentifications and erroneous naming of new species. Polymerase chain reaction (PCR) fragment amplified from the mitochondrial cytochrome oxidase I (COI) gene is often used for mitochondrial haplotype identification that can be associated with specific species. Our objective was to compare morphometric traits against DNA barcode sequences to develop and implement a diagnostic molecular kit based on a RFLP-PCR method using the COI gene for the rapid identification of whiteflies. This study will allow for the rapid diagnosis of the diverse community of whiteflies attacking plants of economic interest in Colombia. It also provides access to the COI sequence that can be used to develop predator conservation techniques by establishing which predators have a trophic linkage with the focal whitefly pest species. PMID:25614792

  16. Molecular species of phosphatidylethanolamine from continuous cultures of Saccharomyces pastorianus syn. carlsbergensis strains.

    PubMed

    Tosch, W; Lanthaler, K; Boote, V; Stretz, D; Robson, G D; Geiger, E; Drucker, D B

    2006-01-30

    Saccharomyces pastorianus syn. carlsbergensis strain 34/70 is well known to be the most used strain for lager beer production. The difference between this strain and very closely related strain 34/78 is the latter's greater flocculating character. This single physiological trait can cause technical difficulties in beer production. The aim of this study was to determine whether lipid analysis by a combination of thin layer chromatography (TLC) with electrospray ionization mass spectrometry (ESI-MS) could be used as a strain-typing technique in order to distinguish S. pastorianus syn. carlsbergensis strain 34/70 from strain 34/78. Both strains (34/70 and 34/78) were harvested after continuous culture under standard conditions. Polar lipids were then extracted from lyophilized cultures and analysed by TLC in order to separate phospholipid families. Phosphatidylethanolamine (PE) was extracted and investigated using ESI-MS, to gain further information on individual molecular species. Using TLC analysis, lipids were separated corresponding to standards for PE, phosphatidylcholine (PC), phosphatidylglycerol (PG), cardiolipin (CL), phosphatidylserine (PS), phosphatidylinositol (PI), phosphatidic acid (PA) and sphingomyelin (SM). ESI-MS of the PE band, separated by TLC, showed that electrospray mass spectra were highly reproducible for repeat cultures. Novel findings were that both brewing strains displayed major phospholipid peaks with m/z 714, PE (34 : 2) m/z 742, PE (36 : 2) and m/z 758, PE (37 : 1). However, strain 34/78 had additional peaks of m/z 700, PE (33 : 2) and m/z 728, PE (35 : 2). Strain 34/70 had an extra peak with m/z 686 PE (32 : 2). We conclude that combined TLC/ESI-MS can distinguish between S. pastorianus syn. carlsbergensis 34/70 and 34/78 and may be a useful typing technique for differentiation of closely related yeast strains. This novel approach may aid quality assurance and could be suitable for yeast collections and larger industrial companies

  17. Zoonotic Potential and Molecular Epidemiology of Giardia Species and Giardiasis†

    PubMed Central

    Feng, Yaoyu; Xiao, Lihua

    2011-01-01

    Summary: Molecular diagnostic tools have been used recently in assessing the taxonomy, zoonotic potential, and transmission of Giardia species and giardiasis in humans and animals. The results of these studies have firmly established giardiasis as a zoonotic disease, although host adaptation at the genotype and subtype levels has reduced the likelihood of zoonotic transmission. These studies have also identified variations in the distribution of Giardia duodenalis genotypes among geographic areas and between domestic and wild ruminants and differences in clinical manifestations and outbreak potentials of assemblages A and B. Nevertheless, our efforts in characterizing the molecular epidemiology of giardiasis and the roles of various animals in the transmission of human giardiasis are compromised by the lack of case-control and longitudinal cohort studies and the sampling and testing of humans and animals living in the same community, the frequent occurrence of infections with mixed genotypes and subtypes, and the apparent heterozygosity at some genetic loci for some G. duodenalis genotypes. With the increased usage of multilocus genotyping tools, the development of next-generation subtyping tools, the integration of molecular analysis in epidemiological studies, and an improved understanding of the population genetics of G. duodenalis in humans and animals, we should soon have a better appreciation of the molecular epidemiology of giardiasis, the disease burden of zoonotic transmission, the taxonomy status and virulences of various G. duodenalis genotypes, and the ecology of environmental contamination. PMID:21233509

  18. Molecular Characterization of Eimeria Species Naturally Infecting Egyptian Baldi Chickens

    PubMed Central

    GADELHAQ, Sahar M; ARAFA, Waleed M; ABOELHADID, Shawky M

    2015-01-01

    Background: Coccidiosis is a serious protozoal disease of poultry. The identification of Eimeria species has important implications for diagnosis and control as well as for epidemiology. The molecular characterization of Eimeria species infecting Egyptian baladi chickens was investigated. Methods: Eimeria species oocysts were harvested from intestines of naturally infected Egyptian baldi chickens. The morphometry characterization of oocysts along with COCCIMORPH software was done. The DNA was extracted initially by freezing and thawing then the prepared samples was subjected to commercial DNA kits. The DNA products were analyzed through conventional polymerase chain reaction by using amplified region (SCAR) marker. Results: The PCR results confirmed the presence of 7 Eimeria species in the examined fecal samples of Egyptian baldi breed with their specific ampilicon sizes being E. acervulina (811bp), E. brunette (626bp), E. tenella (539bp), E. maxima (272bp), E. necatrix (200bp), E. mitis (327bp) and E. praecopx (354bp). A sequencing of the two most predominant species of Eimeria was done, on E. tenella and E. máxima. Analysis of the obtained sequences revealed high identities 99% between Egyptian isolates and the reference one. Similarly, E. maxima isolated from Egyptian baldi chickens showed 98% nucleotide identities with the reference strain. Only single nucleotide substitution was observed among the Egyptian E. tenella isolates (A181G) when compared to the reference one. The Egyptian isolates acquired 4 unique mutations (A68T, C164T, G190A and C227G) in compared with the reference sequence. Conclusion: This is the first time to identify the 7 species of Eimeria from Egyptian baladi chickens. PMID:25904950

  19. Determination of phosphatidylcholine and disaturated phosphatidylcholine content in lung surfactant by high performance liquid chromatography.

    PubMed

    Scarim, J; Ghanbari, H; Taylor, V; Menon, G

    1989-04-01

    A rapid isocratic method for determining the total phosphatidylcholine and disaturated phosphatidylcholine levels in lung surfactant preparations by high performance liquid chromatography (HPLC) is described. The analysis was performed on a 3.9 x 300 mm mu-Porasil column with detection by refractive index. The lipids were eluted with a solvent system of chloroform-acetonitrile-methanol-water-85% phosphoric acid 650:650:500:130:2 (v/v/v/v/v). A 4.6 x 30 mm silica guard column was used in place of an injector loop which served as a sample concentrator and purifier. Phosphatidylinositol, phosphatidylserine, phosphatidylethanolamine, and phosphatidylglycerol, all known components of lung surfactants, were eluted from the loop column and were prevented from reaching the analytical column. Sphingomyelin and lysophosphatidylcholine elute later than the phosphatidylcholines on the analytical column. The method was developed so that phosphatidylcholines elute as a single peak regardless of the fatty acid chain length (C12-C20). When the sample was first oxidized with a potassium permanganate-potassium metaperiodate solution, and potentially interfering oxidation products were removed by extraction into a basic aqueous phase, then only the disaturated phosphatidylcholines were analyzed. PMID:2754340

  20. Mass spectrometry images acylcarnitines, phosphatidylcholines, and sphingomyelin in MDA-MB-231 breast tumor models.

    PubMed

    Chughtai, Kamila; Jiang, Lu; Greenwood, Tiffany R; Glunde, Kristine; Heeren, Ron M A

    2013-02-01

    The lipid compositions of different breast tumor microenvironments are largely unknown due to limitations in lipid imaging techniques. Imaging lipid distributions would enhance our understanding of processes occurring inside growing tumors, such as cancer cell proliferation, invasion, and metastasis. Recent developments in MALDI mass spectrometry imaging (MSI) enable rapid and specific detection of lipids directly from thin tissue sections. In this study, we performed multimodal imaging of acylcarnitines, phosphatidylcholines (PC), a lysophosphatidylcholine (LPC), and a sphingomyelin (SM) from different microenvironments of breast tumor xenograft models, which carried tdTomato red fluorescent protein as a hypoxia-response element-driven reporter gene. The MSI molecular lipid images revealed spatially heterogeneous lipid distributions within tumor tissue. Four of the most-abundant lipid species, namely PC(16:0/16:0), PC(16:0/18:1), PC(18:1/18:1), and PC(18:0/18:1), were localized in viable tumor regions, whereas LPC(16:0/0:0) was detected in necrotic tumor regions. We identified a heterogeneous distribution of palmitoylcarnitine, stearoylcarnitine, PC(16:0/22:1), and SM(d18:1/16:0) sodium adduct, which colocalized primarily with hypoxic tumor regions. For the first time, we have applied a multimodal imaging approach that has combined optical imaging and MALDI-MSI with ion mobility separation to spatially localize and structurally identify acylcarnitines and a variety of lipid species present in breast tumor xenograft models. PMID:22930811

  1. Number of ancestral human species: a molecular perspective.

    PubMed

    Curnoe, D; Thorne, A

    2003-01-01

    Despite the remarkable developments in molecular biology over the past three decades, anthropological genetics has had only limited impact on systematics in human evolution. Genetics offers the opportunity to objectively test taxonomies based on morphology and may be used to supplement conventional approaches to hominid systematics. Our analyses, examining chromosomes and 46 estimates of genetic distance, indicate there may have been only around 4 species on the direct line to modern humans and 5 species in total. This contrasts with current taxonomies recognising up to 23 species. The genetic proximity of humans and chimpanzees has been used to suggest these species are congeneric. Our analysis of genetic distances between them is consistent with this proposal. It is time that chimpanzees, living humans and all fossil humans be classified in Homo. The creation of new genera can no longer be a solution to the complexities of fossil morphologies. Published genetic distances between common chimpanzees and bonobos, along with evidence for interbreeding, suggest they should be assigned to a single species. The short distance between humans and chimpanzees also places a strict limit on the number of possible evolutionary 'side branches' that might be recognised on the human lineage. All fossil taxa were genetically very close to each other and likely to have been below congeneric genetic distances seen for many mammals. Our estimates of genetic divergence suggest that periods of around 2 million years are required to produce sufficient genetic distance to represent speciation. Therefore, Neanderthals and so-called H. erectus were genetically so close to contemporary H. sapiens they were unlikely to have been separate species. Thus, it is likely there was only one species of human (H. sapiens) for most of the last 2 million years. We estimate the divergence time of H. sapiens from 16 genetic distances to be around 1.7 Ma which is consistent with evidence for the earliest

  2. Molecular Species Delimitation in the Racomitrium canescens Complex (Grimmiaceae) and Implications for DNA Barcoding of Species Complexes in Mosses

    PubMed Central

    Stech, Michael; Veldman, Sarina; Larraín, Juan; Muñoz, Jesús; Quandt, Dietmar; Hassel, Kristian; Kruijer, Hans

    2013-01-01

    In bryophytes a morphological species concept is still most commonly employed, but delimitation of closely related species based on morphological characters is often difficult. Here we test morphological species circumscriptions in a species complex of the moss genus Racomitrium, the R. canescens complex, based on variable DNA sequence markers from the plastid (rps4-trnT-trnL region) and nuclear (nrITS) genomes. The extensive morphological variability within the complex has led to different opinions about the number of species and intraspecific taxa to be distinguished. Molecular phylogenetic reconstructions allowed to clearly distinguish all eight currently recognised species of the complex plus a ninth species that was inferred to belong to the complex in earlier molecular analyses. The taxonomic significance of intraspecific sequence variation is discussed. The present molecular data do not support the division of the R. canescens complex into two groups of species (subsections or sections). Most morphological characters, albeit being in part difficult to apply, are reliable for species identification in the R. canescens complex. However, misidentification of collections that were morphologically intermediate between species questioned the suitability of leaf shape as diagnostic character. Four partitions of the molecular markers (rps4-trnT, trnT-trnL, ITS1, ITS2) that could potentially be used for molecular species identification (DNA barcoding) performed almost equally well concerning amplification and sequencing success. Of these, ITS1 provided the highest species discrimination capacity and should be considered as a DNA barcoding marker for mosses, especially in complexes of closely related species. Molecular species identification should be complemented by redefining morphological characters, to develop a set of easy-to-use molecular and non-molecular identification tools for improving biodiversity assessments and ecological research including mosses. PMID

  3. Molecular analysis of phylogenetic relationships among Myrmecophytic macaranga species (Euphorbiaceae).

    PubMed

    Blattner, F R; Weising, K; Bänfer, G; Maschwitz, U; Fiala, B

    2001-06-01

    Many species of the paleotropical pioneer tree genus Macaranga Thou. (Euphorbiaceae) live in association with ants. Various types of mutualistic interactions exist, ranging from the attraction of unspecific ant visitors to obligate myrmecophytism. In the latter, nesting space and food bodies are exchanged for protection by highly specific ant partners (mainly species of the myrmicine genus Crematogaster). As a first step toward elucidating the coevolution of ant-plant interactions in the Macaranga-Crematogaster system, we have initiated a molecular investigation of the plant partners' phylogeny. Nuclear ribosomal DNA internal transcribed spacer (ITS) sequences were analyzed for 73 accessions from 47 Macaranga species, representing 17 sections or informally described species groups. Three accessions from the putative sister taxon Mallotus Lour, were included as outgroups. Cladograms of the ITS data revealed Macaranga to be nested within Mallotus. ITS sequences are highly similar within section Pachystemon s.str., suggesting a relatively recent and rapid radiation of obligate myrmecophytes within this section. Forty-three accessions, mainly of ant-inhabited species, were additionally investigated by random amplified polymorphic DNA (RAPD) and microsatellite-primed PCR (MP-PCR) techniques. Phenetic analysis of RAPD and MP-PCR banding profiles generally confirmed the ITS results. Best resolutions for individual clades were obtained when ITS and RAPD/MP-PCR data were combined into a single matrix and analyzed phenetically. The combined analysis suggests multiple (four) rather than a single evolutionary origin of myrmecophytism, at least one reversal from obligate myrmecophytism to nonmyrmecophytism, and one loss of mutualistic specifity. PMID:11399144

  4. Dimyristoyl Phosphatidylcholine: A Remarkable Exception to Tocopherol s Membrane Presence

    SciTech Connect

    Marquardt, Drew; Williams, Justin; Kinnun, Justin A.; Kucerka, Norbert; Atkinson, Jeffrey; Wassall, Stephen; Katsaras, John; Harroun, Thad

    2014-01-01

    Using data obtained from different physical techniques (i.e., neutron diffraction, NMR and UV spectroscopy), we present evidence which explains some of the conflicting and inexplicable data found in the literature regarding -tocopherol s (aToc s) behavior in dimyristoyl phosphatidylcholine (di-14:0PC) bilayers. Without exception, the data point to aToc s active chromanol moiety residing deep in the hydrophobic core of di-14:0PC bilayers, a location that is in stark contrast to aToc s location in other PC bilayers. Our result is a clear example of the importance of lipid species diversity in biological membranes and importantly, it suggests that measurements of aToc s oxidation kinetics, and its associated byproducts observed in di-14:0PC bilayers, should be reexamined, this time taking into account its noncanonical location in this bilayer.

  5. Molecular parentage of radical species in the comae of comets

    NASA Astrophysics Data System (ADS)

    Lewis, Benjamin K.

    Understanding the chemical composition of comets is of great interest to the scientific community. In this work, an integral field unit (IFU) spectrograph is used to detect emissions of C2, C3, CH, CN, and NH2. The azimuthal average profile (line integral of the column density as a function of radial distance from the center of the nucleus) is simulated by the Haser model. The Haser model simulates the outgassing and photo-dissociate of molecular species in the coma. In this work, the lifetime of the parent molecule in the photo-dissociation chain is set as a free parameter. The best fit parent lifetimes for observations of comets 4P/Faye, 10P/Tempel 2, and C/2009 P1 Garradd are obtained. The results are compared to parent lifetimes cited in other studies. HCN as a likely dominant parent for CN is eliminated. Constraints on likely parent molecules for C3 and NH 2 are discussed.

  6. Isoniazid interaction with phosphatidylcholine-based membranes

    NASA Astrophysics Data System (ADS)

    Marques, Amanda Vicente; Marengo Trindade, Paulo; Marques, Sheylla; Brum, Tainá; Harte, Etienne; Rodrigues, Marieli Oliveira; D'Oca, Marcelo Gonçalves Montes; da Silva, Pedro Almeida; Pohlmann, Adriana R.; Alves, Isabel Dantas; de Lima, Vânia Rodrigues

    2013-11-01

    Interaction between the anti-tuberculosis drug isoniazid (INH) and phosphatidylcholine membranes was investigated in terms of: (i) drug affinity to a lipid bilayer and (ii) drug-induced changes in the dynamic properties of liposomes, such as membrane hydration state, polar head and non-polar acyl chain order and lipid phase transition behavior. These parameters were studied by plasmon waveguide resonance spectroscopy (PWR), UV-visible, horizontal attenuated total reflectance-Fourier transform infrared (HATR-FTIR), nuclear magnetic resonance (NMR) and differential scanning calorimetry (DSC) techniques. PWR measurements showed an INH membrane dissociation constant value of 0.031 μM to phosphatidylcholine bilayers. INH induced higher membrane perturbation in the plane which is perpendicular to the membrane plane. The INH saturation concentration in phosphatidylcholine liposomes was 170 μM. At this concentration, HATR-FTIR and NMR findings showed that INH may interact with the lipid polar head, increasing the number of hydrogen bonds in the phosphate region and enhancing the choline motional freedom. DSC measurements showed that, at 115 μM, INH was responsible for a decrease in lipid phase transition temperature of approximately 2 °C and had no influence in the lipid enthalpy variation (ΔH). However, at 170 μM, INH induced the reduction of the ΔH by approximately 52%, suggesting that the drug may increase the distance among lipid molecules and enhance the freedom of the lipid acyl chains methylene groups. This paper provides information on the effects of INH on membrane dynamics which is important to understand liposome targeting of the drug and for the development of anti-TB pharmacologic systems that not only are less susceptible to resistance but also have low toxicity.

  7. Spectral identification/elimination of molecular species in spacecraft glow

    NASA Technical Reports Server (NTRS)

    Green, B. D.; Marinelli, W. J.; Rawlins, W. T.

    1985-01-01

    Computer models of molecular electronic and vibrational emission intensities were developed. Known radiative emission rates (Einstein coefficients) permit the determination of relative excited state densities from spectral intensities. These codes were applied to the published spectra of glow above shuttle surface and to the Spacelab 1 results of Torr and Torr. The theoretical high-resolution spectra were convolved with the appropriate instrumental slit functions to allow accurate comparison with data. The published spacelab spectrum is complex but N2+ Meinel emission can be clearly identified in the ram spectrum. M2 First Positive emission does not correlate well with observed features, nor does the CN Red System. Spectral overlay comparisons are presented. The spectrum of glow above shuttle surfaces, in contrast to the ISO data, is not highly structured. Diatomic molecular emission was matched to the observed spectral shape. Source excitation mechanisms such as (oxygen atom)-(surface species) reaction product chemiluminescence, surface recombination, or resonance fluorescent re-emission will be discussed for each tentative assignment. These assignments are the necessary first analytical step toward mechanism identification. Different glow mechanisms will occur above surfaces under different orbital conditions.

  8. Molecular and Cytogenetic Characterization of Wild Musa Species

    PubMed Central

    Čížková, Jana; Hřibová, Eva; Christelová, Pavla; Van den Houwe, Ines; Häkkinen, Markku; Roux, Nicolas; Swennen, Rony; Doležel, Jaroslav

    2015-01-01

    The production of bananas is threatened by rapid spreading of various diseases and adverse environmental conditions. The preservation and characterization of banana diversity is essential for the purposes of crop improvement. The world's largest banana germplasm collection maintained at the Bioversity International Transit Centre (ITC) in Belgium is continuously expanded by new accessions of edible cultivars and wild species. Detailed morphological and molecular characterization of the accessions is necessary for efficient management of the collection and utilization of banana diversity. In this work, nuclear DNA content and genomic distribution of 45S and 5S rDNA were examined in 21 diploid accessions recently added to ITC collection, representing both sections of the genus Musa. 2C DNA content in the section Musa ranged from 1.217 to 1.315 pg. Species belonging to section Callimusa had 2C DNA contents ranging from 1.390 to 1.772 pg. While the number of 45S rDNA loci was conserved in the section Musa, it was highly variable in Callimusa species. 5S rRNA gene clusters were found on two to eight chromosomes per diploid cell. The accessions were genotyped using a set of 19 microsatellite markers to establish their relationships with the remaining accessions held at ITC. Genetic diversity done by SSR genotyping platform was extended by phylogenetic analysis of ITS region. ITS sequence data supported the clustering obtained by SSR analysis for most of the accessions. High level of nucleotide diversity and presence of more than two types of ITS sequences in eight wild diploids pointed to their origin by hybridization of different genotypes. This study significantly expands the number of wild Musa species where nuclear genome size and genomic distribution of rDNA loci is known. SSR genotyping identified Musa species that are closely related to the previously characterized accessions and provided data to aid in their classification. Sequence analysis of ITS region

  9. Extreme isotopologue disequilibrium in molecular SIMS species during SHRIMP geochronology

    NASA Astrophysics Data System (ADS)

    Magee, Charles W., Jr.; Danišík, Martin; Mernagh, Terry

    2016-04-01

    Isotopologue deficits of up to 200 ‰ below ideal mixing are observed in UO2+ species during SIMS gechronological analyses using the SHRIMP IIe instrument. These are identified by bombarding natural U-bearing minerals with an 18O2-primary beam. The large anomalies are associated with repeat analyses down a single SIMS sputtering crater (Compston et al., 1984), analysis of high-uranium, radiation damaged zircon, and analysis of baddeleyite. Analysis of zircon under routine conditions yield UO2+ isotopologue anomalies generally within a few percent of equilibrium. The conditions under which the isotopologue anomalies are observed are also conditions in which the UOx-based corrections, or calibration, for relative U vs. Pb ionization efficiencies fail. The existence of these isotopologue anomalies suggest that failure of the various UOx species to equilibrate with each other is the reason that none of them will successfully correct the U / Pb ratio. No simple isotopologue-based correction is apparent. However, isotopologue disequilibrium appears to be a more sensitive tool for detecting hi U calibration breakdowns than Raman spectroscopy, which showed sharper peaks for ~ 37 Ma high uranium 20 zircons than for reference zircons OG1 and Temora. U-Th-Sm/He ages were determined for aliquots of reference zircons OG1 (755 ± 71 Ma) and Temora (323 ± 43 Ma), suggesting that the broader Raman lines for the Temora reference zircons may be due to something other than accumulated radiation damage. Isotopologue abundances for UO+ and ThO+ and their energy spectra are consistent with most or all molecular species being 25 the product of atomic recombination when the primary beam impact energy is greater than 5.7 kV. This, in addition with the large UO2+ instrumentally generated isotopologue disequilibria, suggest any attempts to use SIMS to detect naturally occurring isotopologue deviations could be tricky.

  10. Molecular instability induced by aluminum stress in Plantago species.

    PubMed

    Correia, Sofia; Matos, Manuela; Ferreira, Vanessa; Martins, Neusa; Gonçalves, Sandra; Romano, Anabela; Pinto-Carnide, Olinda

    2014-08-01

    Aluminum (Al) is one of the most abundant metals on earth's crust and Al toxicity represents one of the major factors that limit plant growth and productivity in acid soils (with a pH≤5.0). In this study the mutagenic/genotoxic effects of Al were evaluated in roots and leaves of two Plantago, species, Plantago almogravensis and Plantago lagopus, using ISSRs markers. Both species were exposed to 400 μM Al during 7 and 21 days. Ten ISSR primers produced polymorphic bands. In P. almogravensis, a total of 257 and 258 bands in roots and 255 and 265 bands in leaves were produced in the presence and absence of Al, respectively. In P. lagopus were produced 279 and 278 a total bands in roots and 275 and 274 bands in leaves, under the same conditions. The changes in ISSR profiles after Al treatment were considered as gain and/or loss of bands compared with the controls. The results suggest that changes in genomic template stability (GTS) could be detected with ISSR profiles. This molecular marker proved to be a good tool to detect the effects of Al on DNA profiles. It seems that Al did not interfere significantly with DNA integrity in both species but generated less ISSR stability in P. almogravensis than in P. lagopus. The results confirm the tolerance of P. almogravensis and suggest the same behavior of P. lagopus. Although further studies are required for confirmation the Al tolerance behavior of P. lagopus, a potential application for phytoremediation can be also considered due its wide distribution. PMID:25344171

  11. Acyl-chain remodeling of dioctanoyl-phosphatidylcholine in Saccharomyces cerevisiae mutant defective in de novo and salvage phosphatidylcholine synthesis

    SciTech Connect

    Kishino, Hideyuki; Eguchi, Hiroki; Takagi, Keiko; Horiuchi, Hiroyuki; Fukuda, Ryouichi; Ohta, Akinori

    2014-03-07

    Highlights: • Dioctanoyl-PC (diC8PC) supported growth of a yeast mutant defective in PC synthesis. • diC8PC was converted to PC species containing longer acyl residues in the mutant. • Both acyl residues of diC8PC were replaced by longer fatty acids in vitro. • This system will contribute to the elucidation of the acyl chain remodeling of PC. - Abstract: A yeast strain, in which endogenous phosphatidylcholine (PC) synthesis is controllable, was constructed by the replacement of the promoter of PCT1, encoding CTP:phosphocholine cytidylyltransferase, with GAL1 promoter in a double deletion mutant of PEM1 and PEM2, encoding phosphatidylethanolamine methyltransferase and phospholipid methyltransferase, respectively. This mutant did not grow in the glucose-containing medium, but the addition of dioctanoyl-phosphatidylcholine (diC8PC) supported its growth. Analyses of the metabolism of {sup 13}C-labeled diC8PC ((methyl-{sup 13}C){sub 3}-diC8PC) in this strain using electrospray ionization tandem mass spectrometry revealed that it was converted to PC species containing acyl residues of 16 or 18 carbons at both sn-1 and sn-2 positions. In addition, both acyl residues of (methyl-{sup 13}C){sub 3}-diC8PC were replaced with 16:1 acyl chains in the in vitro reaction using the yeast cell extract in the presence of palmitoleoyl-CoA. These results indicate that PC containing short acyl residues was remodeled to those with acyl chains of physiological length in yeast.

  12. The role of phosphatidylcholine in fatty acid exchange and desaturation in Brassica napus L. leaves.

    PubMed Central

    Williams, J P; Imperial, V; Khan, M U; Hodson, J N

    2000-01-01

    The role of phosphatidylcholine (PC) in fatty acid exchange and desaturation was examined and compared with that of monogalactosyldiacylglycerol (MGDG) in Brassica napus leaves using (14)C-labelling in vivo. Data are presented which indicate that in the chloroplast newly formed saturated (palmitic acid, 16:0) and monounsaturated (oleic acid, 18:1) fatty acid is incorporated into MGDG and desaturated in situ. In the non-plastidic compartments, however, newly formed fatty acid is exchanged with polyunsaturated fatty acid in PC, the probable major site of subsequent desaturation. The unsaturated fatty acid is released to the acyl-CoA pool, which is then used to synthesize diacylglycerol (DAG) containing a high level of unsaturated fatty acid. This highly unsaturated DAG may be the source for the biosynthesis of other cellular glycerolipids. The generally accepted pathway in which PC is synthesized from molecular species of DAG containing 16:0 and 18:1 followed by desaturation of the 18:1 to linoleic (18:2) and linolenic (18:3) acids is questioned. PMID:10861220

  13. Regulation of Phosphatidylcholine Biosynthesis in Saccharomyces cerevisiae

    PubMed Central

    Waechter, Charles J.; Lester, Robert L.

    1971-01-01

    Evidence is presented which indicates that the biosynthesis of phosphatidylcholine by the methylation pathway in growing cultures of Saccharomyces cerevisiae is repressed by the presence of choline in the growth medium. This result, obtained previously for glucose-grown cells, was also observed for lactate-grown cells, of which half of the phosphatidylcholine is mitochondrial. A respiration-deficient mutant of the parent wild-type strain has been studied, and its inability to form functional mitochondria cannot be due to an impaired methylation pathway, as it has been shown to incorporate 14C-CH3-methionine into all of the methylated glycerophosphatides. The incorporation rate is depressed by the inclusion of 1 mm choline in the growth medium, suggesting a regulatory effect similar to that demonstrated for the wild-type strain. The effects of choline on the glycerophospholipid composition of lactate and glucose-grown cells is presented. The repressive effects of the two related bases, mono- and dimethylethanolamine, were examined, and reduced levels of 14C-CH3-methionine incorporation were found for cells grown in the presence of these bases. The effect of choline on the methylation rates is reversible and glucosegrown cells regain the nonrepressed level of methylation activity in 60 to 80 min after removal of choline from the growth medium. Images PMID:5547992

  14. Hypolipidemic drugs are inhibitors of phosphatidylcholine synthesis.

    PubMed Central

    Parthasarathy, S; Kritchevsky, D; Baumann, W J

    1982-01-01

    Clofibric acid (CPIB) and several other systemic hypolipidemic drugs are shown to block phosphatidylcholine synthesis by inhibiting cholinephosphotransferase (ChoPTase; CDPcholine:1,2-diacylglycerol cholinephosphotransferase, EC 2.7.8.2) and particularly lysolecithin acyltransferase (LLAcylTase; acyl-CoA:1-acylglycero-3-phosphocholine O-acyltransferase, EC 2.3.1.23) of rat liver microsomes. Whereas millimolar drug concentrations are required to affect de novo lecithin synthesis catalyzed by ChoPTase, reacylation of lysolecithin by LLAcylTase is inhibited at micromolar levels. Increasing effectiveness in ChoPTase inhibition is observed in the series CPIB, SaH-42-348, tibric acid, S-321328, WY-14643, S-8527, and DH-990, with IC50 ranging from 22 mM (CPIB) to 0.3 mM (DH-990). LLAcylTase inhibition by the hypolipidemic drugs follows the same general pattern, but IC50 concentrations range from 9 mM (CPIB) to 40 microM (DH-990). The agents inhibit ChoPTase (Ki, 25-0.25 mM) and LLAcylTase (Ki, 10-0.025 mM) noncompetitively. The data suggest that inhibition of phosphatidylcholine synthesis, particularly by the LLAcylTase pathway, may be related to a drug's effectiveness in decreasing serum triglyceride and cholesterol levels by blocking lipoprotein synthesis. PMID:6294663

  15. Integrating a Numerical Taxonomic Method and Molecular Phylogeny for Species Delimitation of Melampsora Species (Melampsoraceae, Pucciniales) on Willows in China

    PubMed Central

    Zhao, Peng; Wang, Qing-Hong; Tian, Cheng-Ming; Kakishima, Makoto

    2015-01-01

    The species in genus Melampsora are the causal agents of leaf rust diseases on willows in natural habitats and plantations. However, the classification and recognition of species diversity are challenging because morphological characteristics are scant and morphological variation in Melampsora on willows has not been thoroughly evaluated. Thus, the taxonomy of Melampsora species on willows remains confused, especially in China where 31 species were reported based on either European or Japanese taxonomic systems. To clarify the species boundaries of Melampsora species on willows in China, we tested two approaches for species delimitation inferred from morphological and molecular variations. Morphological species boundaries were determined based on numerical taxonomic analyses of morphological characteristics in the uredinial and telial stages by cluster analysis and one-way analysis of variance. Phylogenetic species boundaries were delineated based on the generalized mixed Yule-coalescent (GMYC) model analysis of the sequences of the internal transcribed spacer (ITS1 and ITS2) regions including the 5.8S and D1/D2 regions of the large nuclear subunit of the ribosomal RNA gene. Numerical taxonomic analyses of 14 morphological characteristics recognized in the uredinial-telial stages revealed 22 morphological species, whereas the GMYC results recovered 29 phylogenetic species. In total, 17 morphological species were in concordance with the phylogenetic species and 5 morphological species were in concordance with 12 phylogenetic species. Both the morphological and molecular data supported 14 morphological characteristics, including 5 newly recognized characteristics and 9 traditionally emphasized characteristics, as effective for the differentiation of Melampsora species on willows in China. Based on the concordance and discordance of the two species delimitation approaches, we concluded that integrative taxonomy by using both morphological and molecular variations was

  16. Molecular characterisation of species and genotypes of Cryptosporidium and Giardia and assessment of zoonotic transmission

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The molecular characterization of species and genotypes of Cryptosporidium and Giardia is essential for accurately identifying organisms and assessing zoonotic transmission. Results of recent molecular epidemiologic studies strongly suggest that zoonotic transmission plays an important role in crypt...

  17. Molecular studies on the species complex of Trichosirocalus horridus in the biological control of Carduinae weeds.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genus Trichosirocalus Colonnelli, 1979, (Coleoptera, Curculionidae, Ceutorhynchinae) includes 17 Palaearctic species mainly feeding on Plantaginaceae and Asteraceae. We studied the taxonomic status of the species complex of Trichosirocalus horridus (TH) by means of molecular markers. We used bot...

  18. Molecular Evidence of Different Rickettsia Species in Villeta, Colombia.

    PubMed

    Faccini-Martínez, Álvaro A; Ramírez-Hernández, Alejandro; Forero-Becerra, Elkin; Cortés-Vecino, Jesús A; Escandón, Patricia; Rodas, Juan D; Palomar, Ana M; Portillo, Aránzazu; Oteo, José A; Hidalgo, Marylin

    2016-02-01

    The aim of this work was to detect and identify Rickettsia species in ticks collected in rural areas of Villeta, Colombia. Tick specimens were collected from domestic animals and walls of houses in five rural villages of Villeta town and from humans in Naranjal village (same town). Moreover, a flea collected from the same area was also processed. DNA was extracted and tested by conventional, semi-nested, and nested PCR reactions targeting rickettsial genes. In the ticks collected from humans from Naranjal village, a nymph of Amblyomma cajennense sensu lato was amplified using primers for ompA and sequenced (100% identity with "Candidatus Rickettsia amblyommii"). Last, three amplicons from the Ctenocephalides felis flea, corresponding to gltA, ompB, and 16S rRNA genes, showed high identity with R. felis (98.5%, 97.3%, and 99.2%, respectively) and "Candidatus Rickettsia asemboensis" (99.7% and 100%, respectively). To our knowledge, these results correspond to the first molecular detection in Colombia of "Candidatus Rickettsia amblyommii" and "Ca. Rickettsia asemboensis" in fleas. PMID:26789730

  19. Rubber molecular weight regulation, in vitro, in plant species that produce high and low molecular weights in vivo.

    PubMed

    Cornish, K; Castillón, J; Scott, D J

    2000-01-01

    In three rubber-producing species, in vitro, the rates of initiation and polymerization and the biopolymer molecular weight produced were affected by the concentration of farnesyl diphosphate (FPP) initiator and isopentenyl diphosphate (IPP) elongation substrate (monomer). Ficus elastica, a low molecular weight-producer in vivo, synthesized rubber polymers approximately twice the molecular weight of those made by Hevea brasiliensis or Parthenium argentatum (which produce high molecular weights in vivo), possibly due to its lower IPP Km. In all species, increasing FPP concentrations increased rubber biosynthetic rate and new molecules initiated but decreased molecular weight by competition with the allylic diphosphate (APP) end of elongating rubber molecules for the APP binding site. Increasing IPP concentrations increased rubber biosynthetic rate and rubber molecular weight, but only when FPP concentrations were below the FPP Km's or where negative cooperativity operated. In conclusion, rubber transferase is not the prime regulator of rubber molecular weight in vivo. PMID:11710193

  20. Phosphatidylcholine: Greasing the Cholesterol Transport Machinery

    PubMed Central

    Lagace, Thomas A.

    2015-01-01

    Negative feedback regulation of cholesterol metabolism in mammalian cells ensures a proper balance of cholesterol with other membrane lipids, principal among these being the major phospholipid phosphatidylcholine (PC). Processes such as cholesterol biosynthesis and efflux, cholesteryl ester storage in lipid droplets, and uptake of plasma lipoproteins are tuned to the cholesterol/PC ratio. Cholesterol-loaded macrophages in atherosclerotic lesions display increased PC biosynthesis that buffers against elevated cholesterol levels and may also facilitate cholesterol trafficking to enhance cholesterol sensing and efflux. These same mechanisms could play a generic role in homeostatic responses to acute changes in membrane free cholesterol levels. Here, I discuss the established and emerging roles of PC metabolism in promoting intracellular cholesterol trafficking and membrane lipid homeostasis. PMID:27081313

  1. Surfactant phosphatidylcholine metabolism and surfactant function in preterm, ventilated lambs

    SciTech Connect

    Jobe, A.H.; Ikegami, M.; Seidner, S.R.; Pettenazzo, A.; Ruffini, L.

    1989-02-01

    Preterm lambs were delivered at 138 days gestational age and ventilated for periods up to 24 h in order to study surfactant metabolism and surfactant function. The surfactant-saturated phosphatidylcholine pool in the alveolar wash was 13 +/- 4 mumol/kg and did not change from 10 min to 24 h after birth. Trace amounts of labeled natural sheep surfactant were mixed with fetal lung fluid at birth. By 24 h, 80% of the label had become lung-tissue-associated, yet there was no loss of label from phosphatidylcholine in the lungs when calculated as the sum of the lung tissue plus alveolar wash. De novo synthesized phosphatidylcholine was labeled with choline given by intravascular injection at 1 h of age. Labeled phosphatidylcholine accumulated in the lung tissue linearly to 24 h, and the labeled phosphatidylcholine moved through lamellar body to alveolar pools. The turnover time for alveolar phosphatidylcholine was estimated to be about 13 h, indicating an active metabolic pool. A less surface-active surfactant fraction recovered as a supernatant after centrifugation of the alveolar washes at 40,000 x g increased from birth to 10 min of ventilation, but no subsequent changes in the distribution of surfactant phosphatidylcholine in surfactant fractions occurred. The results were consistent with recycling pathway(s) that maintained surface-active surfactant pools in preterm ventilated lambs.

  2. The mechanism of intestinal absorption of phosphatidylcholine in rats

    PubMed Central

    Parthasarathy, Sampath; Subbaiah, Papasani V.; Ganguly, Jagannath

    1974-01-01

    1. The mechanism of absorption of phosphatidylcholine was studied in rats by injecting into the intestine phosphatidylcholine specifically labelled either in the fatty acid or in the glycerol moiety or with 32P, when considerable amounts of 1-acyl-lysophosphatidylcholine were found in the intestinal lumen. 2-([14C]Acyl)phosphatidylcholine gave markedly more radioactive unesterified fatty acids in the lumen, compared with the 1-([14C]acyl) derivative. Some of the radioactivity from either the fatty acid or the glycerol moiety of the injected phosphatidylcholine appeared in the mucosal triacylglycerols. 2. Injection of 32P-labelled phosphatidylcholine or 32P-labelled lysophosphatidylcholine led to the appearance of radioactive glycerylphosphorylcholine, glycerophosphate and Pi in the mucosa. 3. Rat mucosa was found to contain a highly active glycerylphosphorylcholine diesterase. 4. It was concluded that the dietary phosphatidylcholine is hydrolysed in the intestinal lumen by the pancreatic phospholipase A to 1-acylglycerylphosphorylcholine, which on entering the mucosal cell is partly reacylated to phosphatidylcholine, and the rest is further hydrolysed to glycerylphosphorylcholine, glycerophosphate, glycerol and Pi. The fatty acids and glycerophosphate are then reassembled to give triacylglycerols via the Kennedy (1961) pathway. PMID:4374941

  3. Molecular species of diacylglycerols and triacylglycerols containing dihydroxy fatty acids in castor oil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The identification of four molecular species of diacylglycerols and eight molecular species of triacylglycerols containing dihydroxy fatty acids in castor oil was reported. The structures of the three dihydroxy fatty acids were proposed as 11,12-dihydroxy-9-octadecenoic acid, 11,12-dihydroxy-9,13-oc...

  4. IDENTIFICATION AND QUANTIFICATION OF THE MOLECULAR SPECIES OF ACYLGLYCEROLS IN CASTOR OIL BY HPLC USING ELSD

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sixteen molecular species of acylglycerols (AG) in castor oil have been identified and quantified using HPLC. ELSD (evaporative light scattering detection) responses of different amounts of the standards of molecular species of AG were nearly linear and similar. In general, the addition of a double ...

  5. Element selective detection of molecular species applying chromatographic techniques and diode laser atomic absorption spectrometry.

    PubMed

    Kunze, K; Zybin, A; Koch, J; Franzke, J; Miclea, M; Niemax, K

    2004-12-01

    Tunable diode laser atomic absorption spectroscopy (DLAAS) combined with separation techniques and atomization in plasmas and flames is presented as a powerful method for analysis of molecular species. The analytical figures of merit of the technique are demonstrated by the measurement of Cr(VI) and Mn compounds, as well as molecular species including halogen atoms, hydrogen, carbon and sulfur. PMID:15561625

  6. Biliary phosphatidylcholine and lysophosphatidylcholine profiles in sclerosing cholangitis

    PubMed Central

    Gauss, Annika; Ehehalt, Robert; Lehmann, Wolf-Dieter; Erben, Gerhard; Weiss, Karl-Heinz; Schaefer, Yvonne; Kloeters-Plachky, Petra; Stiehl, Adolf; Stremmel, Wolfgang; Sauer, Peter; Gotthardt, Daniel Nils

    2013-01-01

    AIM: To analyze phospholipid profiles in intrahepatic bile from patients with primary sclerosing cholangitis (PSC) and secondary sclerosing cholangitis (SSC). METHODS: Intrahepatic bile specimens collected via endoscopic retrograde cholangiography from 41 patients were analyzed. Fourteen of these patients were diagnosed with PSC, 10 with SSC, 11 with choledocholithiasis or no identifiable biliary disease, and 6 with cholangiocellular carcinoma (CCC). Bile acid, cholesterol, protein, and bilirubin contents as well as pancreas lipase activity in bile were determined by biochemical methods. Phosphatidylcholine (PC) and lysophosphatidylcholine (LPC) species were quantified using nano-electrospray ionization tandem mass spectrometry. RESULTS: Bile from all the examined patient groups showed a remarkably similar PC and LPC species composition, with only minor statistical differences. Total biliary PC concentrations were highest in controls (8030 ± 1843 μmol/L) and lowest in patients with CCC (1969 ± 981 μmol/L) (P = 0.005, controls vs SSC and CCC, respectively, P < 0.05). LPC contents in bile were overall low (4.2% ± 1.8%). Biliary LPC/PC ratios and ratios of biliary PC to bilirubin, PC to cholesterol, PC to protein, and PC to bile acids showed no intergroup differences. CONCLUSION: PC and LPC profiles being similar in patients with or without sclerosing cholangitis, these phospholipids are likely not of major pathogenetic importance in this disease group. PMID:24023488

  7. Biosynthetic preparation of selectively deuterated phosphatidylcholine in genetically modified Escherichia coli

    PubMed Central

    Maric, Selma; Thygesen, Mikkel B.; Schiller, Jürgen; Marek, Magdalena; Moulin, Martine; Haertlein, Michael; Forsyth, V. Trevor; Bogdanov, Mikhail; Dowhan, William; Arleth, Lise

    2014-01-01

    Phosphatidylcholine (PC) is a major component of eukaryotic cell membranes and one of the most commonly used phospholipids for reconstitution of membrane proteins into carrier systems such as lipid vesicles, micelles and nanodiscs. Selectively deuterated versions of this lipid have many applications, especially in structural studies using techniques such as NMR, neutron reflectivity and small-angle neutron scattering. Here we present a comprehensive study of selective deuteration of phosphatidylcholine through biosynthesis in a genetically modified strain of Escherichia coli. By carefully tuning the deuteration level in E. coli growth media and varying the deuteration of supplemented carbon sources, we show that it is possible to achieve a controlled deuteration for three distinct parts of the PC lipid molecule, namely the (a) lipid head group, (b) glycerol backbone and (c) fatty acyl tail. This biosynthetic approach paves the way for the synthesis of specifically deuterated, physiologically relevant phospholipid species which remain difficult to obtain through standard chemical synthesis. PMID:25301578

  8. Phylogenetic molecular species delimitations unravel potential new species in the pest genus Spodoptera Guenée, 1852 (Lepidoptera, Noctuidae).

    PubMed

    Dumas, Pascaline; Barbut, Jérôme; Le Ru, Bruno; Silvain, Jean-François; Clamens, Anne-Laure; d'Alençon, Emmanuelle; Kergoat, Gael J

    2015-01-01

    Nowadays molecular species delimitation methods promote the identification of species boundaries within complex taxonomic groups by adopting innovative species concepts and theories (e.g. branching patterns, coalescence). As some of them can efficiently deal with large single-locus datasets, they could speed up the process of species discovery compared to more time consuming molecular methods, and benefit from the existence of large public datasets; these methods can also particularly favour scientific research and actions dealing with threatened or economically important taxa. In this study we aim to investigate and clarify the status of economically important moths species belonging to the genus Spodoptera (Lepidoptera, Noctuidae), a complex group in which previous phylogenetic analyses and integrative approaches already suggested the possible occurrence of cryptic species and taxonomic ambiguities. In this work, the effectiveness of innovative (and faster) species delimitation approaches to infer putative species boundaries has been successfully tested in Spodoptera, by processing the most comprehensive dataset (in terms of number of species and specimens) ever achieved; results are congruent and reliable, irrespective of the set of parameters and phylogenetic models applied. Our analyses confirm the existence of three potential new species clusters (for S. exigua (Hübner, 1808), S. frugiperda (J.E. Smith, 1797) and S. mauritia (Boisduval, 1833)) and support the synonymy of S. marima (Schaus, 1904) with S. ornithogalli (Guenée, 1852). They also highlight the ambiguity of the status of S. cosmiodes (Walker, 1858) and S. descoinsi Lalanne-Cassou & Silvain, 1994. This case study highlights the interest of molecular species delimitation methods as valuable tools for species discovery and to emphasize taxonomic ambiguities. PMID:25853412

  9. Phylogenetic Molecular Species Delimitations Unravel Potential New Species in the Pest Genus Spodoptera Guenée, 1852 (Lepidoptera, Noctuidae)

    PubMed Central

    Dumas, Pascaline; Barbut, Jérôme; Le Ru, Bruno; Silvain, Jean-François; Clamens, Anne-Laure; d’Alençon, Emmanuelle; Kergoat, Gael J.

    2015-01-01

    Nowadays molecular species delimitation methods promote the identification of species boundaries within complex taxonomic groups by adopting innovative species concepts and theories (e.g. branching patterns, coalescence). As some of them can efficiently deal with large single-locus datasets, they could speed up the process of species discovery compared to more time consuming molecular methods, and benefit from the existence of large public datasets; these methods can also particularly favour scientific research and actions dealing with threatened or economically important taxa. In this study we aim to investigate and clarify the status of economically important moths species belonging to the genus Spodoptera (Lepidoptera, Noctuidae), a complex group in which previous phylogenetic analyses and integrative approaches already suggested the possible occurrence of cryptic species and taxonomic ambiguities. In this work, the effectiveness of innovative (and faster) species delimitation approaches to infer putative species boundaries has been successfully tested in Spodoptera, by processing the most comprehensive dataset (in terms of number of species and specimens) ever achieved; results are congruent and reliable, irrespective of the set of parameters and phylogenetic models applied. Our analyses confirm the existence of three potential new species clusters (for S. exigua (Hübner, 1808), S. frugiperda (J.E. Smith, 1797) and S. mauritia (Boisduval, 1833)) and support the synonymy of S. marima (Schaus, 1904) with S. ornithogalli (Guenée, 1852). They also highlight the ambiguity of the status of S. cosmiodes (Walker, 1858) and S. descoinsi Lalanne-Cassou & Silvain, 1994. This case study highlights the interest of molecular species delimitation methods as valuable tools for species discovery and to emphasize taxonomic ambiguities. PMID:25853412

  10. The yeast phospholipid N-methyltransferases catalyzing the synthesis of phosphatidylcholine preferentially convert di-C16:1 substrates both in vivo and in vitro.

    PubMed

    Boumann, Henry A; Chin, Patrick T K; Heck, Albert J R; De Kruijff, Ben; De Kroon, Anton I P M

    2004-09-24

    Phosphatidylcholine (PC) is an important and abundant structural component of the membranes of eukaryotic cells. In the yeast Saccharomyces cerevisiae, the primary route for the biosynthesis of PC consists of three consecutive methylation steps of phosphatidylethanolamine (PE) catalyzed by the phospholipid N-methyltransferases Cho2p and Opi3p. To investigate how these biosynthetic enzymes contribute to the composition of the PC species profile, the precursor-product relationships between PE and newly synthesized PC were determined at the level of the molecular species by using electrospray ionization tandem mass spectrometry and stable isotope labeling. In vivo labeling of yeast cells for 10 min with [methyl-D3]methionine revealed the preferential methylation of di-C16:1 PE over a range of PE species compositions. A similar preferential conversion of di-C16:1 PE to PC was found in vitro upon incubating isolated microsomes with S-adenosyl[methyl-D3]methionine. Yeast opi3 and cho2 deletion strains were used to distinguish between the substrate selectivities of Cho2p and Opi3p, respectively. Both biosynthetic enzymes were found to participate in the speciesselective methylation with Cho2p contributing the most. The combined results indicate that the selective methylation of PE species by the methyltransferases plays an important role in shaping the steady-state profile of PC molecular species in yeast. PMID:15258140

  11. Elucidation of molecular dynamics of invasive species of rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cultivated rice fields are aggressively invaded by weedy rice in the U.S. and worldwide. Weedy rice results in loss of yield and seed contamination. The molecular dynamics of the evolutionary adaptive traits of weedy rice are not fully understood. To understand the molecular basis and identify the i...

  12. Interaction of dipalmitoyl phosphatidylcholine (DPPC) liposomes and insulin

    NASA Astrophysics Data System (ADS)

    Mady, Mohsen M.; Elshemey, Wael M.

    2011-06-01

    Insulin, a peptide that has been used for decades in the treatment of diabetes, has well-defined properties and delivery requirements. Liposomes, which are lipid bilayer vesicles, have gained increasing attention as drug carriers which reduce the toxicity and increase the pharmacological activity of various drugs. The molecular interaction between (uncharged lipid) dipalmitoyl phosphatidylcholine (DPPC) liposomes and insulin has been characterized by using Fourier transform infrared spectroscopy (FTIR) and X-ray diffraction. The characteristic protein absorption band peaks, Amide I (at about 1660 cm-1) and Amide II band (at about 1546 cm-1) are potentially reduced in the liposome insulin complex. Wide-angle x-ray scattering measurements showed that the association of insulin with DPPC lipid of liposomes still maintains the characteristic DPPC diffraction peaks with almost no change in relative intensities or change in peak positions. The absence of any shift in protein peak positions after insulin being associated with DPPC liposomes indicates that insulin is successfully forming complex with DPPC liposomes with possibly no pronounced alterations in the structure of insulin molecule.

  13. Phosphatidylcholine and the CDP-Choline Cycle

    PubMed Central

    Fagone, Paolo; Jackowski, Suzanne

    2012-01-01

    The CDP-choline pathway of phosphatidylcholine (PtdCho) biosynthesis was first described more than 50 years ago. Investigation of the CDP-choline pathway in yeast provides a basis for understanding the CDP-choline pathway in mammals. PtdCho is considered as an intermediate in a cycle of synthesis and degradation, and the activity of a CDP-choline cycle is linked to subcellular membrane lipid movement. The components of the mammalian CDP-choline pathway include choline transport, choline kinase, phosphocholine cytidylyltransferase, and choline phosphotransferase activities. The protein isoforms and biochemical mechanisms of regulation of the pathway enzymes are related to their cell and tissue-specific functions. Regulated PtdCho turnover mediated by phospholipases or neuropathy target esterase participates in the mammalian CDP-choline cycle. Knockout mouse models define the biological functions of the CDP-choline cycle in mammalian cells and tissues. This article is part of a Special Issue entitled Phospholipids and Phospholipid Metabolism. PMID:23010477

  14. Regulation of phosphatidylcholine synthesis in rat liver endoplasmic reticulum.

    PubMed Central

    Sribney, M; Knowles, C L; Lyman, E M

    1976-01-01

    The biosynthesis of phosphatidylcholine in rat liver microsomal preparations catalysed by CDP-choline-1,2-diacylglycerol cholinephosphotransferase (EC 2.7.8.2) was inhibited by a combination of ATP and CoA or ATP and pantetheine. ATP alone at high concentrations (20 mM) inhibits phosphatidylcholine formation to the extent of 70%. In the presence of 0.1 mM-CoA, ATP (2 mM) inhibits to the extent of 80% and in the presence of 1 mM-pantetheine to the extent of 90%. ADP and other nucleotide triphosphates in combination with either CoA or pantetheine are only 10-30% as effective in inhibiting phosphatidylcholine synthesis. AMP(CH2)PP [adenosine 5'-(alphabeta-methylene)triphosphate] together with CoA inhibits to the extent of 59% and with pantetheine by 48%. AMP-P(CH2)P [adenosine 5'-(betagamma-methylene)triphosphate] together with either CoA or pantetheine had no significant effect on phosphatidylcholine formation. Other closely related derivatives of pantothenic acid were without effect either alone or in the presence of ATP, as were thiol compounds such as cysteine, homocysteine, cysteamine, dithiothreitol and glutathione. Several mechanisms by which this inhibition might take place were ruled out and it is concluded that ATP together with either CoA or pantetheine interacts reversibly with phosphatidylcholine synthetase to cause temporarily the inhibition of phosphatidylcholine formation. PMID:182154

  15. Ecology has contrasting effects on genetic variation within species versus rates of molecular evolution across species in water beetles.

    PubMed

    Fujisawa, Tomochika; Vogler, Alfried P; Barraclough, Timothy G

    2015-01-22

    Comparative analysis is a potentially powerful approach to study the effects of ecological traits on genetic variation and rate of evolution across species. However, the lack of suitable datasets means that comparative studies of correlates of genetic traits across an entire clade have been rare. Here, we use a large DNA-barcode dataset (5062 sequences) of water beetles to test the effects of species ecology and geographical distribution on genetic variation within species and rates of molecular evolution across species. We investigated species traits predicted to influence their genetic characteristics, such as surrogate measures of species population size, latitudinal distribution and habitat types, taking phylogeny into account. Genetic variation of cytochrome oxidase I in water beetles was positively correlated with occupancy (numbers of sites of species presence) and negatively with latitude, whereas substitution rates across species depended mainly on habitat types, and running water specialists had the highest rate. These results are consistent with theoretical predictions from nearly-neutral theories of evolution, and suggest that the comparative analysis using large databases can give insights into correlates of genetic variation and molecular evolution. PMID:25621335

  16. Ecology has contrasting effects on genetic variation within species versus rates of molecular evolution across species in water beetles

    PubMed Central

    Fujisawa, Tomochika; Vogler, Alfried P.; Barraclough, Timothy G.

    2015-01-01

    Comparative analysis is a potentially powerful approach to study the effects of ecological traits on genetic variation and rate of evolution across species. However, the lack of suitable datasets means that comparative studies of correlates of genetic traits across an entire clade have been rare. Here, we use a large DNA-barcode dataset (5062 sequences) of water beetles to test the effects of species ecology and geographical distribution on genetic variation within species and rates of molecular evolution across species. We investigated species traits predicted to influence their genetic characteristics, such as surrogate measures of species population size, latitudinal distribution and habitat types, taking phylogeny into account. Genetic variation of cytochrome oxidase I in water beetles was positively correlated with occupancy (numbers of sites of species presence) and negatively with latitude, whereas substitution rates across species depended mainly on habitat types, and running water specialists had the highest rate. These results are consistent with theoretical predictions from nearly-neutral theories of evolution, and suggest that the comparative analysis using large databases can give insights into correlates of genetic variation and molecular evolution. PMID:25621335

  17. The selective utilization of substrates in vivo by the phosphatidylethanolamine and phosphatidylcholine biosynthetic enzymes Ept1p and Cpt1p in yeast.

    PubMed

    Boumann, Henry A; de Kruijff, Ben; Heck, Albert J R; de Kroon, Anton I P M

    2004-07-01

    In yeast, the aminoalcohol phosphotransferases Ept1p and Cpt1p catalyze the final steps in the CDP-ethanolamine and CDP-choline routes leading to phosphatidylethanolamine (PE) and phosphatidylcholine (PC), respectively. To determine how these enzymes contribute to the molecular species profiles of PE and PC in vivo, wild-type, cpt1Delta, and ept1Delta cells were pulse labeled with deuterated ethanolamine and choline. Analysis of newly synthesized PE and PC using electrospray ionization tandem mass spectrometry revealed that PE and PC produced by Ept1p and Cpt1p have different species compositions, demonstrating that the enzymes consume distinct sets of diacylglycerol species in vivo. Using the characteristic phospholipid species profiles produced by Ept1p and Cpt1p as molecular fingerprints, it was also shown that in vivo CDP-monomethylethanolamine is preferentially used as substrate by Ept1p, whereas CDP-dimethylethanolamine and CDP-propanolamine are converted by Cpt1p. PMID:15225629

  18. Molecular relationships between closely related strains and species of nematodes

    NASA Technical Reports Server (NTRS)

    Butler, M. H.; Wall, S. M.; Luehrsen, K. R.; Fox, G. E.; Hecht, R. M.

    1981-01-01

    Electrophoretic comparisons have been made for 24 enzymes in the Bergerac and Bristol strains of Caenorhabditis elegans and the related species, Caenorhabditis briggsae. No variation was detected between the two strains of C. elegans. In contrast, the two species, C. elegans and C. briggsae exhibited electrophoretic differences in 22 of 24 enzymes. A consensus 5S rRNA sequence was determined for C. elegans and found to be identical to that from C. briggsae. By analogy with other species with relatively well established fossil records it can be inferred that the time of divergence between the two nematode species is probably in the tens of millions of years. The limited anatomical evolution during a time period in which proteins undergo extensive changes supports the hypothesis that anatomical evolution is not dependent on overall protein changes.

  19. Molecular Phylogenetic Analysis of the Amiota taurusata Species Group within the Chinese Species, with Descriptions of Two New Species

    PubMed Central

    Shao, Zhen-fang; Li, Tong; Jiang, Jian-jun; Lu, Jin-ming; Chen, Hong-wei

    2014-01-01

    The relationships among six species of the Amiota taurusata Takada, Beppu, & Toda (Diptera: Drosophilidae) species group were investigated based on DNA sequence data of the mitochondrial NADH dehydrogenase subunit 2 (ND2) gene, using three species of the genus Amiota as outgroups. A mitochondrial gene, cytochrome c oxidase I (COI), can be used to discriminate between species of the taurusata group. Two new species are described from South China: A. protuberantis Shao et Chen, sp. nov. and A. shennongi Shao et Chen, sp. nov. A key to all the species of the taurusata group based on morphological characters is provided. PMID:25373180

  20. Molecular evidence for ten species and Oligo-Miocene vicariance within a nominal Australian gecko species (Crenadactylus ocellatus, Diplodactylidae)

    PubMed Central

    2010-01-01

    Background Molecular studies have revealed that many putative 'species' are actually complexes of multiple morphologically conservative, but genetically divergent 'cryptic species'. In extreme cases processes such as non-adaptive diversification (speciation without divergent selection) could mask the existence of ancient lineages as divergent as ecologically and morphologically diverse radiations recognised as genera or even families in related groups. The identification of such ancient, but cryptic, lineages has important ramifications for conservation, biogeography and evolutionary biology. Herein, we use an integrated multilocus genetic dataset (allozymes, mtDNA and nuclear DNA) to test whether disjunct populations of the widespread nominal Australian gecko species Crenadactylus ocellatus include distinct evolutionary lineages (species), and to examine the timing of diversification among these populations. Results We identify at least 10 deeply divergent lineages within the single recognised species Crenadactylus ocellatus, including a radiation of five endemic to the Kimberley region of north-west Australia, and at least four known from areas of less than 100 km2. Lineages restricted to geographically isolated ranges and semi-arid areas across central and western Australia are estimated to have began to diversify in the late Oligocene/early Miocence (~20-30 mya), concurrent with, or even pre-dating, radiations of many iconic, broadly sympatric and much more species-rich Australian vertebrate families (e.g. venomous snakes, dragon lizards and kangaroos). Conclusions Instead of a single species, Crenadactylus is a surprisingly speciose and ancient vertebrate radiation. Based on their deep divergence and no evidence of recent gene flow, we recognise each of the 10 main lineages as candidate species. Molecular dating indicates that the genus includes some of the oldest vertebrate lineages confounded within a single species yet identified by molecular assessments of

  1. Molecular identification of Entamoeba species in savanna woodland chimpanzees (Pan troglodytes schweinfurthii).

    PubMed

    Jirků-Pomajbíková, Kateřina; Čepička, Ivan; Kalousová, Barbora; Jirků, Milan; Stewart, Fiona; Levecke, Bruno; Modrý, David; Piel, Alex K; Petrželková, Klára J

    2016-05-01

    To address the molecular diversity and occurrence of pathogenic species of the genus Entamoeba spp. in wild non-human primates (NHP) we conducted molecular-phylogenetic analyses on Entamoeba from wild chimpanzees living in the Issa Valley, Tanzania. We compared the sensitivity of molecular [using a genus-specific polymerase chain reaction (PCR)] and coproscopic detection (merthiolate-iodine-formaldehyde concentration) of Entamoeba spp. We identified Entamoeba spp. in 72 chimpanzee fecal samples (79%) subjected to species-specific PCRs for six Entamoeba species/groups (Entamoeba histolytica, Entamoeba nuttalli, Entamoeba dispar, Entamoeba moshkovskii, Entamoeba coli and Entamoeba polecki ST2). We recorded three Entamoeba species: E. coli (47%), E. dispar (16%), Entamoeba hartmanni (51%). Coproscopically, we could only distinguish the cysts of complex E. histolytica/dispar/moshkovskii/nuttalli and E. coli. Molecular prevalence of entamoebas was higher than the prevalence based on the coproscopic examination. Our molecular phylogenies showed that sequences of E. dispar and E. coli from Issa chimpanzees are closely related to sequences from humans and other NHP from GenBank. The results showed that wild chimpanzees harbour Entamoeba species similar to those occurring in humans; however, no pathogenic species were detected. Molecular-phylogenetic methods are critical to improve diagnostics of entamoebas in wild NHP and for determining an accurate prevalence of Entamoeba species. PMID:26935395

  2. Studies on ozone-treated phosphatidylcholine

    SciTech Connect

    Butterman, J.A.

    1982-01-01

    A major target of ozone reactivity is the unsaturated acyl side chains of phospholipids. In this study, a model system was established to characterize some of the toxic products generated. When ozone is allowed to react with liposomes prepared from purified phosphatidylcholine, at least two types of hemolytic agents are formed. One type is rapidly produced at 0/sup 0/ in the presence or absence of EDTA. A second type is evolved during storage at 37/sup 0/ in the absence of EDTA. A number of physical and chemical characteristics of the initial hemolytic agents were found: (1) They are heat-labile and are rapidly destroyed at 37/sup 0/ at neutral pH or at 0/sup 0/ above pH 8. (2) The active substances are not volatile and are associated with the light liposomes. (3) They could be extracted into chloroform, but attempts at purification by chromatographic techniques were not successful. (4) Their activity was not associated with hydroperoxides or the majority of the TBA reactive material. The heat-labile hemolytic agents appear to contain carbonyl functional groups which can form hemiaminals or Schiff bases with amines. There appears to be two types of mechanisms which can inhibit the hemolysis induced by the heat-labile hemolytic agents. The first class, consisting of substances such as cysteine, polyamines, heptylamine, semicarbazide, and tryptophan appear to act by chemically reacting with an essential functional group in the hemolytic agent. The second class, of consisting BHT and ascorbic acid appears to quench the propagation of a free radical reaction in the membrane.

  3. Molecular characterization of DSC1 orthologs in invertebrate species.

    PubMed

    Cui, Ying-Jun; Yu, Lin-Lin; Xu, Hai-Jun; Dong, Ke; Zhang, Chuan-Xi

    2012-05-01

    DSC1 and BSC1 are two founding members of a novel family of invertebrate voltage-gated cation channels with close structural and evolutionary relationships to voltage-gated sodium and calcium channels. In this study, we searched the published genome sequences for DSC1 orthologs. DSC1 orthologs were found in all 48 insect species, and in other invertebrate species belonging to phyla Mollusca, Cnidaria, Hemichordata and Echinodermata. However, DSC1 orthologs were not found in four arachnid species, Ixodes scapularis, Rhipicephalus microplus, Tetranychus urticae and Varroa destructor, two species in Annelida or any vertebrate species. We then cloned and sequenced NlSC1 and BmSC1 full-length cDNAs from the brown planthopper (Nilaparvata lugens) and the silkworm (Bombyx mori), respectively. NlSC1 and BmSC1 share about 50% identity with DSC1, and the expression of NlSC1 and BmSC1 transcripts was most abundant in the head and antenna in adults. All DSC1 orthologs contain a unique and conserved DEEA motif, instead of the EEEE or EEDD motif in classical calcium channels or the DEKA motif in sodium channels. Phylogenetic analyses revealed that DSC1 and its orthologs form a separate group distinct from the classical voltage-gated sodium and calcium channels and constitute a unique family of cation channels. The DSC1/BSC1-family channels could be potential targets of new and safe insecticides for pest control. PMID:22321571

  4. Retarded release phosphatidylcholine benefits patients with chronic active ulcerative colitis

    PubMed Central

    Stremmel, W; Merle, U; Zahn, A; Autschbach, F; Hinz, U; Ehehalt, R

    2005-01-01

    Background and aims: We examined the hypothesis of an anti-inflammatory effect of phosphatidylcholine in ulcerative colitis. Methods: A phase IIA, double blind, randomised, placebo controlled study was performed in 60 patients with chronic active, non steroid dependent, ulcerative colitis, with a clinical activity index (CAI) of ⩾4. Retarded release phosphatidylcholine rich phospholipids and placebo were administered at a dose of 6 g daily over three months. The primary end point was a change in CAI towards clinical remission (CAI ⩽3) or CAI improvement by ⩾50%. Secondary end points included ⩾50% changes in endoscopic activity index (EAI), histology, and quality of life scores. Results: Induction of clinical remission (CAI ⩽3) as the primary outcome variable was attained by 16 (53%) patients in the phosphatidylcholine treated group compared with three (10%) in the placebo group (p<0.00001). The rate of clinical remission and CAI improvement was 90% in the phosphatidylcholine group and only 10% in the placebo group. A median drop of seven points in the CAI score (70% improvement) was recorded in the phosphatidylcholine group compared with no change in the placebo group. Secondary end point analysis revealed concomitant drops in EAI and histology scores (p = 0.00016 and p = 0.0067 compared with placebo, respectively). Improvement in quality of life was reported by 16 of 29 evaluated patients in the phosphatidylcholine group compared with two of 30 in the placebo group (p = 0.00005). Conclusion: Retarded release oral phosphatidylcholine is effective in alleviating inflammatory activity caused by ulcerative colitis. PMID:15951544

  5. Molecular Detection of a Potentially Toxic Diatom Species

    PubMed Central

    Dhar, Bidhan Chandra; Cimarelli, Lucia; Singh, Kumar Saurabh; Brandi, Letizia; Brandi, Anna; Puccinelli, Camilla; Marcheggiani, Stefania; Spurio, Roberto

    2015-01-01

    A few diatom species produce toxins that affect human and animal health. Among these, members of the Pseudo-nitzschia genus were the first diatoms unambiguously identified as producer of domoic acid, a neurotoxin affecting molluscan shell-fish, birds, marine mammals, and humans. Evidence exists indicating the involvement of another diatom genus, Amphora, as a potential producer of domoic acid. We present a strategy for the detection of the diatom species Amphora coffeaeformis based on the development of species-specific oligonucleotide probes and their application in microarray hybridization experiments. This approach is based on the use of two marker genes highly conserved in all diatoms, but endowed with sufficient genetic divergence to discriminate diatoms at the species level. A region of approximately 450 bp of these previously unexplored marker genes, coding for elongation factor 1-a (eEF1-a) and silicic acid transporter (SIT), was used to design oligonucleotide probes that were tested for specificity in combination with the corresponding fluorescently labeled DNA targets. The results presented in this work suggest a possible use of this DNA chip technology for the selective detection of A. coffeaeformis in environmental settings where the presence of this potential toxin producer may represent a threat to human and animal health. In addition, the same basic approach can be adapted to a wider range of diatoms for the simultaneous detection of microorganisms used as biomarkers of different water quality levels. PMID:25955528

  6. Molecular Structure and Stability of Dissolved Lithium Polysulfide Species

    SciTech Connect

    Vijayakumar, M.; Govind, Niranjan; Walter, Eric D.; Burton, Sarah D.; Shukla, Anil K.; Devaraj, Arun; Xiao, Jie; Liu, Jun; Wang, Chong M.; Karim, Ayman M.; Thevuthasan, Suntharampillai

    2014-01-01

    Ability to predict the solubility and stability of lithium polysulfide is vital in realizing longer lasting lithium-sulfur batteries. Herein we report a combined computational and experimental spectroscopic analysis to understand the dissolution mechanism of lithium polysulfide species in an aprotic solvent medium. Multinuclear NMR and sulfur K-edge X-ray absorption (XAS) analysis reveals that the lithium exchange between polysulfide species and solvent molecule constitutes the first step in the dissolution process. Lithium exchange leads to de-lithiated polysulfide ions which subsequently forms highly reactive free radicals through disproportion reaction. The energy required for the disproportion and possible dimer formation reactions of the polysulfide species are analyzed using density functional theory (DFT) calculations. We validate our calculations with variable temperature electron spin resonance (ESR) measurements. Based on these findings, we discuss approaches to optimize the electrolyte in order to control the polysulfide solubility. The energy required for the disproportion and possible dimer formation reactions of the polysulfide species are analyzed using density functional theory (DFT) calculations. We validate our calculations with variable temperature electron spin resonance (ESR) measurements. Based on these findings, we discuss approaches to optimize the electrolyte in order to control the polysulfide solubility.

  7. Diabetes-induced changes in specific lipid molecular species in rat myocardium.

    PubMed Central

    Han, X; Abendschein, D R; Kelley, J G; Gross, R W

    2000-01-01

    Intrinsic cardiac dysfunction during the diabetic state has been causally linked to changes in myocardial lipid metabolism. However, the precise alterations in the molecular species of myocardial polar and non-polar lipids during the diabetic state and their responses to insulin have not been investigated. Herein we demonstrate four specific alterations in rat myocardial lipid molecular species after induction of the diabetic state by streptozotocin treatment: (i) a massive remodelling of triacylglycerol molecular species including a >5-fold increase in tripalmitin mass and a 60% decrease in polyunsaturated triacylglycerol molecular species mass (i.e. triacylglycerols containing at least one acyl residue with more than two double bonds); (ii) a 46% increase in myocardial phosphatidylinositol mass; (iii) a 44% increase in myocardial plasmenylethanolamine mass and (iv) a 22% decrease in 1-stearoyl-2-arachidonoyl phosphatidylethanolamine content. Each of the changes in phospholipid classes, subclasses and individual molecular species were prevented by insulin treatment after induction of the diabetic state. In sharp contrast, the alterations in triacylglycerol molecular species were not preventable by peripheral insulin treatment after induction of the diabetic state. These results segregate diabetes-induced alterations in myocardial lipid metabolism into changes that can be remedied or not by routine peripheral insulin treatment and suggest that peripheral insulin therapy alone may not be sufficient to correct all of the metabolic alterations present in diabetic myocardium. PMID:11062060

  8. Susceptibility Patterns and Molecular Identification of Trichosporon Species

    PubMed Central

    Rodriguez-Tudela, Juan L.; Diaz-Guerra, Teresa M.; Mellado, Emilia; Cano, Virginia; Tapia, Cecilia; Perkins, Alexander; Gomez-Lopez, Alicia; Rodero, Laura; Cuenca-Estrella, Manuel

    2005-01-01

    The physiological patterns, the sequence polymorphisms of the internal transcriber spacer (ITS), and intergenic spacer regions (IGS) of the rRNA genes and the antifungal susceptibility profile were evaluated for their ability to identify Trichosporon spp. and their specificity for the identification of 49 clinical isolates of Trichosporon spp. Morphological and biochemical methodologies were unable to differentiate among the Trichosporon species. ITS sequencing was also unable to differentiate several species. However, IGS1 sequencing unambiguously identified all Trichosporon isolates. Following the results of DNA-based identification, Trichosporon asahii was the species most frequently isolated from deep sites (15 of 25 strains; 60%). In the main, other Trichosporon species were recovered from cutaneous samples. The majority of T. asahii, T. faecale, and T. coremiiforme clinical isolates exhibited resistance in vitro to amphotericin B, with geometric mean (GM) MICs >4 μg/ml. The other species of Trichosporon did not show high MICs of amphotericin B, and GM MICs were <1 μg/ml. Azole agents were active in vitro against the majority of clinical strains. The most potent compound in vitro was voriconazole, with a GM MIC ≤0.14 μg/ml. The sequencing of IGS correctly identified Trichosporon isolates; however, this technique is not available in many clinical laboratories, and strains should be dispatched to reference centers where these complex methods are available. Therefore, it seems to be more practical to perform antifungal susceptibility testing of all isolates belonging to Trichosporon spp., since correct identification could take several weeks, delaying the indication of an antifungal agent which exhibits activity against the infectious strain. PMID:16189076

  9. Molecular organization of terminal repetitive DNA in Beta species.

    PubMed

    Dechyeva, Daryna; Schmidt, Thomas

    2006-01-01

    We have isolated families of subtelomeric satellite DNA sequences from species of four sections of the genus Beta and from spinach, a related Chenopodiaceae. Twenty-five clones were sequenced and representative repeats of each family were characterized by Southern blotting and FISH. The families of ApaI restriction satellite repeats were designated pAv34, pAc34, the families of RsaI repeats pRp34, pRn34 and pRs34. The repeating units are 344-362 bp long and 45.7-98.8% homologous with a clear species-specific divergence. Each satellite monomer consists of two subrepeats SR1 and SR2 of 165-184 bp, respectively. The repeats of each subrepeat group are highly identical across species, but share only a homology of 40.8-54.8% with members of the other subrepeat group. Two evolutionary steps could be supposed in the phylogeny of the subtelomeric satellite family: the diversification of an ancestor satellite into groups representing SR1 and SR2 in the progenitor of Beta and Spinacea species, followed by the dimerization and diversification of the resulting 360 bp repeats into section-specific satellite DNA families during species radiation. The chromosomal localization of telomeric, subtelomeric and rDNA tandem repeats was investigated by multi-colour FISH. High-resolution analysis by fibre FISH revealed a unique physical organization of B. vulgaris chromosome ends with telomeric DNA and subtelomeric satellites extending over a maximum of 63 kb and 125 kb, respectively. PMID:17195925

  10. Molecular Method for Bartonella Species Identification in Clinical and Environmental Samples▿

    PubMed Central

    García-Esteban, Coral; Gil, Horacio; Rodríguez-Vargas, Manuela; Gerrikagoitia, Xeider; Barandika, Jesse; Escudero, Raquel; Jado, Isabel; García-Amil, Cristina; Barral, Marta; García-Pérez, Ana L.; Bhide, Mangesh; Anda, Pedro

    2008-01-01

    A new, efficient molecular method for detection of Bartonella, based on the 16S-23S rRNA intergenic spacer and 16S rRNA amplification by multiplex PCR combined with reverse line blotting, was designed. This assay could simultaneously detect 20 different known species and other Bartonella species not described previously. PMID:18094134

  11. Molecular epidemiology of Cryptosporidium species in livestock in Ireland.

    PubMed

    Mirhashemi, Marzieh Ezzaty; Zintl, Annetta; Grant, Tim; Lucy, Frances; Mulcahy, Grace; De Waal, Theo

    2016-01-30

    Cryptosporidium is a protozoan that can cause gastro-intestinal illness with diarrhoea in a wide range of hosts. In fact some species of Cryptosporidium can infect the broad range of hosts. The current paper is focused to investigate monthly prevalence and diversity of Cryptosporidium spp. during the spring and early summer (March-June) in 2009 and 2010 in farms with no history of cryptosporidiosis. Animal samples were analyzed to elucidate the prevalence of Cryptosporidium in two regions, West and the East catchments in Ireland. Our investigation demonstrates the prevalence ranges from 14% to 26% an early summer peak (June) was observed. Based on the findings of this study Cryptosporidium ryanae (in cattle, horses), and Cryptosporidium bovis/xiaoi followed by Cryptosporidium parvum (in sheep) were found to be the predominant species in asymptomatic cases. The circulation of other Cryptosporidium species such as C. parvum, C. bovis, C. ubiquitum, C. andersoni and Cryptosporidium horse and pig genotypes in livestock was investigated. PMID:26801590

  12. Synthesis of phosphatidylcholine under possible primitive earth conditions

    NASA Technical Reports Server (NTRS)

    Rao, M.; Eichberg, J.; Oro, J.

    1982-01-01

    Using a primitive earth evaporating pond model, the synthesis of phosphatidylcholine was accomplished when a reaction mixture of choline chloride and disodium phosphatidate, in the presence of cyanamide and traces of acid, was evaporated and heated at temperatures ranging from 25 to 100 C for 7 hours. Optimum yields of about 15% were obtained at 80 C. Phosphatidylcholine was identified by chromatographic, chemical and enzymatic degradation methods. On enzymatic hydrolysis with phospholipase A2 and phospholipase C, lysophosphatidylcholine and phosphorylcholine were formed, respectively. Alkaline hydrolysis gave glycerophosphorylcholine. The synthesis of phosphatidylcholine as the major compound was accompanied by the formation of lysophosphatidylcholine in smaller amounts. Cyanamide was found to be essential for the formation of phosphatidylcholine, and only traces of HCl, of the order of that required to convert the disodium phosphatidate to free phosphatidic acid were found necessary for the synthesis. This work suggests that phosphatidylcholine, which is an essential component of most biological membranes, could have been synthesized on the primitive earth.

  13. Molecular characterization of Babesia and Cytauxzoon species in wild South-African meerkats.

    PubMed

    Leclaire, Sarah; Menard, Sandie; Berry, Antoine

    2015-04-01

    Piroplasms, including Babesia, Cytauxzoon and Theileria species, frequently infect domestic and wild mammals. At present, there is no information on the occurrence and molecular identity of these tick-borne blood parasites in the meerkat, one of South Africa's most endearing wildlife celebrities. Meerkats live in territorial groups, which may occur on ranchland in close proximity to humans, pets and livestock. Blood collected from 46 healthy meerkats living in the South-African Kalahari desert was screened by microscopy and molecular methods, using PCR and DNA sequencing of 18S rRNA and ITS1 genes. We found that meerkats were infected by 2 species: one species related to Babesia sp. and one species related to Cytauxzoon sp. Ninety one percent of the meerkats were infected by the Cytauxzoon and/or the Babesia species. Co-infection occurred in 46% of meerkats. The pathogenicity and vectors of these two piroplasm species remains to be determined. PMID:25374302

  14. Discordance between morphological and molecular species boundaries among Caribbean species of the reef sponge Callyspongia.

    PubMed

    DeBiasse, Melissa B; Hellberg, Michael E

    2015-02-01

    Sponges are among the most species-rich and ecologically important taxa on coral reefs, yet documenting their diversity is difficult due to the simplicity and plasticity of their morphological characters. Genetic attempts to identify species are hampered by the slow rate of mitochondrial sequence evolution characteristic of sponges and some other basal metazoans. Here we determine species boundaries of the Caribbean coral reef sponge genus Callyspongia using a multilocus, model-based approach. Based on sequence data from one mitochondrial (COI), one ribosomal (28S), and two single-copy nuclear protein-coding genes, we found evolutionarily distinct lineages were not concordant with current species designations in Callyspongia. While C. fallax,C. tenerrima, and C. plicifera were reciprocally monophyletic, four taxa with different morphologies (C. armigera,C. longissima,C. eschrichtii, and C. vaginalis) formed a monophyletic group and genetic distances among these taxa overlapped distances within them. A model-based method of species delimitation supported collapsing these four into a single evolutionary lineage. Variation in spicule size among these four taxa was partitioned geographically, not by current species designations, indicating that in Callyspongia, these key taxonomic characters are poor indicators of genetic differentiation. Taken together, our results suggest a complex relationship between morphology and species boundaries in sponges. PMID:25691989

  15. Discordance between morphological and molecular species boundaries among Caribbean species of the reef sponge Callyspongia

    PubMed Central

    DeBiasse, Melissa B; Hellberg, Michael E

    2015-01-01

    Sponges are among the most species-rich and ecologically important taxa on coral reefs, yet documenting their diversity is difficult due to the simplicity and plasticity of their morphological characters. Genetic attempts to identify species are hampered by the slow rate of mitochondrial sequence evolution characteristic of sponges and some other basal metazoans. Here we determine species boundaries of the Caribbean coral reef sponge genus Callyspongia using a multilocus, model-based approach. Based on sequence data from one mitochondrial (COI), one ribosomal (28S), and two single-copy nuclear protein-coding genes, we found evolutionarily distinct lineages were not concordant with current species designations in Callyspongia. While C. fallax,C. tenerrima, and C. plicifera were reciprocally monophyletic, four taxa with different morphologies (C. armigera,C. longissima,C. eschrichtii, and C. vaginalis) formed a monophyletic group and genetic distances among these taxa overlapped distances within them. A model-based method of species delimitation supported collapsing these four into a single evolutionary lineage. Variation in spicule size among these four taxa was partitioned geographically, not by current species designations, indicating that in Callyspongia, these key taxonomic characters are poor indicators of genetic differentiation. Taken together, our results suggest a complex relationship between morphology and species boundaries in sponges. PMID:25691989

  16. Structure and properties of mixed-chain phosphatidylcholine bilayers.

    PubMed

    Shah, J; Sripada, P K; Shipley, G G

    1990-05-01

    The structural and thermotropic properties of the hydrated mixed-chain phosphatidylcholines (PCs), C(8):C(18)-PC and C(10):C(18)-PC, have been studied by X-ray diffraction and differential scanning calorimetry. For fully hydrated C(8):C(18)-PC, the reversible chain melting transition is observed at 9.9 degrees C (delta H = 7.3 kcal/mol). X-ray diffraction at 0 degrees C (below the chain melting transition) shows a small bilayer repeat distance, d = 51.0 A, and a sharp, symmetric wide-angle reflection at 4.1 A, characteristic of a mixed interdigitated bilayer gel phase [see McIntosh, T. J., Simon, S. A., Ellington, J. C., Jr., & Porter, N. A. (1984) Biochemistry 23, 4038-4044; Hui, S. W., Mason, J. T., & Huang, C. (1984) Biochemistry 23, 5570-5577]. At 30 degrees C (above the chain melting transition), a diffuse band is observed at 4.5 A characteristic of an L alpha phase but with an increased bilayer periodicity, d = 61 A. Both the calculated lipid bilayer thickness (d1) and that determined directly from electron density profiles (dp-p) show unusual increases as a consequence of chain melting. In contrast, fully hydrated C(10):C(18)-PC shows an asymmetric endothermic transition at 11.8 degrees C. Below the chain melting transition, two lamellar phases are present, corresponding to coexisting interdigitated (d = 52.3 A) and noninterdigitated (d = 62.5 A) bilayer gel phases. The relative amounts of these phases depend upon the low-temperature incubation and/or hydration conditions, suggesting conversions, albeit kinetically complex, between metastable, and stable phases. The different behavior of C(8):C(18)-PC and C(10):C(18)-PC, as well as their positional isomers, is rationalized in terms of the molecular conformation of PC. PMID:2361142

  17. Efficacy of phosphatidylcholine in the modulation of motion sickness susceptibility

    NASA Technical Reports Server (NTRS)

    Kohl, R. L.; Ryan, P.; Homick, J. L.

    1985-01-01

    This study evaluated the efficacy of pharmacological doses of phosphatidylcholine (lecithin) in the modulation of motion sickness induced by exposure to coriolis stimulation in a rotating chair. Subjects received daily dietary supplements of 25 grams of lecithin (90 percent phosphatidylcholine) and were tested for their susceptibility to motion sickness after 4 h, 2 d, and 21 d. A small but statistically significant increase in susceptibility (+15 percent) was noted 4 h after supplemental phosphatidylcholine, with four of nine subjects demonstrating a marked increase in susceptibility. This finding was attributed to choline's stimulatory action on cholinergic systems, an action which opposes that of the classical antimotion sickness drug scopolamine. Chronic lecithin loading revealed a trend towards reduced susceptibility, possibly indicating the occurrence of adaptive mechanisms such as receptor down-regulation. Withdrawal from lecithin loading, perhaps coupled with anticholinergic treatment, might prove to be a potent prophylactic regimen and ought to be tested.

  18. How to describe a cryptic species? Practical challenges of molecular taxonomy

    PubMed Central

    2013-01-01

    Background Molecular methods of species delineation are rapidly developing and widely considered as fast and efficient means to discover species and face the 'taxonomic impediment’ in times of biodiversity crisis. So far, however, this form of DNA taxonomy frequently remains incomplete, lacking the final step of formal species description, thus enhancing rather than reducing impediments in taxonomy. DNA sequence information contributes valuable diagnostic characters and –at least for cryptic species – could even serve as the backbone of a taxonomic description. To this end solutions for a number of practical problems must be found, including a way in which molecular data can be presented to fulfill the formal requirements every description must meet. Multi-gene barcoding and a combined molecular species delineation approach recently revealed a radiation of at least 12 more or less cryptic species in the marine meiofaunal slug genus Pontohedyle (Acochlidia, Heterobranchia). All identified candidate species are well delimited by a consensus across different methods based on mitochondrial and nuclear markers. Results The detailed microanatomical redescription of Pontohedyle verrucosa provided in the present paper does not reveal reliable characters for diagnosing even the two major clades identified within the genus on molecular data. We thus characterize three previously valid Pontohedyle species based on four genetic markers (mitochondrial cytochrome c oxidase subunit I, 16S rRNA, nuclear 28S and 18S rRNA) and formally describe nine cryptic new species (P. kepii sp. nov., P. joni sp. nov., P. neridae sp. nov., P. liliae sp. nov., P. wiggi sp. nov., P. wenzli sp. nov., P. peteryalli sp. nov., P. martynovi sp. nov., P. yurihookeri sp. nov.) applying molecular taxonomy, based on diagnostic nucleotides in DNA sequences of the four markers. Due to the minute size of the animals, entire specimens were used for extraction, consequently the holotype is a voucher of

  19. Intestinal Microbial Metabolism of Phosphatidylcholine and Cardiovascular Risk

    PubMed Central

    Tang, W.H. Wilson; Wang, Zeneng; Levison, Bruce S.; Koeth, Robert A.; Britt, Earl B.; Fu, Xiaoming; Wu, Yuping; Hazen, Stanley L.

    2013-01-01

    BACKGROUND Recent studies in animals have shown a mechanistic link between intestinal microbial metabolism of the choline moiety in dietary phosphatidylcholine (lecithin) and coronary artery disease through the production of a proatherosclerotic metabolite, trimethylamine-N-oxide (TMAO). We investigated the relationship among intestinal microbiota-dependent metabolism of dietary phosphatidylcholine, TMAO levels, and adverse cardiovascular events in humans. METHODS We quantified plasma and urinary levels of TMAO and plasma choline and betaine levels by means of liquid chromatography and online tandem mass spectrometry after a phosphatidylcholine challenge (ingestion of two hard-boiled eggs and deuterium [d9]-labeled phosphatidylcholine) in healthy participants before and after the suppression of intestinal microbiota with oral broad-spectrum antibiotics. We further examined the relationship between fasting plasma levels of TMAO and incident major adverse cardiovascular events (death, myocardial infarction, or stroke) during 3 years of follow-up in 4007 patients undergoing elective coronary angiography. RESULTS Time-dependent increases in levels of both TMAO and its d9 isotopologue, as well as other choline metabolites, were detected after the phosphatidylcholine challenge. Plasma levels of TMAO were markedly suppressed after the administration of antibiotics and then reappeared after withdrawal of antibiotics. Increased plasma levels of TMAO were associated with an increased risk of a major adverse cardiovascular event (hazard ratio for highest vs. lowest TMAO quartile, 2.54; 95% confidence interval, 1.96 to 3.28; P<0.001). An elevated TMAO level predicted an increased risk of major adverse cardiovascular events after adjustment for traditional risk factors (P<0.001), as well as in lower-risk subgroups. CONCLUSIONS The production of TMAO from dietary phosphatidylcholine is dependent on metabolism by the intestinal microbiota. Increased TMAO levels are associated

  20. Toxicity of oxidized phosphatidylcholines in cultured human melanoma cells.

    PubMed

    Ramprecht, Claudia; Jaritz, Hannah; Streith, Ingo; Zenzmaier, Elfriede; Köfeler, Harald; Hofmann-Wellenhof, Rainer; Schaider, Helmut; Hermetter, Albin

    2015-07-01

    The oxidized phospholipids (oxPL) 1-palmitoyl-2-glutaroyl-sn-glycero-3-phosphocholine (PGPC) and 1-palmitoyl-2-(5-oxovaleroyl)-sn-glycero-3-phosphocholine (POVPC) are generated from 1-palmitoyl-2-arachidonoyl-phosphatidylcholine under conditions of oxidative stress. These oxPL are components of oxidized low density lipoprotein. They are cytotoxic in cells of the arterial wall thus playing an important role in the development and progression of atherosclerosis. The toxic lipid effects include inflammation and under sustained exposure apoptosis. The aim of this study was to find out whether such toxic effects, especially apoptosis, are also elicited by oxPL in melanocytic cells in order to assess their potential for therapeutic intervention. FACS analysis after staining with fluorescent markers was performed to identify the mode of lipid-induced cell death. Activation of sphingomyelinase which generates apoptotic ceramide was measured using an established fluorescence assay. Ceramide profiles were determined by mass spectrometry. We found that 50μM POVPC induce cell death in human melanoma cells isolated from different stages of tumor progression but affect primary human melanocytes to a much lesser extent. In contrast, 50μM PGPC was only apoptotic in two out of four cell lines used in this study. The toxicity of both compounds was associated with efficient lipid uptake into the tumor cells and activation of acid sphingomyelinase. In several but not all melanoma cell lines used in this study, activation of the sphingomyelin degrading enzyme correlated with an increase in the concentration of the apoptotic mediator ceramide. The individual patterns of the newly formed ceramide species were also cell line-specific. PGPC and POVPC may be considered potential drug candidates for topical skin cancer treatment. They are toxic in malignant cells. The respective oxidized phospholipids are naturally formed in the body and resistance to these compounds is not likely to occur

  1. Hybridization and endangered species protection in the molecular era.

    PubMed

    Wayne, Robert K; Shaffer, H Bradley

    2016-06-01

    After decades of discussion, there is little consensus on the extent to which hybrids between endangered and nonendangered species should be protected by US law. As increasingly larger, genome-scale data sets are developed, we can identify individuals and populations with even trace levels of genetic admixture, making the 'hybrid problem' all the more difficult. We developed a decision-tree framework for evaluating hybrid protection, including both the processes that produced hybrids (human-mediated or natural) and the ecological impact of hybrids on natural ecosystems. We then evaluated our decision tree for four case studies drawn from our own work and briefly discuss several other cases from the literature. Throughout, we highlight the management outcomes that our approach provides and the nuances of hybridization as a conservation problem. PMID:27064931

  2. Molecular and morphologic data reveal multiple species in Peromyscus pectoralis

    PubMed Central

    Bradley, Robert D.; Schmidly, David J.; Amman, Brian R.; Platt, Roy N.; Neumann, Kathy M.; Huynh, Howard M.; Muñiz-Martínez, Raúl; López-González, Celia; Ordóñez-Garza, Nicté

    2015-01-01

    DNA sequence and morphometric data were used to re-evaluate the taxonomy and systematics of Peromyscus pectoralis. Phylogenetic analyses (maximum likelihood and Bayesian inference) of DNA sequences from the mitochondrial cytochrome-b gene in 44 samples of P. pectoralis indicated 2 well-supported monophyletic clades. The 1st clade contained specimens from Texas historically assigned to P. p. laceianus; the 2nd was comprised of specimens previously referable to P. p. collinus, P. p. laceianus, and P. p. pectoralis obtained from northern and eastern Mexico. Levels of genetic variation (~7%) between these 2 clades indicated that the genetic divergence typically exceeded that reported for other species of Peromyscus. Samples of P. p. laceianus north and south of the Río Grande were not monophyletic. In addition, samples representing P. p. collinus and P. p. pectoralis formed 2 clades that differed genetically by 7.14%. Multivariate analyses of external and cranial measurements from 63 populations of P. pectoralis revealed 4 morpho-groups consistent with clades in the DNA sequence analysis: 1 from Texas and New Mexico assignable to P. p. laceianus; a 2nd from western and southern Mexico assignable to P. p. pectoralis; a 3rd from northern and central Mexico previously assigned to P. p. pectoralis but herein shown to represent an undescribed taxon; and a 4th from southeastern Mexico assignable to P. p. collinus. Based on the concordance of these results, populations from the United States are referred to as P. laceianus, whereas populations from Mexico are referred to as P. pectoralis (including some samples historically assigned to P. p. collinus, P. p. laceianus, and P. p. pectoralis). A new subspecies is described to represent populations south of the Río Grande in northern and central Mexico. Additional research is needed to discern if P. p. collinus warrants species recognition. PMID:26937045

  3. Molecular evidence of Sarcocystis species in captive snakes in Japan.

    PubMed

    Abe, Niichiro; Matsubara, Katsuki; Tamukai, Kenichi; Miwa, Yasutsugu; Takami, Kazutoshi

    2015-08-01

    Sarcocystis nesbitti, using snakes as the definitive host, is a causative agent of acute human muscular sarcocystosis in Malaysia. Therefore, it is important to explore the distribution and prevalence of S. nesbitti in snakes. Nevertheless, epizootiological information of S. nesbitti in snakes remains insufficient because few surveys have assessed Sarcocystis infection in snakes in endemic countries. In Japan, snakes are popular exotic pet animals that are imported from overseas, but the degree of Sarcocystis infection in them remains unclear. The possibility exists that muscular sarcocystosis by S. nesbitti occurs in contact with captive snakes in non-endemic countries. For a total of 125 snake faecal samples from 67 snake species collected at animal hospitals, pet shops and a zoo, this study investigated the presence of Sarcocystis using polymerase chain reaction (PCR) for the 18S ribosomal RNA gene (18S rDNA). Four (3.2%) faecal samples were positive by PCR. Phylogenetic analysis of the 18S rDNA sequences obtained from four amplification products revealed one isolate from a beauty snake (Elaphe taeniura), Sarcocystis zuoi, which uses rat snakes as the definitive host. The isolate from a Macklot's python (Liasis mackloti) was closely related with unidentified Sarcocystis sp. from reticulated pythons in Malaysia. The remaining two isolates from tree boas (Corallus spp.) were closely related with Sarcocystis lacertae, Sarcocystis gallotiae and unidentified Sarcocystis sp. from smooth snakes, Tenerife lizards and European shrews, respectively. This report is the first of a study examining the distribution of Sarcocystis species in captive snakes in Japan. PMID:26044884

  4. Metabolic relationships between monogalactosyldiacylglycerol and digalactosyldiacylglycerol molecular species in Dunaliella salina

    SciTech Connect

    Cho, S.H.; Thompson, G.A. Jr.

    1987-06-05

    Dunaliella salina cells were pulse-labeled for 2 min with (/sup 14/C)palmitic acid, (/sup 14/C)oleic acid, or (/sup 14/C)lauric acid in order to trace the pathway of galactolipid biosynthesis and desaturation. Through the use of high performance liquid chromatography it was possible to follow the movement of radioactivity through many individual molecular species of monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG) for periods of 24 h and, in some cases, as much as 120 h. Analysis of the fatty acid fluxes permitted us to refine current views regarding biosynthesis of the predominantly prokaryotic galactolipids. The initial D. salina MGDG molecular species, containing paired oleate and palmitate (18:1/16:0), can follow two metabolic routes. If the palmitoyl chain is desaturated to 16:1, the resulting 18:1/16:1 MGDG is subject to rapid further desaturation to varying degrees, and a part of these products is subsequently galactosylated to DGDG. Contrary to widely held opinions, these DGDG molecular species can themselves be further desaturated toward a 18:3/16:4 final product. In a separate series of reactions, a smaller portion of the nascent 18:1/16:0 MGDG is directly galactosylated to 18:1/16:0 DGDG. This molecular species can then be sequentially desaturated to 18:2/16:0 DGDG and 18:3/16:0 DGDG. However, there is only very limited desaturation of the palmitoyl group attached to these molecular species.

  5. Morphological and molecular characterization of two novel species of Agaricus section Xanthodermatei.

    PubMed

    Callac, Philippe; Guinberteau, Jacques

    2005-01-01

    Agaricus specimens collected in France belong to two novel entities resembling small forms of A. moelleri and A. xanthodermus, two common species in section Xanthodermatei. Molecular (IT1+ITS2 DNA sequence) and morphological comparisons between eight presumed similar taxa of the section support the elevation of both entities to species rank. The new entities are described as A. parvitigrinus and A. xanthodermulus. They form a group with A. laskibarii, a rare species also recently described from France, and A. californicus, a North-American species. The well known A. moelleri and A. xanthodermus are the most related species among the studied sample. Like other species of the section, both new species have a phenolic odor and are probably toxic. PMID:16396349

  6. Molecular species composition of plant cardiolipin determined by liquid chromatography mass spectrometry.

    PubMed

    Zhou, Yonghong; Peisker, Helga; Dörmann, Peter

    2016-07-01

    Cardiolipin (CL), an anionic phospholipid of the inner mitochondrial membrane, provides essential functions for stabilizing respiratory complexes and is involved in mitochondrial morphogenesis and programmed cell death in animals. The role of CL and its metabolism in plants are less well understood. The measurement of CL in plants, including its molecular species composition, is hampered by the fact that CL is of extremely low abundance, and that plants contain large amounts of interfering compounds including galactolipids, neutral lipids, and pigments. We used solid phase extraction by anion exchange chromatography to purify CL from crude plant lipid extracts. LC/MS was used to determine the content and molecular species composition of CL. Thus, up to 23 different molecular species of CL were detected in different plant species, including Arabidopsis, mung bean, spinach, barley, and tobacco. Similar to animals, plant CL is dominated by highly unsaturated species, mostly containing linoleic and linolenic acid. During phosphate deprivation or exposure to an extended dark period, the amount of CL decreased in Arabidopsis, accompanied with an increased degree in unsaturation. The mechanism of CL remodeling during stress, and the function of highly unsaturated CL molecular species, remains to be defined. PMID:27179363

  7. Molecular Evidence for Cryptic Speciation in the Cyclophorus fulguratus (Pfeiffer, 1854) Species Complex (Caenogastropoda: Cyclophoridae) with Description of New Species

    PubMed Central

    Nantarat, Nattawadee; Wade, Christopher M.; Jeratthitikul, Ekgachai; Sutcharit, Chirasak; Panha, Somsak

    2014-01-01

    A high degree of intraspecific variation, both genetic and in shell morphology, of the operculate land snail Cyclophorus fulguratus (Pfeiffer, 1854) suggests that its classification as a single species warrants reconsideration. We sequenced two nuclear (18S and 28S) and two mitochondrial (16S and COI) genes of 46 C. fulguratus specimens and used them to estimate the phylogeny and to determine the validity of species boundaries. Molecular phylogenetic analyses revealed the presence of three lineages corresponding to three geographically disjunctive populations of C. fulguratus in Thailand. Likelihood tests of topologies significantly supported the non-monophyly of the C. fulguratus–complex and Bayesian species delimitation analysis significantly supported the potential representation as distinct species of these three lineages. Discriminant function analysis based on geometric-morphometrics of shell shape allowed for significant distinction of these three candidate species, although they revealed a considerable degree of overlap of shell shape reflecting their crypsis morphologically. The diagnostic characters are provided by color pattern, pattern of protoconch and pattern of jaw. In conclusion, the results support that the C. fulguratus s.l., as currently recognized, consists of three distinct species in Thailand: C. fulguratus s.s., C. rangunensis and C. abditus sp.nov., which are described herein. PMID:25299674

  8. Relationships among 3 Kochia species based on PCR-generated molecular sequences and molecular cytogenetics.

    PubMed

    Lee, B S; Kim, M Y; Wang, R R-C; Waldron, B L

    2005-12-01

    Forage kochia (Kochia prostrata ssp. virescens 'Immigrant' is native to the arid and semiarid regions of central Eurasia. It was introduced into the United States in 1966 as PI 314929 and released as a perennial forage shrub in 1984. Kochia americana is a perennial native to the United States, whereas Kochia scorparia is an introduced annual species that became a weed. To assess both the breeding potential and the possibility of genetic contamination, relationships among the 3 Kochia species were analyzed using random amplified polymorphic DNA (RAPD) markers, sequence tagged site (STS) marker sequences of the chloroplast NADH dehydrogenase gene (ndhF), genomic in situ hybridization (GISH), and multicolor fluorescence in situ hybridization (MC-FISH). Seventy decamer random primers yielded 458 polymorphic bands from 9 plants of K. americana, 20 plants of K. prostrata, and 7 plants of K. scoparia. Fifty-four and 55 species-specific RAPD markers were identified for K. americana and K. prostrata, whereas 80 RAPD markers were specific to K. scoparia. Based on the presence or absence of informative RAPD markers, the 3 species always grouped into 3 distinct clusters in a NTSYSpc2.01b-generated dendrogram. The same relationships were found among the 3 Kochia species based on ndhF DNA sequence divergence. Using a set of 7 STS markers that can identify each Kochia species, we did not find a single interspecific hybrid from artificial hybridizations among the 3 Kochia species. In GISH studies, chromosomes of 1 species fluoresced in green only when they were probed by genomic DNA of the same species. Cross-hybridization by genomic DNA of another species was not observed. In FISH studies using pTa71 (for 18S-5.8S-26S rDNAs) and pScT7 (for 5S rDNA) as probes, there were 1, 1 and 3 pTa71 sites and 2, 1, and 1 pScT7 sites in each haplome of K. prostrata, K. americana, and K. scoparia, respectively. It is concluded that these 3 Kochia species are so genomically distinct that gene

  9. Thermodynamics of interdigitated phases of phosphatidylcholine in glycerol.

    PubMed Central

    Swamy, M J; Marsh, D

    1995-01-01

    Comparison of the electron spin resonance spectra of phosphatidylcholines spin-labeled in the sn-2 chain at a position close to the polar region and close to the methyl terminus indicate that symmetrical saturated diacyl phosphatidylcholines with odd and even chain lengths from 13 to 20 C-atoms (and probably also 12 C-atoms) have gel phases in which the chains are interdigitated when dispersed in glycerol. The chain-length dependences of the chain-melting transition enthalpies and entropies are similar for phosphatidylcholines dispersed in glycerol and in water, but the negative end contributions are smaller for phosphatidylcholines dispersed in glycerol than for those dispersed in water: d delta Ht/dCH2 = 1.48 (1.43) kcal.mol-1, d delta St/dCH2 = 3.9 (4.0) cal.mol-1K-1, and delta H o = -12.9 (-15.0) kcal.mol-1, delta S o = -29 (-40) cal.mol-1K-1, respectively, for dispersions in glycerol (water). These differences reflect the interfacial energetics in glycerol and in water, and the different structure of the interdigitated gel phase. PMID:8534810

  10. Phosphoethanolamine Bases as Intermediates in Phosphatidylcholine Synthesis by Lemna

    PubMed Central

    Mudd, S. Harvey; Datko, Anne H.

    1986-01-01

    The pathway for synthesis of phosphatidylcholine, the dominant methyl-containing end product formed by Lemna paucicostata, has been investigated. Methyl groups originating in methionine are rapidly utilized by intact plants to methylate phosphoethanolamine successively to the mono-, di-, and tri-methyl (i.e. phosphocholine) phosphoethanolamine derivatives. With continued labeling, radioactivity initially builds up in these compounds, then passes on, accumulating chiefly in phosphatidylcholine (34% of the total radioactivity taken up by plants labeled to isotopic equilibrium with l-[14CH3]methionine), and in lesser amounts in soluble choline (6%). Radioactivity was detected in mono- and dimethyl derivatives of free ethanolamine or phosphatidylethanolamine only in trace amounts. Pulse-chase experiments with [14CH3]choline and [3H] ethanolamine confirmed that phosphoethanolamine is rapidly methylated and that phosphocholine is converted to phosphatidylcholine. Initial rates indicate that methylation of phosphoethanolamine predominates over methylation of either phosphatidylethanolamine or free ethanolamine at least 99:1. Although more studies are needed, it is suggested this pathway may well turn out to account for most phosphatidylcholine synthesis in higher plants. Phosphomethylethanolamine and phosphodimethylethanolamine are present in low quantities during steady-state growth (18% and 6%, respectively, of the amount of phosphocholine). Radioactivity was not detected in CDP-choline, probably due to the low steady-state concentration of this nucleotide. PMID:16664979

  11. Cholesterol in condensed and fluid phosphatidylcholine monolayers studied by epifluorescence microscopy.

    PubMed Central

    Worthman, L A; Nag, K; Davis, P J; Keough, K M

    1997-01-01

    Epifluorescence microscopy was used to investigate the effect of cholesterol on monolayers of dipalmitoylphosphatidylcholine (DPPC) and 1 -palmitoyl-2-oleoyl phosphatidylcholine (POPC) at 21 +/- 2 degrees C using 1 mol% 1-palmitoyl-2-[12-[(7-nitro-2-1, 3-benzoxadizole-4-yl)amino]dodecanoyl]phosphatidylcholine (NBD-PC) as a fluorophore. Up to 30 mol% cholesterol in DPPC monolayers decreased the amounts of probe-excluded liquid-condensed (LC) phase at all surface pressures (pi), but did not effect the monolayers of POPC, which remained in the liquid-expanded (LE) phase at all pi. At low pi (2-5 mN/m), 10 mol% or more cholesterol in DPPC induced a lateral phase separation into dark probe-excluded and light probe-rich regions. In POPC monolayers, phase separation was observed at low pi when > or =40 mol% or more cholesterol was present. The lateral phase separation observed with increased cholesterol concentrations in these lipid monolayers may be a result of the segregation of cholesterol-rich domains in ordered fluid phases that preferentially exclude the fluorescent probe. With increasing pi, monolayers could be transformed from a heterogeneous dark and light appearance into a homogeneous fluorescent phase, in a manner that was dependent on pi and cholesterol content. The packing density of the acyl chains may be a determinant in the interaction of cholesterol with phosphatidylcholine (PC), because the transformations in monolayer surface texture were observed in phospholipid (PL)/sterol mixtures having similar molecular areas. At high pi (41 mN/m), elongated crystal-like structures were observed in monolayers containing 80-100 mol% cholesterol, and these structures grew in size when the monolayers were compressed after collapse. This observation could be associated with the segregation and crystallization of cholesterol after monolayer collapse. Images FIGURE 3 FIGURE 4 PMID:9168032

  12. Lipidomic profiling in Crohn's disease: Abnormalities in phosphatidylinositols, with preservation of ceramide, phosphatidylcholine and phosphatidylserine composition

    PubMed Central

    Sewell, Gavin W.; Hannun, Yusuf A.; Han, Xianlin; Koster, Grielof; Bielawski, Jacek; Goss, Victoria; Smith, Philip J.; Rahman, Farooq Z.; Vega, Roser; Bloom, Stuart L.; Walker, Ann P.; Postle, Anthony D.; Segal, Anthony W.

    2012-01-01

    Crohn's disease is a chronic inflammatory condition largely affecting the terminal ileum and large bowel. A contributing cause is the failure of an adequate acute inflammatory response as a result of impaired secretion of pro-inflammatory cytokines by macrophages. This defective secretion arises from aberrant vesicle trafficking, misdirecting the cytokines to lysosomal degradation. Aberrant intestinal permeability is also well-established in Crohn's disease. Both the disordered vesicle trafficking and increased bowel permeability could result from abnormal lipid composition. We thus measured the sphingo- and phospholipid composition of macrophages, using mass spectrometry and stable isotope labelling approaches. Stimulation of macrophages with heat-killed Escherichia coli resulted in three main changes; a significant reduction in the amount of individual ceramide species, an altered composition of phosphatidylcholine, and an increased rate of phosphatidylcholine synthesis in macrophages. These changes were observed in macrophages from both healthy control individuals and patients with Crohn's disease. The only difference detected between control and Crohn's disease macrophages was a reduced proportion of newly-synthesised phosphatidylinositol 16:0/18:1 over a defined time period. Shotgun lipidomics analysis of macroscopically non-inflamed ileal biopsies showed a significant decrease in this same lipid species with overall preservation of sphingolipid, phospholipid and cholesterol composition. PMID:22728312

  13. A new Sparassis species from Spain described using morphological and molecular data.

    PubMed

    Blanco-Dios, Jaime B; Wang, Zheng; Binder, Manfred; Hibbett, David S

    2006-10-01

    Sparassis miniensis, collected in Pinus pinaster forests in Galicia (northwest Iberian Peninsula) is described as a new species, based on morphological and molecular data. Sparassis miniensis is morphologically distinct from all other species in the genus Sparassis based on scattered flabellae, which are strongly laciniated, azonate, and arise from an orange to rose-purplish base. The sporadic presence of clamp connections is restricted to subhymenial hyphae. Molecular data from LSU-rDNA, ITS and partial gene coding RNA polymerase subunit II (rpb2) suggest a close relationship between the new species S. miniensis and S. brevipes, another European species producing large fruiting bodies but with entire flabellae and no clamp connections. PMID:17018255

  14. Method of molecular specie alteration by nonresonant laser induced dielectric breakdown

    DOEpatents

    Ronn, Avigdor M.

    1980-01-01

    Irradiation of a molecular specie by itself or in the presence of a secondary material at a pressure above a threshold value for the particular system by a laser of predetermined minimum power and having a frequency displaced from an absorption line of the specie causes severance of the weakest bond and a yield of products containing at least one dissociative fragment from said specie. A Rogowski type TEA CO.sub.2 --N.sub.2 --He laser has been used successfully on a wide variety of molecular species. Solid, liquid and gaseous end products have been obtained depending upon the starting materials. When solids have been produced they are in the form of microfine particles or microfine aggregates. A neodymium glass laser has also been used successfully.

  15. Molecular Species Delimitation and Morphology of Aquatic and Sub-Aquatic Bugs (Heteroptera) in Cameroon.

    PubMed

    Meyin A Ebong, Solange; Petit, Elsa; Le Gall, Philippe; Chen, Ping-Ping; Nieser, Nico; Guilbert, Eric; Njiokou, Flobert; Marsollier, Laurent; Guégan, Jean-François; Pluot-Sigwalt, Dominique; Eyangoh, Sara; Harry, Myriam

    2016-01-01

    Aquatic and semi-aquatic bugs (Heteroptera) represent a remarkable diversity and a resurging interest has been given to documenting at the species level these insects inhabiting Cameroon in Central Africa due to their potential implication in the transmission of the bacterium Mycobacterium ulcerans, the causal agent of Buruli ulcer, an emerging human disease. A survey was carried out over two years in Cameroon. Morphological analyses were done in two steps. A first step consisted in separating the specimens based on broadly shared characters into morphotypes. The specimens were then separated into two independent batches containing each the same representation of each morphotype. One batch (309 specimens) was used by taxonomy experts on aquatic bugs for species level identification and/or to reconcile nymph with their corresponding adult species. The second batch (188 specimens) was used to define species based on the COI DNA sequences (standard sequence used for "DNA barcoding") and using the Automatic Barcode Gap Discovery (ABGD) method. The first morphological analysis step separated the specimens into 63 different morphotypes (49 adults and 14 nymphs), which were then found to belong to 54 morphological species in the infra-orders Gerromorpha and Nepomorpha based on the species-level morphological identification, and 41-45 putative molecular species according to the gap value retained in the ABGD. Integrating morphology and "DNA barcoding" reconciled all the specimens into 62 aquatic bug species in Cameroon. Generally, we obtained a good congruence between species a priori identified based on morphology from adult morphotypes and molecular putative species. Moreover, molecular identification has allowed the association of 86% of nymphs with adults. This work illustrates the importance of integrative taxonomy. PMID:27149077

  16. Molecular Species Delimitation and Morphology of Aquatic and Sub-Aquatic Bugs (Heteroptera) in Cameroon

    PubMed Central

    Le Gall, Philippe; Chen, Ping-Ping; Nieser, Nico; Guilbert, Eric; Njiokou, Flobert; Marsollier, Laurent; Guégan, Jean-François; Pluot-Sigwalt, Dominique; Eyangoh, Sara; Harry, Myriam

    2016-01-01

    Aquatic and semi-aquatic bugs (Heteroptera) represent a remarkable diversity and a resurging interest has been given to documenting at the species level these insects inhabiting Cameroon in Central Africa due to their potential implication in the transmission of the bacterium Mycobacterium ulcerans, the causal agent of Buruli ulcer, an emerging human disease. A survey was carried out over two years in Cameroon. Morphological analyses were done in two steps. A first step consisted in separating the specimens based on broadly shared characters into morphotypes. The specimens were then separated into two independent batches containing each the same representation of each morphotype. One batch (309 specimens) was used by taxonomy experts on aquatic bugs for species level identification and/or to reconcile nymph with their corresponding adult species. The second batch (188 specimens) was used to define species based on the COI DNA sequences (standard sequence used for “DNA barcoding”) and using the Automatic Barcode Gap Discovery (ABGD) method. The first morphological analysis step separated the specimens into 63 different morphotypes (49 adults and 14 nymphs), which were then found to belong to 54 morphological species in the infra-orders Gerromorpha and Nepomorpha based on the species-level morphological identification, and 41–45 putative molecular species according to the gap value retained in the ABGD. Integrating morphology and “DNA barcoding” reconciled all the specimens into 62 aquatic bug species in Cameroon. Generally, we obtained a good congruence between species a priori identified based on morphology from adult morphotypes and molecular putative species. Moreover, molecular identification has allowed the association of 86% of nymphs with adults. This work illustrates the importance of integrative taxonomy. PMID:27149077

  17. Comparative molecular species delimitation in the charismatic Nawab butterflies (Nymphalidae, Charaxinae, Polyura).

    PubMed

    Toussaint, Emmanuel F A; Morinière, Jérôme; Müller, Chris J; Kunte, Krushnamegh; Turlin, Bernard; Hausmann, Axel; Balke, Michael

    2015-10-01

    The charismatic tropical Polyura Nawab butterflies are distributed across twelve biodiversity hotspots in the Indomalayan/Australasian archipelago. In this study, we tested an array of species delimitation methods and compared the results to existing morphology-based taxonomy. We sequenced two mitochondrial and two nuclear gene fragments to reconstruct phylogenetic relationships within Polyura using both Bayesian inference and maximum likelihood. Based on this phylogenetic framework, we used the recently introduced bGMYC, BPP and PTP methods to investigate species boundaries. Based on our results, we describe two new species Polyura paulettae Toussaint sp. n. and Polyura smilesi Toussaint sp. n., propose one synonym, and five populations are raised to species status. Most of the newly recognized species are single-island endemics likely resulting from the recent highly complex geological history of the Indomalayan-Australasian archipelago. Surprisingly, we also find two newly recognized species in the Indomalayan region where additional biotic or abiotic factors have fostered speciation. Species delimitation methods were largely congruent and succeeded to cross-validate most extant morphological species. PTP and BPP seem to yield more consistent and robust estimations of species boundaries with respect to morphological characters while bGMYC delivered contrasting results depending on the different gene trees considered. Our findings demonstrate the efficiency of comparative approaches using molecular species delimitation methods on empirical data. They also pave the way for the investigation of less well-known groups to unveil patterns of species richness and catalogue Earth's concealed, therefore unappreciated diversity. PMID:26021440

  18. Use of Repetitive Sequences for Molecular and Cytogenetic Characterization of Avena Species from Portugal.

    PubMed

    Tomás, Diana; Rodrigues, Joana; Varela, Ana; Veloso, Maria Manuela; Viegas, Wanda; Silva, Manuela

    2016-01-01

    Genomic diversity of Portuguese accessions of Avena species--diploid A. strigosa and hexaploids A. sativa and A. sterilis--was evaluated through molecular and cytological analysis of 45S rDNA, and other repetitive sequences previously studied in cereal species--rye subtelomeric sequence (pSc200) and cereal centromeric sequence (CCS1). Additionally, retrotransposons and microsatellites targeting methodologies--IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microsatellite amplified polymorphism)--were performed. A very high homology was detected for ribosomal internal transcribed sequences (ITS1 and ITS2) between the species analyzed, although nucleolar organizing regions (NOR) fluorescent in situ hybridization (FISH) analysis revealed distinct number of Nor loci between diploid and hexaploid species. Moreover, morphological diversity, evidenced by FISH signals with different sizes, was observed between distinct accessions within each species. pSc200 sequences were for the first time isolated from Avena species but proven to be highly similar in all genotypes analyzed. The use of primers designed for CCS1 unraveled a sequence homologous to the Ty3/gypsy retrotransposon Cereba, that was mapped to centromeric regions of diploid and hexaploid species, being however restricted to the more related A and D haplomes. Retrotransposon-based methodologies disclosed species- and accessions-specific bands essential for the accurate discrimination of all genotypes studied. Centromeric, IRAP and REMAP profiles therefore allowed accurate assessment of inter and intraspecific variability, demonstrating the potential of these molecular markers on future oat breeding programs. PMID:26861283

  19. Integrating molecular and morphological approaches for characterizing parasite cryptic species: implications for parasitology.

    PubMed

    Nadler, Steven A; DE León, Gerardo Pérez-Ponce

    2011-11-01

    Herein we review theoretical and methodological considerations important for finding and delimiting cryptic species of parasites (species that are difficult to recognize using traditional systematic methods). Applications of molecular data in empirical investigations of cryptic species are discussed from an historical perspective, and we evaluate advantages and disadvantages of approaches that have been used to date. Developments concerning the theory and practice of species delimitation are emphasized because theory is critical to interpretation of data. The advantages and disadvantages of different molecular methodologies, including the number and kind of loci, are discussed relative to tree-based approaches for detecting and delimiting cryptic species. We conclude by discussing some implications that cryptic species have for research programmes in parasitology, emphasizing that careful attention to the theory and operational practices involved in finding, delimiting, and describing new species (including cryptic species) is essential, not only for fully characterizing parasite biodiversity and broader aspects of comparative biology such as systematics, evolution, ecology and biogeography, but to applied research efforts that strive to improve development and understanding of epidemiology, diagnostics, control and potential eradication of parasitic diseases. PMID:21281559

  20. Molecular phylogeny of the Drosophila obscura species group, with emphasis on the Old World species

    PubMed Central

    Gao, Jian-jun; Watabe, Hide-aki; Aotsuka, Tadashi; Pang, Jun-feng; Zhang, Ya-ping

    2007-01-01

    Background Species of the Drosophila obscura species group (e.g., D. pseudoobscura, D. subobscura) have served as favorable models in evolutionary studies since the 1930's. Despite numbers of studies conducted with varied types of data, the basal phylogeny in this group is still controversial, presumably owing to not only the hypothetical 'rapid radiation' history of this group, but also limited taxon sampling from the Old World (esp. the Oriental and Afrotropical regions). Here we reconstruct the phylogeny of this group by using sequence data from 6 loci of 21 species (including 16 Old World ones) covering all the 6 subgroups of this group, estimate the divergence times among lineages, and statistically test the 'rapid radiation' hypothesis. Results Phylogenetic analyses indicate that each of the subobscura, sinobscura, affinis, and pseudoobscura subgroups is monophyletic. The subobscura and microlabis subgroups form the basal clade in the obscura group. Partial species of the obscura subgroup (the D. ambigua/D. obscura/D. tristis triad plus the D. subsilvestris/D. dianensis pair) forms a monophyletic group which appears to be most closely related to the sinobscura subgroup. The remaining basal relationships in the obscura group are not resolved by the present study. Divergence times on a ML tree based on mtDNA data are estimated with a calibration of 30–35 Mya for the divergence between the obscura and melanogaster groups. The result suggests that at least half of the current major lineages of the obscura group originated by the mid-Miocene time (~15 Mya), a time of the last developing and fragmentation of the temperate forest in North Hemisphere. Conclusion The obscura group began to diversify rapidly before invading into the New World. The subobscura and microlabis subgroups form the basal clade in this group. The obscura subgroup is paraphyletic. Partial members of this subgroup (D. ambigua, D. obscura, D. tristis, D. subsilvestris, and D. dianensis) form a

  1. Molecular species identification of Astrotoma agassizii from planktonic embryos: further evidence for a cryptic species complex.

    PubMed

    Heimeier, Dorothea; Lavery, Shane; Sewell, Mary A

    2010-01-01

    The phrynophiurid brittle star Astrotoma agassizii is abundant in the cold temperate Magellanic region of South America and has a circumpolar Antarctic distribution. Three genetically distinct lineages were recently identified, with one in Antarctica geographically and genetically isolated from both South American lineages (Hunter R, Halanych KM. 2008. Evaluating connectivity in the brooding brittle star Astrotoma agassizii across the Drake Passage in the Southern Ocean. J Hered. 99:137-148.). Despite being an apparent brooding species, A. agassizii displayed a high genetic homogeneity at 2 mitochondrial markers (16s and COII) across a geographical range of more than 500 km along the Antarctic Peninsula. Here, using 16s ribosomal RNA sequences, we match a variety of early developmental stages (fertilized eggs, embryos; n = 12) collected from plankton samples in the Ross Sea to sequences of A. agassizii from the Antarctic Peninsula. The single 16s haplotype reported here is an identical match to one 16s haplotype found for A. agassizii from the Antarctic Peninsula, more than 5000 km away. Based on the regular occurrence of A. agassizii developmental stages in plankton samples, we propose that the Antarctic lineage of this species has a planktonic dispersive stage, with brooding restricted to the South American lineages. A different developmental mode would provide further evidence for cryptic speciation in this brittle star. PMID:20576922

  2. Molecular characterization of the species Salvinia (Salviniaceae) from the upper Paraná River floodplain.

    PubMed

    Machado, S A; Oliveira, A V; Fabrin, T M C; Prioli, S M A P; Prioli, A J

    2016-01-01

    The pteridophytes Salvinia minima, S. herzogii, and S. auriculata are among the most abundant aquatic macrophytes in the upper Paraná River floodplain. Since some species have highly similar morphological features, it is very difficult to identify members of this genus to the species level. An indication of this difficulty is a set of poorly differentiated taxa comprising S. auriculata and S. herzogii known as the 'S. auriculata complex', which is found in the Paraná River together with other Salvinia species such as S. biloba and S. molesta. Some authors have reported the existence of inter-species hybrids. Despite the complex Salvinia taxonomy, few genetic studies have been performed on purported species within the genus to resolve this complexity. The present study was conducted to determine useful molecular sequences for the discrimination of Salvinia species of the upper Paraná River floodplain. Molecular data were compared with data of other species of the genus to clarify phylogenetic relationships, employing the nucleotide sequence trnL-trnF from the chloroplast DNA. The results revealed that Salvinia populations in the upper Paraná River floodplain belong to different species and indicated that species of the S. auriculata complex may be distinguished from one another after the division of the S. minima group, corroborating results by other researchers. Although the taxonomic position of S. oblongifolia was clarified, as high closeness between S. oblongifolia and the S. auriculata complex was reported, Salvinia kinship is still not thoroughly established and further investigations in morphology and molecular diversity are required. PMID:27525952

  3. Association of Fusobacterium species in pancreatic cancer tissues with molecular features and prognosis

    PubMed Central

    Mitsuhashi, Kei; Nosho, Katsuhiko; Sukawa, Yasutaka; Matsunaga, Yasutaka; Ito, Miki; Kurihara, Hiroyoshi; Kanno, Shinichi; Igarashi, Hisayoshi; Naito, Takafumi; Adachi, Yasushi; Tachibana, Mami; Tanuma, Tokuma; Maguchi, Hiroyuki; Shinohara, Toshiya; Hasegawa, Tadashi; Imamura, Masafumi; Kimura, Yasutoshi; Hirata, Koichi; Maruyama, Reo; Suzuki, Hiromu; Imai, Kohzoh

    2015-01-01

    Recently, bacterial infection causing periodontal disease has attracted considerable attention as a risk factor for pancreatic cancer. Fusobacterium species is an oral bacterial group of the human microbiome. Some evidence suggests that Fusobacterium species promote colorectal cancer development; however, no previous studies have reported the association between Fusobacterium species and pancreatic cancer. Therefore, we examined whether Fusobacterium species exist in pancreatic cancer tissue. Using a database of 283 patients with pancreatic ductal adenocarcinoma (PDAC), we tested cancer tissue specimens for Fusobacterium species. We also tested the specimens for KRAS, NRAS, BRAF and PIK3CA mutations and measured microRNA-21 and microRNA-31. In addition, we assessed epigenetic alterations, including CpG island methylator phenotype (CIMP). Our data showed an 8.8% detection rate of Fusobacterium species in pancreatic cancers; however, tumor Fusobacterium status was not associated with any clinical and molecular features. In contrast, in multivariate Cox regression analysis, compared with the Fusobacterium species-negative group, we observed significantly higher cancer-specific mortality rates in the positive group (p = 0.023). In conclusion, Fusobacterium species were detected in pancreatic cancer tissue. Tumor Fusobacterium species status is independently associated with a worse prognosis of pancreatic cancer, suggesting that Fusobacterium species may be a prognostic biomarker of pancreatic cancer. PMID:25797243

  4. Atomic and molecular effects on spherically convergent ion flow. II. Multiple molecular species

    NASA Astrophysics Data System (ADS)

    Emmert, Gilbert A.; Santarius, John F.

    2010-01-01

    A theoretical model for the effect of molecular interactions on the flow of molecular ions in spherically convergent geometry where the inner grid (cathode) is at a large negative potential and the outer grid (anode) is grounded has been developed. The model assumes a weakly ionized deuterium plasma composed of D+, D2+, and D3+ ions that interact with the dominant background gas (D2). The interactions included are charge exchange, ionization, and dissociative processes. The formalism developed includes the bouncing motion of the ions in the electrostatic well and sums over all generations of subsequent ions produced by atomic and molecular processes. This leads to a set of two coupled Volterra integral equations, which are solved numerically. From the solution of the Volterra equations, one can obtain quantities of interest, such as the energy spectra of the ions and fast neutral atoms and molecules, and the fusion reaction rate. To provide an experimental test, the model is applied to inertial electrostatic devices and the calculated neutron production rate is compared to previously reported measurements for one University of Wisconsin inertial electrostatic confinement device [D. C. Donovan et al., Fusion Sci. Technol. 56, 507 (2009)]. The results show general agreement with the experimental results, but significant differences remain to be resolved.

  5. Delimiting Species Boundaries within a Paraphyletic Species Complex: Insights from Morphological, Genetic, and Molecular Data on Paramecium sonneborni (Paramecium aurelia species complex, Ciliophora, Protozoa).

    PubMed

    Przyboś, Ewa; Tarcz, Sebastian; Rautian, Maria; Sawka, Natalia

    2015-09-01

    The demarcation of boundaries between protist species is often problematic because of the absence of a uniform species definition, the abundance of cryptic diversity, and the occurrence of convergent morphology. The ciliates belonging to the Paramecium aurelia complex, consisting of 15 species, are a good model for such systematic and evolutionary studies. One member of the complex is P. sonneborni, previously known only from one stand in Texas (USA), but recently found in two new sampling sites in Cyprus (creeks running to Salt Lake and Oroklini Lake near Larnaca). The studied Paramecium sonneborni strains (from the USA and Cyprus) reveal low viability in the F1 and F2 generations of interstrain hybrids and may be an example of ongoing allopatric speciation. Despite its molecular distinctiveness, we postulate that P. sonneborni should remain in the P. aurelia complex, making it a paraphyletic taxon. Morphological studies have revealed that some features of the nuclear apparatus of P. sonneborni correspond to the P. aurelia spp. complex, while others are similar to P. jenningsi and P. schewiakoffi. The observed discordance indicates rapid splitting of the P. aurelia-P. jenningsi-P. schewiakoffi group, in which genetic, morphological, and molecular boundaries between species are not congruent. PMID:26277215

  6. Three novel species of Stemphylium from Sinkiang, China: their morphological and molecular characterization

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Three new species of Stemphylium were isolated from diseased leaves of Luffa cylindrica, Lycium chinense and Cucumis melo growing in the Sinkiang province of Northwest China. Stemphylium luffae, S. lycii and S. cucumis are described by morphological and molecular phylogenetic analyses. The principal...

  7. Quantification of the molecular species of tetraacylglycerols in lesquerella (Physaria fendleri) Oil by HPLC and MS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Thirteen molecular species of tetraacylglycerols in the seed oil of Physaria fendleri were recently identified. We report here the quantification of these tetraacylglycerols using HPLC with evaporative light scattering detector and the MS of the HPLC fractions. Ion signal intensities of MS1 from th...

  8. Wheat digalactosyldiacylglycerol molecular species profiling using porous graphitic carbon stationary phase.

    PubMed

    Deschamps, Frantz S; Gaudin, Karen; Baillet, Arlette; Chaminade, Pierre

    2004-11-01

    The potential of porous graphitic carbon stationary phase (PGC) was assessed for the separation of molecular species of digalactosyldiacylglycerol (DGDG). Detection was by an evaporative light scattering detector (ELSD). A conventional optimization strategy allowed definition of a quaternary non-aqueous mobile phase and separation of 9 wheat DGDG molecular species with isocratic elution: methanol/toluene/tetrahydrofuran/chloroform 64.3/21.5/13.7/0.5 v/v with 0.1% of triethylamine and a stoichiometric amount of formic acid. The molecular species were identified by LC/MS. The chromatographic behavior of DGDG on PGC was then compared to previous studies. The addition of a carbon double bond on the alkyl chain decreased the retention. This contribution was less important when the number of unsaturations increased in the alkyl chain. The consequence of this retention behavior with PGC was an elution order of molecular species which did not agree with the partition number as observed with C18 grafted stationary phases. PMID:15587281

  9. EMERGING MOLECULAR AND COMPUTATIONAL APPROACHES FOR CROSS-SPECIES EXTRAPLATIONS: A WORKSHOP SUMMARY REPORT

    EPA Science Inventory

    Benson, W.H., R.T. Di Giulio, J.C. Cook, J. Freedman, R.L. Malek, C. Thompson and D. Versteeg. In press. Emerging Molecular and Computational Approaches for Cross-Species Extrapolations: A Workshop Summary Report (Abstract). To be presented at the SETAC Fourth World Congress, 14-...

  10. Ratios of the molecular species of triacylglycerols in lesquerella (Physaria fendleri) oil estimated by mass spectrometry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The ratios of regioisomers of 72 molecular species of triacylglycerols (TAG) in lesquerella oil were estimated using the electrospray ionization mass spectrometry of the lithium adducts of TAG in the HPLC fractions of lesquerella oil. The ratios of ion signal intensities (or relative abundances) of ...

  11. Ratios of the molecular species of triacylglycerols in lesquerella (Physaria fendleri) oil estimated by mass spectrometry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The ratios of regioisomers of 74 molecular species of triacylglycerols (TAG) in lesquerella oil were estimated using HPLC and the electrospray ionization mass spectrometry of the lithium adducts of TAG in the HPLC fractions of lequerella oil. The ratios of relative abundances of the fragment ions fr...

  12. Molecular shifts in limb identity underlie development of feathered feet in two domestic avian species.

    PubMed

    Domyan, Eric T; Kronenberg, Zev; Infante, Carlos R; Vickrey, Anna I; Stringham, Sydney A; Bruders, Rebecca; Guernsey, Michael W; Park, Sungdae; Payne, Jason; Beckstead, Robert B; Kardon, Gabrielle; Menke, Douglas B; Yandell, Mark; Shapiro, Michael D

    2016-01-01

    Birds display remarkable diversity in the distribution and morphology of scales and feathers on their feet, yet the genetic and developmental mechanisms governing this diversity remain unknown. Domestic pigeons have striking variation in foot feathering within a single species, providing a tractable model to investigate the molecular basis of skin appendage differences. We found that feathered feet in pigeons result from a partial transformation from hindlimb to forelimb identity mediated by cis-regulatory changes in the genes encoding the hindlimb-specific transcription factor Pitx1 and forelimb-specific transcription factor Tbx5. We also found that ectopic expression of Tbx5 is associated with foot feathers in chickens, suggesting similar molecular pathways underlie phenotypic convergence between these two species. These results show how changes in expression of regional patterning genes can generate localized changes in organ fate and morphology, and provide viable molecular mechanisms for diversity in hindlimb scale and feather distribution. PMID:26977633

  13. Persistence of phase coexistence in disaturated phosphatidylcholine monolayers at high surface pressures.

    PubMed Central

    Crane, J M; Putz, G; Hall, S B

    1999-01-01

    Prior reports that the coexistence of the liquid-expanded (LE) and liquid-condensed (LC) phases in phospholipid monolayers terminates in a critical point have been compromised by experimental difficulties with Langmuir troughs at high surface pressures and temperatures. The studies reported here used the continuous interface of a captive bubble to minimize these problems during measurements of the phase behavior for monolayers containing the phosphatidylcholines with the four different possible combinations of palmitoyl and/or myristoyl acyl residues. Isothermal compression produced surface pressure-area curves for dipalmitoyl phosphatidylcholine (DPPC) that were indistinguishable from previously published data obtained with Langmuir troughs. During isobaric heating, a steep increase in molecular area corresponding to the main LC-LE phase transition persisted for all four compounds to 45 mN/m, at which collapse of the LE phase first occurred. No other discontinuities to suggest other phase transitions were apparent. Isobars for DPPC at higher pressures were complicated by collapse of the monolayer, but continued to show evidence up to 65 mN/m for at least the onset of the LC-LE transition. The persistence of the main phase transition to high surface pressures suggests that a critical point for these monolayers of disaturated phospholipids is either nonexistent or inaccessible at an air-water interface. PMID:10585934

  14. Persistence of phase coexistence in disaturated phosphatidylcholine monolayers at high surface pressures.

    PubMed

    Crane, J M; Putz, G; Hall, S B

    1999-12-01

    Prior reports that the coexistence of the liquid-expanded (LE) and liquid-condensed (LC) phases in phospholipid monolayers terminates in a critical point have been compromised by experimental difficulties with Langmuir troughs at high surface pressures and temperatures. The studies reported here used the continuous interface of a captive bubble to minimize these problems during measurements of the phase behavior for monolayers containing the phosphatidylcholines with the four different possible combinations of palmitoyl and/or myristoyl acyl residues. Isothermal compression produced surface pressure-area curves for dipalmitoyl phosphatidylcholine (DPPC) that were indistinguishable from previously published data obtained with Langmuir troughs. During isobaric heating, a steep increase in molecular area corresponding to the main LC-LE phase transition persisted for all four compounds to 45 mN/m, at which collapse of the LE phase first occurred. No other discontinuities to suggest other phase transitions were apparent. Isobars for DPPC at higher pressures were complicated by collapse of the monolayer, but continued to show evidence up to 65 mN/m for at least the onset of the LC-LE transition. The persistence of the main phase transition to high surface pressures suggests that a critical point for these monolayers of disaturated phospholipids is either nonexistent or inaccessible at an air-water interface. PMID:10585934

  15. Structural Characterization of Unsaturated Phosphatidylcholines Using Traveling Wave Ion Mobility Spectrometry

    PubMed Central

    Kim, Hugh I.; Kim, Hyungjun; Pang, Eric S.; Ryu, Ernest K.; Beegle, Luther W.; Loo, Joseph A.; Goddard, William A.; Kanik, Isik

    2009-01-01

    A number of phosphatidylcholine (PC) cations spanning a mass range of 400 to 1000 Da are investigated using electrospray ionization mass spectrometry coupled with traveling wave ion mobility spectrometry (TWIMS). A high correlation between mass and mobility is demonstrated with saturated phosphatidylcholine cations in N2. A significant deviation from this mass-mobility correlation line is observed for the unsaturated PC cation. We found that the double bond in the acyl chain causes a 5% reduction in drift time. The drift time is reduced at a rate of ~1% for each additional double bond. Theoretical collision cross sections of PC cations exhibit good agreement with experimentally evaluated values. Collision cross sections are determined using the recently derived relationship between mobility and drift time in TWIMS stacked ring ion guide (SRIG) and compared to estimate collision cross-sections using empiric calibration method. Computational analysis was performed using the modified trajectory (TJ) method with nonspherical N2 molecules as the drift gas. The difference between estimated collision cross-sections and theoretical collision cross-sections of PC cations is related to the sensitivity of the PC cation collision cross-sections to the details of the ion-neutral interactions. The origin of the observed correlation and deviation between mass and mobility of PC cations is discussed in terms of the structural rigidity of these molecules using molecular dynamic simulations. PMID:19764704

  16. Molecular strategies for detection and quantification of mycotoxin-producing Fusarium species: a review.

    PubMed

    Gong, Liang; Jiang, Yueming; Chen, Feng

    2015-07-01

    Fusarium contamination is considered a major agricultural problem, which could not only significantly reduce yield and quality of agricultural products, but produce mycotoxins that are virulence factors responsible for many diseases of humans and farm animals. One strategy to identify toxigenic Fusarium species is the use of modern molecular methods, which include the analysis of DNA target regions for differentiation of the Fusarium species, particularly the mycotoxin-producing Fusarium species such as F. verticillioides and F. graminearum. Additionally, polymerase chain reaction assays are used to determine the genes involved in the biosynthesis of the toxins in order to facilitate a qualitative and quantitative detection of Fusarium-producing mycotoxins. Also, it is worth mentioning that some factors that modulate the biosynthesis of mycotoxins are not only determined by their biosynthetic gene clusters, but also by environmental conditions. Therefore, all of the aforementioned factors which may affect the molecular diagnosis of mycotoxins will be reviewed and discussed in this paper. PMID:25255897

  17. Quantitative degenerate four-wave mixing spectroscopy: Probes for molecular species

    SciTech Connect

    Farrow, R.; Rakestraw, D.; Paul, P.; Lucht, R.; Danehy, P.; Friedman-Hill, E.; Germann, G.

    1993-12-01

    Resonant degenerate four-wave mixing (DFWM) is currently the subject of intensive investigation as a sensitive diagnostic tool for molecular species. DFWM has the advantage of generating a coherent (beam-like) signal which results in null-background detection and provides excellent immunity to background-light interference. Since multiple one-photon resonances are involved in the signal generation process, the DFWM technique can allow sensitive detection of molecules via electronic, vibrational or rotational transitions. These properties combine to make DFWM a widely applicable diagnostic technique for the probing of molecular species. The authors are conducting fundamental and applied investigations of DFWM for quantitative measurements of trace species in reacting gases. During the past year, efforts have been focussed in two areas: (1) understanding the effects of collisional processes on the DFWM signal generation process, and (2) exploring the applicability of infrared DFWM to detect polyatomic molecules via rovibrational transitions.

  18. Refined OPLS all-atom force field for saturated phosphatidylcholine bilayers at full hydration.

    PubMed

    Maciejewski, Arkadiusz; Pasenkiewicz-Gierula, Marta; Cramariuc, Oana; Vattulainen, Ilpo; Rog, Tomasz

    2014-05-01

    We report parametrization of dipalmitoyl-phosphatidylcholine (DPPC) in the framework of the Optimized Parameters for Liquid Simulations all-atom (OPLS-AA) force field. We chose DPPC as it is one of the most studied phospholipid species and thus has plenty of experimental data necessary for model validation, and it is also one of the highly important and abundant lipid types, e.g., in lung surfactant. Overall, PCs have not been previously parametrized in the OPLS-AA force field; thus, there is a need to derive its bonding and nonbonding parameters for both the polar and nonpolar parts of the molecule. In the present study, we determined the parameters for torsion angles in the phosphatidylcholine and glycerol moieties and in the acyl chains, as well the partial atomic charges. In these calculations, we used three methods: (1) Hartree-Fock (HF), (2) second order Møller-Plesset perturbation theory (MP2), and (3) density functional theory (DFT). We also tested the effect of the polar environment by using the polarizable continuum model (PCM), and for acyl chains the van der Waals parameters were also adjusted. In effect, six parameter sets were generated and tested on a DPPC bilayer. Out of these six sets, only one was found to be able to satisfactorily reproduce experimental data for the lipid bilayer. The successful DPPC model was obtained from MP2 calculations in an implicit polar environment (PCM). PMID:24745688

  19. Morphological and molecular affinities of two East Asian species of Stenhelia (Crustacea, Copepoda, Harpacticoida).

    PubMed

    Karanovic, Tomislav; Kim, Kichoon; Lee, Wonchoel

    2014-01-01

    Definition of monophyletic supraspecific units in the harpacticoid subfamily Stenheliinae Brady, 1880 has been considered problematic and hindered by the lack of molecular or morphology based phylogenies, as well as by incomplete original descriptions of many species. Presence of a modified seta on the fifth leg endopod has been suggested recently as a synapomorphy of eight species comprising the redefined genus Stenhelia Boeck, 1865, although its presence was not known in S. pubescens Chislenko, 1978. We redescribe this species in detail here, based on our freshly collected topotypes from the Russian Far East. The other species redescribed in this paper was collected from the southern coast of South Korea and identified as the Chinese S. taiae Mu & Huys, 2002, which represents its second record ever and the first one in Korea. A fragment of the mtCOI gene was successfully PCR-amplified from two specimens of each species, which represents the first molecular data for this genus, and from additional 19 specimens belonging to six different species of other stenheliins from Korea and Russia. Reconstructed phylogenies confirm previously postulated monophyly of Stenhelia and polyphyly of the closely related genus Delavalia Brady, 1869. Average pairwise maximum likelihood distances between S. pubescens and S. taiae are only slightly above 10%, suggesting a very close relationship despite numerous newly discovered micro-morphological differences and despite macro-morphological similarities being probable plesiomorphies. PMID:24899857

  20. Use of Repetitive Sequences for Molecular and Cytogenetic Characterization of Avena Species from Portugal

    PubMed Central

    Tomás, Diana; Rodrigues, Joana; Varela, Ana; Veloso, Maria Manuela; Viegas, Wanda; Silva, Manuela

    2016-01-01

    Genomic diversity of Portuguese accessions of Avena species—diploid A. strigosa and hexaploids A. sativa and A. sterilis—was evaluated through molecular and cytological analysis of 45S rDNA, and other repetitive sequences previously studied in cereal species—rye subtelomeric sequence (pSc200) and cereal centromeric sequence (CCS1). Additionally, retrotransposons and microsatellites targeting methodologies—IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microsatellite amplified polymorphism)—were performed. A very high homology was detected for ribosomal internal transcribed sequences (ITS1 and ITS2) between the species analyzed, although nucleolar organizing regions (NOR) fluorescent in situ hybridization (FISH) analysis revealed distinct number of Nor loci between diploid and hexaploid species. Moreover, morphological diversity, evidenced by FISH signals with different sizes, was observed between distinct accessions within each species. pSc200 sequences were for the first time isolated from Avena species but proven to be highly similar in all genotypes analyzed. The use of primers designed for CCS1 unraveled a sequence homologous to the Ty3/gypsy retrotransposon Cereba, that was mapped to centromeric regions of diploid and hexaploid species, being however restricted to the more related A and D haplomes. Retrotransposon-based methodologies disclosed species- and accessions-specific bands essential for the accurate discrimination of all genotypes studied. Centromeric, IRAP and REMAP profiles therefore allowed accurate assessment of inter and intraspecific variability, demonstrating the potential of these molecular markers on future oat breeding programs. PMID:26861283

  1. Molecular identification of onchocerciasis vector sibling species in black flies (Diptera: Simuliidae).

    PubMed

    Brockhouse, C L; Vajime, C G; Marin, R; Tanguay, R M

    1993-07-30

    A number of sibling species in the Simulium damnosum species complex transmit River Blindness (onchocerciasis) in tropical Africa. Black fly sibling species can be reliably recognized only through analysis of the larval polytene chromosomes. The routine, unambiguous assignment of the potentially disease-transmitting adult females to a particular species is virtually impossible. Two molecular assays to identify the sibling species of biting female flies are presented. The first relies on PCR-mediated amplification of internal transcribed spacers of the nuclear rDNA loci while the second involves immunoblotting of silk proteins which are expressed in both larvae and adult females. Both assays yield sibling-specific size markers that can be used to identify the sibling species of biting adult females. To illustrate the use of these assays, a molecular characterization is given for two S. damnosum siblings (squamosum, sirbanum) collected from cytologically verified populations, and a partial characterization of a third sibling (damnosum s. str.) found as a contaminant in these samples. PMID:8343149

  2. Morphological and molecular affinities of two East Asian species of Stenhelia (Crustacea, Copepoda, Harpacticoida)

    PubMed Central

    Karanovic, Tomislav; Kim, Kichoon; Lee, Wonchoel

    2014-01-01

    Abstract Definition of monophyletic supraspecific units in the harpacticoid subfamily Stenheliinae Brady, 1880 has been considered problematic and hindered by the lack of molecular or morphology based phylogenies, as well as by incomplete original descriptions of many species. Presence of a modified seta on the fifth leg endopod has been suggested recently as a synapomorphy of eight species comprising the redefined genus Stenhelia Boeck, 1865, although its presence was not known in S. pubescens Chislenko, 1978. We redescribe this species in detail here, based on our freshly collected topotypes from the Russian Far East. The other species redescribed in this paper was collected from the southern coast of South Korea and identified as the Chinese S. taiae Mu & Huys, 2002, which represents its second record ever and the first one in Korea. A fragment of the mtCOI gene was successfully PCR-amplified from two specimens of each species, which represents the first molecular data for this genus, and from additional 19 specimens belonging to six different species of other stenheliins from Korea and Russia. Reconstructed phylogenies confirm previously postulated monophyly of Stenhelia and polyphyly of the closely related genus Delavalia Brady, 1869. Average pairwise maximum likelihood distances between S. pubescens and S. taiae are only slightly above 10%, suggesting a very close relationship despite numerous newly discovered micro-morphological differences and despite macro-morphological similarities being probable plesiomorphies. PMID:24899857

  3. Coupled biophysical global ocean model and molecular genetic analyses identify multiple introductions of cryptogenic species.

    PubMed

    Dawson, Michael N; Sen Gupta, Alex; England, Matthew H

    2005-08-23

    The anthropogenic introduction of exotic species is one of the greatest modern threats to marine biodiversity. Yet exotic species introductions remain difficult to predict and are easily misunderstood because knowledge of natural dispersal patterns, species diversity, and biogeography is often insufficient to distinguish between a broadly dispersed natural population and an exotic one. Here we compare a global molecular phylogeny of a representative marine meroplanktonic taxon, the moon-jellyfish Aurelia, with natural dispersion patterns predicted by a global biophysical ocean model. Despite assumed high dispersal ability, the phylogeny reveals many cryptic species and predominantly regional structure with one notable exception: the globally distributed Aurelia sp.1, which, molecular data suggest, may occasionally traverse the Pacific unaided. This possibility is refuted by the ocean model, which shows much more limited dispersion and patterns of distribution broadly consistent with modern biogeographic zones, thus identifying multiple introductions worldwide of this cryptogenic species. This approach also supports existing evidence that (i) the occurrence in Hawaii of Aurelia sp. 4 and other native Indo-West Pacific species with similar life histories is most likely due to anthropogenic translocation, and (ii) there may be a route for rare natural colonization of northeast North America by the European marine snail Littorina littorea, whose status as endemic or exotic is unclear. PMID:16103373

  4. Molecular identification and classification of Trichophyton mentagrophytes complex strains isolated from humans and selected animal species.

    PubMed

    Ziółkowska, Grażyna; Nowakiewicz, Aneta; Gnat, Sebastian; Trościańczyk, Aleksandra; Zięba, Przemysław; Dziedzic, Barbara Majer

    2015-03-01

    Species differentiation within Trichophyton mentagrophytes complex group currently poses a major diagnostic challenge, with molecular methods increasingly supplementing classical identification based on the morphological and physiological properties of the fungi. Diagnostic and epidemiological research aimed at determining the source and means of transmission of dermatophytoses in both humans and animals requires not only species differentiation of isolates but also differentiation within species. The study was conducted on 24 isolates originating in humans and various animal species with clinical symptoms of dermatophytosis. The analysis included phenotypical identification methods and molecular methods: internal transcribed spacer sequencing and ITS-restriction fragment length polymorphism (RFLP) with multi-enzyme restriction. ITS sequence analysis identified the isolates to species - Trichophyton interdigitale, Arthroderma benhamiae and A. vanbreuseghemii, and ITS-RFLP detected six different genotypes. Genotypes I, II and III characterised strains belonging to A. benhamiae, genotype IV characterised the A. vanbreuseghemii strain, and genotypes V and VI occurred only within the species T. interdigitale. Strains isolated from guinea pigs were dominant within genotype I, while genotype II was found mainly in strains from foxes. Multi-enzyme restriction analysis of this region enables intraspecific differentiation, which may be useful in epidemiological research, particularly in determining the source of infections. PMID:25643744

  5. Species delimitation of Chinese hop-hornbeams based on molecular and morphological evidence.

    PubMed

    Lu, Zhiqiang; Zhang, Dan; Liu, Siyu; Yang, Xiaoyue; Liu, Xue; Liu, Jianquan

    2016-07-01

    Species delimitation through which infers species boundaries is emerging as a major work in modern systematics. Hop-hornbeam species in Ostrya (Betulaceae) are well known for their hard and heavy woods. Five species were described in China and their interspecific delimitations remain unclear. In this study, we firstly explored their distributions in all recorded field sites distributed in China. We then selected 110 samples from 22 natural populations of five species from this genus and one type specimen of O. yunnanensis, for molecular barcoding analyses. We sequenced four chloroplast (cp) DNA fragments (trnH-psbA, trnL-trnF, rps16, and trnG) and the nuclear internal transcribed spacer (ITS) region for all samples. Sequence variations of Ostrya from four cpDNA fragments identified three groups that showed no correspondence to any morphological delimitation because of the incomplete lineage sorting and/or possible interspecific introgression in the history. However, phylogenetic analyses of ITS sequence variations discerned four species, O. japonica, O. rehderiana, O. trichocarpa, and O. multinervis while O. yunnanensis nested within O. multinervis. Morphological clustering also discerned four species and showed the complete consistency with molecular evidence. Moreover, our phylogenetic analyses-based ITS sequence variations suggested that O. trichocarpa comprised an isolated lineage different from the other Eurasian ones. Based on these results, hop-hornbeams in China should be treated as four separate species. Our results further highlight the importance of ITS sequence variations in delimitating and discerning the closely related species in plants. PMID:27547308

  6. Molecular epidemiology of isolates of the Cryptococcus neoformans species complex from Spain.

    PubMed

    Frasés, Susana; Ferrer, Consuelo; Sánchez, Manuel; Colom-Valiente, María Francisca

    2009-06-30

    To study genetic diversity of Cryptococcus neoformans species complex in Spain, 97 isolates of the yeast recovered from human, animal and environmental samples have been analysed using three molecular epidemiological techniques. One of these, URA5 gene fragment length polymorphism (RFLP) analysis, has been previously described as a molecular epidemiology tool. Thus, standard profiles and reference strains have been defined for it. In addition, 5S rDNA/IGS RFLP and [GACA](4) microsatellite PCR fingerprinting were also used. Our results show five of the previously defined URA5 genotypes with a high frequency (33%) of the VNI type, which is in concordance with other studies. The high presence of VNIII pattern (28.9%) among our strains is remarkable and could be a specific feature of the isolates from our country. 5S rDNA/IGS RFLP showed a low intra-species discriminative power. Three different molecular profiles (S1-3), which showed a good correlation with the different species, varieties and genotypes, were obtained. [GACA](4) microsatellite PCR-fingerprinting analysis showed a high variability of patterns among the studied strains. Molecular profiles represented in a dendrogram clustered strains in four main groups related with the source of the yeast and also in concordance with some of the described genotypes (VNI-IV and VGI). PMID:19631160

  7. Species identification in cell culture: a two-pronged molecular approach.

    PubMed

    Cooper, Jason K; Sykes, Greg; King, Steve; Cottrill, Karin; Ivanova, Natalia V; Hanner, Robert; Ikonomi, Pranvera

    2007-01-01

    Species identification of cell lines and detection of cross-contamination are crucial for scientific research accuracy and reproducibility. Whereas short tandem repeat profiling offers a solution for a limited number of species, primarily human and mouse, the standard method for species identification of cell lines is enzyme polymorphism. Isoezymology, however, has its own drawbacks; it is cumbersome and the data interpretation is often difficult. Furthermore, the detection sensitivity for cross-contamination is low; it requires large amounts of the contaminant present and cross-contamination within closely related species may go undetected. In this paper, we describe a two-pronged molecular approach that addresses these issues by targeting the mitochondrial genome. First, we developed a multiplex PCR-based assay to rapidly identify the most common cell culture species and quickly detect cross-contaminations among these species. Second, for speciation and identification of a wider variety of cell lines, we amplified and sequenced a 648-bp region, often described as the "barcode region" by using a universal primer mix targeted at conserved sequences of the cytochrome C oxidase I gene (COI). This method was challenged with a panel of 67 cell lines from 45 diverse species. Implementation of these assays will accurately determine the species of cell lines and will reduce the problems of misidentification and cross-contamination that plague research efforts. PMID:17934781

  8. Molecular evidence for convergent evolution and allopolyploid speciation within the Physcomitrium-Physcomitrella species complex

    PubMed Central

    2014-01-01

    Background The moss Physcomitrella patens (Hedw.) Bruch & Schimp. is an important experimental model system for evolutionary-developmental studies. In order to shed light on the evolutionary history of Physcomitrella and related species within the Funariaceae, we analyzed the natural genetic diversity of the Physcomitrium-Physcomitrella species complex. Results Molecular analysis of the nuclear single copy gene BRK1 reveals that three Physcomitrium species feature larger genome sizes than Physcomitrella patens and encode two expressed BRK1 homeologs (polyploidization-derived paralogs), indicating that they may be allopolyploid hybrids. Phylogenetic analyses of BRK1 as well as microsatellite simple sequence repeat (SSR) data confirm a polyphyletic origin for three Physcomitrella lineages. Differences in the conservation of mitochondrial editing sites further support hybridization and cryptic speciation within the Physcomitrium-Physcomitrella species complex. Conclusions We propose a revised classification of the previously described four subspecies of Physcomitrella patens into three distinct species, namely Physcomitrella patens, Physcomitrella readeri and Physcomitrella magdalenae. We argue that secondary reduction of sporophyte complexity in these species is due to the establishment of an ecological niche, namely spores resting in mud and possible spore dispersal by migratory birds. Besides the Physcomitrium-Physcomitrella species complex, the Funariaceae are host to their type species, Funaria hygrometrica, featuring a sporophyte morphology which is more complex. Their considerable developmental variation among closely related lineages and remarkable trait evolution render the Funariaceae an interesting group for evolutionary and genetic research. PMID:25015729

  9. Molecular Phylogeny of the Pseudallescheria boydii Species Complex: Proposal of Two New Species†

    PubMed Central

    Gilgado, Felix; Cano, Josep; Gené, Josepa; Guarro, Josep

    2005-01-01

    Pseudallescheria boydii (anamorph Scedosporium apiospermum) is the species responsible for human scedosporiosis, a fungal infection with a high mortality rate and which is difficult to treat. Recently, it has been demonstrated that high genetic variation exists within this species. We have performed a morphological and molecular study involving numerous strains of clinical or environmental origins and from different countries. The analysis of partial sequences of the β-tubulin (two loci) and calmodulin genes and the internal transcribed spacer region of the rRNA gene has demonstrated that P. boydii is a species complex. The combined analysis of the sequences of the four loci of 60 strains has showed the presence of 44 haplotypes in the ingroup. Three species morphologically related to P. boydii sensu stricto, i.e., Pseudallescheria angusta, Pseudallescheria ellipsoidea, and Pseudallescheria fusoidea, which had previously been considered synonyms, could be differentiated genetically from P. boydii in our study. It is relevant that two of the three strains now included in P. ellipsoidea have caused invasive infections. The species Pseudallescheria minutispora and Scedosporium aurantiacum are clearly phylogenetically separated from the other species studied and are here proposed as new. Morphological features support this proposal. All the strains included in S. aurantiacum species have a clinical origin, while those included in P. minutispora are environmental. Further studies are needed to demonstrate whether all the species included in the P. boydii complex have different clinical spectra and antifungal susceptibility. PMID:16207945

  10. A molecular identification protocol for roots of boreal forest tree species1

    PubMed Central

    Randall, Morgan J.; Karst, Justine; Pec, Gregory J.; Davis, Corey S.; Hall, Jocelyn C.; Cahill, James F.

    2014-01-01

    • Premise of the study: Roots play a key role in many ecological processes, yet our ability to identify species from bulk root samples is limited. Molecular tools may be used to identify species from root samples, but they have not yet been developed for most systems. Here we present a PCR-based method previously used to identify roots of grassland species, modified for use in boreal forests. • Methods: We used repeatable interspecific size differences in fluorescent amplified fragment length polymorphisms of three noncoding chloroplast DNA regions to identify seven woody species common to boreal forests in Alberta, Canada. • Results: Abies balsamea, Alnus crispa, Betula papyrifera, Pinus contorta, and Populus tremuloides were identifiable to species, while Picea glauca and Picea mariana were identifiable to genus. In mixtures of known composition of foliar DNA, species were identified with 98% accuracy using one region. Mixed root samples of unknown composition were identified with 100% accuracy; four species were identified using one region, while three species were identified using two regions. • Discussion: This methodology is accurate, efficient, and inexpensive, and thus a valuable approach for ecological studies of roots. Furthermore, this method has now been validated for both grassland and boreal forest systems, and thus may also have applications in any plant community. PMID:25383267

  11. Chronopotentiometric studies of phosphatidylcholine bilayers modified by ergosterol.

    PubMed

    Naumowicz, Monika; Petelska, Aneta Dorota; Figaszewski, Zbigniew Artur

    2011-01-01

    We have monitored the effect of ergosterol on electrical capacitance and electrical resistance of the phosphatidylcholine bilayer membranes using chronopotentiometry method. The chronopotentiometric characteristic of the bilayers depends on constant-current flow through the membranes. For low current values, no electroporation takes place and the membrane voltage rises exponentially to a constant value described by the Ohm's law. Based on these kinds of chronopotentiometric curves, a method of the membrane capacitance and the membrane resistance calculations is presented. PMID:21641920

  12. Molecular profiling for genetic variability in Capsicum species based on ISSR and RAPD markers.

    PubMed

    Thul, Sanjog T; Darokar, Mahendra P; Shasany, Ajit K; Khanuja, Suman P S

    2012-06-01

    The taxonomic identity of Capsicum species is found to be difficult as it displays variations at morpho-chemical characters. Twenty-two accessions of six Capsicum species, namely, C. annuum, C. baccatum, C. chinense, C. eximium, C. frutescens, and C. luteum were investigated for phenotypic diversity based on flower color and for genetic differences by molecular makers. The genetic cluster analyses of 27 RAPD and eight ISSR primers, respectively, revealed genetic similarities in the ranges of 23-88% and 11-96%. Principal component analysis of the pooled RAPD and ISSR data further supports the genetic similarity and groupings. Different species showed variations in relation to corolla shade of flower. C. annuum accessions formed a single cluster in the molecular analysis as maintaining their flower characteristic. C. chinense accession shared flower features with the accessions of C. frutescens and were found to be closer at genotypic level. C. luteum was found to be rather closer to C. baccatum complex, both phenotypically and genetically. The only accession of C. eximium presenting purple flowers falls apart from the groupings. The floral characteristics and the molecular markers are found to be useful toward the delineation of the species specificity in Capsicum collection and identification of genetic stock. PMID:21861246

  13. Cosmopolitan versus cryptic meiofaunal polychaete species: an approach to a molecular taxonomy

    NASA Astrophysics Data System (ADS)

    Westheide, W.; Schmidt, H.

    2002-08-01

    Polychaete taxonomy is characterised by a high number of apparently cosmopolitan species. Detection of subtle but diagnostic ultrastructural differences and - in recent years - investigations at the molecular level have revealed that many of these "species" are actually complexes of morphologically identical or almost identical cryptic species. To disregard their existence would lead to an underestimation of global meiofauna diversity and undermine the value of many scientific studies. Therefore, we strongly recommend that they be given formal taxonomic recognition, beyond their published presentation as "operational taxonomic units", "types" or by alphabetic or numerical designators. Since there are neither generally accepted practical procedures nor any established consensus regarding the application of genetic data in taxonomy, we here provide examples of, and suggestions for, the treatment of meiofaunal species that are distinguished exclusively by molecular data, e.g. by genetic distance values, cluster analyses, diagnostic (= autapomorphic) DNA fragments from DNA fingerprinting procedures (RAPD) and/or DNA sequence differences (e.g. of ITS 2). Although no holotype material may be available because the molecular procedures require the preparation of entire specimens, practical taxonomic problems can be overcome and the recommendations of the Zoological Code of Nomenclature satisfied, by adopting the following procedures: (1) deposition of band-patterns of an individual obtained with the primers used to find diagnostic markers; (2) deposition of DNA in ethanol of one syntype individual; (3) deposition of fixed specimens (syntypes) from the locus typicus.

  14. Stability of drug-carrier emulsions containing phosphatidylcholine mixtures.

    PubMed

    Trotta, Michele; Pattarino, Franco; Ignoni, Terenzio

    2002-03-01

    Lipid emulsion particles containing 10% of medium chain triglycerides were prepared using 2% w/w of a mixture 1:1 w/w of purified soya phosphatidylcholine and 2-hexanoyl phosphatidylcholine as emulsifier mixture, for use as drug carriers. The mean droplet sizes of emulsions, prepared using an Ultra Turrax or a high-pressure homogenizer, were about 288 and 158 nm, respectively, compared with 380 and 268 nm for emulsions containing lecithin, or 325 and 240 nm for those containing 6-phosphatidylcholine. The stability of the emulsions, determined by monitoring the decrease of a lipophilic marker at a specified level within the emulsion, and observing coalescence over time, was also greatly increased using the emulsifier mixture. The emulsion stability did not notably change in the presence of a model destabilizing drug, indomethacin. The use of a second hydrophilic surfactant to adjust the packing properties of the lecithin at the oil-water interface provided an increase in the stability of lipid emulsions, and this may be of importance in the formulation of drug delivery systems. PMID:11880004

  15. Molecular Phylogeny of the Neotropical Genus Christensonella (Orchidaceae, Maxillariinae): Species Delimitation and Insights into Chromosome Evolution

    PubMed Central

    Koehler, Samantha; Cabral, Juliano S.; Whitten, W. Mark; Williams, Norris H.; Singer, Rodrigo B.; Neubig, Kurt M.; Guerra, Marcelo; Souza, Anete P.; Amaral, Maria do Carmo E.

    2008-01-01

    Background and Aims Species' boundaries applied within Christensonella have varied due to the continuous pattern of variation and mosaic distribution of diagnostic characters. The main goals of this study were to revise the species' delimitation and propose a more stable classification for this genus. In order to achieve these aims phylogenetic relationships were inferred using DNA sequence data and cytological diversity within Christensonella was examined based on chromosome counts and heterochromatin patterns. The results presented describe sets of diagnostic morphological characters that can be used for species' identification. Methods Phylogenetic studies were based on sequence data of nuclear and plastid regions, analysed using maximum parsimony and maximum likelihood criteria. Cytogenetic observations of mitotic cells were conducted using CMA and DAPI fluorochromes. Key Results Six of 21 currently accepted species were recovered. The results also support recognition of the ‘C. pumila’ clade as a single species. Molecular phylogenetic relationships within the ‘C. acicularis–C. madida’ and ‘C. ferdinandiana–C. neowiedii’ species' complexes were not resolved and require further study. Deeper relationships were incongruent between plastid and nuclear trees, but with no strong bootstrap support for either, except for the position of C. vernicosa. Cytogenetic data indicated chromosome numbers of 2n = 36, 38 and 76, and with substantial variation in the presence and location of CMA/DAPI heterochromatin bands. Conclusions The recognition of ten species of Christensonella is proposed according to the molecular and cytogenetic patterns observed. In addition, diagnostic morphological characters are presented for each recognized species. Banding patterns and chromosome counts suggest the occurrence of centric fusion/fission events, especially for C. ferdinandiana. The results suggest that 2n = 36 karyotypes evolved from 2n = 38 through descendent

  16. Species identification refined by molecular scatology in a community of sympatric carnivores in Xinjiang, China

    PubMed Central

    LAGUARDIA, Alice; WANG, Jun; SHI, Fang-Lei; SHI, Kun; RIORDAN, Philip

    2015-01-01

    Many ecological studies and conservation management plans employ noninvasive scat sampling based on the assumption that species’ scats can be correctly identified in the field. However, in habitats with sympatric similarly sized carnivores, misidentification of scats is frequent and can lead to bias in research results. To address the scat identification dilemma, molecular scatology techniques have been developed to extract DNA from the donor cells present on the outer lining of the scat samples. A total of 100 samples were collected in the winter of 2009 and 2011 in Taxkorgan region of Xinjiang, China. DNA was extracted successfully from 88% of samples and genetic species identification showed that more than half the scats identified in the field as snow leopard (Panthera uncia) actually belonged to fox (Vulpes vulpes). Correlation between scat characteristics and species were investigated, showing that diameter and dry weight of the scat were significantly different between the species. However it was not possible to define a precise range of values for each species because of extensive overlap between the morphological values. This preliminary study confirms that identification of snow leopard feces in the field is misleading. Research that relies upon scat samples to assess distribution or diet of the snow leopard should therefore employ molecular scatology techniques. These methods are financially accessible and employ relatively simple laboratory procedures that can give an indisputable response to species identification from scats. PMID:25855225

  17. Molecular phylogeny of extant horseshoe crabs (Xiphosura, Limulidae) indicates Paleogene diversification of Asian species.

    PubMed

    Obst, Matthias; Faurby, Søren; Bussarawit, Somchai; Funch, Peter

    2012-01-01

    Horseshoe crabs are marine invertebrates well known for their exceptionally low rates of diversification during their entire evolutionary history. Despite the low species diversity in the group, the phylogenetic relationships among the extant species, especially among the three Asian species are still unresolved. Here we apply a new set of molecular genetic data in combination with a wide geographic sampling of the intra-specific diversity to reinvestigate the evolutionary history among the four living limulid xiphosurans. Our analysis of the intraspecific diversity reveals low levels of connectivity among Carcinoscorpius rotundicauda lineages, which can be explained by the estuarine-bound ecology of this species. Moreover, a clear genetic break across the Thai-Malay Peninsula suggests the presence of cryptic species in C. rotundicauda. The limulid phylogeny finds strong support for a monophyletic genus Tachypleus and a diversification of the three Asian species during the Paleogene period, with speciation events well separated in time by several million years. The tree topology suggests that the three Asian species originated in central South East Asia from a marine stem group that inhabited the shallow coastal waters between the Andaman Sea, Vietnam, and Borneo. In this region C. rotundicauda probably separated from the Tachypleus stem group by invading estuarine habitats, while Tachypleus tridentatus most likely migrated northeast along the Southern coast of China and towards Japan. PMID:21939777

  18. Comprehensive and quantitative analysis of lysophospholipid molecular species present in obese mouse liver by shotgun lipidomics

    PubMed Central

    Wang, Chunyan; Wang, Miao; Han, Xianlin

    2015-01-01

    Shotgun lipidomics exploits the unique chemical and physical properties of lipid classes and individual molecular species to facilitate the high-throughput analysis of a cellular lipidome on a large scale directly from the extracts of biological samples. A platform for comprehensive analysis of lysophospholipid (LPL) species based on shotgun lipidomics has not been established. Herein, after extensive characterization of the fragmentation pattern of individual LPL class and optimization of all experimental conditions including developing new methods for optimization of collision energy, and recovery and enrichment of LPL classes from the aqueous phase after solvent extraction, a new method for comprehensive and quantitative analysis of LPL species was developed. This newly developed method was applied for comprehensive analysis of LPL species present in mouse liver samples. Remarkably, the study revealed significant accumulation of LPL species in the liver of ob/ob mice. Taken together, by exploiting the principles of shotgun lipidomics in combination with a novel strategy of sample preparation, LPL species present in biological samples can be determined by the established method. We believe that this development is significant and useful for understanding the pathways of phospholipid metabolism and for elucidating the role of LPL species in signal transduction and other biological functions. PMID:25860968

  19. Molecular perspective on the American transisthmian species of Macrobrachium (Caridea, Palaemonidae)

    PubMed Central

    Pileggi, Leonardo G.; Rossi, Natália; Wehrtmann, Ingo S.; Mantelatto, Fernando L.

    2014-01-01

    Abstract The closure of the Isthmus of Panama (about 3.1 million years ago) separated previously continuous populations and created two groups of extant species, which live now in the Pacific and Atlantic drainage systems. This relatively recent event was a trigger to diversification of various species in the Neotropics, nonetheless there are exemplars that do not show sufficient morphologic variability to separate them by traditional morphological tools. About 60 years ago, some freshwater decapod species with high morphological similarity were separate by previous researchers, based on geographical distribution, in Pacific and Atlantic and considered as “sister species”. However, the complete isolation of these prawns by this geographical barrier is questionable, and it has generated doubts about the status of the following transisthmian pairs of sibling species: Macrobrachium occidentale × Macrobrachium heterochirus, Macrobrachium americanum × Macrobrachium carcinus, Macrobrachium digueti × Macrobrachium olfersii, Macrobrachium hancocki × Macrobrachium crenulatum, Macrobrachium tenellum × Macrobrachium acanthurus and Macrobrachium panamense × Macrobrachium amazonicum. Here we evaluated the relation among these pairs of sibling species in a molecular phylogenetic context. We generated 95 new sequences: 26 sequences of 16S rDNA, 25 of COI mtDNA and 44 of 18S nDNA. In total, 181 sequences were analyzed by maximum likelihood phylogenetic method, including 12 Macrobrachium transisthmian species, as well as seven other American Macrobrachium species, and two other palaemonids. Our analysis corroborated the morphological proximity of the sibling species. Despite the high degree of morphological similarities and considerable genetic diversification encountered among the transisthmian sister species, our data support the conclusion that all species included in sibling groups studied herein are valid taxonomic entities, but not all pairs of siblings form natural

  20. Taxonomic and Molecular Identification of Mesocriconema and Criconemoides Species (Nematoda: Criconematidae)

    PubMed Central

    Cordero, Marco A.; Robbins, Robert T.; Szalanski, Allen L.

    2012-01-01

    Populations of Mesocriconema curvatum, M. kirjanovae, M. onoense, M. ornatum, M. sphaerocephala, M. surinamense, M. vadense, M. xenoplax, and Criconemoides informis from different geographical areas in the continental United States were characterized morphologically and molecularly. A new ring nematode from Washington County, Arkansas, is also described and named Mesocriconema ozarkiense n. sp., This new species is characterized by females with small flattened submedian lobes, lower than or at the same level as the labial disc, vagina straight, very well developed spermatheca without sperm, no more than one anastomoses, L=379-512 μm, V=89-93, stylet length = 49-61 μm, R=107-119, annuli with slightly crenate margins on tail portion and a simple anterior vulval lip. The molecular characterization of M. ozarkiense n. sp. using the ITS rRNA gene sequence and the phylogenesis relationship of this new species with the ring nematodes included in this study are provided. PMID:23482878

  1. On the nature of hydrogen bonding between the phosphatidylcholine head group and water and dimethylsulfoxide

    NASA Astrophysics Data System (ADS)

    Dabkowska, Aleksandra P.; Lawrence, M. Jayne; McLain, Sylvia E.; Lorenz, Christian D.

    2013-01-01

    Molecular dynamics simulations are used to provide a detailed investigation of the hydrogen bond networks around the phosphatidylcholine (PC) head group in 1,2-dipropionyl-sn-glycero-3-phosphocholine in pure water, 10 mol.% and 30 mol.% dimethylsulfoxide (DMSO)-water solutions. Specifically, it is observed that DMSO replaces those water molecules that are within the first solvation shell of the choline, phosphate and ester groups of the PC head group, but are not hydrogen-bonded to the group. The effect of the presence of DMSO on the hydrogen bond network around the PC head groups of the lipid changes with the concentration of DMSO. In comparison to the hydrogen bond network observed in the pure water system, the number of hydrogen-bonded chains of solvent molecules increases slightly for the 10 mol.% DMSO system, while, in the 30 mol.% DMSO system, the number of hydrogen-bonded chains of solvent molecules decreases.

  2. Molecular Diversity of Seed-borne Fusarium Species Associated with Maize in India.

    PubMed

    Aiyaz, Mohammed; Divakara, Shetty Thimmappa; Mudili, Venkataramana; Moore, Geromy George; Gupta, Vijai Kumar; Yli-Mattila, Tapani; Nayaka, Siddaiah Chandra; Niranjana, Siddapura Ramachandrappa

    2016-04-01

    A total of 106 maize seed samples were collected from different agro-climatic regions of India. Sixty-two Fusarium isolates were recovered, 90% of which were identified as Fusarium verticillioides based on morphological and molecular characters. Use of the tef-1α gene corrected/refined the morphological species identifications of 11 isolates, and confirmed those of the remaining isolates. Genetic diversity among the Fusarium isolates involved multilocus fingerprinting profiles by Inter Simple Sequence Repeats (ISSR) UPGMA and tef-1α gene phenetic analyses; for which, we observed no significant differences among the isolates based on geographic origin or fumonisin production; most of the subdivision related to species. Genotyping was performed on the F. verticillioides isolates, using 12 primer sets from the fumonisin pathway, to elucidate the molec-ular basis of fumonisin production or non-production. One fumonisin-negative isolate, UOMMF-16, was unable to amplify nine of the 12 fumonisin cluster genes tested. We also used the CD-ELISA method to confirm fumonisin production for our 62 Fusarium isolates. Only 15 isolates were found to be fumonisin-negative. Interestingly, genotypic characterization re-vealed six isolates with various gene deletion patterns that also tested positive for the production of fumonisins via CD-ELISA. Our findings confirm the importance of molecular studies for species delimitation, and for observing genetic and phenotypic diversity, among the Fusaria. PMID:27226769

  3. The species flocks of East African cichlid fishes: recent advances in molecular phylogenetics and population genetics

    NASA Astrophysics Data System (ADS)

    Salzburger, Walter; Meyer, Axel

    With more than 3,000 species, the fish family Cichlidae is one of the most species-rich families of vertebrates. Cichlids occur in southern and central America, Africa, Madagascar, and India. The hotspot of their biodiversity is East Africa, where they form adaptive radiations composed of hundreds of endemic species in several lakes of various sizes and ages. The unparalleled species richness of East African cichlids has been something of a conundrum for evolutionary biologists and ecologists, since it has been in doubt whether these hundreds of species arose by allopatric speciation or whether it is necessary to invoke somewhat less traditional models of speciation, such as micro-allopatric, peripatric, or even sympatric speciation or evolution through sexual selection mediated by female choice. Ernst Mayr's analyses of these evolutionary uniquely diverse species assemblages have contributed to a more direct approach to this problem and have led to a deeper understanding of the patterns and processes that caused the formation of these huge groups of species. We review here recent molecular data on population differentiation and phylogenetics, which have helped to unravel, to some extent, the patterns and processes that led to the formation and ecological maintenance of cichlid species flocks. It is becoming apparent that sexually selected traits do play an important role in speciation in micro-allopatric or even sympatric settings. Species richness seems to be roughly correlated with the surface area, but not the age, of the lakes. We observe that the oldest lineages of a species flock of cichlids are often less species-rich and live in the open water or deepwater habitats. While the species flocks of the Lake Malawai and the Lake Victoria areas were shown to be monophyletic, the cichlid assemblage of Lake Tanganyika seems to consist of several independent species flocks. Cichlids emerge as an evolutionary model system in which many fundamental questions in

  4. Morphological and molecular evidence for cryptic species of springsnails [genus Pseudamnicola ( Corrosella) (Mollusca, Caenogastropoda, Hydrobiidae)

    PubMed Central

    Delicado, Diana; Ramos, Marian A.

    2012-01-01

    Abstract Several Pseudamnicola (Corrosella) populations of the central and eastern Iberian Peninsula have been ascribed to Pseudamnicola (Corrosella) astieri (Dupuy, 1851), though recent evidence demonstrates the species could be endemic to the departments of Var and Alpes-Maritimes in France. Through the identification of cryptic species using a combined morphological and phylogenetic approach, this paper provides a detailed morphological description of Pseudamnicola (Corrosella) astieri, clarifying its taxonomic boundaries and confirming it as a French endemic. In parallel, by comparing Pseudamnicola (Corrosella) populations from the provinces of Castellón and Valencia in Eastern Spain, it was observed that rather than Pseudamnicola (Corrosella) astieri they represented a new species here described as Pseudamnicola (Corrosella) hauffei sp. n. Among other characters, the two species show marked differences in shell shape, male and female genital systems, radular formula and concentration of the nervous system. Pseudamnicola (Corrosella) hauffei sp. n. was also compared morphologically to another two Pseudamnicola (Corrosella) species living in nearby areas [Pseudamnicola (Corrosella) hinzi Boeters, 1986 and Pseudamnicola (Corrosella) navasiana (Fagot, 1907)], molecularly to Pseudamnicola (Corrosella) falkneri (Boeters, 1970), the type species of the subgenus, and to the rest of the Pseudamnicola (Corrosella) species described so far. Morphological differentiation between the species is supported by a genetic divergence of 7.4% inferred from a partial sequence (658 bp) of the mitochondrial gene cytochrome c oxidase subunit I (COI). On the basis of an average 8% (5.39 to 11.15%) divergence estimated for the COI gene in other Pseudamnicola (Corrosella) species reported in GenBank, the existence of two specific entities is here proposed, which will have impact on conservation policies both in France and in Spain. PMID:22639531

  5. The bladed Bangiales (Rhodophyta) of the South Eastern Pacific: Molecular species delimitation reveals extensive diversity.

    PubMed

    Guillemin, Marie-Laure; Contreras-Porcia, Loretto; Ramírez, María Eliana; Macaya, Erasmo C; Contador, Cristian Bulboa; Woods, Helen; Wyatt, Christopher; Brodie, Juliet

    2016-01-01

    A molecular taxonomic study of the bladed Bangiales of the South Eastern Pacific (coast of Chile) was undertaken based on sequence data of the mitochondrial COI and chloroplast rbcL for 193 specimens collected from Arica (18°S) in the north to South Patagonia (53°S) in the south. The results revealed for the first time that four genera, Porphyra, Pyropia, Fuscifolium and Wildemania were present in the region. Species delimitation was determined based on a combination of a General Mixed Yule Coalescence model (GMYC) and Automatic Barcode Gap Discovery (ABGD) coupled with detection of monophyly in tree reconstruction. The overall incongruence between the species delimitation methods within each gene was 29%. The GMYC method led to over-splitting groups, whereas the ABGD method had a tendency to lump groups. Taking a conservative approach to the number of putative species, at least 18 were recognized and, with the exception of the recently described Pyropia orbicularis, all were new to the Chilean flora. Porphyra and Pyropia were the most diverse genera with eight 'species' each, whereas only a 'single' species each was found for Fuscifolium and Wildemania. There was also evidence of recently diverging groups: Wildemania sp. was distinct but very closely related to W. amplissima from the Northern Hemisphere and raises questions in relation to such disjunct distributions. Pyropia orbicularis was very closely related to two other species, making species delimitation very difficult but provides evidence of an incipient speciation. The difference between the 'species' discovered and those previously reported for the region is discussed in relation to the difficulty of distinguishing species based on morphological identification. PMID:26484942

  6. Molecular Identification and Prevalence of Malassezia Species in Pityriasis Versicolor Patients From Kashan, Iran

    PubMed Central

    Talaee, Rezvan; Katiraee, Farzad; Ghaderi, Maryam; Erami, Mahzad; Kazemi Alavi, Azam; Nazeri, Mehdi

    2014-01-01

    Background: Malassezia species are lipophilic yeasts found on the skin surface of humans and other warm-blooded vertebrates. It is associated with various human diseases, especially pityriasis versicolor, which is a chronic superficial skin disorder. Objectives: The aim of the present study was to identify Malassezia species isolated from patients’ samples affected by pityriasis versicolor, using molecular methods in Kashan, Iran. Patients and Methods: A total of 140 subjects, suspected of having pityriasis versicolor from Kashan, were clinically diagnosed and then confirmed by direct microscopic examination. The scraped skin specimens were inoculated in modified Dixon’s medium. DNA was extracted from the colonies and PCR amplification was carried out for the 26s rDNA region. PCR products were used to further restriction fragment length polymorphism by CfoI enzyme. Results: Direct examination was positive in 93.3% of suspected pityriasis versicolor lesions. No statistically significant difference was observed in the frequency of Malassezia species between women and men. The highest prevalence of tinea versicolor was seen in patients 21–30 years-of-age. No difference could be seen in the frequency of Malassezia species depending on the age of the patients. In total, 65% of patients with pityriasis versicolor had hyperhidrosis. The most commonly isolated Malassezia species in the pityriasis versicolor lesions were; Malassezia globosa (66%), M. furfur (26%), M. restricta (3%), M. sympodialis (3%), and M. slooffiae (2%). Malassezia species were mainly isolated from the neck and chest. Conclusions: This study showed M. globosa to be the most common Malassezia species isolated from Malassezia skin disorders in Kashan, Iran. The PCR-RFLP method was useful in the rapid identification of the Malassezia species. By using these methods, the detection and identification of individual Malassezia species from clinical samples was substantially easier. PMID:25485051

  7. Species limits in Diaporthe: molecular re-assessment of D. citri, D. foeniculina and D. rudis with a new species on Citrus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Species of Diaporthe are important plant pathogens associated with a wide range of hosts throughout the world. In the present study, the species causing melanose and stem end rot diseases on Citrus spp. were revised. Morphology and molecular phylogenetic analyses of the complete nuclear ribosomal in...

  8. Unexpected diversity of Anopheles species in Eastern Zambia: implications for evaluating vector behavior and interventions using molecular tools

    PubMed Central

    Lobo, Neil F.; Laurent, Brandyce St.; Sikaala, Chadwick H.; Hamainza, Busiku; Chanda, Javan; Chinula, Dingani; Krishnankutty, Sindhu M.; Mueller, Jonathan D.; Deason, Nicholas A.; Hoang, Quynh T.; Boldt, Heather L.; Thumloup, Julie; Stevenson, Jennifer; Seyoum, Aklilu; Collins, Frank H.

    2015-01-01

    The understanding of malaria vector species in association with their bionomic traits is vital for targeting malaria interventions and measuring effectiveness. Many entomological studies rely on morphological identification of mosquitoes, limiting recognition to visually distinct species/species groups. Anopheles species assignments based on ribosomal DNA ITS2 and mitochondrial DNA COI were compared to morphological identifications from Luangwa and Nyimba districts in Zambia. The comparison of morphological and molecular identifications determined that interpretations of species compositions, insecticide resistance assays, host preference studies, trap efficacy, and Plasmodium infections were incorrect when using morphological identification alone. Morphological identifications recognized eight Anopheles species while 18 distinct sequence groups or species were identified from molecular analyses. Of these 18, seven could not be identified through comparison to published sequences. Twelve of 18 molecularly identified species (including unidentifiable species and species not thought to be vectors) were found by PCR to carry Plasmodium sporozoites - compared to four of eight morphological species. Up to 15% of morphologically identified Anopheles funestus mosquitoes in insecticide resistance tests were found to be other species molecularly. The comprehension of primary and secondary malaria vectors and bionomic characteristics that impact malaria transmission and intervention effectiveness are fundamental in achieving malaria elimination. PMID:26648001

  9. Unexpected diversity of Anopheles species in Eastern Zambia: implications for evaluating vector behavior and interventions using molecular tools.

    PubMed

    Lobo, Neil F; St Laurent, Brandyce; Sikaala, Chadwick H; Hamainza, Busiku; Chanda, Javan; Chinula, Dingani; Krishnankutty, Sindhu M; Mueller, Jonathan D; Deason, Nicholas A; Hoang, Quynh T; Boldt, Heather L; Thumloup, Julie; Stevenson, Jennifer; Seyoum, Aklilu; Collins, Frank H

    2015-01-01

    The understanding of malaria vector species in association with their bionomic traits is vital for targeting malaria interventions and measuring effectiveness. Many entomological studies rely on morphological identification of mosquitoes, limiting recognition to visually distinct species/species groups. Anopheles species assignments based on ribosomal DNA ITS2 and mitochondrial DNA COI were compared to morphological identifications from Luangwa and Nyimba districts in Zambia. The comparison of morphological and molecular identifications determined that interpretations of species compositions, insecticide resistance assays, host preference studies, trap efficacy, and Plasmodium infections were incorrect when using morphological identification alone. Morphological identifications recognized eight Anopheles species while 18 distinct sequence groups or species were identified from molecular analyses. Of these 18, seven could not be identified through comparison to published sequences. Twelve of 18 molecularly identified species (including unidentifiable species and species not thought to be vectors) were found by PCR to carry Plasmodium sporozoites - compared to four of eight morphological species. Up to 15% of morphologically identified Anopheles funestus mosquitoes in insecticide resistance tests were found to be other species molecularly. The comprehension of primary and secondary malaria vectors and bionomic characteristics that impact malaria transmission and intervention effectiveness are fundamental in achieving malaria elimination. PMID:26648001

  10. Molecular Characterization of Natural Hybrids Formed between Five Related Indigenous Clade 6 Phytophthora Species

    PubMed Central

    Burgess, Treena I.

    2015-01-01

    Most Phytophthora hybrids characterized to date have emerged from nurseries and managed landscapes, most likely generated as a consequence of biological invasions associated with the movement of living plants and germplasm for ornamental, horticultural and agricultural purposes. Presented here is evidence for natural hybridization among a group of five closely related indigenous clade 6 Phytophthora species isolated from waterways and riparian ecosystems in Western Australia. Molecular characterization of hybrids consisted of cloning and sequencing two nuclear genes (ITS and ASF), sequencing of two further nuclear loci (BT and HSP) and of two mitochondrial loci (COI and NADH). Additionally, phenotypic traits including morphology of sporangia and optima and maxima temperatures for growth were also determined. In most cases the nuclear genes were biparentally and in all cases the mtDNA were uniparentally inherited, indicating hybrid formation through sexual crosses. Some isolates bear the molecular signature of three parents suggesting additional hybrid events, although it cannot be determined from the data if these were sequential or simultaneous. These species and their hybrids co-exist in riparian ecosystems and waterways where their ability for rapid asexual proliferation would enable them to rapidly colonize green plant litter. The apparent ease of hybridization could eventually lead to the merging of species through introgression. However, at this point in time, species integrity has been maintained and a more likely scenario is that the hybrids are not stable evolutionary lineages, but rather transient hybrid clones. PMID:26248187

  11. A simplified protocol for molecular identification of Eimeria species in field samples.

    PubMed

    Haug, Anita; Thebo, Per; Mattsson, Jens G

    2007-05-15

    This study aimed to find a fast, sensitive and efficient protocol for molecular identification of chicken Eimeria spp. in field samples. Various methods for each of the three steps of the protocol were evaluated: oocyst wall rupturing methods, DNA extraction methods, and identification of species-specific DNA sequences by PCR. We then compared and evaluated five complete protocols. Three series of oocyst suspensions of known number of oocysts from Eimeria mitis, Eimeria praecox, Eimeria maxima and Eimeria tenella were prepared and ground using glass beads or mini-pestle. DNA was extracted from ruptured oocysts using commercial systems (GeneReleaser, Qiagen Stoolkit and Prepman) or phenol-chloroform DNA extraction, followed by identification of species-specific ITS-1 sequences by optimised single species PCR assays. The Stoolkit and Prepman protocols showed insufficient repeatability, and the former was also expensive and relatively time-consuming. In contrast, both the GeneReleaser protocol and phenol-chloroform protocols were robust and sensitive, detecting less than 0.4 oocysts of each species per PCR. Finally, we evaluated our new protocol on 68 coccidia positive field samples. Our data suggests that rupturing the oocysts by mini-pestle grinding, preparing the DNA with GeneReleaser, followed by optimised single species PCR assays, makes a robust and sensitive procedure for identifying chicken Eimeria species in field samples. Importantly, it also provides minimal hands-on-time in the pre-PCR process, lower contamination risk and no handling of toxic chemicals. PMID:17386979

  12. Species and hybrid identification of sturgeon caviar: a new molecular approach to detect illegal trade.

    PubMed

    Boscari, E; Barmintseva, A; Pujolar, J M; Doukakis, P; Mugue, N; Congiu, L

    2014-05-01

    Overexploitation of wild populations due to the high economic value of caviar has driven sturgeons to near extinction. The high prices commanded by caviar on world markets have made it a magnet for illegal and fraudulent caviar trade, often involving low-value farmed caviar being sold as top-quality caviar. We present a new molecular approach for the identification of pure sturgeon species and hybrids that are among the most commercialized species in Europe and North America. Our test is based on the discovery of species-specific single nucleotide polymorphisms (SNPs) in the ribosomal protein S7, supplemented with the Vimentin gene and the mitochondrial D-loop. Test validations performed in 702 specimens of target and nontarget sturgeon species demonstrated a 100% identification success for Acipenser naccarii, A. fulvescens, A. stellatus, A. sinensis and A. transmontanus. In addition to species identification, our approach allows the identification of Bester and AL hybrids, two of the most economically important hybrids in the world, with 80% and 100% success, respectively. Moreover, the approach has the potential to identify many other existing sturgeon hybrids. The development of a standardized sturgeon identification tool will directly benefit trade law enforcement, providing the tools to monitor and regulate the legal trade of caviar and protect sturgeon stocks from illicit producers and traders, hence contributing to safeguarding this group of heavily threatened species. PMID:24219811

  13. Molecular and morphological identification of mealybug species (Hemiptera: Pseudococcidae) in Brazilian vineyards.

    PubMed

    Pacheco da Silva, Vitor C; Bertin, Aline; Blin, Aurélie; Germain, Jean-François; Bernardi, Daniel; Rignol, Guylène; Botton, Marcos; Malausa, Thibaut

    2014-01-01

    Mealybugs (Hemiptera: Pseudococcidae) are pests constraining the international trade of Brazilian table grapes. They damage grapes by transmitting viruses and toxins, causing defoliation, chlorosis, and vigor losses and favoring the development of sooty mold. Difficulties in mealybug identification remain an obstacle to the adequate management of these pests. In this study, our primary aim was to identify the principal mealybug species infesting the major table grape-producing regions in Brazil, by morphological and molecular characterization. Our secondary aim was to develop a rapid identification kit based on species-specific Polymerase Chain Reactions, to facilitate the routine identification of the most common pest species. We surveyed 40 sites infested with mealybugs and identified 17 species: Dysmicoccus brevipes (Cockerell), Dysmicoccus sylvarum Williams and Granara de Willink, Dysmicoccus texensis (Tinsley), Ferrisia cristinae Kaydan and Gullan, Ferrisia meridionalis Williams, Ferrisia terani Williams and Granara de Willink, Phenacoccus baccharidis Williams, Phenacoccus parvus Morrison, Phenacoccus solenopsis Tinsley, Planococcus citri (Risso), Pseudococcus viburni (Signoret), Pseudococcus cryptus Hempel, four taxa closely related each of to Pseudococcus viburni, Pseudococcus sociabilis Hambleton, Pseudococcus maritimus (Ehrhorn) and Pseudococcus meridionalis Prado, and one specimen from the genus Pseudococcus Westwood. The PCR method developed effectively identified five mealybug species of economic interest on grape in Brazil: D. brevipes, Pl. citri, Ps. viburni, Ph. solenopsis and Planococcus ficus (Signoret). Nevertheless, it is not possible to assure that this procedure is reliable for taxa that have not been sampled already and might be very closely related to the target species. PMID:25062012

  14. Molecular and Morphological Identification of Mealybug Species (Hemiptera: Pseudococcidae) in Brazilian Vineyards

    PubMed Central

    Pacheco da Silva, Vitor C.; Bertin, Aline; Blin, Aurélie; Germain, Jean-François; Bernardi, Daniel; Rignol, Guylène; Botton, Marcos; Malausa, Thibaut

    2014-01-01

    Mealybugs (Hemiptera: Pseudococcidae) are pests constraining the international trade of Brazilian table grapes. They damage grapes by transmitting viruses and toxins, causing defoliation, chlorosis, and vigor losses and favoring the development of sooty mold. Difficulties in mealybug identification remain an obstacle to the adequate management of these pests. In this study, our primary aim was to identify the principal mealybug species infesting the major table grape-producing regions in Brazil, by morphological and molecular characterization. Our secondary aim was to develop a rapid identification kit based on species-specific Polymerase Chain Reactions, to facilitate the routine identification of the most common pest species. We surveyed 40 sites infested with mealybugs and identified 17 species: Dysmicoccus brevipes (Cockerell), Dysmicoccus sylvarum Williams and Granara de Willink, Dysmicoccus texensis (Tinsley), Ferrisia cristinae Kaydan and Gullan, Ferrisia meridionalis Williams, Ferrisia terani Williams and Granara de Willink, Phenacoccus baccharidis Williams, Phenacoccus parvus Morrison, Phenacoccus solenopsis Tinsley, Planococcus citri (Risso), Pseudococcus viburni (Signoret), Pseudococcus cryptus Hempel, four taxa closely related each of to Pseudococcus viburni, Pseudococcus sociabilis Hambleton, Pseudococcus maritimus (Ehrhorn) and Pseudococcus meridionalis Prado, and one specimen from the genus Pseudococcus Westwood. The PCR method developed effectively identified five mealybug species of economic interest on grape in Brazil: D. brevipes, Pl. citri, Ps. viburni, Ph. solenopsis and Planococcus ficus (Signoret). Nevertheless, it is not possible to assure that this procedure is reliable for taxa that have not been sampled already and might be very closely related to the target species. PMID:25062012

  15. Delimiting species in the Phacus longicauda complex (Euglenida) through morphological and molecular analyses.

    PubMed

    Łukomska-Kowalczyk, Maja; Karnkowska, Anna; Milanowski, Rafał; Łach, Łukasz; Zakryś, Bożena

    2015-12-01

    Although Phacus longicauda is the type species of the genus Phacus and one of the most common species among autotrophic euglenids, its correct identification is nearly impossible. Over 30 morphologically similar taxa appear in the literature, but there are no good diagnostic features to distinguish them. Using environmental sampling and whole genome amplification, we delimited species within the Phacus longicauda complex. Morphological and molecular characters were analyzed for 36 strains isolated from environmental samples (mainly from Poland). DNA was obtained from a small number of cells (20-30) isolated with a micropipette from every sample (i.e., without setting up laboratory cultures), and phylogenetic analyses were based on variation in nSSU rDNA. Apart from Phacus longicauda, three other species (Phacus circumflexus, Phacus helikoides, and Phacus tortus) were distinguished. Phacus cordata comb. nov. Zakryś et M. Łukomska and Phacus rotunda comb. nov. Zakryś et M. Łukomska had their taxonomic ranks changed and two species new to science, Phacus cristatus sp. nov. Zakryś et M. Łukomska and Phacus crassus sp. nov. Zakryś et M. Łukomska, were described. For all verified species, diagnostic descriptions were amended and epitypes designated. PMID:26987009

  16. Multigene Molecular Systematics Confirm Species Status of Morphologically Convergent Pagurus Hermit Crabs

    PubMed Central

    Matzen da Silva, Joana; dos Santos, Antonina; Cunha, Marina R.; Costa, Filipe O.; Creer, Simon; Carvalho, Gary R.

    2011-01-01

    Introduction In spite of contemporary morphological taxonomy appraisals, apparent high morphological similarity raises uncertainty about the species status of certain Pagurus hermit crabs. This is exemplified between two European species, Pagurus excavatus (Herbst, 1791) and Pagurus alatus (Fabricius 1775), whose species status is still difficult to resolve using morphological criteria alone. Methodology/Principal Findings To address such ambiguities, we used combinations of Maximum Likelihood (ML) and Bayesian Inference (BI) methods to delineate species boundaries of P. alatus and P. excavatus and formulate an intermediate Pagurus phylogenetic hypothesis, based upon single and concatenated mitochondrial (cytochrome oxidase I [COI]) and nuclear (16S and 28s ribosomal RNA) gene partitions. The molecular data supported the species status of P. excavatus and P. alatus and also clearly resolved two divergent clades within hermit crabs from the Northeast Atlantic Ocean and the Mediterranean Sea. Conclusions/Significance Despite the abundance and prominent ecological role of hermit crabs, Pagurus, in North East Atlantic Ocean and Mediterranean Sea ecosystems, many important aspects of their taxonomy, biology, systematics and evolution remain poorly explored. The topologies presented here should be regarded as hypotheses that can be incorporated into the robust and integrated understanding of the systematic relationships within and between species of the genus Pagurus inhabiting the Northeast Atlantic Ocean and the Mediterranean Sea. PMID:22174780

  17. Detection of peroxy species in ultra-high-molecular-weight polyethylene by Raman spectroscopy.

    PubMed

    Chenery, D H

    1997-03-01

    Samples of gamma-sterilized ultra-high-molecular-weight polyethylene (UHMWPE) have been examined using infrared and Raman spectroscopies. Infrared spectra of microtomed sections of a thick segment of material exhibited carbonyl bands whose intensity was consistent with published data. Raman spectroscopy has been used for the first time to detect oxidized precursors to the commonly found carbonyl species. Gamma-sterilized plates examined as soon as possible after sterilization exhibited bands consistent with epoxide, alcohol and three different peroxy-containing species. The detection of these species in irradiated UHMWPE is reported for the first time and demonstrates that oxidation of this material proceeds via a gamma-induced free radical mechanism, as has been widely assumed. PMID:9061182

  18. Morphological and Molecular Phylogenetic Data Reveal a New Species of Primula (Primulaceae) from Hunan, China.

    PubMed

    Xu, Yuan; Yu, Xun-Lin; Hu, Chi-Ming; Hao, Gang

    2016-01-01

    A new species of Primulaceae, Primula undulifolia, is described from the hilly area of Hunan province in south-central China. Its morphology and distributional range suggest that it is allied to P. kwangtungensis, both adapted to subtropical climate, having contiguous distribution and similar habitat, growing on shady and moist cliffs. Petioles, scapes and pedicels of them are densely covered with rusty multicellular hairs, but the new species can be easily distinguished by its smaller flowers and narrowly oblong leaves with undulate margins. Molecular phylogenetic analysis based on four DNA markers (ITS, matK, trnL-F and rps16) confirmed the new species as an independent lineage and constitutes a main clade together with P. kwangtungensis, P. kweichouensis, P. wangii and P. hunanensis of Primula sect. Carolinella. PMID:27579832

  19. Morphological and Molecular Characterization of a New Trichuris Species (Nematoda- Trichuridae), and Phylogenetic Relationships of Trichuris Species of Cricetid Rodents from Argentina

    PubMed Central

    Robles, María del Rosario; Cutillas, Cristina; Panei, Carlos Javier; Callejón, Rocío

    2014-01-01

    Populations of Trichuris spp. isolated from six species of sigmodontine rodents from Argentina were analyzed based on morphological characteristics and ITS2 (rDNA) region sequences. Molecular data provided an opportunity to discuss the phylogenetic relationships among the Trichuris spp. from Noth and South America (mainly from Argentina). Trichuris specimens were identified morphologically as Trichuris pardinasi, T. navonae, Trichuris sp. and Trichuris new species, described in this paper. Sequences analyzed by Maximum Parsimony, Maximum Likelihood and Bayesian inference methods showed four main clades corresponding with the four different species regardless of geographical origin and host species. These four species from sigmodontine rodents clustered together and separated from Trichuris species isolated from murine and arvicoline rodents (outgroup). Different genetic lineages observed among Trichuris species from sigmodontine rodents which supported the proposal of a new species. Moreover, host distribution showed correspondence with the different tribes within the subfamily Sigmodontinae. PMID:25393618

  20. Molecular evidence for cryptic candidate species in Iberian Pelodytes (Anura, Pelodytidae).

    PubMed

    Díaz-Rodríguez, Jesús; Gonçalves, Helena; Sequeira, Fernando; Sousa-Neves, Tiago; Tejedo, Miguel; Ferrand, Nuno; Martínez-Solano, Iñigo

    2015-02-01

    Species delineation is a central topic in evolutionary biology, with current efforts focused on developing efficient analytical tools to extract the most information from molecular data and provide objective and repeatable results. In this paper we use a multilocus dataset (mtDNA and two nuclear markers) in a geographically comprehensive population sample across Iberia and Western Europe to delineate candidate species in a morphologically cryptic species group, Parsley frogs (genus Pelodytes). Pelodytes is the sole extant representative of an ancient, historically widely distributed anuran clade that currently includes three species: P. caucasicus in the Caucasus; P. punctatus in Western Europe, from Portugal to North-Western Italy; and P. ibericus in Southern Iberia. Phylogenetic analyses recovered four major well-supported haplotype clades in Western Europe, corresponding to well demarcated geographical subdivisions and exhibiting contrasting demographic histories. Splitting times date back to the Plio-Pleistocene and are very close in time. Species-tree analyses recovered one of these species lineages, corresponding to P. ibericus (lineage B), as the sister taxon to the other three major species lineages, distributed respectively in: western Iberian Peninsula, along the Atlantic coast and part of central Portugal (lineage A); Central and Eastern Spain (lineage C); and North-eastern Spain, France and North-western Italy (lineage D). The latter is in turn subdivided into two sub-clades, one in SE France and NW Italy and the other one from NE Spain to NW France, suggesting the existence of a Mediterranean-Atlantic corridor along the Garonne river. An information theory-based validation approach implemented in SpedeSTEM supports an arrangement of four candidate species, suggesting the need for a taxonomic revision of Western European Pelodytes. PMID:25541245

  1. Import of phosphatidylserine to and export of phosphatidylethanolamine molecular species from mitochondria.

    PubMed

    Kainu, Ville; Hermansson, Martin; Hänninen, Satu; Hokynar, Kati; Somerharju, Pentti

    2013-02-01

    Heavy isotope-labeled ethanolamine and serine as well as exogenous PE and PS species were used to study trafficking of phosphatidylethanolamine (PE) and -serine (PS) molecular species between the endoplasmic reticulum (ER) and mitochondria in HeLa cells. Import of both endogenous and exogenous PS to IMM was a relatively slow process (T1/2=several hours), but depended on the acyl chains. In particular, the 38:4 and 38:5 species were imported more efficiently compared to the other PS species. Knock-down of Mitofusin 2 or Mitostatin had no detectable effect on PS import to mitochondria, suggesting that the ER-mitochondria contacts regulated by these proteins are not essential. Knock-down of PS synthase 1 inhibited PS decarboxylation, suggesting that import of PS to mitochondria is coupled to its synthesis. Also the export of PE from IMM to microsomes is a relatively slow process, but again depends markedly on the acyl chain structure. Most notably, the polyunsaturated 38:4 and 38:5 PE species were less efficiently exported, which together with rapid import of the PS precursors most probably explains their enrichment in IMM. PE synthesized via the CDP-ethanolamine was also imported to IMM, but most of the PE in this membrane derives from imported PS. In contrast to PS, all PC species made in Golgi/ER translocated similarly and rapidly to IMM. In conclusion, selective translocation of PS species and PS-derived PE species between ER and mitochondria plays a major role in phospholipid homeostasis of these organelles. PMID:23159415

  2. A test of color-based taxonomy in nudibranchs: Molecular phylogeny and species delimitation of the Felimida clenchi (Mollusca: Chromodorididae) species complex.

    PubMed

    Padula, Vinicius; Bahia, Juliana; Stöger, Isabella; Camacho-García, Yolanda; Malaquias, Manuel António E; Cervera, Juan Lucas; Schrödl, Michael

    2016-10-01

    Traditionally, species identification in nudibranch gastropods relies heavily on body color pattern. The Felimida clenchi species complex, a group of brightly colored Atlantic and Mediterranean species in the family Chromodorididae, has a history of exceptional controversy and discussion among taxonomists. The most widely accepted hypothesis is that the complex includes four species (Felimida clenchi, F. neona, F. binza and F. britoi), each with a characteristic body color pattern. In this study, we investigated the taxonomic value of coloration in the Felimida clenchi complex, using molecular phylogenetics, species-delimitation analyses (ABGD, GMYC, PTP), haplotype-network methods, and the anatomy of the reproductive system. None of our analyses recovered the traditional separation into four species. Our results indicated the existence of three species, a result inconsistent with previous taxonomic hypotheses. We distinguished an undescribed species of Felimida and redefined the concepts of F. clenchi and F. binza, both highly polychromatic species. For the first time, molecular data support the existence of extreme color polymorphism in chromatic nudibranch species, with direct implications for the taxonomy of the group and its diversity. The polychromatism observed in the F. clenchi complex apparently correlates with the regional occurrence of similar color patterns in congeneric species, suggesting different mimicry circles. This may represent a parallel in the marine environment to the mechanisms that play a major role in the diversification of color in terrestrial and fresh-water chromatic groups, such as heliconian butterflies. PMID:27444708

  3. Molecular phylogeny of some avian species using Cytochrome b gene sequence analysis

    PubMed Central

    Awad, A; Khalil, S. R; Abd-Elhakim, Y. M

    2015-01-01

    Veritable identification and differentiation of avian species is a vital step in conservative, taxonomic, forensic, legal and other ornithological interventions. Therefore, this study involved the application of molecular approach to identify some avian species i.e. Chicken (Gallus gallus), Muskovy duck (Cairina moschata), Japanese quail (Coturnix japonica), Laughing dove (Streptopelia senegalensis), and Rock pigeon (Columba livia). Genomic DNA was extracted from blood samples and partial sequence of the mitochondrial cytochrome b gene (358 bp) was amplified and sequenced using universal primers. Sequences alignment and phylogenetic analyses were performed by CLC main workbench program. The obtained five sequences were deposited in GenBank and compared with those previously registered in GenBank. The similarity percentage was 88.60% between Gallus gallus and Coturnix japonica and 80.46% between Gallus gallus and Columba livia. The percentage of identity between the studied species and GenBank species ranged from 77.20% (Columba oenas and Anas platyrhynchos) to 100% (Gallus gallus and Gallus sonneratii, Coturnix coturnix and Coturnix japonica, Meleagris gallopavo and Columba livia). Amplification of the partial sequence of mitochondrial cytochrome b gene proved to be practical for identification of an avian species unambiguously. PMID:27175180

  4. Molecular phylogeny of some avian species using Cytochrome b gene sequence analysis.

    PubMed

    Awad, A; Khalil, S R; Abd-Elhakim, Y M

    2015-01-01

    Veritable identification and differentiation of avian species is a vital step in conservative, taxonomic, forensic, legal and other ornithological interventions. Therefore, this study involved the application of molecular approach to identify some avian species i.e. Chicken (Gallus gallus), Muskovy duck (Cairina moschata), Japanese quail (Coturnix japonica), Laughing dove (Streptopelia senegalensis), and Rock pigeon (Columba livia). Genomic DNA was extracted from blood samples and partial sequence of the mitochondrial cytochrome b gene (358 bp) was amplified and sequenced using universal primers. Sequences alignment and phylogenetic analyses were performed by CLC main workbench program. The obtained five sequences were deposited in GenBank and compared with those previously registered in GenBank. The similarity percentage was 88.60% between Gallus gallus and Coturnix japonica and 80.46% between Gallus gallus and Columba livia. The percentage of identity between the studied species and GenBank species ranged from 77.20% (Columba oenas and Anas platyrhynchos) to 100% (Gallus gallus and Gallus sonneratii, Coturnix coturnix and Coturnix japonica, Meleagris gallopavo and Columba livia). Amplification of the partial sequence of mitochondrial cytochrome b gene proved to be practical for identification of an avian species unambiguously. PMID:27175180

  5. Morphological and molecular marker contributions to disentangling the cryptic Hermeuptychia hermes species complex (Nymphalidae: Satyrinae: Euptychiina).

    PubMed

    Seraphim, N; Marín, M A; Freitas, A V L; Silva-Brandão, K L

    2014-01-01

    The genus Hermeuptychia is common and widespread through the Americas, from Argentina to the southern United States of America. All eight recognized species within Hermeuptychia are small and brown, with very similar interspecific external morphologies and intraspecifically variable ocelli patterns that render taxonomic identification based on morphology difficult. In our study, we surveyed variability within Hermeuptychia, and evaluated species boundaries based on molecular data (sequences of the 'barcode' mitochondrial DNA COI gene) and morphology (mainly male genitalia), using a phylogenetic approach. We found eight DNA-based and 12 morphological groups in our sampling. Species names were assigned based mainly on comparisons with male genitalia morphology descriptions corresponding to name-bearing type specimens. Morphological and DNA variability were highly congruent, with the exception of group H, the Hermeuptychia cucullina complex. Also, the barcode region showed a clear threshold for intra- and interspecific mean distances around 2%. Based on these results, we circumscribe the species boundaries in the genus Hermeuptychia and discuss conflicts between mitochondrial genes and classic morphological approaches for identifying and delimiting species. Our study revealed cryptic diversity within an ubiquitous genus of Neotropical butterflies. PMID:24034669

  6. Phylogenetic relationships among Neoechinorhynchus species (Acanthocephala: Neoechinorhynchidae) from North-East Asia based on molecular data.

    PubMed

    Malyarchuk, Boris; Derenko, Miroslava; Mikhailova, Ekaterina; Denisova, Galina

    2014-02-01

    Phylogenetic and statistical analyses of DNA sequences of two genes, cytochrome oxidase subunit 1 (cox 1) of the mitochondrial DNA and 18S subunit of the nuclear ribosomal RNA (18S rRNA), was used to characterize Neoechinorhynchus species from fishes collected in different localities of North-East Asia. It has been found that four species can be clearly recognized using molecular markers-Neoechinorhynchus tumidus, Neoechinorhynchus beringianus, Neoechinorhynchus simansularis and Neoechinorhynchus salmonis. 18S sequences ascribed to Neoechinorhynchus crassus specimens from North-East Asia were identical to those of N. tumidus, but differed substantially from North American N. crassus. We renamed North-East Asian N. crassus specimens to N. sp., although the possibility that they represent a subspecies of N. tumidus cannot be excluded, taking into account a relatively small distance between cox 1 sequences of North-East Asian specimens of N. crassus and N. tumidus. Maximum likelihood, maximum parsimony and Bayesian inference analyses were performed for phylogeny reconstruction. All the phylogenetic trees showed that North-East Asian species of Neoechinorhynchus analyzed in this study represent independent clades, with the only exception of N. tumidus and N. sp. for 18S data. Phylogenetic analysis has shown that the majority of species sampled (N. tumidus+N. sp., N. simansularis and N. beringianus) are probably very closely related, while N. salmonis occupies separate position in the trees, possibly indicating a North American origin of this species. PMID:24064255

  7. Molecular phylogeny and biogeography of air sac catfishes of the Heteropneustes fossilis species complex (Siluriformes: Heteropneustidae).

    PubMed

    Ratmuangkhwang, Sahat; Musikasinthorn, Prachya; Kumazawa, Yoshinori

    2014-10-01

    The air sac catfish, Heteropneustes fossilis (Siluriformes: Heteropneustidae), is widely distributed in freshwaters of the Indian subcontinent and mainland southeast Asia. No comprehensive molecular studies that cover the broad distributional areas have been carried out to date. Here, we conducted molecular phylogenetic analyses using both mitochondrial and nuclear gene sequences to suggest that the Heteropneustes fossilis species complex consists of three clades that may potentially be separate species with distinct geographical distribution (southeast Asia, northeastern India, and southwestern India). The first and second clades are more closely related to each other than they are to the third clade. Within the first clade there is a basal divergence of a subclade consisting of individuals from the Upper Irrawaddy River basin of Myanmar, which share some morphological traits with members of the Indian clades. Our molecular and morphological data are congruent with hypotheses that the Early-Middle Miocene disconnection between the paleo-Tsangpo River and the Irrawaddy River caused the vicariant divergence between southeast Asian and northeastern Indian clades, and that the southeast Asian Heteropneustes originated from the Upper Irrawaddy. PMID:24875251

  8. Resonance ionization spectroscopy measurement of the vapor pressure of several molecular species

    SciTech Connect

    Capelle, G.A.; Jessup, D.A.; Borella, H.M.; Franks, L.A.

    1984-01-01

    In recent years resonance ionization spectroscopy (RIS) has found increasing application to various problems involving detection of low levels of atomic, and more recently molecular, species. This work demonstrates the usefulness of RIS in measuring vapor pressure curves of molecular species at very low pressures. Specifically, the vapor pressures versus temperature relationship for rubidium iodide (RbI) and potassium iodide (KI) was measured by applying RIS to atomic Rb and K, using a two-laser system. A pulsed molecular nitrogen laser first dissociated the RbI to produce ground-state Rb atoms in the experimental cell. A flashlamp-pumped dye laser then ionized the Rb in a process wherein two photons of the same wavelength are absorbed, the first exciting Rb via an allowed transition to an upper state (5/sup 2/S/sub 1/2/ ..-->.. 6/sup 2//sub 1/2 or 3/2/) lying in energy slightly more than half the distance to the ionization limit, and the second photon ionizing the excited Rb. In the case of KI, an excimer-laser-pumped dye laser was used in a similar way. An applied dc electric field swept the photoelectrons to a proportional counter for subsequent amplification and detection. The photoelectron signal was then related back to RbI and KI concentrations.

  9. Molecular shifts in limb identity underlie development of feathered feet in two domestic avian species

    PubMed Central

    Domyan, Eric T; Kronenberg, Zev; Infante, Carlos R; Vickrey, Anna I; Stringham, Sydney A; Bruders, Rebecca; Guernsey, Michael W; Park, Sungdae; Payne, Jason; Beckstead, Robert B; Kardon, Gabrielle; Menke, Douglas B; Yandell, Mark; Shapiro, Michael D

    2016-01-01

    Birds display remarkable diversity in the distribution and morphology of scales and feathers on their feet, yet the genetic and developmental mechanisms governing this diversity remain unknown. Domestic pigeons have striking variation in foot feathering within a single species, providing a tractable model to investigate the molecular basis of skin appendage differences. We found that feathered feet in pigeons result from a partial transformation from hindlimb to forelimb identity mediated by cis-regulatory changes in the genes encoding the hindlimb-specific transcription factor Pitx1 and forelimb-specific transcription factor Tbx5. We also found that ectopic expression of Tbx5 is associated with foot feathers in chickens, suggesting similar molecular pathways underlie phenotypic convergence between these two species. These results show how changes in expression of regional patterning genes can generate localized changes in organ fate and morphology, and provide viable molecular mechanisms for diversity in hindlimb scale and feather distribution. DOI: http://dx.doi.org/10.7554/eLife.12115.001 PMID:26977633

  10. Taxonomic and Molecular Identification of Hemicaloosia, Hemicycliophora, Gracilacus and Paratylenchus Species (Nematoda: Criconematidae)

    PubMed Central

    Cordero López, Marco A.; Robbins, Robert T.; Szalanski, Allen L.

    2013-01-01

    Populations of Hemicycliophora epicharoides, H. gigas, H. labiata, H. pruni, H. shepherdi, H. vidua, H. zuckermani, Gracilacus straeleni, and Paratylenchus labiosus were obtained from different geographical areas in the continental United States and characterized morphological and molecularly. Two new species of Hemicycliophorinae: Hemicaloosia uarki n. sp from Pinetree, St. Francis County, Arkansas, and Hemicycliophora wyei n. sp from Wayne County, North Carolina, are also described. Hemicaloosia uarki n. sp. is characterized by having two lip annuli separated from the rest of body and directed anteriorly, a long stylet (106-124 μm), long body length (1,081-1,326 μm) and a single lateral fields demarcated by interruptions of the body annuli. Hemicycliophora wyei n. sp. showed a lateral fields demarked by two faint lines with transverse anastomoses and/or breaks of the striae; an elongated not offset conical tail with distinct annulations and a rounded tip and long vulval lips with a vulval sleeve. The molecular characterizations of the new (H. uarki n. sp. and H. wyei n. sp.) and known species of Criconematidae using the ITS1 rDNA gene sequence and the molecular phylogenetic relationships are provided. PMID:24115782

  11. Taxonomic and Molecular Identification of Bakernema, Criconema, Hemicriconemoides, Ogma and Xenocriconemella Species (Nematoda: Criconematidae)

    PubMed Central

    Cordero, Marco A.; Robbins, Robert T.; Szalanski, Allen L.

    2012-01-01

    Populations of Bakernema inaequale, C. petasum, C. sphagni, C. mutabile, Ogma octangulare, Xenocriconemella macrodora and Hemicriconemoides chitwoodi were identified and re-described from different geographical areas in the continental United States and molecularly characterized. Two new species of spine nematodes Criconema arkaense n. sp. from Washington County and Lee County, Arkansas and Criconema warrenense n. sp from Warren, Bradley County, Arkansas are also described and named. Criconema arkaense is characterize by having a conspicuous lip region offset from the body with two annuli, short rounded tail with a thin cuticular sheath and subterminal anus. Criconema warrenense n. sp. has two lip region annuli about the same width, first annulus directed posteriorly, separated by a narrow neck annulus and a short conoid tail, unilobed non-folded annulus. The molecular characterization of Criconema arkaense and Criconema warrenense using ITS1 rDNA gene sequence and the molecular phylogenetic relationships of these new species along with the known spines nematodes are provided. PMID:23482683

  12. Using Combined Morphological, Allometric and Molecular Approaches to Identify Species of the Genus Raillietiella (Pentastomida)

    PubMed Central

    Kelehear, Crystal; Spratt, David M.; Dubey, Sylvain; Brown, Gregory P.; Shine, Richard

    2011-01-01

    Taxonomic studies of parasites can be severely compromised if the host species affects parasite morphology; an uncritical analysis might recognize multiple taxa simply because of phenotypically plastic responses of parasite morphology to host physiology. Pentastomids of the genus Raillietiella are endoparasitic crustaceans primarily infecting the respiratory system of carnivorous reptiles, but also recorded from bufonid anurans. The delineation of pentastomids at the generic level is clear, but the taxonomic status of many species is not. We collected raillietiellids from lungs of the invasive cane toad (Rhinella marina), the invasive Asian house gecko (Hemidactylus frenatus), and a native tree frog (Litoria caerulea) in tropical Australia, and employed a combination of genetic analyses, and traditional and novel morphological methods to clarify their identity. Conventional analyses of parasite morphology (which focus on raw values of morphological traits) revealed two discrete clusters in terms of pentastome hook size, implying two different species of pentastomes: one from toads and a tree frog (Raillietiella indica) and another from lizards (Raillietiella frenatus). However, these clusters disappeared in allometric analyses that took pentastome body size into account, suggesting that only a single pentastome taxon may be involved. Our molecular data revealed no genetic differences between parasites in toads versus lizards, confirming that there was only one species: R. frenatus. This pentastome (previously known only from lizards) clearly is also capable of maturing in anurans. Our analyses show that the morphological features used in pentastomid taxonomy change as the parasite transitions through developmental stages in the definitive host. To facilitate valid descriptions of new species of pentastomes, future taxonomic work should include both morphological measurements (incorporating quantitative measures of body size and hook bluntness) and molecular data

  13. Relationships of the Woody Medicago Species (Section Dendrotelis) Assessed by Molecular Cytogenetic Analyses

    PubMed Central

    Rosato, Marcela; Castro, Mercedes; Rosselló, Josep A.

    2008-01-01

    Background and Aims The organization of rDNA genes in the woody medic species from the agronomically important Medicago section Dendrotelis was analysed to gain insight into their taxonomic relationships, to assess the levels of infraspecific variation concerning ribosomal loci in a restricted and fragmented insular species (M. citrina) and to assess the nature of its polyploidy. Methods Fluorescence in situ hybridization (FISH) was used for physical mapping of 5S and 45S ribosomal DNA genes in the three species of section Dendrotelis (M. arborea, M. citrina, M. strasseri) and the related M. marina from section Medicago. Genomic in situ hybridization (GISH) was used to assess the genomic relationships of the polyploid M. citrina with the putatively related species from section Dendrotelis. Key Results The diploid (2n = 16) M. marina has a single 45S and two 5S rDNA loci, a pattern usually detected in previous studies of Medicago diploid species. However, polyploid species from section Dendrotelis depart from expectations. The tetraploid species (2n = 32) M. arborea and M. strasseri have one 45S rDNA locus and two 5S rDNA loci, whereas in the hexaploid (2n = 48) M. citrina four 45S rDNA and five 5S rDNA loci have been detected. No single chromosome of M. citrina was uniformly labelled after using genomic probes from M. arborea and M. strasseri. Instead, cross-hybridization signals in M. citrina were restricted to terminal chromosome arms and NOR regions. Conclusions FISH results support the close taxonomic interrelationship between M. arborea and M. strasseri. In these tetraploid species, NOR loci have experienced a diploidization event through physical loss of sequences, a cytogenetic feature so far not reported in other species of the genus. The high number of rDNA loci and GISH results support the specific status for the hexaploid M. citrina, and it is suggested that this species is not an autopolyploid derivative of M. arborea or M. strasseri. Further, molecular

  14. Molecular Techniques for Detection, Species Differentiation, and Phylogenetic Analysis of Microsporidia

    PubMed Central

    Franzen, Caspar; Müller, Andreas

    1999-01-01

    Microsporidia are obligate intracellular protozoan parasites that infect a broad range of vertebrates and invertebrates. These parasites are now recognized as one of the most common pathogens in human immunodeficiency virus-infected patients. For most patients with infectious diseases, microbiological isolation and identification techniques offer the most rapid and specific determination of the etiologic agent. This is not a suitable procedure for microsporidia, which are obligate intracellular parasites requiring cell culture systems for growth. Therefore, the diagnosis of microsporidiosis currently depends on morphological demonstration of the organisms themselves. Although the diagnosis of microsporidiosis and identification of microsporidia by light microscopy have greatly improved during the last few years, species differentiation by these techniques is usually impossible and transmission electron microscopy may be necessary. Immunfluorescent-staining techniques have been developed for species differentiation of microsporidia, but the antibodies used in these procedures are available only at research laboratories at present. During the last 10 years, the detection of infectious disease agents has begun to include the use of nucleic acid-based technologies. Diagnosis of infection caused by parasitic organisms is the last field of clinical microbiology to incorporate these techniques and molecular techniques (e.g., PCR and hybridization assays) have recently been developed for the detection, species differentiation, and phylogenetic analysis of microsporidia. In this paper we review human microsporidial infections and describe and discuss these newly developed molecular techniques. PMID:10194459

  15. Widespread utility of highly informative AFLP molecular markers across divergent shark species.

    PubMed

    Zenger, Kyall R; Stow, Adam J; Peddemors, Victor; Briscoe, David A; Harcourt, Robert G

    2006-01-01

    Population numbers of many shark species are declining rapidly around the world. Despite the commercial and conservation significance, little is known on even the most fundamental aspects of their population biology. Data collection that relies on direct observation can be logistically challenging with sharks. Consequently, molecular methods are becoming increasingly important to obtain knowledge that is critical for conservation and management. Here we describe an amplified fragment length polymorphism method that can be applied universally to sharks to identify highly informative genome-wide polymorphisms from 12 primer pairs. We demonstrate the value of our method on 15 divergent shark species within the superorder Galeomorphii, including endangered species which are notorious for low levels of genetic diversity. Both the endangered sand tiger shark (Carcharodon taurus, N = 18) and the great white shark (Carcharodon carcharias, N = 7) displayed relatively high levels of allelic diversity. A total of 59 polymorphic loci (H(e) = 0.373) and 78 polymorphic loci (H(e) = 0.316) were resolved in C. taurus and C. carcharias, respectively. Results from other sharks (e.g., Orectolobus ornatus, Orectolobus sp., and Galeocerdo cuvier) produced remarkably high numbers of polymorphic loci (106, 94, and 86, respectively) from a limited sample size of only 2. A major constraint to obtaining much needed genetic data from sharks is the time-consuming process of developing molecular markers. Here we demonstrate the general utility of a technique that provides large numbers of informative loci in sharks. PMID:17150982

  16. The Value of Molecular vs. Morphometric and Acoustic Information for Species Identification Using Sympatric Molossid Bats

    PubMed Central

    Gager, Yann; Tarland, Emilia; Lieckfeldt, Dietmar; Ménage, Matthieu; Botero-Castro, Fidel; Rossiter, Stephen J.; Kraus, Robert H. S.; Ludwig, Arne; Dechmann, Dina K. N.

    2016-01-01

    A fundamental condition for any work with free-ranging animals is correct species identification. However, in case of bats, information on local species assemblies is frequently limited especially in regions with high biodiversity such as the Neotropics. The bat genus Molossus is a typical example of this, with morphologically similar species often occurring in sympatry. We used a multi-method approach based on molecular, morphometric and acoustic information collected from 962 individuals of Molossus bondae, M. coibensis, and M. molossus captured in Panama. We distinguished M. bondae based on size and pelage coloration. We identified two robust species clusters composed of M. molossus and M. coibensis based on 18 microsatellite markers but also on a more stringently determined set of four markers. Phylogenetic reconstructions using the mitochondrial gene co1 (DNA barcode) were used to diagnose these microsatellite clusters as M. molossus and M. coibensis. To differentiate species, morphological information was only reliable when forearm length and body mass were combined in a linear discriminant function (95.9% correctly identified individuals). When looking in more detail at M. molossus and M. coibensis, only four out of 13 wing parameters were informative for species differentiation, with M. coibensis showing lower values for hand wing area and hand wing length and higher values for wing loading. Acoustic recordings after release required categorization of calls into types, yielding only two informative subsets: approach calls and two-toned search calls. Our data emphasizes the importance of combining morphological traits and independent genetic data to inform the best choice and combination of discriminatory information used in the field. Because parameters can vary geographically, the multi-method approach may need to be adjusted to local species assemblies and populations to be entirely informative. PMID:26943355

  17. The Value of Molecular vs. Morphometric and Acoustic Information for Species Identification Using Sympatric Molossid Bats.

    PubMed

    Gager, Yann; Tarland, Emilia; Lieckfeldt, Dietmar; Ménage, Matthieu; Botero-Castro, Fidel; Rossiter, Stephen J; Kraus, Robert H S; Ludwig, Arne; Dechmann, Dina K N

    2016-01-01

    A fundamental condition for any work with free-ranging animals is correct species identification. However, in case of bats, information on local species assemblies is frequently limited especially in regions with high biodiversity such as the Neotropics. The bat genus Molossus is a typical example of this, with morphologically similar species often occurring in sympatry. We used a multi-method approach based on molecular, morphometric and acoustic information collected from 962 individuals of Molossus bondae, M. coibensis, and M. molossus captured in Panama. We distinguished M. bondae based on size and pelage coloration. We identified two robust species clusters composed of M. molossus and M. coibensis based on 18 microsatellite markers but also on a more stringently determined set of four markers. Phylogenetic reconstructions using the mitochondrial gene co1 (DNA barcode) were used to diagnose these microsatellite clusters as M. molossus and M. coibensis. To differentiate species, morphological information was only reliable when forearm length and body mass were combined in a linear discriminant function (95.9% correctly identified individuals). When looking in more detail at M. molossus and M. coibensis, only four out of 13 wing parameters were informative for species differentiation, with M. coibensis showing lower values for hand wing area and hand wing length and higher values for wing loading. Acoustic recordings after release required categorization of calls into types, yielding only two informative subsets: approach calls and two-toned search calls. Our data emphasizes the importance of combining morphological traits and independent genetic data to inform the best choice and combination of discriminatory information used in the field. Because parameters can vary geographically, the multi-method approach may need to be adjusted to local species assemblies and populations to be entirely informative. PMID:26943355

  18. Species boundaries of Astreopora corals (Scleractinia, Acroporidae) inferred by mitochondrial and nuclear molecular markers.

    PubMed

    Suzuki, Go; Nomura, Keiichi

    2013-08-01

    The genus Astreopora is a small but ancestral group in Acroporidae, which is one of the most diverse and dominant families of scleractinian coral in Indo-Pacific reefs. We estimated the species boundaries of Astreopora corals using two molecular markers: a mitochondrial non-coding region and a nuclear ribosomal 5.8S region. Seven species (59 specimens) commonly observed around Japan (Astreopora expansa, A. gracilis, A. incrustans, A. listeri, A. myriophthalma, A. cf. suggesta, and Astreopora sp.1) were investigated, and we observed no genetic divergence in the mitochondrial marker, suggesting that these species are closely related, consistent with a species complex or recent divergence, although genotyping by the marker is not so sensitive. In the nuclear 5.8S region, 121 clones consisted of six species were divided into the four major genetic groups. Although there were no monophyletic clades, the two dominant species A. myriophthalma and A. gracilis rarely shared the same haplotypes, suggesting that gene flow is limited between them. However, A. incrustans frequently shared the same haplotypes with A. gracilis although the distributions do not overlap. We found that the ancestral genus Astreopora in Acroporidae shows less genetic variation than traditionally identified morphospecies. Although further research on fertilization rate among these species is required to determine if there are reproductive barriers, the low level of genetic diversification in this genus hints that some ecological differences among acroporid corals play a role in the evolution of scleractinian corals, considering that the other members of this family, Acropora and Montipora, are highly diversified. PMID:23915155

  19. Molecular identification, antifungal susceptibility profile, and biofilm formation of clinical and environmental Rhodotorula species isolates.

    PubMed

    Nunes, Jorge Meneses; Bizerra, Fernando César; Ferreira, Renata Carmona E; Colombo, Arnaldo Lopes

    2013-01-01

    Rhodotorula species are emergent fungal pathogens capable of causing invasive infections, primarily fungemia. They are particularly problematic in immunosuppressed patients when using a central venous catheter. In this study, we evaluated the species distribution of 51 clinical and 8 environmental Rhodotorula species isolates using the ID32C system and internal transcribed spacer (ITS) sequencing. Antifungal susceptibility testing and biofilm formation capability using a crystal violet staining assay were performed. Using ITS sequencing as the gold standard, the clinical isolates were identified as follows: 44 R. mucilaginosa isolates, 2 R. glutinis isolates, 2 R. minuta isolates, 2 R. dairenensis isolates, and 1 Rhodosporidium fluviale isolate. The environmental isolates included 7 R. mucilaginosa isolates and 1 R. slooffiae isolate. Using the ID32C system, along with a nitrate assimilation test, only 90.3% of the isolates tested were correctly identified. In the biofilm formation assay, R. mucilaginosa and R. minuta exhibited greater biofilm formation ability compared to the other Rhodotorula species; the clinical isolates of R. mucilaginosa showed greater biofilm formation compared to the environmental isolates (P = 0.04). Amphotericin B showed good in vitro activity (MIC ≤ 1 μg/ml) against planktonic cells, whereas voriconazole and posaconazole showed poor activity (MIC(50)/MIC(90), 2/4 μg/ml). Caspofungin and fluconazole MICs were consistently high for all isolates tested (≥64 μg/ml and ≥ 4 μg/ml, respectively). In this study, we emphasized the importance of molecular methods to correctly identify Rhodotorula species isolates and non-R. mucilaginosa species in particular. The antifungal susceptibility profile reinforces amphotericin B as the antifungal drug of choice for the treatment of Rhodotorula infections. To our knowledge, this is the first study evaluating putative differences in the ability of biofilm formation among different Rhodotorula

  20. Molecular and Morphological Evidence Demonstrating Two Species of Helicometrina Linton 1910 (Digenea: Opecoelidae) in Northern Chile.

    PubMed

    Oliva, Marcelo E; Valdivia, Isabel M; Chavez, Rosa A; Molina, Horacio; Cárdenas, Leyla

    2015-12-01

    The opecoelid Helicometrina nimia Linton, 1910 has been reported from numerous marine fishes along the Pacific and Atlantic coasts of the Americas. Along the Chilean coast, H. nimia is found in fishes belonging to at least 9 families. This surprisingly low host specificity of H. nimia raises question about the correct identification of specimens assigned to this species. Here we evaluate whether H. nimia specimens isolated from sympatric fish species in northern Chile but with different diets and found in different habitats (water column and demersal) are the same species. Our results demonstrate that specimens from the shallow benthic fish Labrisomus philippii (Steindachner) do not correspond to H. nimia but instead belong to a new species of Helicometrina. This species is described and distinguished from H. nimia using morphological descriptions and 2 molecular markers (the cytochrome c oxidase subunit 1 gene and the V4 region of the SSU rRNA gene). The new species Helicometrina labrisomi (Digenea: Opecoelidae), is found in the intestine of L. philippii (Steindachner, 1866) (Pisces: Labrisomidae), a shallow benthic fish that inhabits the northern coast of Chile. We also studied the related Helicometrina nimia Linton, 1910 from the benthopelagic fishes Paralabrax humeralis (Valenciennes, 1828) and Acanthistius pictus (Tschudi, 1846) (Serranidae). The new species differs from H. nimia by a combination of characters that include ovary shape, number of uterine loops, and position of the genital pore. Our results indicate that morphological characteristics, such as body size, extent of the vitellarium, shape of the testes, and cirrus sac size and extent, traditionally used in the taxonomy of Helicometrina are highly variable. In contrast, meristic and morphological characteristics, such as a lobed ovary, the number of uterine loops, dimensions of the pharynx, and the opening of the genital pore, are highly constant. PMID:26221995

  1. Molecular Identification, Antifungal Susceptibility Profile, and Biofilm Formation of Clinical and Environmental Rhodotorula Species Isolates

    PubMed Central

    Nunes, Jorge Meneses; Bizerra, Fernando César; Ferreira, Renata Carmona e

    2013-01-01

    Rhodotorula species are emergent fungal pathogens capable of causing invasive infections, primarily fungemia. They are particularly problematic in immunosuppressed patients when using a central venous catheter. In this study, we evaluated the species distribution of 51 clinical and 8 environmental Rhodotorula species isolates using the ID32C system and internal transcribed spacer (ITS) sequencing. Antifungal susceptibility testing and biofilm formation capability using a crystal violet staining assay were performed. Using ITS sequencing as the gold standard, the clinical isolates were identified as follows: 44 R. mucilaginosa isolates, 2 R. glutinis isolates, 2 R. minuta isolates, 2 R. dairenensis isolates, and 1 Rhodosporidium fluviale isolate. The environmental isolates included 7 R. mucilaginosa isolates and 1 R. slooffiae isolate. Using the ID32C system, along with a nitrate assimilation test, only 90.3% of the isolates tested were correctly identified. In the biofilm formation assay, R. mucilaginosa and R. minuta exhibited greater biofilm formation ability compared to the other Rhodotorula species; the clinical isolates of R. mucilaginosa showed greater biofilm formation compared to the environmental isolates (P = 0.04). Amphotericin B showed good in vitro activity (MIC ≤ 1 μg/ml) against planktonic cells, whereas voriconazole and posaconazole showed poor activity (MIC50/MIC90, 2/4 μg/ml). Caspofungin and fluconazole MICs were consistently high for all isolates tested (≥64 μg/ml and ≥ 4 μg/ml, respectively). In this study, we emphasized the importance of molecular methods to correctly identify Rhodotorula species isolates and non-R. mucilaginosa species in particular. The antifungal susceptibility profile reinforces amphotericin B as the antifungal drug of choice for the treatment of Rhodotorula infections. To our knowledge, this is the first study evaluating putative differences in the ability of biofilm formation among different Rhodotorula species

  2. Utilization of elongation factor Tu gene (tuf) sequencing and species-specific PCR (SS-PCR) for the molecular identification of Acetobacter species complex.

    PubMed

    Huang, Chien-Hsun; Chang, Mu-Tzu; Huang, Lina; Chu, Wen-Shen

    2014-02-01

    The aim of this study was to use tuf gene as a molecular target for species discrimination in the Acetobacter genus, as well as to develop species-specific PCR method for direct species identification of Acetobacter aceti. The results showed that most Acetobacter species could be clearly distinguished, and the average sequence similarity for the tuf gene (89.5%) among type strains was significantly lower than that of the 16S rRNA gene sequence (98.0%). A pair of species-specific primers were designed and used to specifically identify A. aceti, but none of the other Acetobacter strains. Our data indicate that the phylogenetic relationships of most strains in the Acetobacter genus can be resolved using tuf gene sequencing, and the novel species-specific primer pair could be used to rapidly and accurately identify the species of A. aceti by the PCR based assay. PMID:23969032

  3. Cryptic species of hairworm parasites revealed by molecular data and crowdsourcing of specimen collections.

    PubMed

    Hanelt, Ben; Schmidt-Rhaesa, Andreas; Bolek, Matthew G

    2015-01-01

    Recognizing cryptic species promotes a better understanding of biodiversity, systematics, evolutionary biology, and biogeography. When cryptic species are disease-causing organisms, such as parasites, their correct recognition has important implications for the study of epidemiology, disease ecology, and host-parasite relationships. Freshwater nematomorphs (Nematomorpha: Gordiida) or hairworms, are an enigmatic yet fascinating group of parasites that are known to manipulate host behavior to aid transition from the parasitic phase, within terrestrial insects, to the free-living aquatic stage. Hairworm taxonomy has been hampered by a paucity of informative diagnostic characters and it has long been suspected that this group contains numerous cryptic species. Study of single hairworm species over large geographical areas has been difficult due to extremely rare encounters and unreliable methods of collecting adult worms. Here we report that by using crowdsourcing, citizen scientists have collected and submitted samples of Gordius cf. robustus from throughout its range in North America making its genetic study possible. Combined with our own collections, we examined samples from 28 localities within the USA; despite the collection of numerous hairworms from Canada and Mexico, G. cf. robustus were not collected outside of the contiguous United States. Mitochondrial CO1 genetic distances revealed that specimens grouped into 8 clades separated by 8-24.3%. In addition, molecular evidence from mitochondrial (CO1 and cytB) and nuclear (partial 28S, ITS1, 5.8S and ITS2) DNA suggests that these 8 clades are distinct species and that this group of species is paraphyletic, since the North American species G. attoni and the European species G. aquaticus and G. balticus group among the G. robustus lineages. Furthermore, there was a significant correlation between genetic (CO1) and geographic distance between the 8 Gordius species. This study demonstrates the value of involving the

  4. Molecular basis for species-specific sensitivity to "hot" chili peppers.

    PubMed

    Jordt, Sven-Eric; Julius, David

    2002-02-01

    Chili peppers produce the pungent vanilloid compound capsaicin, which offers protection from predatory mammals. Birds are indifferent to the pain-producing effects of capsaicin and therefore serve as vectors for seed dispersal. Here, we determine the molecular basis for this species-specific behavioral response by identifying a domain of the rat vanilloid receptor that confers sensitivity to capsaicin to the normally insensitive chicken ortholog. Like its mammalian counterpart, the chicken receptor is activated by heat or protons, consistent with the fact that both mammals and birds detect noxious heat and experience thermal hypersensitivity. Our findings provide a molecular basis for the ecological phenomenon of directed deterence and suggest that the capacity to detect capsaicin-like inflammatory substances is a recent acquisition of mammalian vanilloid receptors. PMID:11853675

  5. The genus Leucophenga (Diptera, Drosophilidae), part VI: the argentata species group from the East Asia, with morphological and molecular evidence.

    PubMed

    Huang, Jia; Chen, Hongwei

    2016-01-01

    Six species of the Leucophenga argentata species group from East Asia are examined (including one known and five new ones): L. argentata (de Meijere, 1914); L. bicuspidata sp. nov.; L. fuscivena sp. nov.; L. longipenis sp. nov.; L. quadricuspidata sp. nov.; L. tricuspidata sp. nov.; the diagnoses for Asian species of the argentata group and a key to these species are provided. A total of 44 DNA sequences of the mitochondrial COI (cytochrome c oxidase subunit I) gene with BOLD process ID and GenBank accession numbers are provided for these species. The intra- and interspecific pairwise p-distances are summarized. The NJ (Neighbor-joining) and the Bayesian analyses are used to conduct a molecular phylogenetic analysis for the above-mentioned species. The molecular data are used as complementary evidence for the identification of the argentata group species with sexually dimorphic abdominal tergites. PMID:27615924

  6. Phosphatidylcholine, an edible carrier for nanoencapsulation of unstable thiamine.

    PubMed

    Juveriya Fathima, Syeda; Fathima, Irum; Abhishek, Virat; Khanum, Farhath

    2016-04-15

    Lipid nanoparticles have been used for carrying different therapeutic agents because of the advantage in improved absorption, bioavailability, targeted deliveries and reduction in the quantity of drugs required. The aim of the study was to prepare and characterize nanoliposomes containing thiamine hydrochloride and study their physicochemical stability as this vitamin is highly unstable. Phosphatidylcholine (PC) was used as an edible encapsulant. The average size of nanoliposomes was found to be 150 nm and zeta potential was -34 mV. The encapsulation efficiency was 97%. Atomic force microscopy (AFM) and scanning electron microscopy (SEM) confirmed the size, spherical nature and smooth surface of the nanoliposomes. Differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA) evidenced that the nanoliposomes were stable up to 300°C. The functional groups present were determined by Fourier transformed infrared spectroscopy (FTIR) and the presence of vitamin was confirmed in final formulation by biochemical analysis. The crystalline nature of thiamine was analyzed by X-ray diffraction studies. Storage studies indicated that the nanoliposomes were highly stable up to 3 months at different temperatures. Thus, phosphatidylcholine can be used as carrier vehicle of nutrients especially vitamins, as it can form stable nanoliposomes with 97% encapsulation efficiency. PMID:26616989

  7. Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease

    PubMed Central

    Wang, Zeneng; Klipfell, Elizabeth; Bennett, Brian J.; Koeth, Robert; Levison, Bruce S.; DuGar, Brandon; Feldstein, Ariel E.; Britt, Earl B.; Fu, Xiaoming; Chung, Yoon-Mi; Wu, Yuping; Schauer, Phil; Smith, Jonathan D.; Allayee, Hooman; Tang, W. H. Wilson; DiDonato, Joseph A.; Lusis, Aldons J.; Hazen, Stanley L.

    2011-01-01

    Metabolomics studies hold promise for discovery of pathways linked to disease processes. Cardiovascular disease (CVD) represents the leading cause of death and morbidity worldwide. A metabolomics approach was used to generate unbiased small molecule metabolic profiles in plasma that predict risk for CVD. Three metabolites of the dietary lipid phosphatidylcholine, namely choline, trimethylamine N-oxide (TMAO), and betaine, were identified and then shown to predict risk for CVD in an independent large clinical cohort. Dietary supplementation of mice with choline, TMAO or betaine promoted up-regulation of multiple macrophage scavenger receptors linked to atherosclerosis, and supplementation with choline or TMAO promoted atherosclerosis. Studies using germ-free mice confirmed a critical role for dietary choline and gut flora in TMAO production, augmented macrophage cholesterol accumulation and foam cell formation. Suppression of intestinal microflora in atherosclerosis-prone mice inhibited dietary choline-enhanced atherosclerosis. Genetic variations controlling expression of flavin monooxygenases (FMOs), an enzymatic source of TMAO, segregated with atherosclerosis in hyperlipidemic mice. Discovery of a relationship between gut flora-dependent metabolism of dietary phosphatidylcholine and CVD pathogenesis provides opportunities for development of both novel diagnostic tests and therapeutic approaches for atherosclerotic heart disease. PMID:21475195

  8. Brucella abortus Synthesizes Phosphatidylcholine from Choline Provided by the Host

    PubMed Central

    Comerci, Diego J.; Altabe, Silvia; de Mendoza, Diego; Ugalde, Rodolfo A.

    2006-01-01

    The Brucella cell envelope is characterized by the presence of phosphatidylcholine (PC), a common phospholipid in eukaryotes that is rare in prokaryotes. Studies on the composition of Brucella abortus 2308 phospholipids revealed that the synthesis of PC depends on the presence of choline in the culture medium, suggesting that the methylation biosynthetic pathway is not functional. Phospholipid composition of pmtA and pcs mutants indicated that in Brucella, PC synthesis occurs exclusively via the phosphatidylcholine synthase pathway. Transformation of Escherichia coli with an expression vector containing the B. abortus pcs homologue was sufficient for PC synthesis upon induction with IPTG (isopropyl-β-d-thiogalactopyranoside), while no PC formation was detected when bacteria were transformed with a vector containing pmtA. These findings imply that Brucella depends on choline provided by the host cell to form PC. We could not detect any obvious associated phenotype in the PC-deficient strain under vegetative or intracellular growth conditions in macrophages. However, the pcs mutant strain displays a reproducible virulence defect in mice, which suggests that PC is necessary to sustain a chronic infection process. PMID:16484204

  9. Brucella abortus synthesizes phosphatidylcholine from choline provided by the host.

    PubMed

    Comerci, Diego J; Altabe, Silvia; de Mendoza, Diego; Ugalde, Rodolfo A

    2006-03-01

    The Brucella cell envelope is characterized by the presence of phosphatidylcholine (PC), a common phospholipid in eukaryotes that is rare in prokaryotes. Studies on the composition of Brucella abortus 2308 phospholipids revealed that the synthesis of PC depends on the presence of choline in the culture medium, suggesting that the methylation biosynthetic pathway is not functional. Phospholipid composition of pmtA and pcs mutants indicated that in Brucella, PC synthesis occurs exclusively via the phosphatidylcholine synthase pathway. Transformation of Escherichia coli with an expression vector containing the B. abortus pcs homologue was sufficient for PC synthesis upon induction with IPTG (isopropyl-beta-d-thiogalactopyranoside), while no PC formation was detected when bacteria were transformed with a vector containing pmtA. These findings imply that Brucella depends on choline provided by the host cell to form PC. We could not detect any obvious associated phenotype in the PC-deficient strain under vegetative or intracellular growth conditions in macrophages. However, the pcs mutant strain displays a reproducible virulence defect in mice, which suggests that PC is necessary to sustain a chronic infection process. PMID:16484204

  10. Molecular characterization of Desmodium species--an important ingredient of 'Dashmoola' by RAPD analysis.

    PubMed

    Irshad, Saba; Singh, Jyotsna; Kakkar, Poonam; Mehrotra, Shanta

    2009-03-01

    Identification of medicinal plants by their molecular signature is a fast growing tool. The identification of Desmodium gangeticum (L.) DC. (Shalparni, a constituent of Ayurvedic formulation "Dashmoolarishtha") was carried out using genomic approach. Authentic samples of D. gangeticum(L.) DC., D. velutinum (Willd.) DC. and D. triflorum (L.) DC. were analyzed and compared to commercial samples of various origin. Within twenty primers used, eleven gave 223 RAPD fragments. RAPD profiles of three species showed very low similarity index (0.21-0.39), whereas market samples showed high similarity of 0.82-0.89 with authenticated D. gangeticum. PMID:19100816

  11. New species of xerocomoid boletes (Boletaceae) from Himalayan India based on morphological and molecular evidence.

    PubMed

    Das, Kanad; Chakraborty, Dyutiparna; Baghela, Abhishek; Singh, S K; Dentinger, Bryn T M

    2016-01-01

    Xerocomus doodhcha and Hortiboletus indorubellus (Boletaceae) from broadleaf montane forest in Sikkim, India, are proposed as new. They are described in detail with supporting morphological illustrations and compared with related taxa using molecular phylogenetic analysis of ITS and 28S rDNA sequences. Xerocomus doodhcha is characterized by a pale brown pileus, basidiospores with a finely bacillate surface under SEM, and phylogenetic proximity to the type species of Xerocomus, X. subtomentosus Hortiboletus indorubellus is characterized by a dark brown to reddish brown pileus, context that turns brownish to brownish orange on bruising, and phylogenetic proximity to Hortiboletus rubellus. PMID:27153883

  12. Morphological and molecular evidence for two new species of Laetiporus (Basidiomycota, Polyporales) from southwestern China.

    PubMed

    Song, Jie; Chen, Yuanyuan; Cui, Baokai; Liu, Honggao; Wang, Yuanzhong

    2014-01-01

    Two Laetiporus species, L. ailaoshanensis and L. zonatus spp. nov., are described from southwestern China based on morphological and molecular characters. Laetiporus ailaoshanensis is characterized by orange-yellow to reddish orange pileal surface and cream to buff pores when fresh, azonate to faintly zonate pileus, ovoid to ellipsoid basidiospores (5.0-6.2 × 4.0-5.0 μm), and it has been observed only on Lithocarpus. Laetiporus zonatus is characterized by white to cream pileal surface with buff to clay-buff base when fresh, concentrically zonate basidiocarps, ellipsoid to pyriform or drop-shaped basidiospores (5.8-7.2 × 4.3-5.5 μm), and it has been found only on Quercus. The phylogenetic relationships of all recognized Laetiporus species were inferred from a combined dataset of ITS and nLSU-rDNA sequences, and L. ailaoshanensis and L. zonatus represent two new lineages in this group. PMID:24987130

  13. Molecular Phylogeny and Zoogeography of the Capoeta damascina Species Complex (Pisces: Teleostei: Cyprinidae)

    PubMed Central

    Alwan, Nisreen; Esmaeili, Hamid-Reza; Krupp, Friedhelm

    2016-01-01

    Capoeta damascina was earlier considered by many authors as one of the most common freshwater fish species found throughout the Levant, Mesopotamia, Turkey, and Iran. However, owing to a high variation in morphological characters among and within its various populations, 17 nominal species were described, several of which were regarded as valid by subsequent revising authors. Capoeta damascina proved to be a complex of closely related species, which had been poorly studied. The current study aims at defining C. damascina and the C. damascina species complex. It investigates phylogenetic relationships among the various members of the C. damascina complex, based on mitochondrial and nuclear DNA sequences. Phylogenetic relationships were projected against paleogeographical events to interpret the geographic distribution of the taxa under consideration in relation to the area’s geological history. Samples were obtained from throughout the geographic range and were subjected to genetic analyses, using two molecular markers targeting the mitochondrial cytochrome oxidase I (n = 103) and the two adjacent divergence regions (D1-D2) of the nuclear 28S rRNA genes (n = 65). Six closely related species were recognized within the C. damascina complex, constituting two main lineages: A western lineage represented by C. caelestis, C. damascina, and C. umbla and an eastern lineage represented by C. buhsei, C. coadi, and C. saadii. The results indicate that speciation of these taxa is rather a recent event. Dispersal occurred during the Pleistocene, resulting in present-day distribution patterns. A coherent picture of the phylogenetic relationships and evolutionary history of the C. damascina species complex is drawn, explaining the current patterns of distribution as a result of paleogeographic events and ecological adaptations. PMID:27309854

  14. Prevalence and first molecular identification of Sarcocystis species in cattle and water buffaloes in India.

    PubMed

    Daptardar, Monal; Singh, Balbir Bagicha; Aulakh, Rabinder Singh; Gill, Jatinder Paul Singh

    2016-09-01

    The importance of Sarcocystis hominis in causing zoonotic infections is well known. Recently, S. hominis like cysts have been reported from water buffalo in China. Previous studies indicate prevalence of Sarcocystis species in bovine populations in India but molecular evidence is required for proper species differentiation. We examined two hundred and ninety six cardiac tissue samples of Indian water buffaloes and cattle from northern and western parts of the country. Tissues were examined for Sarcocystis using intact cyst isolation method, pepsin acid digestion method and Sarcocystis 18S rRNA PCR. The combination of primers was used for 18S rRNA PCR amplification followed by sequencing. Twenty five representative samples were sent for sequencing and 19 readable sequences were obtained for phylogenetic analysis. Overall, the Sarcocystis cysts/zoites were recorded in 44% (95% CI 38-49%), 58% (95% CI 53-64%) and 68% (95% CI 63-73%) from both cattle and buffalo samples using intact cyst isolation, pepsin-HCl digestion method and conventional PCR, respectively. The results indicate that pepsin-HCl digestion method and conventional PCR are more sensitive than intact cyst isolation for detection of Sarcocystis species in tissue samples. The prevalence of Sarcocystis species was high in buffalo as compared to cattle intermediate hosts. Phylogenetic analysis indicated that more than one Sarcocystis species are circulating in cattle and water buffaloes in India. The results further indicate that experimental transmission studies are required to re-confirm the identities and host ranges of the Sarcocystis species in cattle and water buffaloes in India. PMID:27447215

  15. Molecular Identification of Closely Related Candida Species Using Two Ribosomal Intergenic Spacer Fingerprinting Methods

    PubMed Central

    Cornet, Muriel; Sendid, Boualem; Fradin, Chantal; Gaillardin, Claude; Poulain, Daniel; Nguyen, Huu-Vang

    2011-01-01

    Recent changes in the epidemiology of candidiasis highlighted an increase in non- Candida albicans species emphasizing the need for reliable identification methods. Molecular diagnostics in fungal infections may improve species characterization, particularly in cases of the closely related species in the Candida complexes. We developed two PCR/restriction fragment length polymorphism assays, targeting either a part of the intergenic spacer 2 or the entire intergenic spacer (IGS) of ribosomal DNA using a panel of 270 isolates. A part of the intergenic spacer was used for discrimination between C. albicans and C. dubliniensis and between species of the C. glabrata complex (C. glabrata/C. bracarensis/C. nivariensis). The whole IGS was applied to C. parapsilosis, C. metapsilosis, and C. orthopsilosis, and to separate C. famata (Debaryomyces hansenii) from C. guilliermondii (Pichia guilliermondii) and from the other species within this complex (ie, C. carpophila, C. fermentati and C. xestobii). Sharing similar biochemical patterns, Pichia norvegensis and C. inconspicua exhibited specific IGS profiles. Our study confirmed that isolates of C. guilliermondii were frequently mis-identified as C. famata. As much as 67% of the clinical isolates phenotypically determined as C. famata were recognized mostly as true P. guilliermondii. Conversely, 44% of the isolates initially identified as C. guilliermondii were corrected by the IGS fingerprints as C. parapsilosis, C. fermentati, or C. zeylanoides. These two PCR/restriction fragment length polymorphism methods may be used as reference tools [either alternatively or adjunctively to the existing ribosomal DNA (26S or ITS) sequence comparisons] for unambiguous determination of the Candida species for which phenotypic characterization remains problematic. PMID:21227390

  16. Molecular Phylogeny and Zoogeography of the Capoeta damascina Species Complex (Pisces: Teleostei: Cyprinidae).

    PubMed

    Alwan, Nisreen; Esmaeili, Hamid-Reza; Krupp, Friedhelm

    2016-01-01

    Capoeta damascina was earlier considered by many authors as one of the most common freshwater fish species found throughout the Levant, Mesopotamia, Turkey, and Iran. However, owing to a high variation in morphological characters among and within its various populations, 17 nominal species were described, several of which were regarded as valid by subsequent revising authors. Capoeta damascina proved to be a complex of closely related species, which had been poorly studied. The current study aims at defining C. damascina and the C. damascina species complex. It investigates phylogenetic relationships among the various members of the C. damascina complex, based on mitochondrial and nuclear DNA sequences. Phylogenetic relationships were projected against paleogeographical events to interpret the geographic distribution of the taxa under consideration in relation to the area's geological history. Samples were obtained from throughout the geographic range and were subjected to genetic analyses, using two molecular markers targeting the mitochondrial cytochrome oxidase I (n = 103) and the two adjacent divergence regions (D1-D2) of the nuclear 28S rRNA genes (n = 65). Six closely related species were recognized within the C. damascina complex, constituting two main lineages: A western lineage represented by C. caelestis, C. damascina, and C. umbla and an eastern lineage represented by C. buhsei, C. coadi, and C. saadii. The results indicate that speciation of these taxa is rather a recent event. Dispersal occurred during the Pleistocene, resulting in present-day distribution patterns. A coherent picture of the phylogenetic relationships and evolutionary history of the C. damascina species complex is drawn, explaining the current patterns of distribution as a result of paleogeographic events and ecological adaptations. PMID:27309854

  17. Molecular Evidence for High Frequency of Multiple Paternity in a Freshwater Shrimp Species Caridina ensifera

    PubMed Central

    Yue, Gen Hua; Chang, Alex

    2010-01-01

    Background Molecular genetic analyses of parentage provide insights into mating systems. Although there are 22,000 members in Malacostraca, not much has been known about mating systems in Malacostraca. The freshwater shrimp Caridina ensifera blue, is a new species belonging to Malacostraca which was discovered recently in Sulawesi, Indonesia. Due to its small body size and low fecundity, this species is an ideal species to study the occurrence and frequency of multiple paternity and to understand of how the low fecundity species persist and evolve. Methodology/Principal Findings In this study, we developed four polymorphic microsatellites from C. ensifera and applied them to investigate the occurrence and frequency of multiple paternity in 20 C. ensifera broods caught from Lake Matano, Sulawesi. By genotyping the mother and all offspring from each brood we discovered multiple paternity in all 20 broods. In most of the 20 broods, fathers contributed skewed numbers of offspring and there was an apparent inverse correlation between reproductive success of sires and their relatedness to mothers. Conclusions/Significance Our results in combination with recent reports on multiple paternity in crayfish, crab and lobster species suggests that multiple paternity is common in Malacostraca. Skewed contribution of fathers to the numbers of offspring and inverse correlation between reproductive success of sires and their relatedness to mothers suggest that sperm competition occurred and/or pre- and postcopulatory female choice happen, which may be important for avoiding the occurrence of inbreeding and optimize genetic variation in offspring and for persistence and evolution of low fecundity species. PMID:20856862

  18. Phylogenomics and Molecular Signatures for Species from the Plant Pathogen-Containing Order Xanthomonadales

    PubMed Central

    Naushad, Hafiz Sohail; Gupta, Radhey S.

    2013-01-01

    The species from the order Xanthomonadales, which harbors many important plant pathogens and some human pathogens, are currently distinguished primarily on the basis of their branching in the 16S rRNA tree. No molecular or biochemical characteristic is known that is specific for these bacteria. Phylogenetic and comparative analyses were conducted on 26 sequenced Xanthomonadales genomes to delineate their branching order and to identify molecular signatures consisting of conserved signature indels (CSIs) in protein sequences that are specific for these bacteria. In a phylogenetic tree based upon sequences for 28 proteins, Xanthomonadales species formed a strongly supported clade with Rhodanobacter sp. 2APBS1 as its deepest branch. Comparative analyses of protein sequences have identified 13 CSIs in widely distributed proteins such as GlnRS, TypA, MscL, LysRS, LipA, Tgt, LpxA, TolQ, ParE, PolA and TyrB that are unique to all species/strains from this order, but not found in any other bacteria. Fifteen additional CSIs in proteins (viz. CoxD, DnaE, PolA, SucA, AsnB, RecA, PyrG, LigA, MutS and TrmD) are uniquely shared by different Xanthomonadales except Rhodanobacter and in a few cases by Pseudoxanthomonas species, providing further support for the deep branching of these two genera. Five other CSIs are commonly shared by Xanthomonadales and 1–3 species from the orders Chromatiales, Methylococcales and Cardiobacteriales suggesting that these deep branching orders of Gammaproteobacteria might be specifically related. Lastly, 7 CSIs in ValRS, CarB, PyrE, GlyS, RnhB, MinD and X001065 are commonly shared by Xanthomonadales and a limited number of Beta- or Gamma-proteobacteria. Our analysis indicates that these CSIs have likely originated independently and they are not due to lateral gene transfers. The Xanthomonadales-specific CSIs reported here provide novel molecular markers for the identification of these important plant and human pathogens and also as potential

  19. First Molecular Characterization of Leishmania Species Causing Visceral Leishmaniasis among Children in Yemen

    PubMed Central

    Mahdy, Mohammed A. K.; Al-Mekhlafi, Abdulsalam M.; Abdul-Ghani, Rashad; Saif-Ali, Reyadh; Al-Mekhlafi, Hesham M.; Al-Eryani, Samira M.; Lim, Yvonne A. L.; Mahmud, Rohela

    2016-01-01

    Visceral leishmaniasis (VL) is a debilitating, often fatal disease caused by Leishmania donovani complex; however, it is a neglected tropical disease. L. donovani complex comprises two closely related species, L. donovani that is mostly anthroponotic and L. infantum that is zoonotic. Differentiation between these two species is critical due to the differences in their epidemiology and pathology. However, they cannot be differentiated morphologically, and their speciation using isoenzyme-based methods poses a difficult task and may be unreliable. Molecular characterization is now the most reliable method to differentiate between them and to determine their phylogenetic relationships. The present study aims to characterize Leishmania species isolated from bone marrows of Yemeni pediatric patients using sequence analysis of the ribosomal internal transcribed spacer-1 (ITS1) gene. Out of 41 isolates from Giemsa-stained bone marrow smears, 25 isolates were successfully amplified by nested polymerase chain reaction and sequenced in both directions. Phylogenetic analysis using neighbor joining method placed all study isolates in one cluster with L. donovani complex (99% bootstrap). The analysis of ITS1 for microsatellite repeat numbers identified L. infantum in 11 isolates and L. donovani in 14 isolates. These data suggest the possibility of both anthroponotic and zoonotic transmission of VL-causing Leishmania species in Yemen. Exploring the possible animal reservoir hosts is therefore needed for effective control to be achieved. PMID:26966902

  20. Clinical significance, antimicrobial susceptibility and molecular identification of Nocardia species isolated from children with cystic fibrosis.

    PubMed

    Betrán, Ana; Villuendas, M Cruz; Rezusta, Antonio; Pereira, Javier; Revillo, M José; Rodríguez-Nava, Verónica

    2016-01-01

    Nocardia is an opportunistic pathogen that causes respiratory infections in immunocompromised patients. The aim of this study was to analyze the epidemiology, clinical significance and antimicrobial susceptibility of Nocardia species isolated from eight children with cystic fibrosis. The isolated species were identified as Nocardia farcinica, Nocardia transvalensis, Nocardia pneumoniae, Nocardia veterana and Nocardia wallacei. N. farcinica was isolated in three patients and all of them presented lung affectation with a chronic colonization and pneumonia. N. farcinica showed resistance against gentamicin, tobramycin, cefotaxime, but was susceptible to trimethoprim-sulfamethoxazole and amikacin. N. transvalensis, which was isolated from two patients, showed an association with chronic colonization. N. transvalensis was resistant to tobramycin and amikacin, but susceptible to ciprofloxacin, trimethoprim-sulfamethoxazole and cefotaxime. N. veterana, N. pneumoniae and N. wallacei were isolated from three different patients and appeared in transitory lung colonization. N. veterana and N. pneumoniae were susceptible to imipenem, trimethoprim-sulfamethoxazole, amikacin, tobramycin, and cefotaxime. N. wallacei was resistant to amikacin, tobramycin, imipenem, and trimethoprim-sulfamethoxazole and susceptible to ciprofloxacin and cefotaxime. All the isolates were identified up to species level by 16S rRNA gene sequencing. The presence of Nocardia in the sputum of patients with cystic fibrosis is not always an indication of an active infection; therefore, the need for a treatment should be evaluated on an individual basis. The detection of multidrug-resistant species needs molecular identification and susceptibility testing, and should be performed for all Nocardia infections. PMID:27155949

  1. Molecular detection of Lactobacillus species in the neovagina of male-to-female transsexual women.

    PubMed

    Petricevic, Ljubomir; Kaufmann, Ulrike; Domig, Konrad J; Kraler, Manuel; Marschalek, Julian; Kneifel, Wolfgang; Kiss, Herbert

    2014-01-01

    There is a general opinion that penile skin lined neovagina of transsexual women is not able to support the growth of lactobacilli. This study was undertaken to prove if lactobacilli strains could survive in neovagina and to characterise the most dominant Lactobacillus species. Sixty three male-to-female transsexual women without abnormal vaginal discharge, clinical signs of infection were recruited on an ongoing basis from among transsexual outpatients in an academic research institution and tertiary care centre. Neovaginal smears were taken for molecular Lactobacillus spp. profiling by denaturing gradient gel electrophoresis (PCR-DGGE). Lactobacillus species were detected from 47/63 transsexual women (75%). The 279 Lactobacillus signals detected by PCR-DGGE technique belonged to 13 different species. Lactobacilli of the L. delbrueckii group (L. gasseri, L. crispatus, L. johnsonii, L. iners, L. jensenii) were predominant. More than 90% of women harboured a combination of two or more neovaginal Lactobacillus species. In this study we report the frequent occurrence of lactobacilli from neovagina of transsexual women. Both, frequency and composition were similar to the normal lactic acid bacterial microflora in both women of reproductive age and postmenopausal women. PMID:24434849

  2. First Molecular Characterization of Leishmania Species Causing Visceral Leishmaniasis among Children in Yemen.

    PubMed

    Mahdy, Mohammed A K; Al-Mekhlafi, Abdulsalam M; Abdul-Ghani, Rashad; Saif-Ali, Reyadh; Al-Mekhlafi, Hesham M; Al-Eryani, Samira M; Lim, Yvonne A L; Mahmud, Rohela

    2016-01-01

    Visceral leishmaniasis (VL) is a debilitating, often fatal disease caused by Leishmania donovani complex; however, it is a neglected tropical disease. L. donovani complex comprises two closely related species, L. donovani that is mostly anthroponotic and L. infantum that is zoonotic. Differentiation between these two species is critical due to the differences in their epidemiology and pathology. However, they cannot be differentiated morphologically, and their speciation using isoenzyme-based methods poses a difficult task and may be unreliable. Molecular characterization is now the most reliable method to differentiate between them and to determine their phylogenetic relationships. The present study aims to characterize Leishmania species isolated from bone marrows of Yemeni pediatric patients using sequence analysis of the ribosomal internal transcribed spacer-1 (ITS1) gene. Out of 41 isolates from Giemsa-stained bone marrow smears, 25 isolates were successfully amplified by nested polymerase chain reaction and sequenced in both directions. Phylogenetic analysis using neighbor joining method placed all study isolates in one cluster with L. donovani complex (99% bootstrap). The analysis of ITS1 for microsatellite repeat numbers identified L. infantum in 11 isolates and L. donovani in 14 isolates. These data suggest the possibility of both anthroponotic and zoonotic transmission of VL-causing Leishmania species in Yemen. Exploring the possible animal reservoir hosts is therefore needed for effective control to be achieved. PMID:26966902

  3. Molecular Diagnosis and Identification of Leishmania Species in Jordan from Saved Dry Samples

    PubMed Central

    Hijjawi, Nawal; Kanani, Kalil A.; Rasheed, Malak; Atoum, Manar; Abdel-Dayem, Mona; Irhimeh, Mohammad R.

    2016-01-01

    Diagnosis of the endemic cutaneous leishmaniasis (CL) in Jordan relies on patient clinical presentation and microscopic identification. Studies toward improved identification of the causative Leishmania species, especially in regions where multiple species exist, and the introduction of these techniques into medical diagnosis is paramount. This study looked at the current epidemiology of CL in Jordan. Clinically diagnosed 41 patients with CL were tested for the presence of Leishmania parasite using both Giemsa staining from skin scraps on glass slides and ITS1-PCR from samples blotted onto storage cards (NucleoCards®). Microscopically, 28 out of the 41 (68.3%) collected samples were positive for amastigotes, whereas the molecular ITS1-PCR amplification successfully identified 30 of the 41 samples (73.2%). Furthermore, PCR-RFLP analysis allowed species identification which is impossible microscopically. Of the 30 PCR positive samples, 28 were Leishmania major positive and the other two samples were Leishmania tropica. This indicates that L. major is the most prevalent species in Jordan and the two L. tropica cases originated from Syria indicating possible future L. tropica outbreaks. Diagnosis of CL based on clinical presentation only may falsely increase its prevalence. Although PCR is more sensitive, it is still not available in our medical laboratories in Jordan. PMID:27403435

  4. Molecular and morphological divergence in a pair of bird species and their ectoparasites.

    PubMed

    Whiteman, Noah K; Dosanjh, Vishal S; Palma, Ricardo L; Hull, Joshua M; Kimball, Rebecca T; Sánchez, Pablo; Sarasola, José Hernán; Parker, Patricia G

    2009-12-01

    In an evolutionary context, parasites tend to be morphologically conservative relative to their hosts. However, the rate of neutral molecular evolution across many parasite lineages is faster than in their hosts. Although this relationship is apparent at the macroevolutionary scale, insight into the processes underpinning it may be gained through investigations at the microevolutionary scale. Birds and their ectoparasitic lice have served as important natural experiments in co-evolution. Here, we compared mitochondrial and morphological divergence in 2 recently diverged avian host lineages and their parasites. Gálapagos hawks (Buteo galapagoensis) are phenotypically divergent from their closest mainland relatives, the Swainson's hawk (Buteo swainsoni). Both species are host to a feather louse species of Craspedorrhynchus (Insecta: Phthiraptera: Ischnocera, Philopteridae). We sequenced the 5′ end of the mitochondrial gene cytochrome oxidase c subunit I (COI) from a set of hawks and lice. Although this fragment allowed unambiguous identification of host and parasite lineages on the islands and the mainland, only a single variable site was present in the 2 hosts, but 2 major Craspedorrhynchus clades divergent by ~10% were recovered that sorted perfectly with host species. We found significant population genetic structure within the Galápagos Craspedorrhynchus lineage. While the host species are highly differentiated phenotypically, the 2 Craspedorrhynchus louse lineages are phenotypically overlapping, although subtle but significant morphological differences exist. PMID:19655998

  5. New molecular evidence supports the species status of Kaempfer’s Woodpecker (Aves, Picidae)

    PubMed Central

    de Sousa Azevedo, Lorena; Aleixo, Alexandre; Santos, Marcos Pérsio Dantas; Sampaio, Iracilda; Schneider, Horacio; Vallinoto, Marcelo; do Rêgo, Péricles Sena

    2013-01-01

    Kaempfer’s Woodpecker (Celeus obrieni) is the only species of the genus Celeus endemic to Brazil. The description of this taxon as a subspecies of the Rufous-headed Woodpecker (Celeus spectabilis) was based on a single specimen. While C. obrieni and C. spectabilis are now considered separate species based on morphological and limited molecular evidence, no study has critically tested the reciprocal monophyly and degree of evolutionary independence between these taxa with several specimens. Herein, fragments of the mitochondrial and nuclear DNA of three recently-collected specimens of C. obrieni were analyzed to evaluate the degree of evolutionary differentiation of this taxon with respect to C. spectabilis. The results confirm the reciprocal monophyly between the specimens of C. obrieni and C. spectabilis. The genetic divergence values for the two taxa also support their classification as independent species, given that they are greater than the values recorded among other closely-related but separate species of the same genus. Estimates of the divergence time between C. obrieni and C. spectabilis indicate that cladogenesis occurred in the mid-Pleistocene, during a period of major climatic fluctuations and landscape change, consistent with the hypothesis of a corridor of open bamboo dominated forests and woodland stretching. PMID:23885201

  6. Molecular detection of Lactobacillus species in the neovagina of male-to-female transsexual women

    PubMed Central

    Petricevic, Ljubomir; Kaufmann, Ulrike; Domig, Konrad J.; Kraler, Manuel; Marschalek, Julian; Kneifel, Wolfgang; Kiss, Herbert

    2014-01-01

    There is a general opinion that penile skin lined neovagina of transsexual women is not able to support the growth of lactobacilli. This study was undertaken to prove if lactobacilli strains could survive in neovagina and to characterise the most dominant Lactobacillus species. Sixty three male-to-female transsexual women without abnormal vaginal discharge, clinical signs of infection were recruited on an ongoing basis from among transsexual outpatients in an academic research institution and tertiary care centre. Neovaginal smears were taken for molecular Lactobacillus spp. profiling by denaturing gradient gel electrophoresis (PCR–DGGE). Lactobacillus species were detected from 47/63 transsexual women (75%). The 279 Lactobacillus signals detected by PCR-DGGE technique belonged to 13 different species. Lactobacilli of the L. delbrueckii group (L. gasseri, L. crispatus, L. johnsonii, L. iners, L. jensenii) were predominant. More than 90% of women harboured a combination of two or more neovaginal Lactobacillus species. In this study we report the frequent occurrence of lactobacilli from neovagina of transsexual women. Both, frequency and composition were similar to the normal lactic acid bacterial microflora in both women of reproductive age and postmenopausal women. PMID:24434849

  7. Morphological and molecular variation in Tylototriton (Caudata: Salamandridae) in Laos, with description of a new species.

    PubMed

    Phimmachak, Somphouthone; Aowphol, Anchalee; Stuart, Bryan L

    2015-01-01

    The salamandrid genus Tylototriton is poorly known in Laos, with one described species and unverified reports of two others. We undertook new fieldwork and obtained samples of Tylototriton at six localities across northern Laos during 2009-2013. Bayesian phylogenetic analysis of mitochondrial DNA, principal component analyses of 13 mensural characters, and qualitative morphological comparisons with samples from across the geographic range of Tylototriton were performed. Samples from Laos fell into four molecular and morphological groups, consisting of T. notialis, T. panhai, T. anguliceps, and a fourth lineage that is hypothesized here to be an undescribed species. Tylototriton podichthys sp. nov. is distinguished from its congeners by having distinct mitochondrial DNA haplotypes and in characteristics of the glandular skin on the head and body, shape of the rib nodules, and coloration of the body and limbs. This study expands the number of confirmed Tylototriton species in Laos from one to four, with the description of one species and extension of the ranges of T. panhai and T. anguliceps to Laos. An improved understanding of the geographic ranges of T. podichthys sp. nov. and T. anguliceps within Laos is needed. PMID:26623768

  8. Diversity of Clonostachys species assessed by molecular phylogenetics and MALDI-TOF mass spectrometry.

    PubMed

    Abreu, Lucas M; Moreira, Gláucia M; Ferreira, Douglas; Rodrigues-Filho, Edson; Pfenning, Ludwig H

    2014-12-01

    We assessed the species diversity among 45 strains of Clonostachys from different substrates and localities in Brazil using molecular phylogenetics, and compared the results with the phenotypic classification of strains obtained from matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Phylogenetic analyses were based on beta tubulin (Tub), ITS-LSU rDNA, and a combined Tub-ITS DNA dataset. MALDI-TOF MS analyses were performed using intact conidia and conidiophores of strains cultivated on oatmeal agar and 4% malt extract agar. Six known species were identified: Clonostachys byssicola, Clonostachys candelabrum, Clonostachys pseudochroleuca, Clonostachys rhizophaga, Clonostachys rogersoniana, and Clonostachys rosea. Two clades and two singleton lineages did not correspond to known species represented in the reference DNA dataset and were identified as Clonostachys sp. 1-4. Multivariate cluster analyses of MALDI-TOF MS data classified the strains into eight clusters and three singletons, corresponding to the ten identified species plus one additional cluster containing two strains of C. rogersoniana that split from the other co-specific strains. The consistent results of MALDI-TOF MS supported the identification of strains assigned to C. byssicola and C. pseudochroleuca, which did not form well supported clades in all phylogenetic analyses, but formed distinct clusters in the MALDI-TOF dendrograms. PMID:25457948

  9. Characterization of Metarhizium species and varieties based on molecular analysis, heat tolerance and cold activity

    USGS Publications Warehouse

    Fernandes, E.K.K.; Keyser, C.A.; Chong, J.P.; Rangel, D.E.N.; Miller, M.P.; Roberts, D.W.

    2010-01-01

    Aims: The genetic relationships and conidial tolerances to high and low temperatures were determined for isolates of several Metarhizium species and varieties. Methods and Results: Molecular-based techniques [AFLP and rDNA (ITS1, ITS2 and 5??8S) gene sequencing] were used to characterize morphologically identified Metarhizium spp. isolates from a wide range of sources. Conidial suspensions of isolates were exposed to wet heat (45 ?? 0??2??C) and plated on potato dextrose agar plus yeast extract (PDAY) medium. After 8-h exposure, the isolates divided clearly into two groups: (i) all isolates of Metarhizium anisopliae var. anisopliae (Ma-an) and Metarhizium from the flavoviride complex (Mf) had virtually zero conidial relative germination (RG), (ii) Metarhizium anisopliae var. acridum (Ma-ac) isolates demonstrated high heat tolerance (c. 70-100% RG). Conidial suspensions also were plated on PDAY and incubated at 5??C for 15 days, during which time RGs for Ma-an and Ma-ac isolates were virtually zero, whereas the two Mf were highly cold active (100% RG). Conclusions: Heat and cold exposures can be used as rapid tools to tentatively identify some important Metarhizium species and varieties. Significance and Impact of the Study: Identification of Metarhizium spp. currently relies primarily on DNA-based methods; we suggest a simple temperature-based screen to quickly obtain tentative identification of isolates as to species or species complexes. ?? 2009 The Society for Applied Microbiology.

  10. Studies of oxygen species in synthetic Todorokite-like manganese oxide octahedral molecular sieves

    SciTech Connect

    Yin, Yuan-Gen; Xu, Wen-Qing; Shen, Yan-Fei; Suib, S.L. ); O'Young, C.L. )

    1994-10-01

    Manganese oxide octahedral molecular sieves of 3 x 3 tunnel structure (OMS-1) doped with various cations possess high thermal stability and were studied by means of temperature-programmed desorption and reduction by H[sub 2] and CO. Different oxygen species can be discerned according to their peak positions in the temperature-programmed desorption and reduction and assigned to chemisorbed dioxygen, oxygen atoms bound to Mn[sup 2+], and those bound to Mn[sup 4+] ions in the framework. Differences in peak positions and availabilities of these species during TPD and TPR can be explained by creation of nascent Mn[sup 2+] ions during TPR. The effects of doping cations on the reactivity and availability of these oxygen species are demonstrated to be more pronounced in TPR in H[sub 2] or CO than in TPD. In some instances, the trends of changes in reactivity and availability of the oxygen species due to doping of Cu[sup 2+], Ni[sup 2+], Zn[sup 2+], and Mg[sup 2+] correlated with the changes in the heat of formation of oxides of these cations. Temperature-programmed reactions with methane show some reactivity of these doped OMS-1 materials. Pulse reactions with CO show higher reactivity of Cu-doped OM-1 than with butane. However, the recovery of Cu-doped OMS-1 by reoxidation with oxygen pulses seems rather incomplete at the same temperature. 27 refs., 9 figs.

  11. Molecular detection and species identification of Alexandrium (Dinophyceae) causing harmful algal blooms along the Chilean coastline

    PubMed Central

    Jedlicki, Ana; Fernández, Gonzalo; Astorga, Marcela; Oyarzún, Pablo; Toro, Jorge E.; Navarro, Jorge M.; Martínez, Víctor

    2012-01-01

    Background and aims On the basis of morphological evidence, the species involved in South American Pacific coast harmful algal blooms (HABs) has been traditionally recognized as Alexandrium catenella (Dinophyceae). However, these observations have not been confirmed using evidence based on genomic sequence variability. Our principal objective was to accurately determine the species of Alexandrium involved in local HABs in order to implement a real-time polymerase chain reaction (PCR) assay for its rapid and easy detection on filter-feeding shellfish, such as mussels. Methodology For species-specific determination, the intergenic spacer 1 (ITS1), 5.8S subunit, ITS2 and the hypervariable genomic regions D1–D5 of the large ribosomal subunit of local strains were sequenced and compared with two data sets of other Alexandrium sequences. Species-specific primers were used to amplify signature sequences within the genomic DNA of the studied species by conventional and real-time PCR. Principal results Phylogenetic analysis determined that the Chilean strain falls into Group I of the tamarensis complex. Our results support the allocation of the Chilean Alexandrium species as a toxic Alexandrium tamarense rather than A. catenella, as currently defined. Once local species were determined to belong to Group I of the tamarensis complex, a highly sensitive and accurate real-time PCR procedure was developed to detect dinoflagellate presence in Mytilus spp. (Bivalvia) samples after being fed (challenged) in vitro with the Chilean Alexandrium strain. The results show that real-time PCR is useful to detect Alexandrium intake in filter-feeding molluscs. Conclusions It has been shown that the classification of local Alexandrium using morphological evidence is not very accurate. Molecular methods enabled the HAB dinoflagellate species of the Chilean coast to be assigned as A. tamarense rather than A. catenella. Real-time PCR analysis based on A. tamarense primers allowed the

  12. Status of Gobiosoma (Teleostei: Gobiidae) from Brazil: description of a new species, redescription of G. hemigymnum, molecular phylogeny of the genus, and key to Atlantic species.

    PubMed

    Van Tassell, James L; Joyeux, Jean-Christophe; Macieira, Raphael Mariano; Tornabene, Luke

    2015-01-01

    It is unclear how many species of Gobiosoma occur in Brazil and what their geographic distributions are. Here we combine data from a comprehensive morphological survey and a molecular analysis to clarify this uncertain taxonomy and place Brazilian Gobiosoma within a phylogenetic framework. Recent collections in Brazil, from the states of Ceará to Santa Catarina, and in Uruguay yielded two allopatric species of Gobiosoma that are distinct in genetics, meristics, morphometrics, scale pattern and coloration. Comparisons were made with types and specimens of Gobiosoma hemigymnum, Garmannia mediocricula, Gobiosoma spilotum and Gobiosoma parri and all other known species of Gobiosoma. We place G. parri in synonomy with G. hemigymnum with a distribution of Rio de Janeiro to Uruguay and Argentina. The northern species, that extends from the states of Espírito Santo to Ceará, is described as a new species, Gobiosoma alfiei. A key to the Atlantic species of Gobiosoma is provided. PMID:26623827

  13. Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies

    PubMed Central

    Patalano, Solenn; Vlasova, Anna; Wyatt, Chris; Ewels, Philip; Camara, Francisco; Ferreira, Pedro G.; Asher, Claire L.; Jurkowski, Tomasz P.; Segonds-Pichon, Anne; Bachman, Martin; González-Navarrete, Irene; Minoche, André E.; Krueger, Felix; Lowy, Ernesto; Marcet-Houben, Marina; Rodriguez-Ales, Jose Luis; Nascimento, Fabio S.; Balasubramanian, Shankar; Gabaldon, Toni; Tarver, James E.; Andrews, Simon; Himmelbauer, Heinz; Hughes, William O. H.; Guigó, Roderic; Reik, Wolf; Sumner, Seirian

    2015-01-01

    Phenotypic plasticity is important in adaptation and shapes the evolution of organisms. However, we understand little about what aspects of the genome are important in facilitating plasticity. Eusocial insect societies produce plastic phenotypes from the same genome, as reproductives (queens) and nonreproductives (workers). The greatest plasticity is found in the simple eusocial insect societies in which individuals retain the ability to switch between reproductive and nonreproductive phenotypes as adults. We lack comprehensive data on the molecular basis of plastic phenotypes. Here, we sequenced genomes, microRNAs (miRNAs), and multiple transcriptomes and methylomes from individual brains in a wasp (Polistes canadensis) and an ant (Dinoponera quadriceps) that live in simple eusocial societies. In both species, we found few differences between phenotypes at the transcriptional level, with little functional specialization, and no evidence that phenotype-specific gene expression is driven by DNA methylation or miRNAs. Instead, phenotypic differentiation was defined more subtly by nonrandom transcriptional network organization, with roles in these networks for both conserved and taxon-restricted genes. The general lack of highly methylated regions or methylome patterning in both species may be an important mechanism for achieving plasticity among phenotypes during adulthood. These findings define previously unidentified hypotheses on the genomic processes that facilitate plasticity and suggest that the molecular hallmarks of social behavior are likely to differ with the level of social complexity. PMID:26483466

  14. Phylogenetic Study of Haemonchus Species from Iran Based On Morpho-Molecular Characterization

    PubMed Central

    MESHGI, Behnam; JALOUSIAN, Fatemeh; MASIH, Zahra

    2015-01-01

    Background: Haemonchosis has a negative effect on the farming industry throughout the world, especially in the tropic and sub-tropic countries. The present study was carried out to differentiate Haemonchus species from its main hosts in Iran, including sheep, goat and camel. Methods: The identification took place based on the morphometrics of the spicules and molecular characters. Two hundred seventy adult male nematodes were collected from the abomasums of different ruminants (90 samples from each animal) at the slaughterhouses from different localities in Iran. Samples were morphologically identified according to the spicules’ morphometric measurements. In the section on molecular study, 10 samples of each Haemonchus isolates were genetically examined. A simple PCR-restriction fragment length polymorphism (PCR-RFLP) assay of the second internal transcribed spacer of ribosomal DNA (ITS2-rDNA) were described to confirm the PCR results. Results: PCR-RFLP profile obtained from the restriction enzyme HPa1 in H. contortus and H. longistipes indicated 1 (278 bp) and 2 (113 and 135 bp) different fragments, respectively. The morphological parameters clearly distinguish H. contortus from H. longistipes. Moreover, regarding the ITS2-rDNA, sequences of 295 bp and 314 bp were obtained from H. contortus and H. longistipes, respectively. Conclusion: The genotypic results are in agreement with the phenotypic findings of both species. PMID:26246816

  15. Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies.

    PubMed

    Patalano, Solenn; Vlasova, Anna; Wyatt, Chris; Ewels, Philip; Camara, Francisco; Ferreira, Pedro G; Asher, Claire L; Jurkowski, Tomasz P; Segonds-Pichon, Anne; Bachman, Martin; González-Navarrete, Irene; Minoche, André E; Krueger, Felix; Lowy, Ernesto; Marcet-Houben, Marina; Rodriguez-Ales, Jose Luis; Nascimento, Fabio S; Balasubramanian, Shankar; Gabaldon, Toni; Tarver, James E; Andrews, Simon; Himmelbauer, Heinz; Hughes, William O H; Guigó, Roderic; Reik, Wolf; Sumner, Seirian

    2015-11-10

    Phenotypic plasticity is important in adaptation and shapes the evolution of organisms. However, we understand little about what aspects of the genome are important in facilitating plasticity. Eusocial insect societies produce plastic phenotypes from the same genome, as reproductives (queens) and nonreproductives (workers). The greatest plasticity is found in the simple eusocial insect societies in which individuals retain the ability to switch between reproductive and nonreproductive phenotypes as adults. We lack comprehensive data on the molecular basis of plastic phenotypes. Here, we sequenced genomes, microRNAs (miRNAs), and multiple transcriptomes and methylomes from individual brains in a wasp (Polistes canadensis) and an ant (Dinoponera quadriceps) that live in simple eusocial societies. In both species, we found few differences between phenotypes at the transcriptional level, with little functional specialization, and no evidence that phenotype-specific gene expression is driven by DNA methylation or miRNAs. Instead, phenotypic differentiation was defined more subtly by nonrandom transcriptional network organization, with roles in these networks for both conserved and taxon-restricted genes. The general lack of highly methylated regions or methylome patterning in both species may be an important mechanism for achieving plasticity among phenotypes during adulthood. These findings define previously unidentified hypotheses on the genomic processes that facilitate plasticity and suggest that the molecular hallmarks of social behavior are likely to differ with the level of social complexity. PMID:26483466

  16. Various Molecular Species of Diacylglycerol Hydroperoxide Activate Human Neutrophils via PKC Activation

    PubMed Central

    Kambayashi, Yasuhiro; Takekoshi, Susumu; Tanino, Yutaka; Watanabe, Keiichi; Nakano, Minoru; Hitomi, Yoshiaki; Takigawa, Tomoko; Ogino, Keiki; Yamamoto, Yorihiro

    2007-01-01

    We have proposed that diacylglycerol hydroperoxide-induced unregulated signal transduction causes oxidative stress-related diseases. In this study, we investigated which molecular species of diacylglycerol hydroperoxide activated human peripheral neutrophils. All diacylglycerol hydroperoxides, diacylglycerol hydroxides, and diacyglycerols tested in the present study induced superoxide production by neutrophils. The ability to activate neutrophils among molecular species containing the same fatty acid composition was as follows; diacylglycerol hydroperoxide>diacylglycerol hydroxide≥diacylglycerol. The diacylglycerol hydroperoxide composed of linoleate was a stronger activator for neutrophils than that composed of arachidonate. 1-Palmitoyl-2-linoleoylglycerol hydroperoxide (PLG-OOH) was the strongest stimulator for neutrophils. We reconfirmed that PLG-OOH activated protein kinase C (PKC) in neutrophils. PLG-OOH induced the phosphorylation of p47phox, a substrate of PKC and a cytosolic component of NADPH oxidase, in neutrophils, as did N-formyl-methionyl-leucyl-phenylalanine or 4β-phorbol-12β-myristate-13α-acetate. Moreover, the time course of p47phox phosphorylation was comparable to that of superoxide production. These results suggest that PLG-OOH activated intracellular protein kinase C. PLG-OOH, produced via an uncontrolled process, can act as a biological second messenger to cause inflammatory disease from oxidative stress. PMID:18392102

  17. Roles of specific lipid species in the cell and their molecular mechanism.

    PubMed

    Kimura, Tomohiro; Jennings, William; Epand, Richard M

    2016-04-01

    Thousands of different molecular species of lipids are present within a single cell, being involved in modulating the basic processes of life. The vast number of different lipid species can be organized into a number of different lipid classes, which may be defined as a group of lipids with a common chemical structure, such as the headgroup, apart from the nature of the hydrocarbon chains. Each lipid class has unique biological roles. In some cases, a relatively small change in the headgroup chemical structure can result in a drastic change in function. Such phenomena are well documented, and largely understood in terms of specific interactions with proteins. In contrast, there are observations that the entire structural specificity of a lipid molecule, including the hydrocarbon chains, is required for biological activity through specific interactions with membrane proteins. Understanding of these phenomena represents a fundamental change in our thinking of the functions of lipids in biology. There are an increasing number of diverse examples of roles for specific lipids in cellular processes including: Signal transduction; trafficking; morphological changes; cell division. We are gaining knowledge and understanding of the underlying molecular mechanisms. They are of growing importance in both basic and applied sciences. PMID:26875545

  18. Molecular Identification of Mucor and Lichtheimia Species in Pure Cultures of Zygomycetes

    PubMed Central

    Ziaee, Ardeshir; Zia, Mohammadali; Bayat, Mansour; Hashemi, Jamal

    2016-01-01

    Background The Mucorales are an important opportunistic fungi that can cause mucormycosis in immunocompromised patients. The fast and precise diagnosis of mucormycosis is very important because, if the diagnosis is not made early enough, dissemination often occurs. It is now well established that molecular methods such as polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) are feasible and reliable tools for the early and accurate diagnosis of mucormycosis agents. Objectives The present study was conducted to evaluate the validity of PCR-RFLP for the identification of Mucorales and some important Mucor and Lichtheimia species in pure cultures of Zygomycetes. Materials and Methods Specific sense and anti-sense primers were used to amplify the Mucorales, Mucor, and Lichtheimia DNA. The PCR products were digested by AfIII, XmnI, and AcII restriction enzymes, and the resultant restriction pattern was analyzed. Results On the basis of the molecular and morphological data, we identified Mucor plumbeus (10.83%), M. circinelloides (9.17%), Lichtheimia corymbifera (9.17%), M. racemosus (5.83%), M. ramosissimus (3.33%), and L. blakesleeana (0.83%). Conclusions It seems that PCR-RFLP is a suitable technique for the identification of Mucorales at the species level. PMID:27284399

  19. Comparative molecular cytogenetics of major repetitive sequence families of three Dendrobium species (Orchidaceae) from Bangladesh

    PubMed Central

    Begum, Rabeya; Alam, Sheikh Shamimul; Menzel, Gerhard; Schmidt, Thomas

    2009-01-01

    Background and Aims Dendrobium species show tremendous morphological diversity and have broad geographical distribution. As repetitive sequence analysis is a useful tool to investigate the evolution of chromosomes and genomes, the aim of the present study was the characterization of repetitive sequences from Dendrobium moschatum for comparative molecular and cytogenetic studies in the related species Dendrobium aphyllum, Dendrobium aggregatum and representatives from other orchid genera. Methods In order to isolate highly repetitive sequences, a c0t-1 DNA plasmid library was established. Repeats were sequenced and used as probes for Southern hybridization. Sequence divergence was analysed using bioinformatic tools. Repetitive sequences were localized along orchid chromosomes by fluorescence in situ hybridization (FISH). Key Results Characterization of the c0t-1 library resulted in the detection of repetitive sequences including the (GA)n dinucleotide DmoO11, numerous Arabidopsis-like telomeric repeats and the highly amplified dispersed repeat DmoF14. The DmoF14 repeat is conserved in six Dendrobium species but diversified in representative species of three other orchid genera. FISH analyses showed the genome-wide distribution of DmoF14 in D. moschatum, D. aphyllum and D. aggregatum. Hybridization with the telomeric repeats demonstrated Arabidopsis-like telomeres at the chromosome ends of Dendrobium species. However, FISH using the telomeric probe revealed two pairs of chromosomes with strong intercalary signals in D. aphyllum. FISH showed the terminal position of 5S and 18S–5·8S–25S rRNA genes and a characteristic number of rDNA sites in the three Dendrobium species. Conclusions The repeated sequences isolated from D. moschatum c0t-1 DNA constitute major DNA families of the D. moschatum, D. aphyllum and D. aggregatum genomes with DmoF14 representing an ancient component of orchid genomes. Large intercalary telomere-like arrays suggest chromosomal

  20. A proposed harmonized LPS molecular-subtyping scheme for Cronobacter species.

    PubMed

    Yan, Qiongqiong; Jarvis, Karen G; Chase, Hannah R; Hébert, Karine; Trach, Larisa H; Lee, Chloe; Sadowski, Jennifer; Lee, Boram; Hwang, Seongeun; Sathyamoorthy, Venugopal; Mullane, Niall; Pava-Ripoll, Monica; Iversen, Carol; Pagotto, Franco; Fanning, Séamus; Tall, Ben D

    2015-09-01

    Cronobacter are opportunistic pathogens, which cause infections in all age groups. To aid the characterization of Cronobacter in foods and environments a harmonized LPS identification scheme for molecular serotyping is needed. To this end, we studied 409 Cronobacter isolates representing the seven Cronobacter species using two previously reported molecular serotyping schemes, described here as Mullane-Jarvis (M-J) and Sun schemes. PCR analysis revealed many overlapping results that were obtained when independently applying the two serotyping schemes. There were complete agreements between the two PCR schemes for Cronobacter sakazakii (Csak) O:1, Csak O:3, and Csak O:7 serotypes. However, only thirty-five of 41 Csak O:4 strains, identified using the M-J scheme, were PCR-positive with the Sun scheme primers. Also the Sun scheme Csak O:5 primers failed to identify this serotype in any of the C. sakazakii strains tested, but did recognize seven Cronobacter turicensis strains, which were identified as Ctur O:3 using the M-J scheme. Similarly, the Sun scheme Csak O:6 primers recognized 30 Cronobacter malonaticus O:2 strains identified with the M-J scheme, but failed to identify this serotype in any C. sakazakii strain investigated. In this report, these findings are summarized and a harmonized molecular-serotyping scheme is proposed which is predicated on the correct identification of Cronobacter species, prior to serotype determination. In summary, fourteen serotypes were identified using the combined protocol, which consists of Csak O:1-O:4, and Csak O:7; Cmal O:1-O:2; Cdub O:1-O:2, Cmuy O:1-O:2, Cuni O:1, as well as Ctur O:1 and Ctur O:3. PMID:25998813

  1. Decreased hepatic contents of coenzyme A molecular species in mice after subchronic mild social defeat stress.

    PubMed

    Kubota, Yoshifumi; Goto, Tatsuhiko; Hagiya, Yuki; Chohnan, Shigeru; Toyoda, Atsushi

    2016-03-01

    Social stress may precipitate psychiatric disorders such as depression, which is related to the occurrence of the metabolic syndrome, including obesity and type 2 diabetes. We have evaluated the effects of social stress on central and peripheral metabolism using a model of depression in mice. In the present study, we focused on coenzyme A (CoA) molecular species [i.e. non-esterified CoA (CoASH), acetyl-CoA and malonyl-CoA] which play important roles in numerous metabolic pathways, and we analyzed changes in expression of these molecules in the hypothalamus and liver of adult male mice (C57BL/6J) subjected to 10 days of subchronic mild social defeat stress (sCSDS) with ICR mice as aggressors. Mice (n = 12) exposed to showed hyperphagia- and polydipsia-like symptoms and increased body weight gain compared with control mice which were not affected by exposure to ICR mice (n = 12). To elucidate the underlying metabolic features in the sCSDS model, acetyl-CoA, malonyl-CoA and CoASH tissue levels were analyzed using the acyl-CoA cycling method. The levels of hypothalamic malonyl-CoA, which decreases feeding behavior, were not influenced by sCSDS. However, sCSDS reduced levels of acetyl-CoA, malonyl-CoA and total CoA (sum of the three CoA molecular species) in the liver. Hence, hyperphagia-like symptoms in sCSDS mice evidently occurred independently of hypothalamic malonyl-CoA, but might consequently lead to down-regulation of hepatic CoA via altered expression of nudix hydrolase 7. Future studies should investigate the molecular mechanism(s) underlying the down-regulation of liver CoA pools in sCSDS mice. PMID:26864137

  2. Molecular typing of environmental Cryptococcus neoformans/C. gattii species complex isolates from Manaus, Amazonas, Brazil.

    PubMed

    Alves, Gleica Soyan Barbosa; Freire, Ana Karla Lima; Bentes, Amaury Dos Santos; Pinheiro, José Felipe de Souza; de Souza, João Vicente Braga; Wanke, Bodo; Matsuura, Takeshi; Jackisch-Matsuura, Ani Beatriz

    2016-08-01

    Cryptococcus neoformans and Cryptococcus gattii are the main causative agents of cryptococcosis, a systemic fungal disease that affects internal organs and skin, and which is acquired by inhalation of spores or encapsulated yeasts. It is currently known that the C. neoformans/C. gattii species complex has a worldwide distribution, however, some molecular types seem to prevail in certain regions. Few environmental studies of Cryptococcus have been conducted in the Brazilian Amazon. This is the first ecological study of the pathogenic fungi C. neoformans/C. gattii species complex in the urban area of Manaus, Amazonas, Brazil. A total of 506 samples from pigeon droppings (n = 191), captive bird droppings (n = 60) and tree hollows (n = 255) were collected from June 2012 to January 2014 at schools and public buildings, squares, pet shops, households, the zoo and the bus station. Samples were plated on niger seed agar (NSA) medium supplemented with chloramphenicol and incubated at 25°C for 5 days. Dark-brown colonies were isolated and tested for thermotolerance at 37°C, cycloheximide resistance and growth on canavanine-glycine-bromothymol blue agar. Molecular typing was done by PCR-RFLP. Susceptibility to the antifungal drugs amphotericin B, fluconazole, itraconazole and ketoconazole was tested using Etest(®) strips. In total, 13 positive samples were obtained: one tree hollow (C. gattiiVGII), nine pigeon droppings (C. neoformansVNI) and three captive bird droppings (C. neoformansVNI). The environmental cryptococcal isolates found in this study were of the same molecular types as those responsible for infections in Manaus. PMID:27005969

  3. Particle size interconversion of human low density lipoproteins during incubation of plasma with phosphatidylcholine vesicles

    SciTech Connect

    Shahrokh, Z.; Nichols, A.V.

    1982-09-30

    Incubation of plasma (37/sup 0/C, 6hr) in the presence of increasing amounts of phosphatidylcholine (PC) vesicles, above a threshold concentration, results in an increase in particle diameter of LDL relative to that from nonincubated plasma. With further PC addition, the major peak of LDL in the gradient gel electrophoretic pattern is transformed, first, into a bimodal and, subsequently, into a single peak distribution. PC-induced interconversion of LDL requires factor(s) in the d > 1.20 g/ml fraction and, at PC concentrations below approximately 2 mg/ml, is not inhibited by p-chloromercuriphenylsulfonic acid. Plasma incubation with increasing PC levels also leads to characteristic particle size transformations in HDL/sub 3/ species, with the transformation products ultimately converging to form a single peak pattern within the HDL/sub 2a/ size interval. In certain subjects, incubation of plasma, in the absence of added PC, shifts the particle size distribution of LDL towards smaller species; this can be prevented by addition of PC. We propose that incubation-induced shifts of LDL towards larger or smaller species result from changes in phospholipid (PL) content of LDL.

  4. TNF-α-induced up-regulation of pro-inflammatory cytokines is reduced by phosphatidylcholine in intestinal epithelial cells

    PubMed Central

    2009-01-01

    Background Phosphatidylcholine (PC) is a major lipid of the gastrointestinal mucus layer. We recently showed that mucus from patients suffering from ulcerative colitis has low levels of PC. Clinical studies reveal that the therapeutic addition of PC to the colonic mucus using slow release preparations is beneficial. The positive role of PC in this disease is still unclear; however, we have recently shown that PC has an intrinsic anti-inflammatory property. It could be demonstrated that the exogenous application of PC inhibits membrane-dependent actin assembly and TNF-α-induced nuclear NF-κB activation. We investigate here in more detail the hypothesis that the exogenous application of PC has anti-inflammatory properties. Methods PC species with different fatty acid side chains were applied to differentiated and non-differentiated Caco-2 cells treated with TNF-α to induce a pro-inflammatory response. We analysed TNF-α-induced NF-κB-activation via the transient expression of a NF-κB-luciferase reporter system. Pro-inflammatory gene transcription was detected with the help of a quantitative real time (RT)-PCR analysis. We assessed the binding of TNF-α to its receptor by FACS and analysed lipid rafts by isolating detergent resistant membranes (DRMs). Results The exogenous addition of all PC species tested significantly inhibited TNF-α-induced pro-inflammatory signalling. The expression levels of IL-8, ICAM-1, IP-10, MCP-1, TNF-α and MMP-1 were significantly reduced after PC pre-treatment for at least two hours. The effect was comparable to the inhibition of NF-kB by the NF-kB inhibitor SN 50 and was not due to a reduced binding of TNF-α to its receptor or a decreased surface expression of TNF-α receptors. PC was also effective when applied to the apical side of polarised Caco-2 cultures if cells were stimulated from the basolateral side. PC treatment changed the compartmentation of the TNF-α-receptors 1 and 2 to DRMs. Conclusion PC induces a prolonged

  5. Molecular Assortment of Lens Species with Different Adaptations to Drought Conditions Using SSR Markers.

    PubMed

    Singh, Dharmendra; Singh, Chandan Kumar; Tomar, Ram Sewak Singh; Taunk, Jyoti; Singh, Ranjeet; Maurya, Sadhana; Chaturvedi, Ashish Kumar; Pal, Madan; Singh, Rajendra; Dubey, Sarawan Kumar

    2016-01-01

    The success of drought tolerance breeding programs can be enhanced through molecular assortment of germplasm. This study was designed to characterize molecular diversity within and between Lens species with different adaptations to drought stress conditions using SSR markers. Drought stress was applied at seedling stage to study the effects on morpho-physiological traits under controlled condition, where tolerant cultivars and wilds showed 12.8-27.6% and 9.5-23.2% reduction in seed yield per plant respectively. When juxtaposed to field conditions, the tolerant cultivars (PDL-1 and PDL-2) and wild (ILWL-314 and ILWL-436) accessions showed 10.5-26.5% and 7.5%-15.6% reduction in seed yield per plant, respectively under rain-fed conditions. The reductions in seed yield in the two tolerant cultivars and wilds under severe drought condition were 48-49% and 30.5-45.3% respectively. A set of 258 alleles were identified among 278 genotypes using 35 SSR markers. Genetic diversity and polymorphism information contents varied between 0.321-0.854 and 0.299-0.836, with mean value of 0.682 and 0.643, respectively. All the genotypes were clustered into 11 groups based on SSR markers. Tolerant genotypes were grouped in cluster 6 while sensitive ones were mainly grouped into cluster 7. Wild accessions were separated from cultivars on the basis of both population structure and cluster analysis. Cluster analysis has further grouped the wild accessions on the basis of species and sub-species into 5 clusters. Physiological and morphological characters under drought stress were significantly (P = 0.05) different among microsatellite clusters. These findings suggest that drought adaptation is variable among wild and cultivated genotypes. Also, genotypes from contrasting clusters can be selected for hybridization which could help in evolution of better segregants for improving drought tolerance in lentil. PMID:26808306

  6. Molecular Assortment of Lens Species with Different Adaptations to Drought Conditions Using SSR Markers

    PubMed Central

    Singh, Dharmendra; Singh, Chandan Kumar; Tomar, Ram Sewak Singh; Taunk, Jyoti; Singh, Ranjeet; Maurya, Sadhana; Chaturvedi, Ashish Kumar; Pal, Madan; Singh, Rajendra; Dubey, Sarawan Kumar

    2016-01-01

    The success of drought tolerance breeding programs can be enhanced through molecular assortment of germplasm. This study was designed to characterize molecular diversity within and between Lens species with different adaptations to drought stress conditions using SSR markers. Drought stress was applied at seedling stage to study the effects on morpho-physiological traits under controlled condition, where tolerant cultivars and wilds showed 12.8–27.6% and 9.5–23.2% reduction in seed yield per plant respectively. When juxtaposed to field conditions, the tolerant cultivars (PDL-1 and PDL-2) and wild (ILWL-314 and ILWL-436) accessions showed 10.5–26.5% and 7.5%–15.6% reduction in seed yield per plant, respectively under rain-fed conditions. The reductions in seed yield in the two tolerant cultivars and wilds under severe drought condition were 48–49% and 30.5–45.3% respectively. A set of 258 alleles were identified among 278 genotypes using 35 SSR markers. Genetic diversity and polymorphism information contents varied between 0.321–0.854 and 0.299–0.836, with mean value of 0.682 and 0.643, respectively. All the genotypes were clustered into 11 groups based on SSR markers. Tolerant genotypes were grouped in cluster 6 while sensitive ones were mainly grouped into cluster 7. Wild accessions were separated from cultivars on the basis of both population structure and cluster analysis. Cluster analysis has further grouped the wild accessions on the basis of species and sub-species into 5 clusters. Physiological and morphological characters under drought stress were significantly (P = 0.05) different among microsatellite clusters. These findings suggest that drought adaptation is variable among wild and cultivated genotypes. Also, genotypes from contrasting clusters can be selected for hybridization which could help in evolution of better segregants for improving drought tolerance in lentil. PMID:26808306

  7. Description and molecular diagnosis of a new species of Brunfelsia (Solanaceae) from the Bolivian and Argentinean Andes

    PubMed Central

    Filipowicz, Natalia; Nee, Michael H.; Renner, Susanne S.

    2012-01-01

    Abstract Brunfelsia plowmaniana N.Filipowicz & M.Nee sp. nov., a species from humid and cloud forests of the Bolivian and Argentinean Andes, is described and provided with a molecular diagnosis, using provisions available in the recently approved International Code of Nomenclature for algae, fungi and plants. Specimens belonging to the new species were previously placed in the polymorphic Brunfelsia uniflora (Pohl) D.Don, which a molecular phylogeny revealed as polyphyletic. Revision of numerous collections revealed clear morphological differences between the new species and Brunfelsia uniflora, the type locality of which is in the state of São Paulo, Brazil. PMID:22461731

  8. Description and molecular diagnosis of a new species of Brunfelsia (Solanaceae) from the Bolivian and Argentinean Andes.

    PubMed

    Filipowicz, Natalia; Nee, Michael H; Renner, Susanne S

    2012-01-01

    Brunfelsia plowmaniana N.Filipowicz & M.Nee sp. nov., a species from humid and cloud forests of the Bolivian and Argentinean Andes, is described and provided with a molecular diagnosis, using provisions available in the recently approved International Code of Nomenclature for algae, fungi and plants. Specimens belonging to the new species were previously placed in the polymorphic Brunfelsia uniflora (Pohl) D.Don, which a molecular phylogeny revealed as polyphyletic. Revision of numerous collections revealed clear morphological differences between the new species and Brunfelsia uniflora, the type locality of which is in the state of São Paulo, Brazil. PMID:22461731

  9. Reproductive mode evolution in nematodes: insights from molecular phylogenies and recently discovered species.

    PubMed

    Denver, D R; Clark, K A; Raboin, M J

    2011-11-01

    The Phylum Nematoda has long been known to contain a great diversity of species that vary in reproductive mode, though our understanding of the evolutionary origins, causes and consequences of nematode reproductive mode change have only recently started to mature. Here we bring together and analyze recent progress on reproductive mode evolution throughout the phylum, resulting from the application of molecular phylogenetic approaches and newly discovered nematode species. Reproductive mode variation is reviewed in multiple free-living, animal-parasitic and plant-parasitic nematode groups. Discussion ranges from the model nematode Caenorhabditis elegans and its close relatives, to the plant-parasitic nematodes of the Meloidogyne genus where there is extreme variation in reproductive mode between and even within species, to the vertebrate-parasitic genus Strongyloides and related genera where reproductive mode varies across generations (heterogony). Multiple evolutionary transitions from dioecous (obligately outcrossing) to hermaphroditism and parthenogenesis in the phylum are discussed, along with one case of an evolutionary transition from hermaphroditism to doioecy in the Oscheius genus. We consider the roles of underlying genetic mechanisms in promoting reproductive plasticity in this phylum, as well as the potential evolutionary forces promoting transitions in reproductive mode. PMID:21787872

  10. Morphological and Molecular Discrimination of Fasciola Species Isolated From Domestic Ruminants of Urmia City, Iran

    PubMed Central

    YAKHCHALI, Mohammad; MALEKZADEH-VIAYEH, Reza; IMANI-BARAN, Abbas; MARDANI, Karim

    2015-01-01

    Background: The trematodes of the genus Fasciola (the liver flukes) are among the well-known instances of food-borne parasites worldwide. Differentiation of Fasciola species is important because of their different transmission and epidemiological characteristics. The current study was undertaken to discriminate Fasciola species in the domestic ruminants of Urmia city, Iran. Methods: Adult flukes were isolated from the naturally infected livers of the slaughtered water buffaloes and sheep. The flukes were initially identified based on morphological and morphometric parameters. A 618-bp-long fragment of the 28SrRNA gene of Fasciola was amplified by polymerase chain reaction (PCR). The amplified fragment was digested by DraII or AvaII enzymes for a restriction fragment length polymorphism (RFLP) analysis and sequenced for the phylogenetic tree construction. Results: Based on the morphometric examination, the flukes belonged to F. hepatica, F. gigantica and an intermediate Fasciola form. The PCR-RFLP analysis was able to differentiate F. hepatica from F. gigantica. While the phylogenetic reconstruction justified, to some extent, the morphological diagnosis, it failed to segregate F. hepatica from F. gigantica identified in this and the previous studies. Conclusion: To resolve fully the problem of taxonomy and evolution in Fasciola species, employing a broad range of molecular and morphological approaches is necessary. This is crucial for epidemiological surveys and successful clinical management of their infection. PMID:25904945

  11. Development of New Candidate Gene and EST-Based Molecular Markers for Gossypium Species.

    PubMed

    Buyyarapu, Ramesh; Kantety, Ramesh V; Yu, John Z; Saha, Sukumar; Sharma, Govind C

    2011-01-01

    New source of molecular markers accelerate the efforts in improving cotton fiber traits and aid in developing high-density integrated genetic maps. We developed new markers based on candidate genes and G. arboreum EST sequences that were used for polymorphism detection followed by genetic and physical mapping. Nineteen gene-based markers were surveyed for polymorphism detection in 26 Gossypium species. Cluster analysis generated a phylogenetic tree with four major sub-clusters for 23 species while three species branched out individually. CAP method enhanced the rate of polymorphism of candidate gene-based markers between G. hirsutum and G. barbadense. Two hundred A-genome based SSR markers were designed after datamining of G. arboreum EST sequences (Mississippi Gossypium arboreum  EST-SSR: MGAES). Over 70% of MGAES markers successfully produced amplicons while 65 of them demonstrated polymorphism between the parents of G. hirsutum and G. barbadense RIL population and formed 14 linkage groups. Chromosomal localization of both candidate gene-based and MGAES markers was assisted by euploid and hypoaneuploid CS-B analysis. Gene-based and MGAES markers were highly informative as they were designed from candidate genes and fiber transcriptome with a potential to be integrated into the existing cotton genetic and physical maps. PMID:22315588

  12. Development of New Candidate Gene and EST-Based Molecular Markers for Gossypium Species

    PubMed Central

    Buyyarapu, Ramesh; Kantety, Ramesh V.; Yu, John Z.; Saha, Sukumar; Sharma, Govind C.

    2011-01-01

    New source of molecular markers accelerate the efforts in improving cotton fiber traits and aid in developing high-density integrated genetic maps. We developed new markers based on candidate genes and G. arboreum EST sequences that were used for polymorphism detection followed by genetic and physical mapping. Nineteen gene-based markers were surveyed for polymorphism detection in 26 Gossypium species. Cluster analysis generated a phylogenetic tree with four major sub-clusters for 23 species while three species branched out individually. CAP method enhanced the rate of polymorphism of candidate gene-based markers between G. hirsutum and G. barbadense. Two hundred A-genome based SSR markers were designed after datamining of G. arboreum EST sequences (Mississippi Gossypium arboreum  EST-SSR: MGAES). Over 70% of MGAES markers successfully produced amplicons while 65 of them demonstrated polymorphism between the parents of G. hirsutum and G. barbadense RIL population and formed 14 linkage groups. Chromosomal localization of both candidate gene-based and MGAES markers was assisted by euploid and hypoaneuploid CS-B analysis. Gene-based and MGAES markers were highly informative as they were designed from candidate genes and fiber transcriptome with a potential to be integrated into the existing cotton genetic and physical maps. PMID:22315588

  13. Morphological and molecular description of three new species of the cyrtophorid genus Chlamydodon (Ciliophora, Cyrtophoria).

    PubMed

    Pan, Hongbo; Li, Lifang; Al-Rasheid, Khaled A S; Song, Weibo

    2013-01-01

    This study investigates the morphology and molecular characteristics of three new cyrtophorid ciliates isolated from China seas: Chlamydodon salinus n. sp., Chlamydodon caudatus n. sp., and Chlamydodon paramnemosyne n. sp. Of these, C. salinus n. sp. differs from its congeners through a combination of body size, a cross-striated band that is not continuous, the presence of 30-34 somatic kineties, 11-15 nematodesmal rods, and 13 contractile vacuoles. Chlamydodon caudatus n. sp., meanwhile, is characterized by having a conspicuous tail, a continuous cross-striated band, 34-40 somatic kineties, about 15 contractile vacuoles, and 20-24 nematodesmal rods. Compared with other Chlamydodon species, the third new one, C. paramnemosyne n. sp., could be identified by its continuous cross-striated band, 16-18 somatic kineties, 5 contractile vacuoles, and 9-12 nematodesmal rods. Based on the sequence of the small subunit (SSU) rRNA gene, the phylogeny of these three new species was analyzed, indicating that they all clustered with other congeners to form a monophyletic assemblage. Based on previous studies and the present work, a brief revision of the genus Chlamydodon is supplied, and a key to aid the identification of Chlamydodon species is given. PMID:23289638

  14. Innovative molecular diagnosis of Trichinella species based on β-carbonic anhydrase genomic sequence.

    PubMed

    Zolfaghari Emameh, Reza; Kuuslahti, Marianne; Näreaho, Anu; Sukura, Antti; Parkkila, Seppo

    2016-03-01

    Trichinellosis is a helminthic infection where different species of Trichinella nematodes are the causative agents. Several molecular assays have been designed to aid diagnostics of trichinellosis. These assays are mostly complex and expensive. The genomes of Trichinella species contain certain parasite-specific genes, which can be detected by polymerase chain reaction (PCR) methods. We selected β-carbonic anhydrase (β-CA) gene as a target, because it is present in many parasites genomes but absent in vertebrates. We developed a novel β-CA gene-based method for detection of Trichinella larvae in biological samples. We first identified a β-CA protein sequence from Trichinella spiralis by bioinformatic tools using β-CAs from Caenorhabditis elegans and Drosophila melanogaster. Thereafter, 16 sets of designed primers were tested to detect β-CA genomic sequences from three species of Trichinella, including T. spiralis, Trichinella pseudospiralis and Trichinella nativa. Among all 16 sets of designed primers, the primer set No. 2 efficiently amplified β-CA genomic sequences from T. spiralis, T. pseudospiralis and T. nativa without any false-positive amplicons from other parasite samples including Toxoplasma gondii, Toxocara cati and Parascaris equorum. This robust and straightforward method could be useful for meat inspection in slaughterhouses, quality control by food authorities and medical laboratories. PMID:26639312

  15. Molecular characterization and physical localization of highly repetitive DNA sequences from Brazilian Alstroemeria species.

    PubMed

    Kuipers, A G J; Kamstra, S A; de Jeu, M J; Visser, R G F

    2002-01-01

    Highly repetitive DNA sequences were isolated from genomic DNA libraries of Alstroemeria psittacina and A. inodora. Among the repetitive sequences that were isolated, tandem repeats as well as dispersed repeats could be discerned. The tandem repeats belonged to a family of interlinked Sau3A subfragments with sizes varying from 68-127 bp, and constituted a larger HinfI repeat of approximately 400 bp. Southern hybridization showed a similar molecular organization of the tandem repeats in each of the Brazilian Alstroemeria species tested. None of the repeats hybridized with DNA from Chilean Alstroemeria species, which indicates that they are specific for the Brazilian species. In-situ localization studies revealed the tandem repeats to be localized in clusters on the chromosomes of A. inodora and A. psittacina: distal hybridization sites were found on chromosome arms 2PS, 6PL, 7PS, 7PL and 8PL, interstitial sites on chromosome arms 2PL, 3PL, 4PL and 5PL. The applicability of the tandem repeats for cytogenetic analysis of interspecific hybrids and their role in heterochromatin organization are discussed. PMID:12296521

  16. Molecular characterization of various trichomonad species isolated from humans and related mammals in Indonesia.

    PubMed

    Kamaruddin, Mudyawati; Tokoro, Masaharu; Rahman, Md Moshiur; Arayama, Shunsuke; Hidayati, Anggi P N; Syafruddin, Din; Asih, Puji B S; Yoshikawa, Hisao; Kawahara, Ei

    2014-10-01

    Trichomonad species inhabit a variety of vertebrate hosts; however, their potential zoonotic transmission has not been clearly addressed, especially with regard to human infection. Twenty-one strains of trichomonads isolated from humans (5 isolates), pigs (6 isolates), rodents (6 isolates), a water buffalo (1 isolate), a cow (1 isolate), a goat (1 isolate), and a dog (1 isolate) were collected in Indonesia and molecularly characterized. The DNA sequences of the partial 18S small subunit ribosomal RNA (rRNA) gene or 5.8S rRNA gene locus with its flanking regions (internal transcribed spacer region, ITS1 and ITS2) were identified in various trichomonads; Simplicimonas sp., Hexamastix mitis, and Hypotrichomonas sp. from rodents, and Tetratrichomonas sp. and Trichomonas sp. from pigs. All of these species were not detected in humans, whereas Pentatrichomonas hominis was identified in humans, pigs, the dog, the water buffalo, the cow, and the goat. Even when using the high-resolution gene locus of the ITS regions, all P. hominis strains were genetically identical; thus zoonotic transmission between humans and these closely related mammals may be occurring in the area investigated. The detection of Simplicimonas sp. in rodents (Rattus exulans) and P. hominis in water buffalo in this study revealed newly recognized host adaptations and suggested the existence of remaining unrevealed ranges of hosts in the trichomonad species. PMID:25352694

  17. Molecular characterization of patulin producing and non-producing Penicillium species in apples from Morocco.

    PubMed

    Rharmitt, Sanae; Hafidi, Majida; Hajjaj, Hassan; Scordino, Fabio; Giosa, Domenico; Giuffrè, Letterio; Barreca, Davide; Criseo, Giuseppe; Romeo, Orazio

    2016-01-18

    The isolation of patulin-producing Penicillia in apples collected in different markets in four localities in Morocco is reported. Fungi were identified by β-tubulin sequencing and further characterized using a specific PCR-based method targeting the isoepoxydon dehydrogenase (IDH) gene to discriminate between patulin-producing and non-producing strains. Production of patulin was also evaluated using standard cultural and biochemical methods. Results showed that 79.5% of contaminant fungi belonged to the genus Penicillium and that Penicillium expansum was the most isolated species (83.9%) followed by Penicillium chrysogenum (~9.7%) and Penicillium crustosum (~6.4%). Molecular analysis revealed that 64.5% of the Penicillium species produced the expected IDH-amplicon denoting patulin production in these strains. However, patulin production was not chemically confirmed in all P. expansum strains. The isolation of IDH(-)/patulin(+) strains poses the hypothesis that gentisylaldehyde is not a direct patulin precursor, supporting previous observations that highlighted the importance of the gentisyl alcohol in the production of this mycotoxin. Total agreement between IDH-gene detection and cultural/chemical methods employed was observed in 58% of P. expansum strains and for 100% of the other species isolated. Overall the data reported here showed a substantial genetic variability within P. expansum population from Morocco. PMID:26513254

  18. Interesterification of phosphatidylcholine with lipases in organic media.

    PubMed

    Svensson, I; Adlercreutz, P; Mattiasson, B

    1990-06-01

    Lipases were investigated with respect to their ability to catalyse the incorporation of fatty acids into phosphatidylcholine (PC) by interesterification reactions. The enzymes were dried onto solid support materials and the conversions were carried out in water-saturated toluene. Three lipases (two fungal and one plant enzyme) had the desired activity; immobilized lipase from Mucor miehei (Lipozyme) was the most active enzyme. The Lipozyme-catalysed interesterification was selective for the sn-1 position of PC and during 48 h of reaction around 50% of the fatty acids in this position were replaced with heptadecanoic acid, a fatty acid which was practically absent in the original phospholipid. Due to adsorption on the support material and the competing hydrolysis reaction the total amount of PC in the reaction solution decreased to about 40% of the original amount. Higher interesterification rates were obtained with free fatty acids as acyl donors than with fatty acid esters. PMID:1366637

  19. Antibiotic-loaded phosphatidylcholine inhibits staphylococcal bone infection

    PubMed Central

    Jennings, Jessica Amber; Beenken, Karen E; Skinner, Robert A; Meeker, Daniel G; Smeltzer, Mark S; Haggard, Warren O; Troxel, Karen S

    2016-01-01

    AIM To test antibiotic-loaded coating for efficacy in reducing bacterial biofilm and development of osteomyelitis in an orthopaedic model of implant infection. METHODS Phosphatidylcholine coatings loaded with 25% vancomycin were applied to washed and sterilized titanium wires 20 mm in length. A 10 mm segment was removed from rabbit radius (total = 9; 5 coated, 4 uncoated), and the segment was injected with 1 × 106 colony forming units (CFUs) of Staphylococcus aureus (UAMS-1 strain). Titanium wires were inserted through the intramedullary canal of the removed segment and into the proximal radial segment and the segment was placed back into the defect. After 7 d, limbs were removed, X-rayed, swabbed for tissue contamination. Wires were removed and processed to determine attached CFUs. Tissue was swabbed and streaked on agar plates to determine bacteriological score. RESULTS Antibiotic-loaded coatings resulted in significantly reduced biofilm formation (4.7 fold reduction in CFUs; P < 0.001) on titanium wires and reduced bacteriological score in surrounding tissue (4.0 ± 0 for uncoated, 1.25 ± 0.5 for coated; P = 0.01). Swelling and pus formation was evident in uncoated controls at the 7 d time point both visually and radiographically, but not in antibiotic-loaded coatings. CONCLUSION Active antibiotic was released from coated implants and significantly reduced signs of osteomyelitic symptoms. Implant coatings were well tolerated in bone. Further studies with additional control groups and longer time periods are warranted. Antibiotic-loaded phosphatidylcholine coatings applied at the point of care could prevent implant-associated infection in orthopaedic defects. PMID:27622146

  20. Molecular Identification of Fusarium Species in Gibberella fujikuroi Species Complex from Rice, Sugarcane and Maize from Peninsular Malaysia

    PubMed Central

    Hsuan, Heng Mei; Salleh, Baharuddin; Zakaria, Latiffah

    2011-01-01

    The objective of this study was to identify Fusarium species in the Gibberella fujikuroi species complex from rice, sugarcane and maize as most of the Fusarium species in the species complex are found on the three crops. Isolates used were collected from the field and obtained from culture collection. The Fusarium isolates were initially sorted based on morphology and identifications confirmed based on the DNA sequence of the translation elongation factor 1-α (TEF-1α) gene. Based on the closest match of BLAST analysis, five species were recovered, namely, F. sacchari, F. fujikuroi, F. proliferatum, F. andiyazi and F. verticillioides. This is the first report regarding F. andiyazi from rice in Malaysia and Southeast Asia. The phylogenetic tree generated by using the neighbor joining method showed that isolates from the same species were grouped in the same clade. The present study indicated that Fusarium species in the G. fujikuroi species complex are widespread in rice, sugarcane and maize in Peninsular Malaysia. The findings also suggest that the use of morphological characters for identification of Fusarium species in the G. fujikuroi species complex from the three crops will lead to incorrect species designation. PMID:22072914

  1. Investigation of the local structure of mixtures of an ionic liquid with polar molecular species through molecular dynamics: cluster formation and angular distributions.

    PubMed

    Carrete, Jesús; Méndez-Morales, Trinidad; Cabeza, Óscar; Lynden-Bell, Ruth M; Gallego, Luis J; Varela, Luis M

    2012-05-24

    In this work, we used molecular dynamics simulations to analyze in detail the spatial distributions of the different constituents in mixtures of 1-butyl-3-methylimidazolium tetrafluoroborate with three polar molecular species: water and two alcohols of different chain lengths (methanol and ethanol). In particular, we report results regarding the influence of the chosen species and its concentration on the formation of ionic and molecular clusters over the whole miscibility range, as well as on the angular distribution of polar molecules around the anion and the cation in these systems. Both analyses showed that addition of a molecular species breaks down the polar network of the pure ionic liquid in clusters whose mean size decreases progressively as more molecules are added. At very high concentrations of the molecular species, the ions are found to be isolated in mixtures with water and methanol, but they tend to form pairs in ethanol. In mixtures with water we identified large clusters that form a water network at very high water concentrations, while at low water concentrations polar molecules tend to form smaller aggregates. In contrast, in mixtures with alkanols there is no evidence of the formation of large alcohol clusters at any concentration. Spatial order in alcohol was also studied by means of the Kirkwood G factor, reaching the conclusion that the angular correlations which appear in pure alcohols due to dipole interactions are destroyed by the ionic liquid, even when present only in tiny amounts. PMID:22587330

  2. Molecular Characterization of Cryptosporidium Species and Giardia duodenalis from Symptomatic Cambodian Children

    PubMed Central

    Moore, Catrin E.; Elwin, Kristin; Phot, Nget; Seng, Chanthou; Mao, Saroeun; Suy, Kuong; Kumar, Varun; Nader, Johanna; Bousfield, Rachel; Perera, Sanuki; Bailey, J. Wendi; Beeching, Nicholas J.; Day, Nicholas P. J.; Parry, Christopher M.; Chalmers, Rachel M.

    2016-01-01

    Background In a prospective study, 498 single faecal samples from children aged under 16 years attending an outpatient clinic in the Angkor Hospital for Children, northwest Cambodia, were examined for Cryptosporidium oocysts and Giardia cysts using microscopy and molecular assays. Methodology/Principal Findings Cryptosporidium oocysts were detected in 2.2% (11/498) of samples using microscopy and in 7.7% (38/498) with molecular tests. Giardia duodenalis cysts were detected in 18.9% (94/498) by microscopy and 27.7% (138/498) by molecular tests; 82% of the positive samples (by either method) were from children aged 1–10 years. Cryptosporidium hominis was the most common species of Cryptosporidium, detected in 13 (34.2%) samples, followed by Cryptosporidium meleagridis in 9 (23.7%), Cryptosporidium parvum in 8 (21.1%), Cryptosporidium canis in 5 (13.2%), and Cryptosporidium suis and Cryptosporidium ubiquitum in one sample each. Cryptosporidium hominis and C. parvum positive samples were subtyped by sequencing the GP60 gene: C. hominis IaA16R6 and C. parvum IIeA7G1 were the most abundant subtypes. Giardia duodenalis was typed using a multiplex real-time PCR targeting assemblages A and B. Assemblage B (106; 76.8% of all Giardia positive samples) was most common followed by A (12.3%) and mixed infections (5.1%). Risk factors associated with Cryptosporidium were malnutrition (AOR 9.63, 95% CI 1.67–55.46), chronic medical diagnoses (AOR 4.51, 95% CI 1.79–11.34) and the presence of birds in the household (AOR 2.99, 95% CI 1.16–7.73); specifically C. hominis (p = 0.03) and C. meleagridis (p<0.001) were associated with the presence of birds. The use of soap was protective against Giardia infection (OR 0.74, 95% CI 0.58–0.95). Conclusions/Significance This is the first report to describe the different Cryptosporidium species and subtypes and Giardia duodenalis assemblages in Cambodian children. The variety of Cryptosporidium species detected indicates both

  3. Molecular Simulation of the Diffusion of Uranyl Carbonate Species in Aqueous Solution

    SciTech Connect

    Kerisit, Sebastien N.; Liu, Chongxuan

    2010-09-01

    Molecular dynamics simulations of aqueous uranyl carbonate species were carried out with two different potential models to gain molecular-level insight into the hydration properties of these species and evaluate the ability of the two models to reproduce published ab initio and experimental data. The simulation results were used to estimate the self-diffusion coefficients of uranyl carbonate species that often dominate uranyl speciation in groundwater systems. The first potential model was based on a series of shell models developed by Parker and co-workers (including (DE LEEUW and PARKER, 1998; KERISIT and PARKER, 2004; PAVESE et al., 1996). The second potential model was a rigid-ion model based on the flexible SPC water model (TELEMAN et al., 1987), the uranyl model of Guilbaud and Wipff (GUILBAUD and WIPFF, 1996), and the parameters for the carbonate ion given by Greathouse and co-workers (GREATHOUSE and CYGAN, 2005; GREATHOUSE et al., 2002). Analysis of structural (mean interatomic distances and coordination numbers) and dynamical (water residence times in hydration shell and self-diffusion coefficients) properties showed that, overall, the first potential model performed best when compared to published data, although the only major discrepancy with the second model was a misrepresentation of the configuration adopted by the alkaline-earth uranyl carbonate ions. The diffusion coefficients obtained for the alkaline-earth cations and the uranyl ion were compared with three variants of the Stokes-Einstein (SE) equation and it was found that none of the three SE models were able to reproduce both the absolute values and the overall trend determined from the molecular dynamics simulations. However, as would be expected based on the SE equation, a plot of the diffusion coefficients of the uranyl carbonate complexes as a function of the inverse of the equivalent spherical radius showed a general linear dependence with the two models yielding almost identical gradients

  4. Interactions of egg yolk phosphatidylcholine with cholesteryl polyethoxy neoglycolipids containing N-acetyl- D-glucosamine

    NASA Astrophysics Data System (ADS)

    Kemoun, Rachida; Gelhausen, Micaèle; Besson, Françoise; Lafont, Dominique; Buchet, René; Boullanger, Paul; Roux, Bernard

    1999-03-01

    Series of neoglycolipids containing cholesteryl and N-acetyl- D-glucosaminyl groups were synthesized with various ethoxy linkers. Their self aggregations and intermolecular interactions, without and with egg yolk phosphatidylcholine (EYPC), were characterized in dry and hydrated states, by using infrared spectroscopy. The neoglycolipids in the dry state formed intermolecular hydrogen bonds between the CO and N-H or O-H groups of N-acetyl- D-glucosamine (GlcNAc). In the presence of EYPC, these intermolecular interactions were broken and new hydrogen bonds, involving the phosphate group of EYPC and N-H or O-H groups of GlcNAc of neoglycolipid, were formed. The presence of water molecules altered these intermolecular hydrogen bonds. The CO groups of EYPC were not affected by the presence of neoglycolipids, either in hydrated or in dry states, indicating that the GlcNAc polar groups interacted mostly with EYPC phosphate residues. The phase transition-temperature of mixtures of EYPC containing either cholesterol or neoglycolipid were similar, indicating that the cholesteryl group of the neoglycolipid interacted in the same manner as cholesterol with hydrocarbon chains of EYPC. Some structural models of molecular interactions of neoglycolipids were discussed in relation with the molecular recognition of wheat germ agglutinin.

  5. De novo Transcriptome Analysis and Molecular Marker Development of Two Hemarthria Species

    PubMed Central

    Huang, Xiu; Yan, Hai-Dong; Zhang, Xin-Quan; Zhang, Jian; Frazier, Taylor P.; Huang, De-Jun; Lu, Lu; Huang, Lin-Kai; Liu, Wei; Peng, Yan; Ma, Xiao; Yan, Yan-Hong

    2016-01-01

    Hemarthria R. Br. is an important genus of perennial forage grasses that is widely used in subtropical and tropical regions. Hemarthria grasses have made remarkable contributions to the development of animal husbandry and agro-ecosystem maintenance; however, there is currently a lack of comprehensive genomic data available for these species. In this study, we used Illumina high-throughput deep sequencing to characterize of two agriculturally important Hemarthria materials, H. compressa “Yaan” and H. altissima “1110.” Sequencing runs that used each of four normalized RNA samples from the leaves or roots of the two materials yielded more than 24 million high-quality reads. After de novo assembly, 137,142 and 77,150 unigenes were obtained for “Yaan” and “1110,” respectively. In addition, a total of 86,731 “Yaan” and 48,645 “1110” unigenes were successfully annotated. After consolidating the unigenes for both materials, 42,646 high-quality SNPs were identified in 10,880 unigenes and 10,888 SSRs were identified in 8330 unigenes. To validate the identified markers, high quality PCR primers were designed for both SNPs and SSRs. We randomly tested 16 of the SNP primers and 54 of the SSR primers and found that the majority of these primers successfully amplified the desired PCR product. In addition, high cross-species transferability (61.11–87.04%) of SSR markers was achieved for four other Poaceae species. The amount of RNA sequencing data that was generated for these two Hemarthria species greatly increases the amount of genomic information available for Hemarthria and the SSR and SNP markers identified in this study will facilitate further advancements in genetic and molecular studies of the Hemarthria genus. PMID:27148320

  6. Molecular Analysis of the In Situ Growth Rates of Subsurface Geobacter Species

    PubMed Central

    Giloteaux, Ludovic; Barlett, Melissa; Chavan, Milind A.; Smith, Jessica A.; Williams, Kenneth H.; Wilkins, Michael; Long, Philip; Lovley, Derek R.

    2013-01-01

    Molecular tools that can provide an estimate of the in situ growth rate of Geobacter species could improve understanding of dissimilatory metal reduction in a diversity of environments. Whole-genome microarray analyses of a subsurface isolate of Geobacter uraniireducens, grown under a variety of conditions, identified a number of genes that are differentially expressed at different specific growth rates. Expression of two genes encoding ribosomal proteins, rpsC and rplL, was further evaluated with quantitative reverse transcription-PCR (qRT-PCR) in cells with doubling times ranging from 6.56 h to 89.28 h. Transcript abundance of rpsC correlated best (r2 = 0.90) with specific growth rates. Therefore, expression patterns of rpsC were used to estimate specific growth rates of Geobacter species during an in situ uranium bioremediation field experiment in which acetate was added to the groundwater to promote dissimilatory metal reduction. Initially, increased availability of acetate in the groundwater resulted in higher expression of Geobacter rpsC, and the increase in the number of Geobacter cells estimated with fluorescent in situ hybridization compared well with specific growth rates estimated from levels of in situ rpsC expression. However, in later phases, cell number increases were substantially lower than predicted from rpsC transcript abundance. This change coincided with a bloom of protozoa and increased attachment of Geobacter species to solid phases. These results suggest that monitoring rpsC expression may better reflect the actual rate that Geobacter species are metabolizing and growing during in situ uranium bioremediation than changes in cell abundance. PMID:23275510

  7. Molecular characterisation of Mycoplasma species isolated from the genital tract of Dorper sheep in South Africa.

    PubMed

    Kalshingi, Habu A; Bosman, Anna-Mari; Gouws, Johan; van Vuuren, Moritz

    2015-01-01

    Biochemical and molecular analysis were conducted on 34 strains of Mycoplasma species isolated between 2003 and 2009 from the genital tract of clinically healthy Dorper sheep and sheep with ulcerative vulvitis and balanitis. Earlier publications identified the causative agent as Mycoplasma mycoides mycoides large colony (MmmLC) and Arcanobacterium pyogenes. The aims of the study were to characterise Mycoplasma species isolated from the genital tract of Dorper sheep with polymerase chain reaction assay, cloning and gene sequencing. Basic Local Alignment Search Tool (BLAST) results revealed six predominant Mycoplasma species: Mycoplasma arginini, Mycoplasma bovigenitalium, Arcanobacterium laidlawii, MmmLC, Mycoplasma sp. ovine/caprine serogroup II and M. canadense. Sequencing of the 34 isolates were analysed using phylogenetic methods, and 18 (50%) were identified as M. arginini with 99% - 100% similarity to M. arginini from England and Sweden. Six isolates showed 99% similarity to M. bovigenitalium strains from Turkey and Germany. Two isolates had 99% similarity to an M. sp. ovine/caprine sero group II from the United Kingdom. BLAST for two isolates revealed 99% similarity to Acholeplasma laidlawii from India, another two were 99% similar to MmmLC strain from Sweden, two showed 98% similarity to Mycoplasma sp. Usp 120 from Brazil, and two isolates have a 97% - 99% similarity to M. mm. Jcv1 strain from the United States of America. Finally, one isolate showed similarity of 99% to Mycoplasma canadense strain from Italy. The findings support the hypothesis that ulcerative vulvitis and balanitis of Dorper sheep in South Africa (SA) is a multifactorial disease with involvement of different Mycoplasma species. PMID:26244581

  8. Characterization of molecular and atomic species adsorbed on ferroelectric and semiconductor surfaces

    NASA Astrophysics Data System (ADS)

    Bharath, Satyaveda Chavi

    In order to clarify the mechanisms behind the adsorption of atomic and molecular species adsorbed on ferroelectric surfaces, single crystalline lithium niobate (LiNbO3, LN), 'Z-cut' along the (0001) plane, has been prepared, characterized and subsequently exposed to molecular and atomic species. 4-n-octyl-4'-cyanobiphenyl (8CB) liquid crystal was chosen as a polar molecule for our model system for this study. Low-energy electron diffraction (LEED), atomic force microscopy (AFM), surface contact angles (CA), and X-ray photoelectron spectroscopy (XPS) were used to characterize the surface of LN as well as the nature of the liquid crystal films grown on the surface. Atomically flat LN surfaces were prepared as a support for monolayer thick, 8CB molecular domains. Also, for the purpose of gaining a fundamental understanding of low coverage interactions of metal atoms on ferroelectric surfaces, we choose to deposit gold onto the LN surface. These gold atomic layers were grown under UHV conditions and characterized. Understanding anchoring mechanisms and thin film organization for LC molecules and metal atoms on uniformly poled surfaces allows for a fuller appreciation of how molecular deposition of other polarizable molecules on patterned poled LN surfaces would occur as well as yielding greater insight on the atomic characteristics of metal on ferroelectric interfaces. Also, to reveal the mechanisms involved in the adsorption of organic aromatic molecules on high-index Si surfaces, thiophene (C4H 4S) and pyrrole (C4H5N) molecules were dosed on prepared Si(5 5 12)-2x1 surfaces as our experimental system. The Si(5 5 12) surface was prepared to produce a 2x1 reconstruction after which molecules were dosed at low exposure to observe the preferred adsorption sites on the surface. All surface preparation and experiments were performed in UHV and measurements of the surface before and after deposition were performed using scanning tunneling microscopy (STM). Fundamental

  9. A molecular method to identify species of fine roots and to predict the proportion of a species in mixed samples in subtropical forests

    PubMed Central

    Zeng, Weixian; Zhou, Bo; Lei, Pifeng; Zeng, Yeling; Liu, Yan; Liu, Cong; Xiang, Wenhua

    2015-01-01

    Understanding of belowground interactions among tree species and the fine root (≤2 mm in diameter) contribution of a species to forest ecosystem production are mostly restricted by experimental difficulties in the quantification of the species composition. The available approaches have various defects. By contrast, DNA-based methods can avoid these drawbacks. Quantitative real-time polymerase chain reaction (PCR) is an advanced molecular technology, but it is difficult to develop specific primer sets. The method of next-generation sequencing has several limitations, such as inaccurate sequencing of homopolymer regions, as well as being time-consuming, and requiring special knowledge for data analysis. This study evaluated the potential of the DNA-sequence-based method to identify tree species and to quantify the relative proportion of each species in mixed fine root samples. We discriminated the species by isolating DNA from individual fine roots and amplifying the plastid trnL(UAA; i.e., tRNA-Leu-UAA) intron using the PCR. To estimate relative proportions, we extracted DNA from fine root mixtures. After the plastid trnL(UAA) intron amplification and TA-cloning, we sequenced the positive clones from each mixture. Our results indicated that the plastid trnL(UAA) intron spacer successfully distinguished tree species of fine roots in subtropical forests. In addition, the DNA-sequence-based approach could reliably estimate the relative proportion of each species in mixed fine root samples. To our knowledge, this is the first time that the DNA-sequence-based method has been used to quantify tree species proportions in mixed fine root samples in Chinese subtropical forests. As the cost of DNA-sequencing declines and DNA-sequence-based methods improve, the molecular method will be more widely used to determine fine root species and abundance. PMID:25999977

  10. Fiber optic apparatus for detecting molecular species by surface enhanced Raman spectroscopy

    DOEpatents

    Angel, S.M.; Sharma, S.K.

    1987-11-30

    Optrode apparatus for detecting constituents of a fluid medium includes an optical fiber having a metal coating on at least a portion of a light transmissive core. The metal is one, such as silver, gold or copper, which enhances emission of Raman signal frequencies by molecules adsorbed on the surface of the coating when monochromatic probe light of a different frequency is scattered by such molecules and the metal coating is sufficiently thin to transmit light between the adsorbed molecules and the core of the fiber. Probe light is directed into one end of the fiber and a detector analyzes light emitted from the fiber for Raman frequencies that identify one or more particular molecular species. In one form, the optrode may function as a working electrode of an electrochemical cell while also serving to detect the products of oxidation or reduction reactions which occur at the electrode surface. 6 figs.

  11. Fiber optic apparatus for detecting molecular species by surface enhanced Raman spectroscopy

    DOEpatents

    Angel, S.M.; Sharma, S.K.

    1988-11-01

    Optrode apparatus for detecting constituents of a fluid medium includes an optical fiber having a metal coating on at least a portion of a light transmissive core. The metal is one, such as silver, gold or copper, which enhances emission of Raman signal frequencies by molecules adsorbed on the surface of the coating when monochromatic probe light of a different frequency is scattered by such molecules and the metal coating is sufficiently thin to transmit light between the absorbed molecules and the core of the fiber. Probe light is directed into one end of the fiber and a detector analyzes light emitted from the fiber for Raman frequencies that identify one or more particular molecular species. In one form, the optrode may function as a working electrode of an electrochemical cell while also serving to detect the products of oxidation or reduction reactions which occur at the electrode surface. 6 figs.

  12. Molecular phylogeny and morphology reveal a new species of Amyloporia (Basidiomycota) from China.

    PubMed

    Cui, Bao-Kai; Dai, Yu-Cheng

    2013-11-01

    Amyloporia pinea sp. nov. is described and illustrated on the basis of collections from southern China. Morphology and phylogenetic analysis of rDNA ITS sequences support this new species. Morphologically, it is characterized by resupinate, annual basidiocarps, cream to yellowish buff pore surface when fresh, which becomes yellowish brown to clay-buff upon drying, a dimitic hyphal system with clamped generative hyphae and inamyloid skeletal hyphae, fusoid cystidioles, and cylindrical basidiospores; moreover, it causes a brown rot. Molecular phylogeny inferred from ITS sequence data suggested a close relationship between A. pinea and Amyloporia crassa sensu lato. Antrodia subxantha has amyloid skeletal hyphae, and grouped within the Amyloporia clade, hence, it is transferred to Amyloporia, and a new combination Amyloporia subxantha is proposed. PMID:23912447

  13. High-temperature micro liquid chromatography for lipid molecular species analysis with evaporative light scattering detection.

    PubMed

    Hazotte, Aurélie; Libong, Danielle; Chaminade, Pierre

    2007-01-26

    The need for a rapid and sensitive chromatographic technique for analyzing lipid molecular species, has led to the development of an high-temperature micro liquid chromatographic system (HTLC) coupled to an evaporative light scattering detector. The increased diffusion coefficients and reduced viscosity at higher temperatures allowed lipids to be analyzed rapidly with solvents differing from those classically used in lipids chemistry. Hypercarb, a reverse phase material, was used for its different properties including heat resistance in high temperature micro HPLC. We have investigated the temperature effect on kinetic performances in HTLC, established pure solvents eluent strength at high temperature and studied different classes of lipids with seven pure solvents. We found that it was possible to use alcohols solvents in the mobile phase to elute lipids without the use of chlorinated solvents. A quick and simple method was developed to analyze a complex lipid simple, ceramide type III and type IV. PMID:17161844

  14. Molecular identification of novel intermediate host species of Angiostrongylus vasorum in Greater London.

    PubMed

    Patel, Zainab; Gill, A Christina; Fox, Mark T; Hermosilla, Carlos; Backeljau, Thierry; Breugelmans, Karin; Keevash, Esther; McEwan, Claudia; Aghazadeh, Mahdis; Elson-Riggins, Jocelyn G

    2014-12-01

    Angiostrongylus vasorum is a parasitic nematode that can cause serious and potentially fatal disease in dogs and other canids. The aim of this study was to determine the intermediate slug species infected in nature by sampling sites in Greater London and Hertfordshire located within a known hyperendemic region. Overall, A. vasorum larvae were recovered from 6/381 slugs (1.6%) by tissue digestion, and their identity was confirmed by PCR. Infected slugs originated from three different sites in the Greater London area: one in Waltham Forest and two in Bromley. Slugs parasitised by A. vasorum were identified by a combination of external morphological characteristics and molecular techniques and belonged to three different families: the Arionidae, the Milacidae and the Limacidae. This includes two new host records for the parasite: Arion distinctus and Tandonia sowerbyi. This is the first record of A. vasorum in the family Milacidae, indicating that the parasite has a broader intermediate host range than previously recognised. PMID:25195057

  15. Molecular systematics and ultrastructural characterization of a forgotten species: Chattonidium setense (Ciliophora, Heterotrichea)

    PubMed Central

    Modeo, Letizia; Rosati, Giovanna; Andreoli, Ilaria; Gabrielli, Simone; Verni, Franco; Petroni, Giulio

    2006-01-01

    In the present paper we redescribe the ciliate Chattonidium setense Villeneuve 1937 combining morphological observations (live, stained, scanning, and transmission electron microscope) with behavioral notes and molecular data. Ultrastructural analysis revealed remarkable similarities between Chattonidium and representative members of the class Heterotrichea in cortical structure and cytoplasmic organization. The most similar genus for these aspects appears to be Condylostoma. To verify this relatedness, 18S rRNA genes from Chattonidium and from one Condylostoma species were sequenced. Phylogenetic analysis indicates Chattonidium belongs to the class Heterotrichea defined according to the modern taxonomy, and confirms its relatedness with Condylostoma already hypothesized by Villeneuve-Brachon (1940). The presence of the aboral cavity complex, a unique feature never described in other ciliates, and its peculiar organization revealed by ultrastructural analysis fully justify, in our opinion, the maintenance of Chattonidium in the separate family Chattonidiidae, established by Villeneuve-Brachon in 1940. PMID:25792797

  16. A SEARCH FOR CO-EVOLVING ION AND NEUTRAL GAS SPECIES IN PRESTELLAR MOLECULAR CLOUD CORES

    SciTech Connect

    Tassis, Konstantinos; Hezareh, Talayeh; Willacy, Karen

    2012-11-20

    A comparison between the widths of ion and neutral molecule spectral lines has been recently used to estimate the strength of the magnetic field in turbulent star-forming regions. However, the ion (HCO{sup +}) and neutral (HCN) species used in such studies may not be necessarily co-evolving at every scale and density, and thus, may not trace the same regions. Here, we use coupled chemical/dynamical models of evolving prestellar molecular cloud cores including non-equilibrium chemistry, with and without magnetic fields, to study the spatial distribution of HCO{sup +} and HCN, which have been used in observations of spectral line width differences to date. In addition, we seek new ion-neutral pairs that are good candidates for such observations, because they have similar evolution and are approximately co-spatial in our models. We identify three such good candidate pairs: HCO{sup +}/NO, HCO{sup +}/CO, and NO{sup +}/NO.

  17. Studies for the Loss of Atomic and Molecular Species from IO

    NASA Technical Reports Server (NTRS)

    Combi, Michael R.

    1999-01-01

    The general objective of this project has been to advance our theoretical understanding of lo's atmosphere and how various atomic and molecular species are lost from this atmosphere and are distributed in the circumplanetary environment of Jupiter. This grant has provided support for the activities of Dr. Michael Combi at the University of Michigan to serve as a small part in collaboration with a larger project awarded to Atmospheric & Environmental Research, Inc., with primary principal investigator Dr. William H. Smyth. Dr. Combi is the Principal Investigator and Project Manager for the Michigan grant NAG5-6187. This Michigan grant has provided for a continuation of a collaboration between Drs. Smyth and Combi in related efforts beginning in 1981, and with the object to develop and apply sophisticated theoretical models to interpret and to relate a number of new and exciting observations for the atmospheric gases of the satellite. The ability to interpret and then to relate through the theoretical fabric a number of these otherwise independent observations are a central strength of this program. This comprehensive approach provides a collective power, extracting more from the sum of the parts and seeing beyond various limitations that are inherent in any one observation. Although the approach is designed to unify, the program is divided into well-defined studies for the likely dominant atmospheric gases involving species of the SO2 family (SO2, SO, O2, S and O) and for the trace atmospheric gas atomic sodium and a likely escaping molecular ion NaX(+) (where Na(X) is the atmospheric molecule and X represents one or more atoms).Attachments: IO's sodium corona and spatially cloud: a consistent flux speed distribution. and Io's plasma environment during the Galileo flyby: global three-dimensional MHD modeling with adaptive mesh refinement.

  18. The molecular evolution of four anti-malarial immune genes in the Anopheles gambiae species complex

    PubMed Central

    2008-01-01

    Background If the insect innate immune system is to be used as a potential blocking step in transmission of malaria, then it will require targeting one or a few genes with highest relevance and ease of manipulation. The problem is to identify and manipulate those of most importance to malaria infection without the risk of decreasing the mosquito's ability to stave off infections by microbes in general. Molecular evolution methodologies and concepts can help identify such genes. Within the setting of a comparative molecular population genetic and phylogenetic framework, involving six species of the Anopheles gambiae complex, we investigated whether a set of four pre-selected immunity genes (gambicin, NOS, Rel2 and FBN9) might have evolved under selection pressure imposed by the malaria parasite. Results We document varying levels of polymorphism within and divergence between the species, in all four genes. Introgression and the sharing of ancestral polymorphisms, two processes that have been documented in the past, were verified in this study in all four studied genes. These processes appear to affect each gene in different ways and to different degrees. However, there is no evidence of positive selection acting on these genes. Conclusion Considering the results presented here in concert with previous studies, genes that interact directly with the Plasmodium parasite, and play little or no role in defense against other microbes, are probably the most likely candidates for a specific adaptive response against P. falciparum. Furthermore, since it is hard to establish direct evidence linking the adaptation of any candidate gene to P. falciparum infection, a comparative framework allowing at least an indirect link should be provided. Such a framework could be achieved, if a similar approach like the one involved here, was applied to all other anopheline complexes that transmit P. falciparum malaria. PMID:18325105

  19. Molecular Properties of the Anti-Aromatic Species Cyclopentadienone, C5H5=0

    NASA Astrophysics Data System (ADS)

    Ormond, Thomas; Ellison, Barney; Daily, John W.; Stanton, John F.; Ahmed, Musahid; Zwier, Timothy S.; Hemberger, Patrick

    2015-06-01

    A common intermediate in the high temperature combustion of benzene is cyclopentadienone, C5H4=O. Cyclopentadienone is considered to be an "anti-aromatic" molecule. It is certainly a metastable species; samples persist at LN2 temperatures but dimerize upon warming to -80°C. It is of great interest to physically characterize this "anti-aromatic" species. The microwave spectrum, the infrared spectrum, the ionization energy, and the electron affinity of cyclopentadienone have been measured. Flash pyrolysis of o-phenylene sulfite (C6H4O2SO) provides molecular beams of C5H4=O entrained in a rare gas carrier. The beams are interrogated with time-of-flight photoionization mass spectrometry, confirming the clean, intense production of C5H4=O. a) Chirped-pulse Fourier transform microwave spectroscopy and CCSD(T) electronic structure calculations have combined to determine the re molecular structure of C5H4=O. b) Guided by CCSD(T) electronic structure calculations, the matrix infrared absorbance spectrum of C5H4=O isolated in a 4 K neon matrix has been used to assign 20 of the 24 fundamental vibrational frequencies. c) Imaging photoelectron photoion coincidence (iPEPICO) spectra of cyclopentadienone establishes the ionization energy, IE(C5H4=O), to be 9.41 ± 0.01 eV. d) Prof. A. Sanov's group has reported the electron affinity, EA(C5H4=O), to be 1.06 ± 0.01 eV. Kidwell et al. J. Phys. Chem. Letts. 2201 (2014) Ormond et al. J. Phys. Chem. A 118, 708 (2014) Ormond et al. Mol. Phys. in press (2015) Khuseynov et al. J. Phys. Chem. A 118, 6965 (2014)

  20. Studies for the loss of atomic and molecular species from Io

    NASA Technical Reports Server (NTRS)

    Combi, Michael R.

    1994-01-01

    The general objective of this project is to advance theoretical understanding of Io's atmosphere and how various atomic and molecular species are lost from this atmosphere and are distributed in the circumplanetary environment of Jupiter. The major task for the University of Michigan portion of this work is the generalization of the Io sodium cloud model to simulate the ion-precursor of sodium that is the apparent source of the fast sodium jet observed by Schneider et al. (1991). The goal is a quantitative test of the molecular ion hypothesis with a model that is comparable to a general sodium cloud model published previously. A detailed comparison of observations with such a model will help to probe the feasibility of such a source and to examine the rates and scale lengths associated with the decay of the ion precursor so as to possibly uncover the identity of the parent ion. Another important task to be performed at Michigan is more support of AER in the general area of modeling the Na and SO2-family clouds.

  1. Molecular analysis of phylogeographic subspecies in three Ponto-Caspian sturgeon species

    PubMed Central

    Dudu, Andreea; Georgescu, Sergiu Emil; Costache, Marieta

    2014-01-01

    Sturgeons (Order Acipenseriformes) represent an extremely valuable natural resource that is now facing depletion. In the current study we evaluate if the traditional classification in subspecies of Acipenser gueldenstaedtii, Acipenser stellatus and Huso huso, endemic to Ponto-Caspian region is sustained by molecular analysis and if these represent Evolutionary Significant Units (ESUs) that should be managed separately in conservation programs. To examine the classification of taxonomic entities we sequenced a fragment of the mitochondrial control region in case of three sturgeon species that inhabit the North-western of Black Sea and migrate for reproduction in the Lower Danube. Beside these sequences, we used previously published sequences from sturgeon individuals sampled in the Black Sea, Azov Sea and Caspian Sea. We determined the genetic diversity and genetic differentiation, conducted a Population Aggregation Analysis (PAA) and inferred an intraspecific molecular phylogeny and haplotype network. The results indicated a low level of genetic differentiation between the geographically designated subspecies and did not support a significant divergence or reciprocal monophyly between them. Our results confirm previous genetic studies with smaller samples sizes, but additional analyses including nuclear markers should be conducted for proper recommendations aiming at the development of conservation programs. PMID:25249783

  2. Transmission of nocardiosis and molecular typing of Nocardia species: a short review.

    PubMed

    Provost, F; Laurent, F; Blanc, M V; Boiron, P

    1997-02-01

    Nocardia species are ubiquitous in the environment and may be found in the soil. They are generally responsible for sporadic pulmonary diseases acquired by inhalation of spores, with secondary localizations in the central nervous system and subcutaneous tissues. There is no absolute evidence for person to person transmission. Presumptive outbreaks of nocardiosis were observed in immunocompromised patients, more frequently in kidney transplant patients than in cardiac transplant patients. Nocardia spp., being present in dust particles, closure and disinfection of the transplantation unit with formaldehyde arrested the sequence of cases of nocardiosis. The original sources of the Nocardia sp. remain doubtful. Other possible sources of contamination are other patients, medical staff and the hospital environment. The first studies of Nocardia spp. typing were based on the detection of extracellular antigens, on the susceptibility of actinomycete strains to killer yeasts, and on the biochemical profiles with fluorogenic substrate. The use of molecular typing techniques have given very promising results. Analysis of plasmid profiles is an interesting way to compare the identity of isolates, although the reliability of this method depends of the presence of plasmids in the isolates. Other typing methods, including analysis of restriction length fragment polymorphism of total DNA, ribosomal DNA fingerprinting, require further investigations to evaluate their discriminating power or to be easily interpretable, whereas a random amplified polymorphic DNA (RAPD) assay was successful for epidemiological purposes. Progress in epidemiological analysis of cases of nocardiosis will be consistent when an improved diagnosis of this infection (molecular and serological diagnosis) will be available, when the genetic diversity of Nocardia spp. isolates will be better known, and when molecular typing, that hold promise in complementing investigations of outbreak of these infections, will

  3. Molecular phylogeny of the genus Lepidophthalmus (Decapoda, Callianassidae), with re-examination of its species composition.

    PubMed

    Robles, Rafael; Felder, Darryl L

    2015-01-01

    Ghost shrimps (Decapoda: Callianassidae) are common estuarine and marine burrowing organisms of tropical to temperate waters, typically found in intertidal to shallow subtidal habitats. Except for an abbreviated planktonic larval phase, most callianassids live as obligate burrowers and appear to depend on the burrow for shelter, reproduction, and feeding. Recent studies have shown the genus Lepidophthalmus, a group largely restricted to estuaries and river mouths, to be surprisingly speciose, but relationships among these taxa and driving forces for their separation remain poorly understood. We include fifteen described species of Lepidophthalmus in a molecular phylogenetic analysis based upon sequence analyses of the 16S and 12S mitochondrial genes. Our findings clarify the monophyletic membership of the genus and confirm postulated species separations. We reconfirm validity of Lepidophthalmus eiseni, reject two recently proposed new genera for selected members of Lepidophthalmus, and define ecologically and morphologically informative clades among congeners. Limited capability for larval dispersal and regional biogeographic history could well account for high diversity and regional endemism observed within the genus. Biogeographic scenarios, including continental drift, closure of the Panamanian Isthmus, and post-glacial dispersals, are invoked to account for proposed reconstructions of historical relationships. PMID:26624110

  4. Studies for the Loss of Atomic and Molecular Species from Io

    NASA Technical Reports Server (NTRS)

    Smyth, William H.

    1997-01-01

    The general objective of this project is to advance our theoretical understanding of Io's atmosphere by studying how various atomic and molecular species are lost from this atmosphere and are distributed near the satellite and in the circumplanetary environment of Jupiter. The project is divided into well-defined studies described for the likely dominant atmospheric gases involving species of the SO2 family (SO2, SO, 02, 0, S) and for the trace atmospheric gas atomic sodium. The relative abundance of the members of the S02 family and Na (and its parent Na(x)) at the satellite exobase and their relative spatial densities beyond in the extended corona of lo are not well known but will depend upon a number of factors including the upward transport rate of gases from below, the velocity distribution and corresponding escape rate of gases at the exobase, and the operative magnetospheric/solar-photon driven chemistry for the different gases. This question of relative abundance will be studied in this project.

  5. Improved Molecular Typing Assay for Rhinovirus Species A, B, and C

    PubMed Central

    Grindle, Kristine; Vang, Fue; Evans, Michael D.; Gern, James E.

    2014-01-01

    Human rhinoviruses (RVs), comprising three species (A, B, and C) of the genus Enterovirus, are responsible for the majority of upper respiratory tract infections and are associated with severe lower respiratory tract illnesses such as pneumonia and asthma exacerbations. High genetic diversity and continuous identification of new types necessitate regular updating of the diagnostic assays for the accurate and comprehensive detection of circulating RVs. Methods for molecular typing based on phylogenetic comparisons of a variable fragment in the 5′ untranslated region were improved to increase assay sensitivity and to eliminate nonspecific amplification of human sequences, which are observed occasionally in clinical samples. A modified set of primers based on new sequence information and improved buffers and enzymes for seminested PCR assays provided higher specificity and sensitivity for virus detection. In addition, new diagnostic primers were designed for unequivocal species and type assignments for RV-C isolates, based on phylogenetic analysis of partial VP4/VP2 coding sequences. The improved assay was evaluated by typing RVs in >3,800 clinical samples. RVs were successfully detected and typed in 99% of the samples that were RV positive in multiplex diagnostic assays. PMID:24789198

  6. Molecular characterization of a new species in the genus Alphacoronavirus associated with mink epizootic catarrhal gastroenteritis

    PubMed Central

    Vlasova, Anastasia N.; Halpin, Rebecca; Wang, Shiliang; Ghedin, Elodie; Spiro, David J.

    2011-01-01

    A coronavirus (CoV) previously shown to be associated with catarrhal gastroenteritis in mink (Mustela vison) was identified by electron microscopy in mink faeces from two fur farms in Wisconsin and Minnesota in 1998. A pan-coronavirus and a genus-specific RT-PCR assay were used initially to demonstrate that the newly discovered mink CoVs (MCoVs) were members of the genus Alphacoronavirus. Subsequently, using a random RT-PCR approach, full-genomic sequences were generated that further confirmed that, phylogenetically, the MCoVs belonged to the genus Alphacoronavirus, with closest relatedness to the recently identified but only partially sequenced (fragments of the polymerase, and full-length spike, 3c, envelope, nucleoprotein, membrane, 3x and 7b genes) ferret enteric coronavirus (FRECV) and ferret systemic coronavirus (FRSCV). The molecular data presented in this study provide the first genetic evidence for a new coronavirus associated with epizootic catarrhal gastroenteritis outbreaks in mink and demonstrate that MCoVs possess high genomic variability and relatively low overall nucleotide sequence identities (91.7 %) between contemporary strains. Additionally, the new MCoVs appeared to be phylogenetically distant from human (229E and NL63) and other alphacoronaviruses and did not belong to the species Alphacoronavirus 1. It is proposed that, together with the partially sequenced FRECV and FRSCV, they comprise a new species within the genus Alphacoronavirus. PMID:21346029

  7. Impact of IgG2 high molecular weight species on neonatal Fc receptor binding assays.

    PubMed

    Zhang, Yuling; Mathur, Abhishek; Maher, Gwen; Arroll, Thomas; Bailey, Robert

    2015-11-15

    A cell-based assay and a solution neonatal Fc receptor (FcRn) binding assay were implemented for the characterization of an IgG2 antibody after observation that different product lots exhibited unexpected differences in FcRn binding in the cell-based format with membrane-bound FcRn. The experiments described here suggest that the apparent differences observed in the FcRn binding across different product lots in the cell-based format can be attributed to the different levels of the higher order high molecular weight species (HMWs) in them. A strong correlation between FcRn binding in the cell-based format and the percentage (%) higher order HMWs suggests that small amounts (∼0.1%) of the latter could cause the enhanced apparent FcRn binding (% relative binding ranging from 50 to 100%) in the format. However, when the binding was assessed with recombinant FcRn in soluble form, avidity effects were minimal and the assay format exhibited less sensitivity toward the differences in higher order HMWs levels across product lots. In conclusion, a solution-based assay may be a more appropriate assay to assess FcRn binding of the dominant species of an Fc-fusion protein or monoclonal antibody if minor differences in product variants such as higher order HMWs are shown to affect the binding significantly. PMID:26255698

  8. Integration of molecular and enzymatic catalysts on graphene for biomimetic generation of antithrombotic species

    NASA Astrophysics Data System (ADS)

    Xue, Teng; Peng, Bo; Xue, Min; Zhong, Xing; Chiu, Chin-Yi; Yang, Si; Qu, Yongquan; Ruan, Lingyan; Jiang, Shan; Dubin, Sergey; Kaner, Richard B.; Zink, Jeffrey I.; Meyerhoff, Mark E.; Duan, Xiangfeng; Huang, Yu

    2014-02-01

    The integration of multiple synergistic catalytic systems can enable the creation of biocompatible enzymatic mimics for cascading reactions under physiologically relevant conditions. Here we report the design of a graphene-haemin-glucose oxidase conjugate as a tandem catalyst, in which graphene functions as a unique support to integrate molecular catalyst haemin and enzymatic catalyst glucose oxidase for biomimetic generation of antithrombotic species. Monomeric haemin can be conjugated with graphene through π-π interactions to function as an effective catalyst for the oxidation of endogenous L-arginine by hydrogen peroxide. Furthermore, glucose oxidase can be covalently linked onto graphene for local generation of hydrogen peroxide through the oxidation of blood glucose. Thus, the integrated graphene-haemin-glucose oxidase catalysts can readily enable the continuous generation of nitroxyl, an antithrombotic species, from physiologically abundant glucose and L-arginine. Finally, we demonstrate that the conjugates can be embedded within polyurethane to create a long-lasting antithrombotic coating for blood-contacting biomedical devices.

  9. Trace species detection: Spectroscopy and molecular energy transfer at high temperature

    SciTech Connect

    Gray, J.A.

    1993-12-01

    Monitoring the concentration of trace species such as atomic and molecular free radicals is essential in forming predictive models of combustion processes. LIF-based techniques have the necessary sensitivity for concentration and temperature measurements but have limited accuracy due to collisional quenching in combustion applications. The goal of this program is to use spectroscopic and kinetic measurements to quantify nonradiative and collisional effects on LIF signals and to develop new background-free alternatives to LIF. The authors have measured the natural linewidth of several OH A-X (3,0) rotational transitions to determine predissociation lifetimes in the upper state, which were presumed to be short compared to quenching lifetimes, and as a result, quantitative predictions about the applicability of predissociation fluorescence methods at high pressures are made. The authors are investigating collisional energy transfer in the A-state of NO. Quenching rates which enable direct corrections to NO LIF quantum yields at high temperature were calculations. These quenching rates are now being used in studies of turbulence/chemistry interactions. The authors have measured the electric dipole moment {mu} of excited-state NO using Stark quantum-beat spectroscopy. {mu} is an essential input to a harpoon model which predicts quenching efficiencies for NO (A) by a variety of combustion-related species. The authors are developing new coherent multiphoton techniques for measurements of atomic hydrogen concentration in laboratory flames to avoid the quenching problems associated with previous multiphoton LIF schemes.

  10. Supported and inserted monomeric niobium oxide species on/in silica: a molecular picture.

    PubMed

    Tranca, Diana C; Wojtaszek-Gurdak, Anna; Ziolek, Maria; Tielens, Frederik

    2015-09-14

    The geometry, energetic, and spectroscopic properties of molecular structures of silica-supported niobium oxide catalysts are studied using periodic density functional calculations (DFT) and compared with experimental data. The calculations are done for Nb oxide species inserted or grafted in/on an amorphous hydroxylated silica surface. Different positions of the Nb atom/atoms in the silica structure have been investigated. By means of DFT calculations the geometry and the degree of hydration of Nb oxide species with oxidation state +5 have been studied. The local Nb geometry depends on different parameters such as the number of Nb-O-Si groups vs. Nb-O-H groups, the formation of H bonds and the distance between Nb atoms. The interaction between the oxide and silanol groups occurs by formation of Si-O-Nb bonds with chemically and thermally stable Brønsted and Lewis acid sites. UV-Vis, reflection absorption infrared vibrational spectra (RAIRS) as well as various thermodynamic properties have also been investigated in order to get a better insight into the system studied and to provide support to possible experimental studies. PMID:26250394

  11. Inhibition of phosphatidylcholine synthesis by vasopressin and angiotensin in rat hepatocytes.

    PubMed Central

    Alemany, S; Varela, I; Mato, J M

    1982-01-01

    The addition of 1 microM-vasopressin or -angiotensin to isolated rat hepatocytes induced a fast transient inhibition of the rate of incorporation of [Me-3H]choline into phosphatidylcholine. The cationophore A23187 induced a similar inhibition of phosphatidylcholine synthesis. The addition of micromolar Ca2+ to rat liver microsomes inhibited the activity of CDP-choline: 1,2-diacylglycerol cholinephosphotransferase. This inhibition is due a decrease in the Vmax. of the enzyme without affecting the Km for CDP-choline. It is concluded that Ca2+ regulates phosphatidylcholine synthesis in rat liver. PMID:6818955

  12. Molecular detection of Setaria tundra (Nematoda: Filarioidea) and an unidentified filarial species in mosquitoes in Germany

    PubMed Central

    2012-01-01

    Background Knowledge of the potential vector role of Culicidae mosquitoes in Germany is very scanty, and until recently it was generally assumed that they are not involved in the transmission of anthroponotic or zoonotic pathogens in this country. However, anticipated changes in the course of global warming and globalization may alter their status. Methods We conducted a molecular mass screening of mosquitoes for filarial parasites using mitochondrial 12S rRNA-based real-time PCR. Results No parasites causing disease in humans such as Dirofilaria spp. were detected in about 83,000 mosquitoes tested, which had been collected in 2009 and 2010 in 16 locations throughout Germany. However, minimum infection rates of up to 24 per 1000 mosquitoes were revealed, which could be attributed to mosquito infection with Setaria tundra and a yet unidentified second parasite. Setaria tundra was found to be widespread in southern Germany in various mosquito species, except Culex spp. In contrast, the unidentified filarial species was exclusively found in Culex spp. in northern Baden-Württemberg, and is likely to be a bird parasite. Conclusions Although dirofilariasis appears to be emerging and spreading in Europe, the absence of Dirofilaria spp. or other zoonotic filariae in our sample allows the conclusion that the risk of autochthonous infection in Germany is still very low. Potential vectors of S. tundra in Germany are Ochlerotatus sticticus, Oc. cantans, Aedes vexans and Anopheles claviger. Technically, the synergism between entomologists, virologists and parasitologists, combined with state-of-the-art methods allows a very efficient near-real-time monitoring of a wide spectrum of both human and veterinary pathogens, including new distribution records of parasite species and the incrimination of their potential vectors. PMID:22236560

  13. Genetic diversity and molecular characterization of several Heliconia species in Colombia.

    PubMed

    Isaza, L; Marulanda, M L; López, A M

    2012-01-01

    Researchers have classified the Heliconia genus as a group of highly variable and diverse plants. Species and cultivars are visually differentiated primarily on the basis of the color and size of inflorescence bracts. At taxonomic level, flower type (parabolic, sigmoid, or erect) and size are taken into account. The vast morphological diversity of heliconias at intra-specific, intra-population, and varietal levels in central-west Colombia prompted the present study. We characterized the genetic variability of 67 genotypes of cultivated heliconias belonging to Heliconia caribaea Lamarck, H. bihai (L.) L., H. orthotricha L. Andersson, H. stricta Huber, H. wagneriana Petersen, and H. psittacorum L. f., as well as that of several interspecific hybrids such as H. psittacorum L. f. x H. spathocircinata Aristeguieta and H. caribaea Lamarck x H. bihai (L.) L. We also created an approximation to their phylogenetic analysis. Molecular analysis using amplified fragment length polymorphism (AFLP) markers revealed a total of 170 bands. Two large, well-defined groups resulted: the first grouped cultivars of the very closely related H. caribaea and H. bihai species with those of H. orthotricha and H. psittacorum, and the second grouped H. stricta and H. wagneriana cultivars. The lowest percentage of polymorphism was found in H. psittacorum (17.65%) and the highest was in H. stricta (55.88%). Using AFLP, phylogenetic analysis of the species studied revealed the monophyletic origin of the Heliconiaceae family, and identified the Heliconia subgenus as monophyletic while providing evidence of the polyphyletic origin of several representatives of the Stenochlamys subgenus. PMID:23212400

  14. Species Boundaries and Host Range of Tortoise Mites (Uropodoidea) Phoretic on Bark Beetles (Scolytinae), Using Morphometric and Molecular Markers

    PubMed Central

    Knee, Wayne; Beaulieu, Frédéric; Skevington, Jeffrey H.; Kelso, Scott; Cognato, Anthony I.; Forbes, Mark R.

    2012-01-01

    Understanding the ecology and evolutionary history of symbionts and their hosts requires accurate taxonomic knowledge, including clear species boundaries and phylogenies. Tortoise mites (Mesostigmata: Uropodoidea) are among the most diverse arthropod associates of bark beetles (Curculionidae: Scolytinae), but their taxonomy and host associations are largely unstudied. We tested the hypotheses that (1) morphologically defined species are supported by molecular data, and that (2) bark beetle uropodoids with a broad host range comprise cryptic species. To do so, we assessed the species boundaries of uropodoid mites collected from 51 host species, across 11 countries and 103 sites, using morphometric data as well as partial cytochrome oxidase I (COI) and nuclear large subunit ribosomal DNA (28S). Overall, morphologically defined species were confirmed by molecular datasets, with a few exceptions. Twenty-nine of the 36 uropodoid species (Trichouropoda, Nenteria and Uroobovella) collected in this study had narrow host ranges, while seven species had putative broad host ranges. In all but one species, U. orri, our data supported the existence of these host generalists, which contrasts with the typical finding that widespread generalists are actually complexes of cryptic specialists. PMID:23071768

  15. Molecular systematics of Serrasalmidae: Deciphering the identities of piranha species and unraveling their evolutionary histories

    USGS Publications Warehouse

    Freeman, B.; Nico, L.G.; Osentoski, M.; Jelks, H.L.; Collins, T.M.

    2007-01-01

    Piranhas and their relatives have proven to be a challenging group from a systematic perspective, with difficulties in identification of species, linking of juveniles to adults, diagnosis of genera, and recognition of higher-level clades. In this study we add new molecular data consisting of three mitochondrial regions for museum vouchered and photo-documented representatives of the Serrasalmidae. These are combined with existing serrasalmid sequences in GenBank to address species and higher-level questions within the piranhas using parsimony and Bayesian methods. We found robust support for the monophyly of Serrasalmus manueli, but not for Serrasalmus gouldingi when GenBank specimens identified as S. gouldingi were included in the analysis. "Serrasalmus gouldingi" sequences in GenBank may, however, be misidentified. Linking of juveniles to adults of the same species was greatly facilitated by the addition of sequence data. Based on our sampling and identifications, our data robustly reject the monophyly of the genera Serrasalmus and Pristobrycon. We found evidence for a well-supported clade comprised of Serrasalmus, Pygocentrus, and Pristobrycon (in part). This clade was robustly supported in separate and combined analyses of gene regions, and was also supported by a unique molecular character, the loss of a tandem repeat in the control region. Analysis of specimens and a literature review suggest this clade is also characterized by the presence of a pre-anal spine and ectopterygoid teeth. A persistent polytomy at the base of this clade was dated using an independent calibration as 1.8 million years old, corresponding to the beginning of the Pleistocene Epoch, and suggesting an origin for this clade more recent than dates cited in the recent literature. The sister group to this clade is also robustly supported, and consists of Catoprion, Pygopristis, and Pristobrycon striolatus. If the term piranha is to refer to a monophyletic clade, it should be restricted to

  16. Molecular phylogeny and taxonomy of the Epictia goudotii Species complex (Serpentes: Leptotyphlopidae: Epictinae) in Middle America and northern South America

    PubMed Central

    McCranie, James R.

    2016-01-01

    Here we review the systematics of the threadsnakes of the Epictia goudotii Species complex in Middle and northern South America using external morphology and molecular data. Two species, Epictia goudotii and E. magnamaculata, are currently recognized from that region, but we provide evidence for recognizing, as species, three other nominal forms usually treated as subspecies of E. goudotii: E. ater, E. bakewelli, and E. phenops. Thus, together with E. columbi (Bahamas), we recognize six species in the Epictia goudotii Species complex. Because E. albifrons from northern South America has been confused with E. goudotii in the past, we also briefly discuss the taxonomic status of that species and its apparent close relative E. tenella, which are not members of the E. goudotii complex. PMID:26788430

  17. Phylogenetic relationships in the Niviventer-Chiromyscus complex (Rodentia, Muridae) inferred from molecular data, with description of a new species.

    PubMed

    Balakirev, Alexander E; Abramov, Alexei V; Rozhnov, Viatcheslav V

    2014-01-01

    Based on molecular data for mitochondrial (Cyt b, COI) and nuclear (IRBP, GHR) genes, and morphological examinations of museum specimens, we examined diversity, species boundaries, and relationships within and between the murine genera Chiromyscus and Niviventer. Phylogenetic patterns recovered demonstrate that Niviventer sensu lato is not monophyletic but instead includes Chiromyscuschiropus, the only previously recognized species of Chiropus. To maintain the genera Niviventer and Chiropus as monophyletic lineages, the scope and definition of the genus Chiromyscus is revised to include at least three distinct species: Chiromyscuschiropus (the type species of Chiromyscus), Chiromyscuslangbianis (previously regarded as a species of Niviventer), and a new species, described in this paper under the name Chiromyscusthomasi sp. n. PMID:25493050

  18. Phylogenetic relationships in the Niviventer-Chiromyscus complex (Rodentia, Muridae) inferred from molecular data, with description of a new species

    PubMed Central

    Balakirev, Alexander E.; Abramov, Alexei V.; Rozhnov, Viatcheslav V.

    2014-01-01

    Abstract Based on molecular data for mitochondrial (Cyt b, COI) and nuclear (IRBP, GHR) genes, and morphological examinations of museum specimens, we examined diversity, species boundaries, and relationships within and between the murine genera Chiromyscus and Niviventer. Phylogenetic patterns recovered demonstrate that Niviventer sensu lato is not monophyletic but instead includes Chiromyscus chiropus, the only previously recognized species of Chiropus. To maintain the genera Niviventer and Chiropus as monophyletic lineages, the scope and definition of the genus Chiromyscus is revised to include at least three distinct species: Chiromyscus chiropus (the type species of Chiromyscus), Chiromyscus langbianis (previously regarded as a species of Niviventer), and a new species, described in this paper under the name Chiromyscus thomasi sp. n. PMID:25493050

  19. A new species of Alopoglossus lizard (Squamata, Gymnophthalmidae) from the tropical Andes, with a molecular phylogeny of the genus

    PubMed Central

    Torres-Carvajal, Omar; Lobos, Simón E.

    2014-01-01

    Abstract We describe a new species of Alopoglossus from the Pacific slopes of the Andes in northern Ecuador based on morphological and molecular evidence. The new species differs most significantly from all other congeners in having a double longitudinal row of widened gular scales, lanceolate dorsal scales in transverse rows, 29–32 dorsal scales in a transverse row at midbody, and 4 longitudinal rows of ventrals at midbody. It is most similar in morphology to A. festae, the only species of Alopoglossus currently recognized in western Ecuador. We analyze the phylogenetic relationships among species of Alopoglossus based on the mitochondrial gene ND4. Cis-Andean [east of the Andes] and Trans-Andean [west of the Andes] species are nested in two separate clades, suggesting that the uplift of these mountains had an important effect in the diversification of Alopoglossus. In addition, we present an updated key to the species of Alopoglossus. PMID:24899852

  20. Mass Spectrometric Analyses of Phosphatidylcholines in Alkali-Exposed Corneal Tissue

    PubMed Central

    Crane, Ashley M.; Hua, Hong-Uyen; Coggin, Andrew D.; Gugiu, Bogdan G.; Lam, Byron L.; Bhattacharya, Sanjoy K.

    2012-01-01

    Purpose. The aims were to determine whether exposure to sodium hydroxide results in predictable changes in phosphatidylcholine (PC) in corneal tissue and if PC profile changes correlate to exposure duration. PCs are major components of the cell membrane lipid bilayer and are often involved in biological processes such as signaling. Methods. Enucleated porcine (n = 140) and cadaver human eyes (n = 20) were exposed to water (control) and 11 M NaOH. The corneas were excised and lipids were extracted using the Bligh and Dyer method with suitable modifications. Class-specific lipid identification was carried out using a ratiometric lipid standard on a TSQ Quantum Access Max mass spectrometer. Protein amounts were determined using Bradford assays. Results. Control and alkali-treated corneas showed reproducible PC spectra for both porcine and human corneas. Over 200 PCs were identified for human and porcine control and each experimental time point. Several PC species (m/z values) consequent upon alkali exposure could not be ascribed to a recorded PC species. Control and treated groups showed 41 and 29 common species among them for porcine and human corneas, respectively. The unique PC species peaked at 12 minutes and at 30 minutes for human and porcine corneas followed by a decline consistent with an interplay of alkali penetration and hydrolyses at various time points. Conclusions. Alkali exposure dramatically changes the PC profile of cornea. Our data are consistent with penetration and hydrolysis as stochastic contributors to changes in PCs due to exposure to alkali for a finite duration and amount. PMID:22956606

  1. Molecular analysis of the Pygospio elegans group of species (Annelida: Spionidae).

    PubMed

    Radashevsky, Vasily I; Pankova, Victoria V; Neretina, Tatyana V; Stupnikova, Alexandra N; Tzetlin, Alexander B

    2016-01-01

    Pygospio elegans Claparède, 1863, the type species of the genus Pygospio, was originally described from Normandy, France, and later widely reported from boreal waters in the northern hemisphere. Sequence data of four gene fragments (2576 bp in total) of the mitochondrial 16S rDNA, nuclear 18S and 28S rDNA, and Histone 3 have shown that individuals from California and Oregon, USA, Scotland and the White Sea, Russia were genetically similar (the average p-distances for the combined data between the four groups ranged from 0.04 to 0.16%, average p = 0.1%). These individuals are considered to be conspecific and the amphiboreal distribution of P. elegans is here confirmed. Adult morphology of the species is briefly described and illustrated. The molecular analysis revealed two genetically distant populations, Pygospio sp. 1 from the Sea of Okhotsk and Pygospio sp. 2 from Oregon. The morphological differences and high average genetic p-distances for the combined data (ranging from 3.06 to 3.18%, average p = 3.12%) between Pygospio sp. 2 and P. elegans suggest the presence of an undescribed Pygospio species co-occurring with P. elegans in Oregon. High morphological similarity and moderate genetic p-distances for the combined data (ranging from 1 to 1.11%, average p = 1.07%) between Pygospio sp. 1 and P. elegans indicate a comparatively recent genetic divergence of the Pygospio population in the Sea of Okhotsk. Taking into account the high genetic similarity of the remote European and North American populations of P. elegans and medial location of the Pygospio sp. 1 population, we suggest the latter to belong to a separate species. However, this conclusion should be verified in further studies on the morphology, reproductive biology and genetics of this population. The present findings show the need to re-examine Pygospio from the Asian Pacific and elsewhere that have been identified as P. elegans. PMID:27394228

  2. Delimiting Species-Poor Data Sets using Single Molecular Markers: A Study of Barcode Gaps, Haplowebs and GMYC.

    PubMed

    Dellicour, Simon; Flot, Jean-François

    2015-11-01

    Most single-locus molecular approaches to species delimitation available to date have been designed and tested on data sets comprising at least tens of species, whereas the opposite case (species-poor data sets for which the hypothesis that all individuals are conspecific cannot by rejected beforehand) has rarely been the focus of such attempts. Here we compare the performance of barcode gap detection, haplowebs and generalized mixed Yule-coalescent (GMYC) models to delineate chimpanzees and bonobos using nuclear sequence markers, then apply these single-locus species delimitation methods to data sets of one, three, or six species simulated under a wide range of population sizes, speciation rates, mutation rates and sampling efforts. Our results show that barcode gap detection and GMYC models are unable to delineate species properly in data sets composed of one or two species, two situations in which haplowebs outperform them. For data sets composed of three or six species, bGMYC and haplowebs outperform the single-threshold and multiple-threshold versions of GMYC, whereas a clear barcode gap is only observed when population sizes and speciation rates are both small. The latter conditions represent a "sweet spot" for molecular taxonomy where all the single-locus approaches tested work well; however, the performance of these methods decreases strongly when population sizes and speciation rates are high, suggesting that multilocus approaches may be necessary to tackle such cases. PMID:25601944

  3. Nuclear Phosphatidylcholine and Sphingomyelin Metabolism of Thyroid Cells Changes during Stratospheric Balloon Flight

    PubMed Central

    Albi, Elisabetta; Cataldi, Samuela; Villani, Maristella; Perrella, Giuseppina

    2009-01-01

    Nuclear sphingomyelin and phosphatidylcholine metabolism is involved in the response to ultraviolet radiation treatment in different ways related to the physiological state of cells. To evaluate the effects of low levels of radiation from the stratosphere on thyroid cells, proliferating and quiescent FRTL-5 cells were flown in a stratospheric balloon (BIRBA mission). After recovery, the activity of neutral sphingomyelinase, phosphatidylcholine-specific phospholipase C, sphingomyelin synthase, and reverse sphingomyelin synthase was assayed in purified nuclei and the nuclei-free fraction. In proliferating FRTL-5, space radiation stimulate nuclear neutral sphingomyelinase and reverse sphingomyelin synthase activity, whereas phosphatidylcholine-specific phospholipase C and sphingomyelin synthase were inhibited, thus inducing sphingomyelin degradation and phosphatidylcholine synthesis. This effect was lower in quiescent cells. The possible role of nuclear lipid metabolism in the thyroid damage induced by space radiations is discussed. PMID:20011661

  4. The Centipede Genus Scolopendra in Mainland Southeast Asia: Molecular Phylogenetics, Geometric Morphometrics and External Morphology as Tools for Species Delimitation

    PubMed Central

    Siriwut, Warut; Edgecombe, Gregory D.; Sutcharit, Chirasak; Panha, Somsak

    2015-01-01

    Seven Scolopendra species from the Southeast Asian mainland delimited based on standard external morphological characters represent monophyletic groups in phylogenetic trees inferred from concatenated sequences of three gene fragments (cytochrome c oxidase subunit 1, 16S rRNA and 28S rRNA) using Maximum likelihood and Bayesian inference. Geometric morphometric description of shape variation in the cephalic plate, forcipular coxosternite, and tergite of the ultimate leg-bearing segment provides additional criteria for distinguishing species. Colouration patterns in some Scolopendra species show a high degree of fit to phylogenetic trees at the population level. The most densely sampled species, Scolopendra dehaani Brandt, 1840, has three subclades with allopatric distributions in mainland SE Asia. The molecular phylogeny of S. pinguis Pocock, 1891, indicated ontogenetic colour variation among its populations. The taxonomic validation of S. dawydoffi Kronmüller, 2012, S. japonica Koch, 1878, and S. dehaani Brandt, 1840, each a former subspecies of S. subspinipes Leach, 1814 sensu Lewis, 2010, as full species was supported by molecular information and additional morphological data. Species delimitation in these taxonomically challenging animals is facilitated by an integrative approach that draws on both morphology and molecular phylogeny. PMID:26270342

  5. The Centipede Genus Scolopendra in Mainland Southeast Asia: Molecular Phylogenetics, Geometric Morphometrics and External Morphology as Tools for Species Delimitation.

    PubMed

    Siriwut, Warut; Edgecombe, Gregory D; Sutcharit, Chirasak; Panha, Somsak

    2015-01-01

    Seven Scolopendra species from the Southeast Asian mainland delimited based on standard external morphological characters represent monophyletic groups in phylogenetic trees inferred from concatenated sequences of three gene fragments (cytochrome c oxidase subunit 1, 16S rRNA and 28S rRNA) using Maximum likelihood and Bayesian inference. Geometric morphometric description of shape variation in the cephalic plate, forcipular coxosternite, and tergite of the ultimate leg-bearing segment provides additional criteria for distinguishing species. Colouration patterns in some Scolopendra species show a high degree of fit to phylogenetic trees at the population level. The most densely sampled species, Scolopendra dehaani Brandt, 1840, has three subclades with allopatric distributions in mainland SE Asia. The molecular phylogeny of S. pinguis Pocock, 1891, indicated ontogenetic colour variation among its populations. The taxonomic validation of S. dawydoffi Kronmüller, 2012, S. japonica Koch, 1878, and S. dehaani Brandt, 1840, each a former subspecies of S. subspinipes Leach, 1814 sensu Lewis, 2010, as full species was supported by molecular information and additional morphological data. Species delimitation in these taxonomically challenging animals is facilitated by an integrative approach that draws on both morphology and molecular phylogeny. PMID:26270342

  6. Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions.

    PubMed

    Botan, Alexandru; Favela-Rosales, Fernando; Fuchs, Patrick F J; Javanainen, Matti; Kanduč, Matej; Kulig, Waldemar; Lamberg, Antti; Loison, Claire; Lyubartsev, Alexander; Miettinen, Markus S; Monticelli, Luca; Määttä, Jukka; Ollila, O H Samuli; Retegan, Marius; Róg, Tomasz; Santuz, Hubert; Tynkkynen, Joona

    2015-12-10

    Phospholipids are essential building blocks of biological membranes. Despite a vast amount of very accurate experimental data, the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulations have the potential to resolve the structures, and to give an arrestingly intuitive interpretation of the experimental data, but only if the simulations reproduce the data within experimental accuracy. In the present work, we simulated phosphatidylcholine (PC) lipid bilayers with 13 different atomistic models, and compared simulations with NMR experiments in terms of the highly structurally sensitive C-H bond vector order parameters. Focusing on the glycerol backbone and choline headgroups, we showed that the order parameter comparison can be used to judge the atomistic resolution structural accuracy of the models. Accurate models, in turn, allow molecular dynamics simulations to be used as an interpretation tool that translates these NMR data into a dynamic three-dimensional representation of biomolecules in biologically relevant conditions. In addition to lipid bilayers in fully hydrated conditions, we reviewed previous experimental data for dehydrated bilayers and cholesterol-containing bilayers, and interpreted them with simulations. Although none of the existing models reached experimental accuracy, by critically comparing them we were able to distill relevant chemical information: (1) increase of choline order parameters indicates the P-N vector tilting more parallel to the membrane, and (2) cholesterol induces only minor changes to the PC (glycerol backbone) structure. This work has been done as a fully open collaboration, using nmrlipids.blogspot.fi as a communication platform; all the scientific contributions were made publicly on this blog. During the open research process, the repository holding our simulation trajectories and files ( https

  7. Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions†

    PubMed Central

    2015-01-01

    Phospholipids are essential building blocks of biological membranes. Despite a vast amount of very accurate experimental data, the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulations have the potential to resolve the structures, and to give an arrestingly intuitive interpretation of the experimental data, but only if the simulations reproduce the data within experimental accuracy. In the present work, we simulated phosphatidylcholine (PC) lipid bilayers with 13 different atomistic models, and compared simulations with NMR experiments in terms of the highly structurally sensitive C–H bond vector order parameters. Focusing on the glycerol backbone and choline headgroups, we showed that the order parameter comparison can be used to judge the atomistic resolution structural accuracy of the models. Accurate models, in turn, allow molecular dynamics simulations to be used as an interpretation tool that translates these NMR data into a dynamic three-dimensional representation of biomolecules in biologically relevant conditions. In addition to lipid bilayers in fully hydrated conditions, we reviewed previous experimental data for dehydrated bilayers and cholesterol-containing bilayers, and interpreted them with simulations. Although none of the existing models reached experimental accuracy, by critically comparing them we were able to distill relevant chemical information: (1) increase of choline order parameters indicates the P–N vector tilting more parallel to the membrane, and (2) cholesterol induces only minor changes to the PC (glycerol backbone) structure. This work has been done as a fully open collaboration, using nmrlipids.blogspot.fi as a communication platform; all the scientific contributions were made publicly on this blog. During the open research process, the repository holding our simulation trajectories and files (https

  8. Comparative Experimental and Computational Study of Monoalkyl Chain Phosphatidylcholine-Containing Thermoresponsive Liposomes.

    PubMed

    Eleftheriou, Kleopatra; Sideratou, Zili; Thanassoulas, Angelos; Papakyriakou, Athanasios; Tsiourvas, Dimitris

    2016-06-23

    Liposomes containing lysophospholipids are intensively studied as drug delivery systems that are stable at normal body temperature but exhibit fast release of their drug load at slightly elevated temperatures. In this study, the stability and release properties of dipalmitoylglycerophosphocholine (DPPC)-based liposomes incorporating the commonly used lysophosphatidylocholine (lyso-PC), and a series of monoalkyl chain ether-linked phosphatidylcholine, i.e., the biologically relevant monoalkyl chain platelet activating factor (PAF) and its derivatives lyso-PAF and methyl-PAF, were investigated. To this end a series of PEGylated small unilamellar liposomes with DPPC:monoalkyl lipid compositions of 5% and 10% molar ratio were prepared and compared with regard to stability (37 °C) and release properties at elevated temperatures (38-43 °C). All systems were characterized with respect to size distribution, ζ-potential, and phase transition characteristics. The presence of ether-lipids endows liposomes with superior (∼10% increase) release properties at 5% incorporation compared to lyso-PC, while at 10% molar ratio the formulations do not differ significantly, the release being close to 90%. The findings are supported by atomistic molecular dynamics simulations that suggest a correlation between the enhanced permeability and increased penetration of water molecules within the bilayers with density fluctuations resulting from the increased area-per-lipid and the disorder of the lysolipids alkyl chains. PMID:27280363

  9. Intermediate structures in the cholate-phosphatidylcholine vesicle-micelle transition

    PubMed Central

    Walter, Anne; Vinson, Phillip K.; Kaplun, Alon; Talmon, Yeshayahu

    1991-01-01

    The vesicle-micelle transition of egg phosphatidylcholine (PC) and sodium cholate was described by comparing cryo-transmission electron microscopic (cryo-TEM) images of the structures formed to the associated turbidity changes. These experiments were designed to identify the morphology of the intermediates between vesicles and small spheroidal mixed micelles. With increasing cholate concentration, the vesicular structures changed size and more multilamellar vesicles were seen. Between the apparent upper and lower phase boundaries, three structures were observed: open vesicles, large bilayer sheets (twenty to several hundred nanometers in diameter), and long (150-300 nm) flexible cylindrical micelles. The cylindrical micelles evolved from the edges of the bilayer sheets. At higher relative cholate concentration, the phase boundary was sharply defined by optical clarification of the egg PC-cholate mixtures. Cryo-TEM revealed only small spheroidal mixed micelles at this transition. These results provide the first direct evidence of the structural pathway or of molecular intermediates between a lamellar and a micellar state. Understanding these specific intermediates and the transitions between them is essential to developing reconstitution protocols and properly analyzing either activity or structural data obtained from cholate-dispersed membrane proteins. ImagesFIGURE 2FIGURE 3FIGURE 4FIGURE 5 PMID:19431813

  10. Revealing Transient Interactions between Phosphatidylinositol-specific Phospholipase C and Phosphatidylcholine--Rich Lipid Vesicles

    NASA Astrophysics Data System (ADS)

    Yang, Boqian; He, Tao; Grauffel, Cédric; Reuter, Nathalie; Roberts, Mary; Gershenson, Anne

    2013-03-01

    Phosphatidylinositol-specific phospholipase C (PI-PLC) enzymes transiently interact with target membranes. Previous fluorescence correlation spectroscopy (FCS) experiments showed that Bacillus thuringiensis PI-PLC specifically binds to phosphatidylcholine (PC)-rich membranes and preferentially interacts with unilamellar vesicles that show larger curvature. Mutagenesis studies combined with FCS measurements of binding affinity highlighted the importance of interfacial PI-PLC tyrosines in the PC specificity. All-atom molecular dynamics simulations of PI-PLC performed in the presence of a PC membrane indicate these tyrosines are involved in specific cation-pi interactions with choline headgroups. To further understand those transient interactions between PI-PLC and PC-rich vesicles, we monitor single fluorescently labeled PI-PLC proteins as they cycle on and off surface-tethered small unilamellar vesicles using total internal reflection fluorescent microscopy. The residence times on vesicles along with vesicle size information, based on vesicle fluorescence intensity, reveal the time scales of PI-PLC membrane interactions as well as the curvature dependence. The PC specificity and the vesicle curvature dependence of this PI-PLC/membrane interaction provide insight into how the interface modulates protein-membrane interactions. This work was supported by the National Institute of General Medical Science of the National Institutes of Health (R01GM060418).

  11. Biosynthesis of phosphatidylcholine by human lysophosphatidylcholine acyltransferase 1.

    PubMed

    Harayama, Takeshi; Shindou, Hideo; Shimizu, Takao

    2009-09-01

    Pulmonary surfactant is a complex of phospholipids and proteins lining the alveolar walls of the lung. It reduces surface tension in the alveoli, and is critical for normal respiration. Pulmonary surfactant phospholipids consist mainly of phosphatidylcholine (PC) and phosphatidylglycerol (PG). Although the phospholipid composition of pulmonary surfactant is well known, the enzyme(s) involved in its biosynthesis have remained obscure. We previously reported the cloning of murine lysophosphatidylcholine acyltransferase 1 (mLPCAT1) as a potential biosynthetic enzyme of pulmonary surfactant phospholipids. mLPCAT1 exhibits lysophosphatidylcholine acyltransferase (LPCAT) and lysophosphatidylglycerol acyltransferase (LPGAT) activities, generating PC and PG, respectively. However, the enzymatic activity of human LPCAT1 (hLPCAT1) remains controversial. We report here that hLPCAT1 possesses LPCAT and LPGAT activities. The activity of hLPCAT1 was inhibited by N-ethylmaleimide, indicating the importance of some cysteine residue(s) for the catalysis. We found a conserved cysteine (Cys(211)) in hLPCAT1 that is crucial for its activity. Evolutionary analyses of the close homologs of LPCAT1 suggest that it appeared before the evolution of teleosts and indicate that LPCAT1 may have evolved along with the lung to facilitate respiration. hLPCAT1 mRNA is highly expressed in the human lung. We propose that hLPCAT1 is the biosynthetic enzyme of pulmonary surfactant phospholipids. PMID:19383981

  12. Origins of extreme boundary lubrication by phosphatidylcholine liposomes.

    PubMed

    Sorkin, Raya; Kampf, Nir; Dror, Yael; Shimoni, Eyal; Klein, Jacob

    2013-07-01

    Phosphatidylcholine (PC) vesicles have been shown to have remarkable boundary lubricating properties under physiologically-high pressures. Here we carry out a systematic study, using a surface force balance, of the normal and shear (frictional) forces between two opposing surfaces bearing different PC vesicles across water, to elucidate the origin of these properties. Small unilamellar vesicles (SUVs, diameters < 100 nm) of the symmetric saturated diacyl PCs DMPC (C(14)), DPPC (C(16)) and DSPC (C(18)) attached to mica surfaces were studied in their solid-ordered (SO) phase on the surface. Overall liposome lubrication ability improves markedly with increasing acyl chain length, and correlates strongly with the liposomes' structural integrity on the substrate surface: DSPC-SUVs were stable on the surface, and provided extremely efficient lubrication (friction coefficient μ ≈ 10(-4)) at room temperature at pressures up to at least 18 MPa. DMPC-SUVs ruptured following adsorption, providing poor high-pressure lubrication, while DPPC-SUVs behavior was intermediate between the two. These results can be well understood in terms of the hydration-lubrication paradigm, but suggest that an earlier conjecture, that highly-efficient lubrication by PC-SUVs depended simply on their being in the SO rather than in the liquid-disordered phase, should be more nuanced. Our results indicate that the resistance of the SUVs to mechanical deformation and rupture is the dominant factor in determining their overall boundary lubrication efficiency in our system. PMID:23623226

  13. Phosphatidylcholine from "Healthful" Egg Yolk Varieties: An Organic Laboratory Experience

    NASA Astrophysics Data System (ADS)

    Hodges, Linda C.

    1995-12-01

    I have added an investigative element to a popular undergraduate experiment. the characterization of phosphatidylcholine (PC) from egg yolks. Varieties of eggs are commercially available which have been obtained from chickens fed a diet containing no animal fat. Presumably, less saturated fat in the diet of the chickens could be reflected in the fatty acid composition of various classes of biological lipids, including phospholipids, in the eggs from these chickens. PC is extracted using conventional methods, the extract is further purified by chromatography on silicic acid, and the column fractions are assayed for the presence and purity of PC by TLC. Fractions containing pure PC are pooled, concentrated, hydrolyzed, and esterified to obtain the fatty acid methyl esters (FAME) which are identified by GLC. Comparing FAMEs derived from PC of yolks of regular eggs to those obtained from the other special brands adds a novel twist to the students' work and generates greater student interest and involvement in both the interpretation of data than a simple isolation of a biological compound alone evokes.

  14. Phosphatidylcholine biosynthesis and insulin release in rat islets of Langerhans

    SciTech Connect

    Hoffman, J.M.

    1988-01-01

    Turnover of phosphatidylcholine (PC) has been demonstrated to play a role in glucose stimulation of insulin release by pancreatic islets of Langerhans. The activity of the islet CDP-choline pathway of PC synthesis was determined by measuring the incorporation of radiolabeled choline or {sup 32}PO{sub 4} into PC, phosphorylcholine and CDP-choline. Concurrently, insulin release was measured by radioimmunoassay to correlate insulin release and PC synthesis. Glucose concentrations greater than 8.5 mM stimulated CDP-choline pathway activity. However, measurement of PC lipid phosphorus tended to decrease, suggesting that stimulation of the CDP-choline pathway was a means of replenishing PC pools diminished by hydrolysis of PC. Inhibition of glucose oxidation by mannoheptulose or incubations under hypoxic conditions prevented stimulation of the CDP-choline pathway, while inhibition of phospholipase A{sub 2} (PLA{sub 2}) and secretion by the removal of extracellular Ca{sup 2+} potentiated the stimulation seen with glucose.

  15. Chlorophyll a triplet-state ESR in frozen phosphatidylcholine vesicles

    SciTech Connect

    Hiromitsu, I.; Kevan, L.

    1988-05-19

    Photoexcited chlorophyll a (Chla) triplet state in rapidly frozen egg phosphatidylcholine (EPC) vesicles is investigated at 77 K by electron spin resonance (ESR) spectroscopy using light intensity modulation. The electron spin polarization (ESP) intensity is stronger for 0.2 mM Chla than for 1.0 mM Chla. The absolute values of the zero field splitting parameter, D, are 283 (+/-1) x 10/sup -4/ and 276 (+/-2) x 10/sup -4/ cm/sup -1/, and the average depopulation rates of the triplet state are 0.671 +/- 0.052 and 1.054 +/- 0.036 ms/sup -1/ for 0.2 mM Chla and 1.0 mM Chla, respectively. This difference can be consistently attributed to faster triplet-state migration between adjacent Chla's at the higher 1.0 mM Chla concentration. A characteristic migration time of 2.6 ms is obtained. The ESP pattern of the Chla triplet state in the frozen EPC vesicles resembles that in polycrystals more than that in glasses. This suggests that the local environment around Chla in the vesicles is more structured than in glasses.

  16. Phosphatidylcholine Supply to Peroxisomes of the Yeast Saccharomyces cerevisiae.

    PubMed

    Flis, Vid V; Fankl, Ariane; Ramprecht, Claudia; Zellnig, Günther; Leitner, Erich; Hermetter, Albin; Daum, Günther

    2015-01-01

    In the yeast Saccharomyces cerevisiae, phosphatidylcholine (PC), the major phospholipid (PL) of all organelle membranes, is synthesized via two different pathways. Methylation of phosphatidylethanolamine (PE) catalyzed by the methyl transferases Cho2p/Pem1p and Opi3p/Pem2p as well as incorporation of choline through the CDP (cytidine diphosphate)-choline branch of the Kennedy pathway lead to PC formation. To determine the contribution of these two pathways to the supply of PC to peroxisomes (PX), yeast mutants bearing defects in the two pathways were cultivated under peroxisome inducing conditions, i.e. in the presence of oleic acid, and subjected to biochemical and cell biological analyses. Phenotype studies revealed compromised growth of both the cho20Δopi3Δ (mutations in the methylation pathway) and the cki1Δdpl1Δeki1Δ (mutations in the CDP-choline pathway) mutant when grown on oleic acid. Analysis of peroxisomes from the two mutant strains showed that both pathways produce PC for the supply to peroxisomes, although the CDP-choline pathway seemed to contribute with higher efficiency than the methylation pathway. Changes in the peroxisomal lipid pattern of mutants caused by defects in the PC biosynthetic pathways resulted in changes of membrane properties as shown by anisotropy measurements with fluorescent probes. In summary, our data define the origin of peroxisomal PC and demonstrate the importance of PC for peroxisome membrane formation and integrity. PMID:26241051

  17. Phosphatidylcholine Supply to Peroxisomes of the Yeast Saccharomyces cerevisiae

    PubMed Central

    Ramprecht, Claudia; Zellnig, Günther; Leitner, Erich; Hermetter, Albin; Daum, Günther

    2015-01-01

    In the yeast Saccharomyces cerevisiae, phosphatidylcholine (PC), the major phospholipid (PL) of all organelle membranes, is synthesized via two different pathways. Methylation of phosphatidylethanolamine (PE) catalyzed by the methyl transferases Cho2p/Pem1p and Opi3p/Pem2p as well as incorporation of choline through the CDP (cytidine diphosphate)-choline branch of the Kennedy pathway lead to PC formation. To determine the contribution of these two pathways to the supply of PC to peroxisomes (PX), yeast mutants bearing defects in the two pathways were cultivated under peroxisome inducing conditions, i.e. in the presence of oleic acid, and subjected to biochemical and cell biological analyses. Phenotype studies revealed compromised growth of both the cho20Δopi3Δ (mutations in the methylation pathway) and the cki1Δdpl1Δeki1Δ (mutations in the CDP-choline pathway) mutant when grown on oleic acid. Analysis of peroxisomes from the two mutant strains showed that both pathways produce PC for the supply to peroxisomes, although the CDP-choline pathway seemed to contribute with higher efficiency than the methylation pathway. Changes in the peroxisomal lipid pattern of mutants caused by defects in the PC biosynthetic pathways resulted in changes of membrane properties as shown by anisotropy measurements with fluorescent probes. In summary, our data define the origin of peroxisomal PC and demonstrate the importance of PC for peroxisome membrane formation and integrity. PMID:26241051

  18. Accelerated interleaflet transport of phosphatidylcholine molecules in membranes under deformation.

    PubMed Central

    Raphael, R M; Waugh, R E

    1996-01-01

    Biological membranes are lamellar structures composed of two leaflets capable of supporting different mechanical stresses. Stress differences between leaflets were generated during micromechanical experiments in which long thin tubes of lipid (tethers) were formed from the surfaces of giant phospholipid vesicles. A recent dynamic analysis of this experiment predicts the relaxation of local differences in leaflet stress by lateral slip between the leaflets. Differential stress may also relax by interleaflet transport of lipid molecules ("flip-flop"). In this report, we extend the former analysis to include interleaflet lipid transport. We show that transmembrane lipid flux will evidence itself as a linear increase in tether length with time after a step reduction in membrane tension. Multiple measurements were performed on 24 different vesicles composed of stearoyl-oleoyl-phosphatidylcholine plus 3% dinitrophenol-linked di-oleoyl-phosphatidylethanolamine. These tethers all exhibited a linear phase of growth with a mean value of the rate of interlayer permeation, cp = 0.009 s-1. This corresponds to a half-time of approximately 8 min for mechanically driven interleaflet transport. This value is found to be consistent with longer times obtained for chemically driven transport if the lipids cross the membrane via transient, localized defects in the bilayer. Images FIGURE 1 FIGURE 7 PMID:8874013

  19. Susceptibility for hydroperoxide formation of phosphatidylcholine and phosphatidylethanolamine in liposomes.

    PubMed

    Wang, J Y; Shibata, T; Ueki, T; Miyazawa, T

    1995-06-01

    To compare the peroxidative susceptibilities of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) in liposomes, multilamellar vesicles (MLVs) were prepared with equimolar L-alpha-dilinoleoyl PC (DLPC) and L-alpha-dilinoleoyl PE (DLPE), and with soya PC and soya PE having a uniform constituent fatty acids. The hydroperoxide formation at 37 degrees C in the presence of a water-soluble radical initiator was examined by chemiluminescence-high-performance liquid chromatography (CL-HPLC), and the effect of heterogeneous distribution of PC and PE on peroxidation was investigated. No difference was found between the hydroperoxidation of PC and PE in MLVs systems, except that soya PC was more susceptible to peroxidation than soya PE in the L-alpha-dipalmitoyl PC (DPPC)-based liposomes. No correlation was found between the amount of phospholipids distributed in the external leaflet of MLVs and hydroperoxide formation. This result suggested that the unsaturation of constituent fatty acids in phospholipids is more important than the difference in the polar head group of phospholipids regarding their peroxidizabilities in liposomes. PMID:7472672

  20. Molecular determination of abundance of infection with Sarcocystis species in slaughtered sheep of Urmia, Iran

    PubMed Central

    Farhang-Pajuh, Farhad; Yakhchali, Mohammad; Mardani, Karim

    2014-01-01

    Sarcocystis is one of the most prevalent parasites of domestic ruminants worldwide. This study was aimed to determine prevalence of Sarcocystis infection and molecular discrimination of Sarcocystis gigantea and Sarcocystis medusiformis infecting domestic sheep. Tissue samples from 638 sheep slaughtered at Urmia abattoir were randomly collected from February 2011 to January 2012. Genomic DNA extraction and polymerase chain reaction (PCR) was performed to amplify a 964 bp fragment of nuclear 18S rRNA gene. The PCR products were subjected to digestion with endonuclease MboII and/or MvaI for discriminating S. medusiformis and S. gigantea. Results indicated that the overall prevalence of Sarcocystis unspecified species was 36.83% (235/638) in which male (7.63%, 38/498) and female (35.00%, 49/140) sheep over 4 years-old had the highest prevalence. There was no significant difference between prevalence of macrosarcocysts and sex. Two macrosarcocysts forms were found as fat (27.90%, 178/638) and thin (8.93%, 57/638) in striated muscles. There was significant difference between frequency of macrosarcocysts and body distribution. Mixed infection with both fat and thin macrosarcocysts was also found in 11.13% (71/638) of infected sheep. There was no significant difference regarding the prevalence of mixed infection in both age classes. The PCR-RFLP patterns showed that fat sarcocysts were S. gigantea (29.31%, 187/638) and thin sarcocysts were S. medusiformis (7.52%, 48/638). It was concluded that ovine Sarcocystis infection was prevalent in Urmia and a combination of conventional methods and molecular study for sheep sarcocysts could be informative. PMID:25568716

  1. Molecular determination of abundance of infection with Sarcocystis species in slaughtered sheep of Urmia, Iran.

    PubMed

    Farhang-Pajuh, Farhad; Yakhchali, Mohammad; Mardani, Karim

    2014-01-01

    Sarcocystis is one of the most prevalent parasites of domestic ruminants worldwide. This study was aimed to determine prevalence of Sarcocystis infection and molecular discrimination of Sarcocystis gigantea and Sarcocystis medusiformis infecting domestic sheep. Tissue samples from 638 sheep slaughtered at Urmia abattoir were randomly collected from February 2011 to January 2012. Genomic DNA extraction and polymerase chain reaction (PCR) was performed to amplify a 964 bp fragment of nuclear 18S rRNA gene. The PCR products were subjected to digestion with endonuclease MboII and/or MvaI for discriminating S. medusiformis and S. gigantea. Results indicated that the overall prevalence of Sarcocystis unspecified species was 36.83% (235/638) in which male (7.63%, 38/498) and female (35.00%, 49/140) sheep over 4 years-old had the highest prevalence. There was no significant difference between prevalence of macrosarcocysts and sex. Two macrosarcocysts forms were found as fat (27.90%, 178/638) and thin (8.93%, 57/638) in striated muscles. There was significant difference between frequency of macrosarcocysts and body distribution. Mixed infection with both fat and thin macrosarcocysts was also found in 11.13% (71/638) of infected sheep. There was no significant difference regarding the prevalence of mixed infection in both age classes. The PCR-RFLP patterns showed that fat sarcocysts were S. gigantea (29.31%, 187/638) and thin sarcocysts were S. medusiformis (7.52%, 48/638). It was concluded that ovine Sarcocystis infection was prevalent in Urmia and a combination of conventional methods and molecular study for sheep sarcocysts could be informative. PMID:25568716

  2. Potential molecular mechanisms underlying muscle fatigue mediated by reactive oxygen and nitrogen species

    PubMed Central

    Debold, Edward P.

    2015-01-01

    Intense contractile activity causes a dramatic decline in the force and velocity generating capacity of skeletal muscle within a few minutes, a phenomenon that characterizes fatigue. Much of the research effort has focused on how elevated levels of the metabolites of ATP hydrolysis might inhibit the function of the contractile proteins. However, there is now growing evidence that elevated levels of reactive oxygen and nitrogen species (ROS/RNS), which also accumulate in the myoplasm during fatigue, also play a causative role in this type of fatigue. The most compelling evidence comes from observations demonstrating that pre-treatment of intact muscle with a ROS scavenger can significantly attenuate the development of fatigue. A clear advantage of this line of inquiry is that the molecular targets and protein modifications of some of the ROS scavengers are well-characterized enabling researchers to begin to identify potential regions and even specific amino acid residues modified during fatigue. Combining this knowledge with assessments of contractile properties from the whole muscle level down to the dynamic motions within specific contractile proteins enable the linking of the structural modifications to the functional impacts, using advanced chemical and biophysical techniques. Based on this approach at least two areas are beginning emerge as potentially important sites, the regulatory protein troponin and the actin binding region of myosin. This review highlights some of these recent efforts which have the potential to offer uniquely precise information on the underlying molecular basis of fatigue. This work may also have implications beyond muscle fatigue as ROS/RNS mediated protein modifications are also thought to play a role in the loss of muscle function with aging and in some acute pathologies like cardiac arrest and ischemia. PMID:26388779

  3. Analysis of Molecular Species Profiles of Ceramide-1-phosphate and Sphingomyelin Using MALDI-TOF Mass Spectrometry.

    PubMed

    Yamashita, Ryouhei; Tabata, Yumika; Iga, Erina; Nakao, Michiyasu; Sano, Shigeki; Kogure, Kentaro; Tokumura, Akira; Tanaka, Tamotsu

    2016-02-01

    Ceramide-1-phosphate (C1P) is a potential signaling molecule that modulates various cellular functions in animals. It has been known that C1P with different N-acyl lengths induce biological responses differently. However, molecular species profiles of the C1P in animal tissues have not been extensively examined yet. Here, we developed a method for determination of the molecular species of a C1P using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry with Phos-tag, a phosphate capture molecule. The amounts of total C1P in skin, brain, liver, kidney and small intestine of mice were determined to be 344, 151, 198, 96 and 90 pmol/g wet weight, respectively. We found a C1P species having an α-hydroxypalmitoyl residue (h-C1P, 44 pmol/g wet weight) in mouse skin. The h-C1P was detected only in the skin, and not other tissues of mice. The same analysis was applied to sphingomyelin after conversion of sphingomyelin to C1P by Streptomyces chromofuscus phospholipase D. We found that molecular species profiles of sphingomyelin in skin, kidney and small intestine of mice were similar to those of C1P in corresponding tissues. In contrast, molecular species profiles of sphingomyelin in liver and brain were quite different from those of C1P in these tissues, indicating selective synthesis or degradation of C1P in these tissues. The method described here will be useful for detection of changes in molecular species profiles of C1P and sphingomyelin. PMID:26694604

  4. Molecular systematics of marine gregarine apicomplexans from Pacific tunicates, with descriptions of five novel species of Lankesteria.

    PubMed

    Rueckert, Sonja; Wakeman, Kevin C; Jenke-Kodama, Holger; Leander, Brian S

    2015-08-01

    The eugregarines are a group of apicomplexan parasites that mostly infect the intestines of invertebrates. The high level of morphological variation found within and among species of eugregarines makes it difficult to find consistent and reliable traits that unite even closely related lineages. Based mostly on traits observed with light microscopy, the majority of described eugregarines from marine invertebrates has been classified into a single group, the Lecudinidae. Our understanding of the overall diversity and phylogenetic relationships of lecudinids is very poor, mainly because only a modest amount of exploratory research has been done on the group and very few species of lecudinids have been characterized at the molecular phylogenetic level. In an attempt to understand the diversity of marine gregarines better, we surveyed lecudinids that infect the intestines of Pacific ascidians (i.e. sea squirts) using ultrastructural and molecular phylogenetic approaches; currently, these species fall within one genus, Lankesteria. We collected lecudinid gregarines from six ascidian host species, and our data demonstrated that each host was infected by a different species of Lankesteria: (i) Lankesteria hesperidiiformis sp. nov., isolated from Distaplia occidentalis, (ii) Lankesteria metandrocarpae sp. nov., isolated from Metandrocarpa taylori, (iii) Lankesteria halocynthiae sp. nov., isolated from Halocynthia aurantium, (iv) Lankesteria herdmaniae sp. nov., isolated from Herdmania momus, (v) Lankesteria cf. ritterellae, isolated from Ritterella rubra, and (vi) Lankesteria didemni sp. nov., isolated from Didemnum vexillum. Visualization of the trophozoites with scanning electron microscopy showed that four of these species were covered with epicytic folds, whereas two of the species were covered with a dense pattern of epicytic knobs. The molecular phylogenetic data suggested that species of Lankesteria with surface knobs form a clade that is nested within a paraphyletic

  5. Feline drug metabolism and disposition: pharmacokinetic evidence for species differences and molecular mechanisms

    PubMed Central

    2013-01-01

    Synopsis Although it is widely appreciated that cats respond differently to certain drugs when compared with other companion animal species, the causes of these differences are poorly understood. This review critically evaluates published evidence for altered drug effects in cats, focusing on pharmacokinetic differences between cats, dogs and humans, and the molecular mechanisms underlying these differences. Pharmacokinetic studies indicate that acetaminophen, propofol, carprofen, and acetylsalicylic acid (aspirin) are cleared significantly more slowly in cats versus dogs and humans. All of these drugs are metabolized by conjugation. Cats lack the major phenol UDP-glucuronosyltransferase (UGT) enzymes, including UGT1A6 and UGT1A9, that glucuronidate acetaminophen and propofol. Deficient glucuronidation may also explain slower carprofen clearance, although there is no direct evidence for this. However, poor aspirin clearance in cats appears to be mainly a consequence of slower glycine conjugation. Cats are also deficient in several other conjugation enzymes, including N-acetyltransferase (NAT) 2 and thiopurine methyltransferase (TMPT). NAT2 deficiency may be the reason cats are more prone to developing methemoglobinemia rather than hepatotoxicity from acetaminophen. TMPT deficiency may predispose cats to azathioprine toxicity. No evidence was found for slower elimination of drugs cleared by oxidation or unchanged into urine or bile. Piroxicam, an oxidized drug, was cleared much more rapidly in cats than humans and dogs, although the mechanism for this difference is unclear. More work is needed to better understand drug metabolism and disposition differences in cats, thereby enabling more rational prescribing of existing medications, and the development of safer drugs for this species. PMID:23890237

  6. A molecular phylogeny of Anopheles annulipes (Diptera: Culicidae) sensu lato: the most species-rich anopheline complex.

    PubMed

    Foley, D H; Wilkerson, R C; Cooper, R D; Volovsek, M E; Bryan, J H

    2007-04-01

    The Australasian Annulipes Complex is the most species-rich among Anopheles mosquitoes, with at least 15 sibling species suspected. Members of this complex are the most likely vectors of malaria in the past in southern Australia and are involved in the spread of myxomatosis among rabbits. In this, the first comprehensive molecular study of the Annulipes Complex, 23 ITS2 rDNA variants were detected from collections throughout Australia and Papua New Guinea, including diagnostic variants for the previously identified An. annulipes species A-G. Specimens of each ITS2 variant were sequenced for portions of the mitochondrial COI, COII and nuclear EF-1alpha genes. Partitioned Bayesian and Maximum Parsimony analyses confirmed the monophyly of the Annulipes Complex and revealed at least 17 clades that we designate species A-Q. These species belong to two major clades, one in the north and one mainly in the south, suggesting that climate was a driver of species radiation. We found that 65% (11) of the 17 sibling species recorded here had unique COI sequences, suggesting that DNA barcoding will be useful for diagnosing species within the Annulipes Complex. A comparison of the taxa revealed morphological characters that may be diagnostic for some species. Our results substantially increase the size of the subgenus Cellia in Australasia, and will assist species-level studies of the Annulipes Complex. PMID:17126567

  7. The labeling of pulmonary surfactant phosphatidylcholine in newborn and adult sheep

    SciTech Connect

    Ikegami, M.; Jobe, A.; Nathanielsz, P.W.

    1981-08-01

    The labeling of the saturated phosphatidylcholine from surfactant with radiolabeled palmitic acid was characterized in seven newborn and seven adult sheep using a repetitive sampling technique. Each animal had a small cannula placed surgically in the trachea. Following the intravenous injection of (3H) palmitic acid, surfactant samples in saline were recovered from the distal airways of each animal with fine plastic catheters over a period of 10 days. The change in specific activity of the saturated phosphatidylcholine (cpm/mumol) was used to define the kinetics of secretion and then disappearance of the labeled saturated phosphatidylcholine. Labeled saturated phosphatidylcholine accumulated in a linear fashion without an apparent initial delay for 27 hr in adult and 44 hr in newborn sheep. The labeled saturated phosphatidylcholine then decayed with mean apparent biological half-life values of 45 hr and 54 hr in adult and newborn sheep, respectively. However, these half-life estimates are compromised by the long secretory phase of the labeling curves. The characteristics of the labeling of surfactant saturated phosphatidylcholine in sheep may be more representative of surfactant metabolism in large mammals than previous studies in small rodents.

  8. Phosphatidylcholine synthesis in castor bean endosperm. I. Metabolism of L-serine. [Ricinus communis

    SciTech Connect

    Kinney, A.J.; Moore, T.S. Jr.

    1987-05-01

    Endosperm halves from 3-day-old castor bean (Ricinus communis var Hale) were incubated for 30 minutes with L(/sup 14/C)serine, after which label was observed in ethanolamine, choline, phosphatidylserine, phosphatidylethanolamine, phosphatidylcholine, ethanolaminephosphate, and CDPethanolamine, but not in cholinephosphate or CDPcholine. Only later did significant amounts of isotope become incorporated into cholinephosphate and CDPcholine. The choline kinase inhibitor hemicholinium-3 prevented the incorporation of label from serine into choline-phosphate and CDPcholine, reduced the incorporation of (/sup 14/C)choline into phosphatidylcholine by 65%, but inhibited the incorporation of label into phosphatidylcholine from serine by only 15%. The inhibitor did not prevent the incorporation of labeled methyl groups from S-adenosyl-L-methionine into phosphatidyldimethylethanolamine plus phosphatidyl-choline. The amount of incorporation of label from the methyl donor was only 8% of that from choline into phosphatidylcholine. The implications of these results for the pathway and regulation of phosphatidylcholine synthesis from the water-soluble precursors are discussed.

  9. Phosphatidylcholine composition of pulmonary surfactant from terrestrial and marine diving mammals

    PubMed Central

    Gutierrez, Danielle B.; Fahlman, Andreas; Gardner, Manuela; Kleinhenz, Danielle; Piscitelli, Marina; Raverty, Stephen; Haulena, Martin; Zimba, Paul V.

    2015-01-01

    Marine mammals are repeatedly exposed to elevated extra-thoracic pressure and alveolar collapse during diving and readily experience alveolar expansion upon inhalation – a unique capability as compared to terrestrial mammals. How marine mammal lungs overcome the challenges of frequent alveolar collapse and recruitment remains unknown. Recent studies indicate that pinniped lung surfactant has more anti-adhesive components compared to terrestrial mammals, which would aid in alveolar opening. However, pulmonary surfactant composition has not yet been investigated in odontocetes, whose physiology and diving behavior differ from pinnipeds. The aim of this study was to investigate the phosphatidylcholine (PC) composition of lung surfactants from various marine mammals and compare these to a terrestrial mammal. We found an increase in anti-adhesive PC species in harp seal (Pagophilus groenlandicus) and California sea lion (Zalophus californianus) compared to dog (Canus lupus familiaris), as well as an increase in the fluidizing PCs 16:0/14:0 and 16:0/16:1 in pinnipeds compared to odontocetes. The harbor porpoise (a representative of the odontocetes) did not have higher levels of fluidizing PCs compared to dog. Our preliminary results support previous findings that pinnipeds may have adapted unique surfactant compositions that allow them to dive at high pressures for extended periods without adverse effects. Future studies will need to investigate the differences in other surfactant components to fully assess the surfactant composition in odontocetes. PMID:25812797

  10. Phosphatidylcholine composition of pulmonary surfactant from terrestrial and marine diving mammals.

    PubMed

    Gutierrez, Danielle B; Fahlman, Andreas; Gardner, Manuela; Kleinhenz, Danielle; Piscitelli, Marina; Raverty, Stephen; Haulena, Martin; Zimba, Paul V

    2015-06-01

    Marine mammals are repeatedly exposed to elevated extra-thoracic pressure and alveolar collapse during diving and readily experience alveolar expansion upon inhalation - a unique capability as compared to terrestrial mammals. How marine mammal lungs overcome the challenges of frequent alveolar collapse and recruitment remains unknown. Recent studies indicate that pinniped lung surfactant has more anti-adhesive components compared to terrestrial mammals, which would aid in alveolar opening. However, pulmonary surfactant composition has not yet been investigated in odontocetes, whose physiology and diving behavior differ from pinnipeds. The aim of this study was to investigate the phosphatidylcholine (PC) composition of lung surfactants from various marine mammals and compare these to a terrestrial mammal. We found an increase in anti-adhesive PC species in harp seal (Pagophilus groenlandicus) and California sea lion (Zalophus californianus) compared to dog (Canus lupus familiaris), as well as an increase in the fluidizing PCs 16:0/14:0 and 16:0/16:1 in pinnipeds compared to odontocetes. The harbor porpoise (a representative of the odontocetes) did not have higher levels of fluidizing PCs compared to dog. Our preliminary results support previous findings that pinnipeds may have adapted unique surfactant compositions that allow them to dive at high pressures for extended periods without adverse effects. Future studies will need to investigate the differences in other surfactant components to fully assess the surfactant composition in odontocetes. PMID:25812797

  11. Melittin-Induced Lipid Extraction Modulated by the Methylation Level of Phosphatidylcholine Headgroups.

    PubMed

    Therrien, Alexandre; Lafleur, Michel

    2016-01-19

    Protein- and peptide-induced lipid extraction from membranes is a critical process for many biological events, including reverse cholesterol transport and sperm capacitation. In this work, we examine whether such processes could display specificity for some lipid species. Melittin, the main component of dry bee venom, was used as a model amphipathic α-helical peptide. We specifically determined the modulation of melittin-induced lipid extraction from membranes by the change of the methylation level of phospholipid headgroups. Phosphatidylcholine (PC) bilayers were demethylated either by substitution with phosphatidylethanolamine (PE) or chemically by using mono- and dimethylated PE. It is shown that demethylation reduces the association of melittin with membranes, likely because of the resulting tighter chain packing of the phospholipids, which reduces the capacity of the membranes to accommodate inserted melittin. This reduced binding of the peptide is accompanied by an inhibition of the lipid extraction caused by melittin. We demonstrate that melittin selectively extracts PC from PC/PE membranes. This selectivity is proposed to be a consequence of a PE depletion in the surroundings of bound melittin to minimize disruption of the interphospholipid interactions. The resulting PC-enriched vicinity of melittin would be responsible for the observed formation of PC-enriched lipid/peptide particles resulting from the lipid efflux. These findings reveal that modulating the methylation level of phospholipid headgroups is a simple way to control the specificity of lipid extraction from membranes by peptides/proteins and thereby modulate the lipid composition of the membranes. PMID:26789763

  12. Cryptic Species in Tropic Sands - Interactive 3D Anatomy, Molecular Phylogeny and Evolution of Meiofaunal Pseudunelidae (Gastropoda, Acochlidia)

    PubMed Central

    Neusser, Timea P.; Jörger, Katharina M.; Schrödl, Michael

    2011-01-01

    Background Towards realistic estimations of the diversity of marine animals, tiny meiofaunal species usually are underrepresented. Since the biological species concept is hardly applicable on exotic and elusive animals, it is even more important to apply a morphospecies concept on the best level of information possible, using accurate and efficient methodology such as 3D modelling from histological sections. Molecular approaches such as sequence analyses may reveal further, cryptic species. This is the first case study on meiofaunal gastropods to test diversity estimations from traditional taxonomy against results from modern microanatomical methodology and molecular systematics. Results The examined meiofaunal Pseudunela specimens from several Indo-Pacific islands cannot be distinguished by external features. Their 3D microanatomy shows differences in the organ systems and allows for taxonomic separation in some cases. Additional molecular analyses based on partial mitochondrial cytochrome c oxidase subunit I (COI) and 16S rRNA markers revealed considerable genetic structure that is largely congruent with anatomical or geographical patterns. Two new species (Pseudunela viatoris and P. marteli spp. nov.) are formally described integrating morphological and genetic analyses. Phylogenetic analysis using partial 16S rRNA, COI and the nuclear 18S rRNA markers shows a clade of Pseudunelidae species as the sister group to limnic Acochlidiidae. Within Pseudunela, two subtypes of complex excretory systems occur. A complex kidney already evolved in the ancestor of Hedylopsacea. Several habitat shifts occurred during hedylopsacean evolution. Conclusions Cryptic species occur in tropical meiofaunal Pseudunela gastropods, and likely in other meiofaunal groups with poor dispersal abilities, boosting current diversity estimations. Only a combined 3D microanatomical and molecular approach revealed actual species diversity within Pseudunela reliably. Such integrative methods are

  13. Molecular and Morphological Differentiation of Common Dolphins (Delphinus sp.) in the Southwestern Atlantic: Testing the Two Species Hypothesis in Sympatry

    PubMed Central

    Cunha, Haydée A.; de Castro, Rocio Loizaga; Secchi, Eduardo R.; Crespo, Enrique A.; Lailson-Brito, José; Azevedo, Alexandre F.; Lazoski, Cristiano; Solé-Cava, Antonio M.

    2015-01-01

    The taxonomy of common dolphins (Delphinus sp.) has always been controversial, with over twenty described species since the original description of the type species of the genus (Delphinus delphis Linnaeus, 1758). Two species and four subspecies are currently accepted, but recent molecular data have challenged this view. In this study we investigated the molecular taxonomy of common dolphins through analyses of cytochrome b sequences of 297 individuals from most of their distribution. We included 37 novel sequences from the Southwestern Atlantic Ocean, a region where the short- and long-beaked morphotypes occur in sympatry, but which had not been well sampled before. Skulls of individuals from the Southwestern Atlantic were measured to test the validity of the rostral index as a diagnostic character and confirmed the presence of the two morphotypes in our genetic sample. Our genetic results show that all common dolphins in the Atlantic Ocean belong to a single species, Delphinus delphis. According to genetic data, the species Delphinus capensis is invalid. Long-beaked common dolphins from the Northeastern Pacific Ocean may constitute a different species. Our conclusions prompt the need for revision of currently accepted common dolphin species and subspecies and of Delphinus delphis distribution. PMID:26559411

  14. Molecular and Morphological Differentiation of Common Dolphins (Delphinus sp.) in the Southwestern Atlantic: Testing the Two Species Hypothesis in Sympatry.

    PubMed

    Cunha, Haydée A; de Castro, Rocio Loizaga; Secchi, Eduardo R; Crespo, Enrique A; Lailson-Brito, José; Azevedo, Alexandre F; Lazoski, Cristiano; Solé-Cava, Antonio M

    2015-01-01

    The taxonomy of common dolphins (Delphinus sp.) has always been controversial, with over twenty described species since the original description of the type species of the genus (Delphinus delphis Linnaeus, 1758). Two species and four subspecies are currently accepted, but recent molecular data have challenged this view. In this study we investigated the molecular taxonomy of common dolphins through analyses of cytochrome b sequences of 297 individuals from most of their distribution. We included 37 novel sequences from the Southwestern Atlantic Ocean, a region where the short- and long-beaked morphotypes occur in sympatry, but which had not been well sampled before. Skulls of individuals from the Southwestern Atlantic were measured to test the validity of the rostral index as a diagnostic character and confirmed the presence of the two morphotypes in our genetic sample. Our genetic results show that all common dolphins in the Atlantic Ocean belong to a single species, Delphinus delphis. According to genetic data, the species Delphinus capensis is invalid. Long-beaked common dolphins from the Northeastern Pacific Ocean may constitute a different species. Our conclusions prompt the need for revision of currently accepted common dolphin species and subspecies and of Delphinus delphis distribution. PMID:26559411

  15. Studies for the Loss of Atomic and Molecular Species from Io

    NASA Technical Reports Server (NTRS)

    Smyth, William H.

    1999-01-01

    A summary discussion of research undertaken in this project is presented and is related to six published papers attached in the appendix. The discussion is divided into six sections describing a variety of studies for the loss of atomic and molecular species from Io. They include studies for: (1) atomic sodium, (2) SO2, (3) O and S, (4) spectacular high-spatial resolution ultraviolet image observations of O, S, and possibly H in Io's atmosphere and/or corona acquired by the Space Telescope Imaging Spectrometer (STIS) of the Hubble Space Telescope (HST), (5) spectacular high-spatial resolution visible Io eclipse image observations acquired by the Solid State Imager (SSI) of Galileo spacecraft, (6) ground-based observations acquired by the Solid State Imager (SSI) of Galileo spacecraft, and (7) ground-based observations of Io's neutral cloud in [OI] 6300 angstrom emission. New source rates at Io's exobase for SO2, O, and H are given and a variety of interesting implications for Io's atmosphere and for the Io plasma torus are discussed. Appendices that are comprised of articles published during the contract are also presented.

  16. Mechanisms and observations for isotope fractionation of molecular species in planetary atmospheres

    SciTech Connect

    Kaye, J.A.

    1987-11-01

    Chemcial and physical processes which may give rise to isotope fractionation of molecular species in the atmospheres of both earth and other planets are reviewed, along with observations of isotopically substituted molecules in planetary atmospheres. Mechanisms for production of isotope fractionation considered include atmospheric escape and the effect of isotope substitution on equilibrium constants (including those of phase changes), photolysis rates, and chemical reaction rates. The isotopes considered for compounds in the terrestrial atmosphere include D, T, C-13, C-14, N-15, O-18, and S-34. Compounds for which data about isotopic composition in the terrestrial atmosphere are summarized include CO, CO2, O3, N2O, NH3, SO2, H2S, H2O, H, H2, and CH4. Planetary atmospheres discussed include those of Venus, Mars, Jupiter, Saturn, Uranus, and Titan; isotopes reviewed are D, C-13, N-15, and O-18. Suggestions for additional research in the area of isotopically substituted molecules in atmospheres are offered.

  17. Studies for the Loss of Atomic and Molecular Species from Io

    NASA Technical Reports Server (NTRS)

    Combi, Michael R.

    1997-01-01

    The general objective of this project has been to advance our theoretical understanding of Io's atmosphere and how various atomic and molecular species are lost from this atmosphere and are distributed in the circumplanetary environment of Jupiter. The scientific objectives of the larger collaborative program between AER, Inc., and the University of Michigan have been to undertake theoretical modeling studies to simulate the distributions of the exospheric gases in Io's corona and extended clouds, to investigate the importance of the various physical processes that shape their relative abundances, and with these tools to analyze observations of O, S and Na obtained by four observers: M.A. McGrath of the Space Telescope Science Institute and G.E. Ballester of the University of Michigan who each have obtained Hubble Space Telescope observations of O and S near Io, F. Scherb who continues an effort to obtain 6300 A OI observations as part of the University of Wisconsin Fabry-Perot program, and N.M. Schneider of the University of Colorado who obtained an extensive set of spectral and spatial observations of the Na emission near Io in the D-lines.

  18. Heterogeneous rates of molecular evolution among cryptic species of the ciliate morphospecies Chilodonella uncinata

    PubMed Central

    Katz, Laura A.; DeBerardinis, Jennifer; Hall, Meaghan S.; Kovner, Alexandra M.; Dunthorn, Micah; Muse, Spencer V.

    2012-01-01

    While molecular analyses have provided insight into the phylogeny of ciliates, the few studies assessing intraspecific variation have largely relied on just a single locus (e.g. nuclear small subunit rDNA (nSSU-rDNA) or mitochondrial cytochrome oxidase I). In this study, we characterize the diversity of several nuclear protein-coding genes plus both nSSU-rDNA and mitochondrial small subunit rDNA (mtSSU-rDNA) of five isolates of the ciliate morphospecies Chilodonella uncinata. Although these isolates have nearly identical nSSU-rDNA sequences, they differ by up to 8.0% in mtSSU-rDNA. Comparative analyses of all loci, including β-tubulin paralogs, indicate a lack of recombination between strains, demonstrating that the morphospecies C. uncinata consists of multiple cryptic species. Further, there is considerable variation in substitution rates among loci as some protein-coding domains are nearly identical between isolates while others differ by up to 13.2% at the amino acid level. Combining insights on macronuclear variation among isolates, the focus of this study, with published data from the micronucleus of two of these isolates indicates that C. uncinata lineages are able to maintain both highly divergent and highly conserved genes within a rapidly evolving germline genome. PMID:22258433

  19. Using deuterated H3+ and other molecular species to understand the formation of stars and planets.

    PubMed

    van der Tak, F F S

    2012-11-13

    The H(3)(+) ion plays a key role in the chemistry of dense interstellar gas clouds where stars and planets are forming. The low temperatures and high extinctions of such clouds make direct observations of H(3)(+) impossible, but lead to large abundances of H(2)D(+) and D(2)H(+) that are very useful probes of the early stages of star and planet formation. Maps of H(2)D(+) and D(2)H(+) pure rotational line emission towards star-forming regions show that the strong deuteration of H(3)(+) is the result of near-complete molecular depletion of CNO-bearing molecules onto grain surfaces, which quickly disappears as cores warm up after stars have formed. In the warmer parts of interstellar gas clouds, H(3)(+) transfers its proton to other neutrals such as CO and N(2), leading to a rich ionic chemistry. The abundances of such species are useful tracers of physical conditions such as the radiation field and the electron fraction. Recent observations of HF line emission towards the Orion Bar imply a high electron fraction, and we suggest that observations of OH(+) and H(2)O(+) emission may be used to probe the electron density in the nuclei of external galaxies. PMID:23028165

  20. Fiber optic apparatus for detecting molecular species by surface enhanced Raman spectroscopy

    DOEpatents

    Angel, Stanley M.; Sharma, Shiv K.

    1988-01-01

    Optrode apparatus for detecting constituents of a fluid medium includes an optical fiber (13, 13a to 13e) having a metal coating (22, 22a to 22e) on at least a portion of a light transmissive core (17, 17a to 17d). The metal is one, such as silver, gold or copper, which enhances emission of Raman signal frequencies by molecules adsorbed on the surface of the coating when monochromatic probe light of a different frequency is scattered by such molecules and the metal coating is sufficiently thin to transmit light between the absorbed molecules and the core of the fiber. Probe light is directed into one end of the fiber and a detector (16, 16d, 16e) analyzes light emitted from the fiber for Raman frequencies that identify one or more particular molecular species. In one form, the optrode (13e) may function as a working electrode of an electrochemical cell (53) while also serving to detect the products of oxidation or reduction reactions which occur at the electrode surface.

  1. Relationship between Extracellular Low-Molecular-Weight Thiols and Mercury Species in Natural Lake Periphytic Biofilms.

    PubMed

    Leclerc, Maxime; Planas, Dolors; Amyot, Marc

    2015-07-01

    The uptake of mercury by microorganisms is a key step in the production of methylmercury, a biomagnifiable toxin. Mercury complexation by low-molecular-weight (LMW) thiols can affect its bioavailability and thus the production of methylmercury. Freshwater biofilms were sampled in the summer using artificial Teflon substrates submerged for over a year to allow natural community colonization in the littoral zone of a Boreal Shield lake. Inside biofilms, concentrations of different extracellular thiol species (thioglycolic acid, l-cysteine-l-glycine, cysteine, and glutathione) were up to 3 orders of magnitude greater than in the surrounding water column, potentially more readily controlling mercury speciation than in the water column. All biofilm thiols except thioglycolic acid were highly correlated to chlorophyll a, likely indicating an algal origin. Extracellular total mercury represented 3 ± 1% of all biofilm mercury and was preferentially found in the capsular fraction. Levels of LMW thiols of presumed algal origins were highly correlated with total mercury in the mobile colloidal fraction of biofilms. We propose that periphytic phototrophic microorganisms such as algae likely affect the bioavailability of mercury through the exudation of LMW thiols, and thus they may play a key role in the production of methylmercury in biofilms. PMID:26011687

  2. Susceptibility and molecular characterization of Candida species from patients with vulvovaginitis.

    PubMed

    Fornari, Gheniffer; Vicente, Vania Aparecida; Gomes, Renata Rodrigues; Muro, Marisol Dominguez; Pinheiro, Rosangela Lameira; Ferrari, Carolina; Herkert, Patricia Fernanda; Takimura, Marcos; Carvalho, Newton Sérgio de; Queiroz-Telles, Flavio

    2016-01-01

    Vulvovaginal candidiasis affects women of reproductive age, which represents approximately 15-25% of vaginitis cases. The present study aimed to isolate and characterize yeast from the patients irrespective of the presentation of clinical symptoms. The isolates were subjected to in vitro susceptibility profile and characterization by molecular markers, which intended to assess the distribution of species. A total of 40 isolates were obtained and identified through the CHROMagar, API20aux and by ITS and D1/D2 regions sequencing of DNAr gene. Candida albicans strains were genotyped by the ABC system and the isolates were divided into two genotypic groups. The identity of the C. albicans, C. glabrata, C. guilliermondii, C. kefyr and Saccharomyces cerevisiae isolates was confirmed by the multilocus analysis. The strains of Candida, isolated from patients with complications, were found to be resistant to nystatin but sensitive to fluconazole, amphotericin B and ketoconazole, as observed by in vitro sensitivity profile. The isolates from asymptomatic patients, i.e., the colonized group, showed a dose-dependent sensitivity to the anti-fungal agents, fluconazole and amphotericin B. However, the isolates of C. albicans that belong to distinct genotypic groups showed the same in vitro susceptibility profile. PMID:26991298

  3. New Molecular Species In Comet C/1995 (Hale-Bopp) Observed with the Caltech Submillimeter Observatory

    NASA Technical Reports Server (NTRS)

    Lis, D. C.; Mehringer, D. M.; Benford, D.; Gardner, M.; Phillips, T. G.; Bockelee-Morvan, D.; Biver, N.; Colom, P.; Crovisier, J.; Despois, D.; Rauer, H.

    1998-01-01

    We present millimeter-wave observations of HNCO, HC3N, SO, NH2CHO, H(13)CN, and H3O(+) in comet C/1995 O1 (Hale-Bopp) obtained in February-April, 1997 with the Caltech Submillimeter Observatory (CSO). HNCO, first detected at the CSO in comet C/1996 B2 (Hyakutake), is securely confirmed in comet Hale-Bopp via observations of three rotational transitions. The derived abundance with respect to H2O is (4-13) x 10(exp -4). HC3N, SO, and NH2CHO are detected for the first time in a comet. The fractional abundance of HC3N based on observations of three rotational lines is (1.9 +/- 0.2) x 10(exp -4). Four transitions of SO are detected and the derived fractional abundance, (2-8) x 10(exp -3), is higher than the upper limits derived from UV observations of previous comets. Observations of NH2CHO imply a fractional abundance of (1-8) x 10(exp -4). H3O(+) is detected for the first time from the ground. The H(13)CN (3-2) transition is also detected and the derived HCN/H(13)CN abundance ratio is 90 +/- 15, consistent with the terrestrial C-13/C-12 ratio. in addition, a number of other molecular species are detected, including HNC, OCS, HCO(+), CO(+), and CN (the last two are first detections in a comet at radio wavelengths).

  4. Formation of Aldehydic Phosphatidylcholines during the Anaerobic Decomposition of a Phosphatidylcholine Bearing the 9-Hydroperoxide of Linoleic Acid

    PubMed Central

    2016-01-01

    Lipid oxidation-derived carbonyl compounds are associated with the development of various physiological disorders. Formation of most of these products has recently been suggested to require further reactions of oxygen with lipid hydroperoxides. However, in rat and human tissues, the formation of 4-hydroxy-2-nonenal is greatly elevated during hypoxic/ischemic conditions. Furthermore, a previous study found an unexpected result that the decomposition of a phosphatidylcholine (PC) bearing the 13-hydroperoxide of linoleic acid under a nitrogen atmosphere afforded 9-oxononanoyl-PC rather than 13-oxo-9,11-tridecadienoyl-PC as the main aldehydic PC. In the present study, products of the anaerobic decomposition of a PC bearing the 9-hydroperoxide of linoleic acid were analysed by electrospray ionization mass spectrometry. 9-Oxononanoyl-PC (ONA-PC) and several well-known bioactive aldehydes including 12-oxo-9-hydroperoxy-(or oxo or hydroxy)-10-dodecenoyl-PCs were detected. Hydrolysis of the oxidized PC products, methylation of the acids obtained thereby, and subsequent gas chromatography-mass spectroscopy with electron impact ionization further confirmed structures of some of the key aldehydic PCs. Novel, hydroxyl radical-dependent mechanisms of formation of ONA-PC and peroxyl-radical dependent mechanisms of formation of the rest of the aldehydes are proposed. The latter mechanisms will mainly be relevant to tissue injury under hypoxic/anoxic conditions, while the former are relevant under both normoxia and hypoxia/anoxia. PMID:27366754

  5. Molecular abundances and low-mass star formation. 1: Si- and S-bearing species toward IRAS 16293-2422

    NASA Technical Reports Server (NTRS)

    Blake, Geoffrey A.; Dishoek, Ewine F. Van; Jansen, David J.; Groesbeck, T. D.; Mundy, Lee G.

    1994-01-01

    Results from millimeter and submillimeter spectral line surveys of the protobinary source Infrared Astronomical Satellite (IRAS) 16293-2422 are presented. Here we outline the abundances of silicon- and sulfur-containing species. A combination of rotation diagram and full statistical equilibrium/radiative transfer calculations is used to constrain the physical conditions toward IRAS 16293 and to construct its beam-averaged chemical composition over a 10 to 20 sec (1600 to 3200 AU) scale. The chemical complexity as judged by species such as SiO, OCS, and H2S, is intermediate between that of dark molecular clouds such as L134N and hot molecular cloud cores such as Orion KL. From the richness of the spectra compared to other young stellar objects of similar luminosity, it is clear that molecular abundances do not scale simply with mass; rather, the chemistry is a strong function of evolutionary state, i.e., age.

  6. Barcoding against a paradox? Combined molecular species delineations reveal multiple cryptic lineages in elusive meiofaunal sea slugs

    PubMed Central

    2012-01-01

    Background Many marine meiofaunal species are reported to have wide distributions, which creates a paradox considering their hypothesized low dispersal abilities. Correlated with this paradox is an especially high taxonomic deficit for meiofauna, partly related to a lower taxonomic effort and partly to a high number of putative cryptic species. Molecular-based species delineation and barcoding approaches have been advocated for meiofaunal biodiversity assessments to speed up description processes and uncover cryptic lineages. However, these approaches show sensitivity to sampling coverage (taxonomic and geographic) and the success rate has never been explored on mesopsammic Mollusca. Results We collected the meiofaunal sea-slug Pontohedyle (Acochlidia, Heterobranchia) from 28 localities worldwide. With a traditional morphological approach, all specimens fall into two morphospecies. However, with a multi-marker genetic approach, we reveal multiple lineages that are reciprocally monophyletic on single and concatenated gene trees in phylogenetic analyses. These lineages are largely concordant with geographical and oceanographic parameters, leading to our primary species hypothesis (PSH). In parallel, we apply four independent methods of molecular based species delineation: General Mixed Yule Coalescent model (GMYC), statistical parsimony, Bayesian Species Delineation (BPP) and Automatic Barcode Gap Discovery (ABGD). The secondary species hypothesis (SSH) is gained by relying only on uncontradicted results of the different approaches (‘minimum consensus approach’), resulting in the discovery of a radiation of (at least) 12 mainly cryptic species, 9 of them new to science, some sympatric and some allopatric with respect to ocean boundaries. However, the meiofaunal paradox still persists in some Pontohedyle species identified here with wide coastal and trans-archipelago distributions. Conclusions Our study confirms extensive, morphologically cryptic diversity among

  7. Molecular phylogeny of the genus Asparagus (Asparagaceae) explains interspecific crossability between the garden asparagus (A. officinalis) and other Asparagus species.

    PubMed

    Kubota, Shosei; Konno, Itaru; Kanno, Akira

    2012-02-01

    The genus Asparagus comprises approximately 200 species, some of which are commercially cultivated, such as the garden asparagus (A. officinalis). Many Asparagus species, including A. officinalis, are dioecious and have been grouped into a subgenus distinct from that of hermaphroditic species. Although many interspecific crossings have been attempted to introduce useful traits into A. officinalis, only some of the dioecious species were found to be cross-compatible with A. officinalis. Here, molecular phylogenetic analyses were conducted to determine whether interspecific crossability is proportional to the genetic distance between the crossing pairs and to further clarify the evolutionary history of the Asparagus genus. A clade with all cross-compatible species and no cross-incompatible species was recovered in the phylogenetic tree based on analyses of non-coding cpDNA regions. In addition, a sex-linked marker developed for A. officinalis amplified a male-specific region in all cross-compatible species. The phylogenetic analyses also provided some insights about the evolutionary history of Asparagus; for example, by indicating that the genus had its origin in southern Africa, subsequently spreading throughout the old world through intensive speciation and dispersal. The results also suggest that dioecious species were derived from a single evolutionary transition from hermaphroditism in Asparagus. These findings not only contribute towards the understanding of the evolutionary history of the genus but may also facilitate future interspecific hybridization programs involving Asparagus species. PMID:21947345

  8. The Equilibria of Diosgenin-Phosphatidylcholine and Diosgenin-Cholesterol in Monolayers at the Air/Water Interface.

    PubMed

    Janicka, Katarzyna; Jastrzebska, Izabella; Petelska, Aneta Dorota

    2016-08-01

    Diosgenin (Dio) has shown many treatment properties, but the most important property is cytotoxic activity in cancer cells. In this study, we investigated monolayers of Dio, cholesterol (Ch), and phosphatidylcholine (PC) at the air/water interface. The measurements were carried with a Langmuir Teflon trough and a Nima 9000 tensiometer program. The surface tension values of pure and mixed monolayers were used to calculate π-A isotherms and determine molecular surface areas. We were able to demonstrate the formation of complexes between Dio and PC and Dio and Ch molecules also. We considered the equilibrium between individual components and the formed complexes. In addition, we established that diosgenin and the lipids formed highly stable 1:1 complexes. PMID:27350149

  9. Half of the European fruit fly species barcoded (Diptera, Tephritidae); a feasibility test for molecular identification

    PubMed Central

    Smit, John; Reijnen, Bastian; Stokvis, Frank

    2013-01-01

    Abstract A feasibility test of molecular identification of European fruit flies (Diptera: Tephritidae) based on COI barcode sequences has been executed. A dataset containing 555 sequences of 135 ingroup species from three subfamilies and 42 genera and one single outgroup species has been analysed. 73.3% of all included species could be identified based on their COI barcode gene, based on similarity and distances. The low success rate is caused by singletons as well as some problematic groups: several species groups within the genus Terellia and especially the genus Urophora. With slightly more than 100 sequences – almost 20% of the total – this genus alone constitutes the larger part of the failure for molecular identification for this dataset. Deleting the singletons and Urophora results in a success-rate of 87.1% of all queries and 93.23% of the not discarded queries as correctly identified. Urophora is of special interest due to its economic importance as beneficial species for weed control, therefore it is desirable to have alternative markers for molecular identification. We demonstrate that the success of DNA barcoding for identification purposes strongly depends on the contents of the database used to BLAST against. Especially the necessity of including multiple specimens per species of geographically distinct populations and different ecologies for the understanding of the intra- versus interspecific variation is demonstrated. Furthermore thresholds and the distinction between true and false positives and negatives should not only be used to increase the reliability of the success of molecular identification but also to point out problematic groups, which should then be flagged in the reference database suggesting alternative methods for identification. PMID:24453563

  10. Molecular responses of Lotus japonicus to parasitism by the compatible species Orobanche aegyptiaca and the incompatible species Striga hermonthica

    PubMed Central

    Hiraoka, Yukihiro; Ueda, Hiroaki; Sugimoto, Yukihiro

    2009-01-01

    Lotus japonicus genes responsive to parasitism by the compatible species Orobanche aegyptiaca and the incompatible species Striga hermonthica were isolated by using the suppression subtractive hybridization (SSH) strategy. O. aegyptiaca and S. hermonthica parasitism specifically induced the expression of genes involved in jasmonic acid (JA) biosynthesis and phytoalexin biosynthesis, respectively. Nodulation-related genes were almost exclusively found among the Orobanche-induced genes. Temporal gene expression analyses revealed that 19 out of the 48 Orobanche-induced genes and 5 out of the 48 Striga-induced genes were up-regulated at 1 dai. Four genes, including putative trypsin protease inhibitor genes, exhibited systemic up-regulation in the host plant parasitized by O. aegyptiaca. On the other hand, S. hermonthica attachment did not induce systemic gene expression. PMID:19088337

  11. A species boundary within the Chinese Kurixalus odontotarsus species group (Anura: Rhacophoridae): New insights from molecular evidence.

    PubMed

    Yu, Guohua; Zhang, Mingwang; Yang, Junxing

    2010-09-01

    We construct the phylogeny of the Kurixalus odontotarsus species group using two mitochondrial (12S rRNA and 16S rRNA) genes in an attempt to delimit species boundaries within the Chinese K. odontotarsus group. With strong support values, three major clades are obtained, and all phylogenetic analyses reject monophyly of K. odontotarsus. The Tibetan lineage of K. odontotarsus was clustered with Kurixalus verrucosus from Myanmar (labeled Clade I); K. odontotarsus haplotypes from the type locality and nearby regions formed a distinct clade (labeled Clade II), and K. odontotarsus haplotypes from other places, together with those from Kurixalus bisacculus, K. verrucosus from Vietnam, and Kurixalus hainanus, formed a distinct clade (labeled Clade III). Clade II is the sister taxon to Clade III. The average uncorrected p-distance of 16S rRNA sequences between these three major clades range from 3.11% to 7.88%, which is obviously higher than that within these three major clades (0.03-1.89%). We propose that K. odontotarsus, K. bisacculus, and K. verrucosus should be treated as three independent species. The Tibetan lineage of K. odontotarsus does not belong to K. odontotarsus, and we tentatively place it in K. verrucosus. Kurixalus hainanus is considered a synonym of K. bisacculus. The distribution range of K. bisacculus should be expanded widely to include most regions of South China, and in China the distribution of K. odontotarsus should be limited to its type locality and nearby regions. PMID:20472079

  12. Intermolecular interactions of lysobisphosphatidic acid with phosphatidylcholine in mixed bilayers.

    PubMed

    Holopainen, Juha M; Söderlund, Tim; Alakoskela, Juha-Matti; Säily, Matti; Eriksson, Ove; Kinnunen, Paavo K J

    2005-01-01

    Lysobisphosphatidic acid (LBPA) can be regarded to represent a unique derivative of phosphatidylglycerol. This lipid is highly enriched in late endosomes where it can comprise up to 10-15 mol% of all lipids and in these membranes, LBPA appears to be segregated into microdomains. We studied the thermotropic behavior of pure dioleoyl-LBPA mono- and bilayers using Langmuir-lipid monolayers, electron microscopy, differential scanning calorimetry (DSC), and fluorescence spectroscopy. LBPA formed metastable, liquid-expanded monolayers at an air/buffer interface, and its compression isotherms lacked any indication for structural phase transitions. Neat LBPA formed multilamellar vesicles with no structural transitions or phase transitions between 10 and 80 degrees C at a pH range of 3.0-7.4. We then proceeded to study mixed LBPA/dipalmitoylphosphatidylcholine (DPPC) bilayers by DSC and fluorescence spectroscopy. Incorporating increasing amounts of LBPA (up to X(LBPA) (molar fraction)=0.10) decreased the co-operativity of the main transition for DPPC, and a decrease in the main phase transition as well as pretransition temperature of DPPC was observed yet with no effect on the enthalpy of this transition. In keeping with the DSC data for DPPC, 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC)/LBPA mixed bilayers were more fluid, and no evidence for lateral phase segregation was observed. These results were confirmed using fluorescence microscopy of Langmuir-lipid films composed of POPC and LBPA up to X(LBPA)=0.50 with no evidence for lateral phase separation. As late endosomes are eminently acidic, we examined the effect of lowering pH on lateral organization of mixed PC/LBPA bilayers by DSC and fluorescence spectroscopy. Even at pH 3.0, we find no evidence of LBPA-induced microdomain formation at LBPA contents found in cellular organelles. PMID:15589226

  13. Alterations in phosphatidylcholine synthesis are associated with taxol resistance

    SciTech Connect

    Sorbara, L.R.

    1986-01-01

    A taxol resistant variant (J7/TAX-50) of the murine macrophage-like cell line J774.2 has been developed in vitro. The LD/sub 50/ of taxol for the resistant cells is 800-fold greater than that for the parental cell line. The J7/TAX-50 cells display phenotypic traits which are associated with multidrug resistance. J7/TAX-50 is unstably resistant and must be maintained in the presence of taxol. Cells grown in the absence of taxol for 30 days revert to drug sensitivity, and the membrane phosphoglycoprotein is lost. In contrast, the return to a normal level of drug accumulation is prolonged and requires over 8 months of growth in the absence of taxol. To characterize further the parental, resistant and revertant cell lines, the major lipids have been analyzed by 2D-chromatography and HPLC. The steady-state level of phosphatidylcholine (PC) in J7/TAX-50 is greater than in the parental or revertant cell lines. Pulse-chase studies performed with /sup 14/C-choline or /sup 32/P-orthophosphate demonstrated an increase in the turnover of PC in J7/TAX-50. Analysis by gas chromatography/mass spectrometry of the composition of the major phospholipids indicated that fatty acids attached to the sn1- and 2-positions of PC are the same in the resistant and parental cell lines. These studies suggest that an increased level of PC in the membrane may be related to drug resistance and responsible for the prolonged decrease in steady-state drug association in J7/TAX-50 grown in the absence of taxol.

  14. Molecular Simulations of the Diffusion of Uranyl Carbonate Species in Nanosized Mineral Fractures

    NASA Astrophysics Data System (ADS)

    Kerisit, S.; Liu, C.

    2010-12-01

    Uranium is a major groundwater contaminant at uranium processing and mining sites as a result of intentional and accidental discharges of uranium-containing waste products into subsurface environments. Recent characterization has shown that uranium preferentially associates with intragrain and intra-aggregate domains in some of the uranium-contaminated sediments collected from the US Department of Energy Hanford Site [1, 2]. In these sediments, uranium existed as precipitated and/or adsorbed phases in grain micropores with nano- to microscale sizes. Desorption and diffusion characterization studies and continuum-scale modeling indicated that ion diffusion in the microfractures is a major mechanism that led to preferential uranium concentration in the microfracture regions and will control the future mobility of uranium in the subsurface sediments [1, 3-4]. However, the diffusion properties of uranyl species in the intragrain regions, especially at the solid-liquid interface, are still poorly understood. Therefore, a general aim of this work is to provide atomic-level insights into the contribution of microscopic surface effects to the slow diffusion process of uranyl species in porous media with nano- to microsized fractures. In this presentation, we will first present molecular dynamics (MD) simulations of feldspar-water interfaces to investigate their interfacial structure and dynamics and establish a theoretical framework for subsequent simulations of water and ion diffusion at these interfaces [5]. We will then report on MD simulations carried out to probe the effects of confinement and of the presence of the mineral surface on the diffusion of water and electrolyte ions in nanosized feldspar fractures [6]. Several properties of the mineral-water interface were varied, such as the fracture width, the ionic strength of the contacting solution, and the surface charge. Our calculations reveal a 2.0-2.5 nm interfacial region within which the diffusion properties of

  15. Insights about α-tocopherol and Trolox interaction with phosphatidylcholine monolayers under peroxidation conditions through Brewster angle microscopy.

    PubMed

    Castro, Carla M; Pinheiro, Marina; Lúcio, Marlene; Giner-Casares, Juan J; Camacho, Luis; Lima, José L F C; Reis, Salette; Segundo, Marcela A

    2013-11-01

    Membranes are major targets to oxidative damage, particularly due to lipid oxidation, which has been associated to aging. The role, efficacy and membrane interaction of antioxidants is still unclear, requiring further understanding of molecular interaction. Hence, the objective of this work was to evaluate the interaction between antioxidants (α-tocopherol and its aqueous soluble analog Trolox) and the monolayer formed by phosphatidylcholine molecules at air/liquid interface upon peroxidation conditions, promoted by peroxyl radicals from thermal decomposition of 2,2'-azobis(2-methylpropionamidine) (AAPH). The interaction with three different monolayers, containing (i) 1,2-dihexadecanoyl-sn-glycero-3-phosphocholine (DPPC), (ii) DDPC+α-linolenic acid, or (iii) egg yolk l-α-phosphatidylcholine (EPC), was ascertain by surface pressure (π)-molecular area (A) isotherms and by monitoring monolayer features through Brewster angle microscopy (BAM). The interaction of antioxidants with DPPC monolayers was confirmed by modifications on DPPC domain shape for α-tocopherol and through the maintenance of typical multilobed domain shape during an extended surface pressure interval for Trolox. Under peroxidation conditions, BAM images showed a clear interaction between components of AAPH subphase with the monolayer through changes on DPPC domain shape and appearance of white dots, located mainly at the frontier between the condensed and expanded liquid phases. White branched structures were also observed whenever both α-linolenic acid and α-tocopherol were present, indicating the segregation of these components within the monolayer, which is highly significant in biological systems. For EPC monolayers, no information from BAM was obtained but π-A isotherms confirmed the existence of the same interactions observed within the other two monolayers. PMID:23907050

  16. Development of two molecular approaches for differentiation of clinically relevant yeast species closely related to Candida guilliermondii and Candida famata.

    PubMed

    Feng, Xiaobo; Wu, Jingsong; Ling, Bo; Yang, Xianwei; Liao, Wanqing; Pan, Weihua; Yao, Zhirong

    2014-09-01

    The emerging pathogens Candida palmioleophila, Candida fermentati, and Debaryomyces nepalensis are often misidentified as Candida guilliermondii or Candida famata in the clinical laboratory. Due to the significant differences in antifungal susceptibilities and epidemiologies among these closely related species, a lot of studies have focused on the identification of these emerging yeast species in clinical specimens. Nevertheless, limited tools are currently available for their discrimination. Here, two new molecular approaches were established to distinguish these closely related species. The first approach differentiates these species by use of restriction fragment length polymorphism analysis of partial internal transcribed spacer 2 (ITS2) and large subunit ribosomal DNA with the enzymes BsaHI and XbaI in a double digestion. The second method involves a multiplex PCR based on the intron size differences of RPL18, a gene coding for a protein component of the large (60S) ribosomal subunit, and species-specific amplification. These two methods worked well in differentiation of these closely related yeast species and have the potential to serve as effective molecular tools suitable for laboratory diagnoses and epidemiological studies. PMID:24951804

  17. Molecular phylogeny and species delimitation within the ciliate genus Spirostomum (Ciliophora, Postciliodesmatophora, Heterotrichea), using the internal transcribed spacer region.

    PubMed

    Shazib, Shahed Uddin Ahmed; Vďačný, Peter; Kim, Ji Hye; Jang, Seok Won; Shin, Mann Kyoon

    2016-09-01

    Morphological and molecular delimitation of Spirostomum species is currently under debate. We addressed species boundaries within the genus Spirostomum, using the ITS1-5.8S-ITS2 region and the secondary structure of the ITS2 molecule, and 18S and 28S (D1D2) sequences additionally. The Spirostomum ITS region is among the shortest within the ciliates hitherto studied. The Spirostomum ITS2 molecule matches the "ring model", but exhibits only two helices radiating from a common loop. According to comparative analyses, they very likely correspond to helices II and III of other eukaryotes. Our phylogenetic analyses of the ITS region revealed a complex genealogical structure within the genus Spirostomum. However, boundaries among Spirostomum species could not be unambiguously determined either by phylogenetic trees, networks or sequence divergence cutoffs, because ITS2 sequences transcended species boundaries of the following morphospecies: S. ambiguum, S. minus, S. subtilis and S. teres. According to molecular diversity analysis, this is very likely caused by polymorphism in S. minus and S. teres, and by the lack of variability in S. ambiguum and S. subtilis. No compensatory base changes (CBCs) were detected in helices of the ITS2 molecule between different Spirostomum species, documenting that CBC analysis per se is not able to effectively discriminate Spirostomum species. PMID:27261253

  18. Molecular phylogeny and chromosome evolution among the creeping herbaceous Oxalis species of sections Corniculatae and Ripariae (Oxalidaceae).

    PubMed

    Vaio, M; Gardner, A; Emshwiller, E; Guerra, M

    2013-08-01

    Oxalis sections Corniculatae DC. and Ripariae Lourteig are composed mainly of creeping herbs. They not only share strong morphological similarities, such as the presence of a reptant stem but also some cytogenetic characteristics. Several species in section Corniculatae share a base chromosome number x=5 with species in section Ripariae, while other species in the former have a x=6. We used a molecular and cytogenetic approach to determine the phylogenetic relationships, test the previous taxonomic classification and study the genome rearrangements that led to the differences in chromosome size and basic chromosome number between both sections. Phylogenetic relationships were inferred based on DNA sequences from chloroplast and nuclear ribosomal ITS. The molecular phylogenetic analyses found that neither of the sections are monophyletic, but do support two clades. The first group contains diploid species with x=5, large chromosomes and high DNA content and the second diploid and polyploidy species with x=6, small chromosomes and low DNA content. The x=5 clade comprises species of both sections, while the x=6 clade was formed mainly by section Corniculatae species and O. serpens from section Ripariae. Our results suggest that x=5 and high DNA content are derived conditions, which may have resulted from descendent disploidy and proliferation of transposable elements. Thus, cytogenetic data superimposed on the phylogeny have shown two different modes of chromosome evolution in both lineages: (1) chromosome rearrangements and increase in genome size in the x=5 lineage and (2) polyploidy playing the main role in chromosome evolution among species in the x=6 species. A taxonomic revision for the two sections is suggested. PMID:23562801

  19. Molecular characterization of cryptic and sympatric lymnaeid species from the Galba/Fossaria group in Mendoza Province, Northern Patagonia, Argentina

    PubMed Central

    2013-01-01

    Background Freshwater lymnaeid snails can act as the intermediate hosts for trematode parasites such as the liver fluke Fasciola hepatica, that cause significant economic and biomedical burden worldwide, particularly through bovine fascioliasis. Transmission potential is tightly coupled to local compatibility with snail hosts, so accurate identification of lymnaeid species is crucial for understanding disease risk, especially when invasive species are encountered. Mendoza Province, in Argentina, is a center of livestock production and also an area of endemic fascioliasis transmission. However, the distribution of lymnaeid species in the region is not well known. Methods This study examined lymnaeid snails from seven localities in the Department of Malarguë, Mendoza Province, using morphological and molecular analyses and also describing ecological variables associated with snail presence. Results While morphological characters identified two species of lymnaeid, Galba truncatula and G. viatrix, molecular data revealed a third, cryptic species, G. neotropica, which was sympatric with G. viatrix. G. truncatula was exclusively found in high altitude (>1900 meters above sea level [masl]) sites, whereas mixed G. neotropica/G. viatrix localities were at middle elevations (1300–1900 masl), and G. viatrix was found alone at the lowest altitude sites (<1300 masl). Phylogenetic analysis using two mitochondrial markers revealed G. neotropica and G. viatrix to be closely related, and given their morphological similarities, their validities as separate taxonomic entities should be questioned. Conclusions This study highlights the need of a robust taxonomic framework for the identification of lymnaeid snails, incorporating molecular, morphological and ecological variables while avoiding nomenclature redundancy. As the three species observed here, including one alien invasive species, are considered hosts of varying susceptibility to Fasciola parasites, and given the economic

  20. Deconstructing a Species-Complex: Geometric Morphometric and Molecular Analyses Define Species in the Western Rattlesnake (Crotalus viridis)

    PubMed Central

    Davis, Mark A.; Douglas, Marlis R.; Collyer, Michael L.; Douglas, Michael E.

    2016-01-01

    Morphological data are a conduit for the recognition and description of species, and their acquisition has recently been broadened by geometric morphometric (GM) approaches that co-join the collection of digital data with exploratory ‘big data’ analytics. We employed this approach to dissect the Western Rattlesnake (Crotalus viridis) species-complex in North America, currently partitioned by mitochondrial (mt)DNA analyses into eastern and western lineages (two and seven subspecies, respectively). The GM data (i.e., 33 dorsal and 50 lateral head landmarks) were gleaned from 2,824 individuals located in 10 museum collections. We also downloaded and concatenated sequences for six mtDNA genes from the NCBI GenBank database. GM analyses revealed significant head shape differences attributable to size and subspecies-designation (but not their interactions). Pairwise shape distances among subspecies were significantly greater than those derived from ancestral character states via squared-change parsimony, with the greatest differences separating those most closely related. This, in turn, suggests the potential for historic character displacement as a diversifying force in the complex. All subspecies, save one, were significantly differentiated in a Bayesian discriminant function analysis (DFA), regardless of whether our priors were uniform or informative (i.e., mtDNA data). Finally, shape differences among sister-clades were significantly greater than expected by chance alone under a Brownian model of evolution, promoting the hypothesis that selection rather than drift was the driving force in the evolution of the complex. Lastly, we combine head shape and mtDNA data so as to derived an integrative taxonomy that produced robust boundaries for six OTUs (operational taxonomic units) of the C. viridis complex. We suggest these boundaries are concomitant with species-status and subsequently provide a relevant nomenclature for its recognition and representation. PMID

  1. Deconstructing a Species-Complex: Geometric Morphometric and Molecular Analyses Define Species in the Western Rattlesnake (Crotalus viridis).

    PubMed

    Davis, Mark A; Douglas, Marlis R; Collyer, Michael L; Douglas, Michael E

    2016-01-01

    Morphological data are a conduit for the recognition and description of species, and their acquisition has recently been broadened by geometric morphometric (GM) approaches that co-join the collection of digital data with exploratory 'big data' analytics. We employed this approach to dissect the Western Rattlesnake (Crotalus viridis) species-complex in North America, currently partitioned by mitochondrial (mt)DNA analyses into eastern and western lineages (two and seven subspecies, respectively). The GM data (i.e., 33 dorsal and 50 lateral head landmarks) were gleaned from 2,824 individuals located in 10 museum collections. We also downloaded and concatenated sequences for six mtDNA genes from the NCBI GenBank database. GM analyses revealed significant head shape differences attributable to size and subspecies-designation (but not their interactions). Pairwise shape distances among subspecies were significantly greater than those derived from ancestral character states via squared-change parsimony, with the greatest differences separating those most closely related. This, in turn, suggests the potential for historic character displacement as a diversifying force in the complex. All subspecies, save one, were significantly differentiated in a Bayesian discriminant function analysis (DFA), regardless of whether our priors were uniform or informative (i.e., mtDNA data). Finally, shape differences among sister-clades were significantly greater than expected by chance alone under a Brownian model of evolution, promoting the hypothesis that selection rather than drift was the driving force in the evolution of the complex. Lastly, we combine head shape and mtDNA data so as to derived an integrative taxonomy that produced robust boundaries for six OTUs (operational taxonomic units) of the C. viridis complex. We suggest these boundaries are concomitant with species-status and subsequently provide a relevant nomenclature for its recognition and representation. PMID:26816132

  2. Phosphatidylcholine kinetics in neonatal rat lungs and the effects of rhuKGF and betamethasone.

    PubMed

    Bernhard, Wolfgang; Gesche, Jens; Raith, Marco; Poets, Christian F

    2016-05-15

    Surfactant, synthesized by type II pneumocytes (PN-II), mainly comprises phosphatidylcholine (PC) and is essential to prevent neonatal respiratory distress. Furthermore, PC is essential to lung tissue growth and maintenance as a membrane component. Recent findings suggest that the lung contributes to systemic lipid homeostasis via PC export through ABC-A1 transporter expression. Hence it is important to consider pharmacological interventions in neonatal lung PC metabolism with respect to such export. Five-day-old rats were treated with carrier (control), intraperitoneal betamethasone, subcutaneous recombinant human keratinocyte growth factor (rhuKGF), or their combination for 48 h. Animals were intraperitoneally injected with 50 mg/kg [D9-methyl]choline chloride 1.5, 3.0, and 6.0 h before death at day 7, and lung lavage fluid (LLF) and tissue were harvested. Endogenous PC, D9-labeled PC species, and their water-soluble precursors (D9-)choline and (D9-)phosphocholine were determined by tandem mass spectrometry. Treatment increased secreted and tissue PC pools but did not change equilibrium composition of PC species in LLF. However, all treatments increased specific surfactant components in tissue. In control rats, peak D9-PC in lavaged lung was reached after 3 h and was decreased at 6 h. Only 13% of this net loss in lavaged lung was found in LLF. Such decrease was not present in lungs treated with betamethasone and/or with rhuKGF. D9-PC loss at 3-6 h and PC synthesis calculated from D9 enrichment of phosphocholine indicated that daily synthesis rate is higher than total pool size. We conclude that lung tissue contributes to systemic PC homeostasis in neonatal rats, which is altered by glucocorticoid and rhuKGF treatment. PMID:26944086

  3. Eriocaenus (Acari: Trombidiformes: Eriophyoidea), a new genus from Equisetum spp. (Equisetaceae): morphological and molecular delimitation of two morphologically similar species.

    PubMed

    Petanović, Radmila U; Amrine, James W; Chetverikov, Philipp E; Cvrković, Tatjana K

    2015-01-01

    Surveys conducted on horsetails, Equisetum spp. (Equisetaceae), in Serbia led to the discovery of a new eriophyoid mite genus while searching for a classical biological control agent against these weeds in New Zealand. Eriocaenus gen. n. is described based on the type species Aceria equiseti Farkas, 1960 (transferred to Eriophyes by Farkas 1965; herein reassigned to the new genus) and Eriocaenus ramosissimi n. sp., a new species discovered on Equisetum ramosissimum Desf. in Serbia. Eriocaenus equiseti (Farkas, 1960), previously only known from Hungary, was found in Serbia for the first time on Equisetum arvense L. and Equisetum telmateia Ehrh., and is redescribed. Species descriptions include line drawings as well as phase contrast (PCLM), differential interference contrast (DIC) and scanning electron (SEM) micrographs. The differential diagnosis between the two Eriocaenus species is supplemented by molecular differentiation of 28S rDNA sequences including D2 fragments for both mites. PMID:26623881

  4. Molecular phylogenetic relationships of the Liolaemus rothi complex and a new species of lizard from Auca Mahuida Volcano (Squamata: Liolaemini).

    PubMed

    Avila, Luciano Javier; Olave, Melisa; Perez, Cristian Hernan Fulvio; Perez, Daniel Roberto; Morando, Mariana

    2013-01-01

    A new species of lizard of the genus Liolaemus from Neuquén Province, western Argentina, is described. The new species is a member of the Liolaemus rothi species complex, and mitochondrial and nuclear molecular data show it as sister taxon of the clade composed of (L. hermannunezi (L. tromen + L. loboi)), differing in size, squamation, coloration, and sexual dimorphism from the other species of this group. Liolaemus sitesi sp. nov. has a dark body coloration with series of notched blotches on the dorsum, with bright spots, and a very iridescent yellow-green coloration in natural light. Liolaemus sitesi sp. nov. is found only in the Auca Mahuida volcano and is terrestrial, dwelling on the stony slopes with sandy soil between 1300 m and the volcano summit. PMID:24614465

  5. Molecular evidence of two cryptic species of Stramonita (Mollusca, Muricidae) in the southeastern Atlantic coast of Brazil

    PubMed Central

    De Biasi, Juliana Beltramin; Tomás, Acácio Ribeiro Gomes; Hilsdorf, Alexandre Wagner Silva

    2016-01-01

    Abstract Snails of the genus Stramonita are commonly found in the rocky intertidal habitat of the western Atlantic Ocean coast. They belong to a monophyletic taxon that occurs along the tropical and warm-temperate Atlantic and eastern Pacific rocky shores. This genus comprises different valid species and members of the S. haemastoma complex. In the present study, samples of Stramonita were collected from three different regions of southeastern Brazil. Partial sequences of two mitochondrial genes, COI and 16S rRNA, were used to compare nucleotides sequences between Stramonita specimens. Levels of nucleotide divergence greater than 2% across the three sampled regions were used for differentiation at the species level. One of the identified species was S. brasiliensis, which has recently been described by molecular analysis; the other species may represent S. haemastoma, not yet described in the southeastern Brazilian coast. PMID:27560649

  6. Molecular evidence of two cryptic species of Stramonita (Mollusca, Muricidae) in the southeastern Atlantic coast of Brazil.

    PubMed

    De Biasi, Juliana Beltramin; Tomás, Acácio Ribeiro Gomes; Hilsdorf, Alexandre Wagner Silva

    2016-01-01

    Snails of the genus Stramonita are commonly found in the rocky intertidal habitat of the western Atlantic Ocean coast. They belong to a monophyletic taxon that occurs along the tropical and warm-temperate Atlantic and eastern Pacific rocky shores. This genus comprises different valid species and members of the S. haemastoma complex. In the present study, samples of Stramonita were collected from three different regions of southeastern Brazil. Partial sequences of two mitochondrial genes, COI and 16S rRNA, were used to compare nucleotides sequences between Stramonita specimens. Levels of nucleotide divergence greater than 2% across the three sampled regions were used for differentiation at the species level. One of the identified species was S. brasiliensis, which has recently been described by molecular analysis; the other species may represent S. haemastoma, not yet described in the southeastern Brazilian coast. PMID:27560649

  7. Species hybridization between a female blue whale (Balaenoptera musculus) and a male fin whale (B. physalus): molecular and morphological documentation.

    PubMed

    Spilliaert, R; Vikingsson, G; Arnason, U; Palsdottir, A; Sigurjonsson, J; Arnason, A

    1991-01-01

    In 1986 a large, pregnant, female balaenopterid whale was caught in Icelandic waters. The animal had morphological characteristics of both the blue and the fin whale. Molecular analyses of the whale showed that it was a hybrid between a female blue whale and a male fin whale. The descent of the species hybrid was established without access to either parental specimen. Analysis of the fetus showed that it had a blue whale father. The present report of species hybridization between the two largest cetacean species, the blue and the fin whale, documents the occurrence of cetacean species hybridization in the wild. It is also the first example of any cetacean hybridization giving rise to a fertile offspring. PMID:1679066

  8. Molecular evidence of two cryptic species of Stramonita (Mollusca, Muricidae) in the southeastern Atlantic coast of Brazil.

    PubMed

    De Biasi, Juliana Beltramin; Tomás, Acácio Ribeiro Gomes; Hilsdorf, Alexandre Wagner Silva

    2016-07-01

    Snails of the genus Stramonita are commonly found in the rocky intertidal habitat of the western Atlantic Ocean coast. They belong to a monophyletic taxon that occurs along the tropical and warm-temperate Atlantic and eastern Pacific rocky shores. This genus comprises different valid species and members of the S. haemastoma complex. In the present study, samples of Stramonita were collected from three different regions of southeastern Brazil. Partial sequences of two mitochondrial genes, COI and 16S rRNA, were used to compare nucleotides sequences between Stramonita specimens. Levels of nucleotide divergence greater than 2% across the three sampled regions were used for differentiation at the species level. One of the identified species was S. brasiliensis, which has recently been described by molecular analysis; the other species may represent S. haemastoma, not yet described in the southeastern Brazilian coast. PMID:27392237

  9. Morphology delimits more species than molecular genetic clusters of invasive Pilosella

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Premise of the study: Reliable identifications of invasive species are essential for effective management. Several species of Pilosella (syn. Hieracium, Asteraceae) hawkweeds invade North America, where unreliable identification hinders their control. Here we ask (i) do morphological traits dependab...

  10. Molecular phylogeny of Niphargus boskovici (Crustacea: Amphipoda) reveals a new species from epikarst.

    PubMed

    Švara, Vid; Delić, Teo; Rađa, Tonći; Fišer, Cene

    2015-01-01

    We describe a new species of an amphipod Niphargus zagorae sp. n. and redescribe its nearest relative and morphologically similar species N. boskovici S. Karaman, 1952. We present the geographic distributions of both species, morphological diagnoses and infer their phylogenetic position within the genus based on COI, 28S and H3 markers. PMID:26250278

  11. MOLECULAR TAXONOMIC KEYS – ARE THEY THE SOLUTION FOR SPECIES IDENTIFICATION IN FORENSIC ENTOMOLOGY?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A functional diagnostic technique must have the ability to unambiguously identify and differentiate insect species. Insect species developing in cadavers are often used to estimate the time since death or postmortem interval (PMI). Accurate identification of the species involved is essential, but ex...

  12. Molecular Tools for Cryptic "Candida" Species Identification with Applications in a Clinical Laboratory

    ERIC Educational Resources Information Center

    Gamarra, Soledad; Dudiuk, Catiana; Mancilla, Estefania; Vera Garate, Maria Veronica; Guerrero, Sergio; Garcia-Effron, Guillermo

    2013-01-01

    "Candida" spp. includes more than 160 species but only 20 species pose clinical problems. "C. albicans" and "C. parapsilosis" account for more than 75% of all the fungemias worldwide. In 1995 and 2005, one "C. albicans" and two "C. parapsilosis"-related species were described, respectively. Using…

  13. Molecular analysis of six Rhynchospio Hartman, 1936 species (Annelida: Spionidae) with comments on the evolution of brooding within the group.

    PubMed

    Radashevsky, Vasily I; Malyar, Vasily V; Pankova, Victoria V; Nuzhdin, Sergey V

    2016-01-01

    Rhynchospio Hartman, 1936 is a small group of spionid polychaetes currently comprising ten described species distributed mainly in the Pacific. Five species examined to date are hermaphrodites producing spermatozoa with long nuclei, oocytes with thin and smooth envelopes, and dorsally brooding their offspring. Since our first molecular analysis of four Rhynchospio species, we have collected additional material from Northern Territory, Australia, and Oregon, USA. Herein, we describe the gamete and adult morphology of the newly collected material and use molecular analyses to provide new insight on the phylogenetic relationships of six Rhynchospio species. Adults of R. cf. foliosa from Oregon are hermaphrodites, but in contrast to other Rhynchospio, they produce spermatozoa with short nuclei (ect-aquasperm), oocytes with thick vesiculate envelopes, and likely have a holopelagic larval development. Analysis of four gene fragments, comprising mitochondrial 16S rDNA, and nuclear 18S, 28S rDNA, and Histone 3 (2516 bp in total) showed Rhynchospio to be a monophyletic group, with R. cf. foliosa being a distant sister to the five other species. Rhynchospio cf. foliosa was closer to M. arctia having ect-aquasperm and vesiculate thick-envelop oocytes (p = 14.40%) than to Spioninae members B. proboscidea and P. elegans, having introsperm and oocytes with thin and smooth envelopes (p = 15.39 and 16.54%, respectively). We hypothesize that brooding might have evolved from free-spawning inside the Rhynchospio clade, but this hypothesis should be tested in a future analysis. PMID:27395642

  14. Effects of sphingomyelin and phosphatidylcholine degradation on cyclodextrin-mediated cholesterol efflux in cultured fibroblasts.

    PubMed

    Ohvo, H; Olsio, C; Slotte, J P

    1997-11-15

    The hydrolysis of plasma membrane sphingomyelin is known to dramatically alter cellular cholesterol homeostasis in different ways, whereas the degradation of plasma membrane phosphatidylcholine has much less or no effects on cell cholesterol homeostasis [Pörn, Ares, Slotte, J. Lipid Res. 34 (1993) 1385-1392]. In this study, we used an efficient extracellular cholesterol acceptor (cyclodextrin) and determined the extent of cholesterol efflux from cultured fibroblasts in which plasma membrane sphingomyelin or phosphatidylcholine was degraded. Treatment of cells with sphingomyelinase reduced the cell sphingomyelin content by about 76% (about 13 nmol SM degraded), and dramatically increased the desorption of [3H]cholesterol from the plasma membrane to 2-hydroxypropyl-beta-cyclodextrin. The corresponding hydrolysis of cell surface phosphatidylcholine (about 12% reduction of the cellular phosphatidylcholine content, corresponding to about 12 nmol degraded PC) had almost no effect on cell [3H]cholesterol efflux. The stimulatory effect of sphingomyelin degradation on cell [3H]cholesterol efflux was reversible, since rates of [3H]cholesterol efflux dropped back to control levels when cells (in this case baby hamster kidney cells) were allowed to restore their sphingomyelin content by re-synthesis in the absence of sphingomyelinase. The findings of this study clearly demonstrate that plasma membrane sphingomyelin markedly affected the rate of cholesterol transfer between cells and an extracellular acceptor (i.e., cyclodextrin), whereas the effect of phosphatidylcholine on cholesterol efflux was much smaller. PMID:9421186

  15. Evidence for superlattice arrangements in fluid phosphatidylcholine/phosphatidylethanolamine bilayers.

    PubMed Central

    Cheng, K H; Ruonala, M; Virtanen, J; Somerharju, P

    1997-01-01

    Recently, evidence for cholesterol and phosphatidylcholine (PC) molecules to adapt superlattice arrangements in fluid lipid bilayers has been presented. Whether superlattice arrangements exist in other biologically relevant lipid membranes, such as phosphatidylethanolamine (PE)/PC, is still speculative. In this study, we have examined the physical properties of fluid 1-palmitoyl-2-oleoyl-PC (POPC) and 1-palmitoyl-2-oleoyl-PE (POPE) binary mixtures as a function of the POPE mole fraction (X(PE)) using fluorescence and Fourier transform infrared spectroscopy. At 30 degrees C, i.e., above the Tm of POPE and POPC, deviations, or dips, as well as local data scattering in the excimer-to-monomer fluorescence intensity ratio of intramolecular excimer forming dipyrenylphosphatidylcholine probe in POPE/POPC mixtures were detected at X(PE) approximately 0.04, 0.11, 0.16, 0.26, 0.33, 0.51, 0.66, 0.75, 0.82, 0.91, and 0.94. The above critical values of X(PE) coincide (within +/-0.03) with the critical mole fractions X(HX,PE) or X(R,PE) predicted by a headgroup superlattice model, which assumes that the lipid headgroups form hexagonal or rectangular superlattice, respectively, in the bilayer. Other spectroscopic data, generalized polarization of Laurdan and infrared carbonyl and phosphate stretching frequency, were also collected. Similar agreements between some of the observed critical values of X(PE) from these data and the X(HX,PE) or X(R,PE) values were also found. However, all techniques yielded critical values of X(PE) (e.g., 0.42 and 0.58) that cannot be explained by the present headgroup superlattice model. The effective cross-sectional area of the PE headgroup is smaller than that of the acyl chains. Hence, the relief of "packing frustration" of PE in the presence of PC (larger headgroup than PE) may be one of the major mechanisms in driving the PE and PC components to superlattice-like lateral distributions in the bilayer. We propose that headgroup superlattices may

  16. The interaction of phosphatidylcholine bilayers with Triton X-100.

    PubMed

    Goñi, F M; Urbaneja, M A; Arrondo, J L; Alonso, A; Durrani, A A; Chapman, D

    1986-11-01

    The interaction of multilamellar phosphatidylcholine vesicles with the non-ionic detergent Triton X-100 has been studied under equilibrium conditions, specially in the sub-lytic range of surfactant concentrations. Equilibrium was achieved in less than 24 h. Estimations of detergent binding to bilayers, using [3H]Triton X-100, indicate that the amphiphile is incorporated even at very low concentrations (below its critical micellar concentration); a dramatic increase in the amount of bound Triton X-100 occurs at detergent concentrations just below those producing membrane solubilization. Solubilization occurs at phospholipid/detergent molar ratios near 0.65 irrespective of lipid concentration. The perturbation produced by the surfactant in the phospholipid bilayer has been studied by differential scanning calorimetry, NMR and Fourier-transform infrared spectroscopy. At low detergent concentration (lipid/detergent molar ratios above 3), a reduction in 2H-NMR quadrupolar splitting occurs, suggesting a decrease in the static order of the acyl chains; the same effect is detected by Fourier-transform infrared spectroscopy in the form of blue shifts of the methylene stretching vibration bands. Simultaneously, the enthalpy variation of the main phospholipid phase transition is decreased by about a third with respect to its value in the pure lipid/water system. For phospholipid/detergent molar ratios between 3 and 1, the decrease in lipid static order does not proceed any further; rather an increase in fluidity is observed, characterized by a marked decrease in the midpoint transition temperature of the gel-to-fluid phospholipid transition. At the same time an isotropic component is apparent in both 31P-NMR and 2H-NMR spectra, and a new low-temperature endotherm is detected in differential scanning calorimetric traces. When phospholipid and Triton X-100 are present at equimolar ratios some bilayer structure persists, as judged from calorimetric observations, but NMR reveals

  17. Properties of ganglioside GM1 in phosphatidylcholine bilayer membranes.

    PubMed

    Reed, R A; Shipley, G G

    1996-03-01

    Gangliosides have been shown to function as cell surface receptors, as well as participating in cell growth, differentiation, and transformation. In spite of their multiple biological functions, relatively little is known about their structure and physical properties in membrane systems. The thermotropic and structural properties of ganglioside GM1 alone and in a binary system with 1,2-dipalmitoyl phosphatidylcholine (DPPC) have been investigated by differential scanning calorimetry (DSC) and x-ray diffraction. By DSC hydrated GM1 undergoes a broad endothermic transition TM = 26 degrees C (delta H = 1.7 kcal/mol GM1). X-ray diffraction below (-2 degrees C) and above (51 degrees C) this transition indicates a micellar structure with changes occurring only in the wide angle region of the diffraction pattern (relatively sharp reflection at 1/4.12 A-1 at -2 degrees C; more diffuse reflection at 1/4.41 A-1 at 51 degrees C). In hydrated binary mixtures with DPPC, incorporation of GM1 (0-30 mol%; zone 1) decreases the enthalpy of the DPPC pretransition at low molar compositions while increasing the TM of both the pre- and main transitions (limiting values, 39 and 44 degrees C, respectively). X-ray diffraction studies indicate the presence of a single bilayer gel phase in zone 1 that can undergo chain melting to an L alpha bilayer phase. A detailed hydration study of GM1 (5.7 mol %)/DPPC indicated a conversion of the DPPC bilayer gel phase to an infinite swelling system in zone 1 due to the presence of the negatively charged sialic acid moiety of GM1. At 30-61 mol % GM1 (zone 2), two calorimetric transitions are observed at 44 and 47 degrees C, suggesting the presence of two phases. The lower transition reflects the bilayer gel --> L alpha transition (zone 1), whereas the upper transition appears to be a consequence of the formation of a nonbilayer, micellar or hexagonal phase, although the structure of this phase has not been defined by x-ray diffraction. At > 61 mol % GM

  18. Molecular phylogeny of commercially important lobster species from Indian coast inferred from mitochondrial and nuclear DNA sequences.

    PubMed

    Jeena, N S; Gopalakrishnan, A; Radhakrishnan, E V; Kizhakudan, Joe K; Basheer, V S; Asokan, P K; Jena, J K

    2016-07-01

    Lobsters constitute low-volume high-value crustacean fishery resource along Indian coast. For the conservation and management of this declining resource, accurate identification of species and larvae is essential. The objectives of this work were to generate species-specific molecular signatures of 11 commercially important species of lobsters of families Palinuridae and Scyllaridae and to reconstruct a phylogeny to clarify the evolutionary relationships among genera and species included in this study. Partial sequences were generated for all the candidate species from sampling sites along the Indian coast using markers like Cytochrome oxidase I (COI), 16SrRNA, 12SrRNA, and 18SrRNA genes, and analyzed. The genetic identities of widely distributed Thenus species along the Indian coast to be Thenus unimaculatus and the sub-species of Panulirus homarus to be P. homarus homarus were confirmed. Phylogeny reconstruction using the individual gene and concatenated mtDNA data set were carried out. The overall results suggested independent monophyly of Scyllaridae and Stridentes of Palinuridae. The interspecific divergence was found to be highest for the 12SrRNA compared with other genes. Significant incongruence between mtDNA and nuclear 18SrRNA gene tree topologies was observed. The results hinted an earlier origin for Palinuridae compared with Scyllaridae. The DNA sequence data generated from this study will aid in the correct identification of lobster larvae and will find application in research related to larval transport and distribution. PMID:26065848

  19. Why is the molecular identification of the forensically important blowfly species Lucilia caesar and L. illustris (family Calliphoridae) so problematic?

    PubMed

    Sonet, Gontran; Jordaens, Kurt; Braet, Yves; Desmyter, Stijn

    2012-11-30

    Species of the fly genus Lucilia are commonly used in forensic investigations to estimate the postmortem interval (PMI). Two close-related species Lucilia caesar and L. illustris are difficult to identify. Previous studies showed that the mitochondrial cytochrome c oxidase subunit I (COI) marker could be used to identify many Lucilia species. However, mixed results were obtained for L. caesar and L. illustris due to some European specimens showing identical haplotypes. Here, we investigated 58 new European male specimens of L. illustris and L. caesar whose morphological identifications were checked and for which COI fragments were sequenced. In addition, two other mitochondrial (cytochrome c oxidase subunit II and 16S) and two nuclear (internal transcribed spacer 2 and 28S ribosomal RNA) markers were obtained for a subset of these samples. For each marker, genetic divergence within each species was in the same range as between species, confirming the close relationship between both species. Moreover, for each of the gene fragments, both species shared at least one haplotype/genotype. Hence, none of the molecular markers tested could be used, alone or in combination, to discriminate between L. illustris and L. caesar. PMID:22964163

  20. Species Delimitation of the Cycas segmentifida Complex (Cycadaceae) Resolved by Phylogenetic and Distance Analyses of Molecular Data

    PubMed Central

    Feng, Xiuyan; Liu, Jian; Gong, Xun

    2016-01-01

    The Cycas segmentifida complex consists of eight species whose distributions overlap in a narrow region in Southwest China. These eight taxa are also morphologically similar and are difficult to be distinguished. Consequently, their taxonomic status has been a matter of discussion in recent years. To study this species complex, we sequenced four plastid intergenic spacers (cpDNA), three nuclear genes and genotyped 12 microsatellites for the eight taxa from 19 different localities. DNA sequences were analyzed using Maximum Likelihood (ML) method and Bayesian Inference (BI), and microsatellites were analyzed using the Neighbor-joining (NJ) and structure inference methods. Results of cpDNA, nuclear gene GTP and microsatellites all rejected the hypotheses that this complex consisted of eight taxa or one distinct lineage (species) but two previously described species were adopted: Cycas guizhouensis K. M. Lan et R. F. Zou and Cycas segmentifida D. Y. Wang et C. Y. Deng. Cycas longlinensis H. T. Chang et Y. C. Zhong was included in C. guizhouensis and the other five taxa were included in C. segmentifida. Our species delimitation inferred from molecular data largely corresponds to morphological differentiation. However, the other two nuclear genes were unable to resolve species boundaries for this complex independently. This study offered evidences from different genomes for dealing with the species boundaries and taxonomical treatment of the C. segmentifida complex in an integrated perspective. PMID:26913044

  1. Molecular analysis of Chinese truffles resembling Tuber californicum in morphology reveals a rich pattern of species diversity with emphasis on four new species.

    PubMed

    Fan, Li; Han, Ling; Zhang, Peng-rui; Yan, Xiang-yuan

    2016-01-01

    In China the species name Tuber californicum is assigned to pale truffles in the genus Tuber that have more or less regularly globose ascospores; however, we recently discovered that the name was misapplied to some specimens collected in China. In the present study we re-examined all available Chinese collections purported to be T. californicum, including herbarium specimens and newly collected materials, with morphological and molecular methods. The accessions separated into seven clusters in a phylogenetic analysis based on sequences of the internal transcribed spacers sequences of these materials. An ML tree generated with ITS, nuc 28S rDNA and translation elongation factor-1α sequences from Chinese and worldwide Tuber species with globose ascospores showed only two clades, the Puberulum clade and Latisporum clade. The Latisporum clade as recognized in this study includes the species known from eastern Asia only and probably represents a new lineage that arose in parallel with the Puberulum, Maculatum and Gibbosum lineages. We concluded that no evidence supports the existence of T. californicum in China and that the specimens misidentified as T. californicum belong to four species newly described herein, T. xuanhuaense, T. jinshajiangense, T. caoi and T. parvomurphium. PMID:26742582

  2. Taxonomic status and molecular phylogeography of two sibling species of Polytremis (Lepidoptera: Hesperiidae)

    PubMed Central

    Jiang, Weibin; He, Haiyan; Li, Yingdong; Ren, Mengyi; Ma, Yazhong; Zheng, Lingli; Zhu, Jianqing; Yu, Weidong

    2016-01-01

    The skipper Polytremis theca species complex is widely distributed in the south of the Qinling Mountains in China. A recent study of the Polytremis genus suggested that this species might encompass two differentiated lineages. We tested this hypothesis, by carrying out a phylogenetic study of this agricultural pest based on nationwide sampling and the evaluation of mitochondrial and nuclear DNA markers. We show that this species is actually an amalgamation of two sibling taxa (P. t. theca and P. t. fukia), which displayed levels of genetic divergence as great as those generally found between sister species in the Polytremis genus, suggesting that they actually correspond to two distinct species. The Divergence time estimates suggest that an active period of speciation within Polytremis occurred within the Pleistocene eras. Based on its distinct phylogenetic placement and geographical isolation, we suggest that the subspecies should be elevated to full species status under the phylogenetic species concept, which has significant management implications. PMID:26860271

  3. Molecular systematics of pinniped hookworms (Nematoda: Uncinaria): species delimitation, host associations and host-induced morphometric variation.

    PubMed

    Nadler, Steven A; Lyons, Eugene T; Pagan, Christopher; Hyman, Derek; Lewis, Edwin E; Beckmen, Kimberlee; Bell, Cameron M; Castinel, Aurelie; Delong, Robert L; Duignan, Padraig J; Farinpour, Cher; Huntington, Kathy Burek; Kuiken, Thijs; Morgades, Diana; Naem, Soraya; Norman, Richard; Parker, Corwin; Ramos, Paul; Spraker, Terry R; Berón-Vera, Bárbara

    2013-12-01

    Hookworms of the genus Uncinaria have been widely reported from juvenile pinnipeds, however investigations of their systematics has been limited, with only two species described, Uncinaria lucasi from northern fur seals (Callorhinus ursinus) and Uncinaria hamiltoni from South American sea lions (Otaria flavescens). Hookworms were sampled from these hosts and seven additional species including Steller sea lions (Eumetopias jubatus), California sea lions (Zalophus californianus), South American fur seals (Arctocephalus australis), Australian fur seals (Arctocephalus pusillus), New Zealand sea lions (Phocarctos hookeri), southern elephant seals (Mirounga leonina), and the Mediterranean monk seal (Monachus monachus). One hundred and thirteen individual hookworms, including an outgroup species, were sequenced for four genes representing two loci (nuclear ribosomal DNA and mitochondrial DNA). Phylogenetic analyses of these sequences recovered seven independent evolutionary lineages or species, including the described species and five undescribed species. The molecular evidence shows that U. lucasi parasitises both C. ursinus and E. jubatus, whereas U. hamiltoni parasitises O. flavescens and A. australis. The five undescribed hookworm species were each associated with single host species (Z. californianus, A. pusillus, P. hookeri, M. leonina and M. monachus). For parasites of otarids, patterns of Uncinaria host-sharing and phylogenetic relationships had a strong biogeographic component with separate clades of parasites from northern versus southern hemisphere hosts. Comparison of phylogenies for these hookworms and their hosts suggests that the association of U. lucasi with northern fur seals results from a host-switch from Steller sea lions. Morphometric data for U. lucasi shows marked host-associated size differences for both sexes, with U. lucasi individuals from E. jubatus significantly larger. This result suggests that adult growth of U. lucasi is reduced within the

  4. Molecular phylogeny of the Afroedura nivaria (Reptilia: Gekkonidae) species complex in South Africa provides insight on cryptic speciation.

    PubMed

    Makhubo, Buyisile G; Tolley, Krystal A; Bates, Michael F

    2015-01-01

    The Afroedura nivaria species complex (A. nivaria, A. karroica, A. amatolica, A. tembulica and A. halli) is a morphologically conservative group of medium-sized flat geckos endemic to South Africa and Lesotho. Species are allopatric, as are some populations within species that are separated by large expanses of unsuitable habitat. Because of this isolation of populations we hypothesised that several cryptic species may be present. To investigate this hypothesis we constructed a molecular phylogeny using multiple markers, and included representatives of other Afroedura species. Bayesian inference and maximum likelihood analyses (439bp 16S, 593bp ND4, 948bp RAG1) strongly supported the genetic distinctiveness of the five described species. However, the A. nivaria species complex as currently described is not monophyletic, as A. karroica was positioned outside a clade containing all other Afroedura species, and A. pondolia (which was presumed to belong to a different species complex) was recovered within the A. nivaria complex. Several distinct clades within A. halli and A. nivaria were also recovered, and the narrowly-distributed A. amatolica consisted of two highly divergent clades. We also conducted a multivariate analysis using 19 morphological characters to investigate whether the clades recovered by the phylogeny were distinct in terms of head, body and limb shape. The analysis showed some variation between clades in terms of locomotor apparatus (forelimbs and feet), head and body dimensions, but overall the morphological differences were minor. This morphological conservatism in the A. nivaria complex may be a result of adaptation to similar microhabitats. Exclusive of A. karroica, the results suggest that there are at least nine species in this complex, of which four are cryptic and undescribed. PMID:25307118

  5. Constituents of ophiuroidea. 1. Isolation and structure of three ganglioside molecular species from the brittle star Ophiocoma scolopendrina.

    PubMed

    Inagaki, M; Shibai, M; Isobe, R; Higuchi, R

    2001-12-01

    Three ganglioside molecular species, OSG-0 (1), OSG-1 (2), and OSG-2 (3) have been obtained from the polar lipid fraction of the chloroform/methanol extract of the brittle star Ophiocoma scolopendrina. The structures of these gangliosides have been determined on the basis of chemical and spectroscopic evidence as 1-O-[(N-glycolyl-alpha-D-neuraminosyl)-(2-->6)-beta-D-glucopyranosyl]-ceramide (1), 1-O-[8-O-sulfo-(N-acetyl-alpha-D-neuraminosyl)-(2-->6)-beta-D-glucopyranosyll-ceramide (2) and 1-O-[(N-glycolyl-alpha-D-neuraminosyl)-(2-->8)-(N-acetyl- and N-glycolyl-alpha-D-neuraminosyl)-(2-->6)-beta-D-glucopyranosyl]-ceramide (3). The ceramide moieties were composed of heterogeneous unsubstituted fatty acid, 2-hydroxy fatty acid and phytosphingosine units. Compounds 2 and 3 represent new ganglioside molecular species. PMID:11767069

  6. Direct molecular mass determination of trehalose monomycolate from 11 species of mycobacteria by MALDI-TOF mass spectrometry.

    PubMed

    Fujita, Yukiko; Naka, Takashi; Doi, Takeshi; Yano, Ikuya

    2005-05-01

    Direct estimation of the molecular mass of single molecular species of trehalose 6-monomycolate (TMM), a ubiquitous cell-wall component of mycobacteria, was performed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. When less than 1 microg TMM was analysed by MALDI-TOF mass spectrometry, quasimolecular ions [M+Na]+ of each molecular species were demonstrated and the numbers of carbons and double bonds (or cyclopropane rings) were determined. Since the introduction of oxygen atoms such as carbonyl, methoxy and ester groups yielded the appropriate shift of mass ions, the major subclasses of mycolic acid (alpha, methoxy, keto and wax ester) were identified without resorting to hydrolytic procedures. The results showed a marked difference in the molecular species composition of TMM among mycobacterial species. Unexpectedly, differing from other mycoloyl glycolipids, TMM from Mycobacterium tuberculosis showed a distinctive mass pattern, with abundant odd-carbon-numbered monocyclopropanoic (or monoenoic) alpha-mycolates besides dicyclopropanoic mycolate, ranging from C75 to C85, odd- and even-carbon-numbered methoxymycolates ranging from C83 to C94 and even- and odd-carbon-numbered ketomycolates ranging from C83 to C90. In contrast, TMM from Mycobacterium bovis (wild strain and BCG substrains) possessed even-carbon-numbered dicyclopropanoic alpha-mycolates. BCG Connaught strain lacked methoxymycolates almost completely. These results were confirmed by MALDI-TOF mass analysis of mycolic acid methyl esters liberated by alkaline hydrolysis and methylation of the original TMM. Wax ester-mycoloyl TMM molecular species were demonstrated for the first time as an intact form in the Mycobacterium avium-intracellulare group, M. phlei and M. flavescens. The M. avium-intracellulare group possessed predominantly C85 and C87 wax ester-mycoloyl TMM, while M. phlei and the rapid growers tested contained C80, C81, C82 and C83 wax ester

  7. Combining Next-Generation Sequencing Strategies for Rapid Molecular Resource Development from an Invasive Aphid Species, Aphis glycines

    PubMed Central

    Bai, Xiaodong; Zhang, Wei; Orantes, Lucia; Jun, Tae-Hwan; Mittapalli, Omprakash; Mian, M. A. Rouf; Michel, Andrew P.

    2010-01-01

    Background Aphids are one of the most important insect taxa in terms of ecology, evolutionary biology, genetics and genomics, and interactions with endosymbionts. Additionally, many aphids are serious pest species of agricultural and horticultural plants. Recent genetic and genomic research has expanded molecular resources for many aphid species, including the whole genome sequencing of the pea aphid, Acrythosiphon pisum. However, the invasive soybean aphid, Aphis glycines, lacks in any significant molecular resources. Methodology/Principal Findings Two next-generation sequencing technologies (Roche-454 and Illumina GA-II) were used in a combined approach to develop both transcriptomic and genomic resources, including expressed genes and molecular markers. Over 278 million bp were sequenced among the two methods, resulting in 19,293 transcripts and 56,688 genomic sequences. From this data set, 635 SNPs and 1,382 microsatellite markers were identified. For each sequencing method, different soybean aphid biotypes were used which revealed potential biotype specific markers. In addition, we uncovered 39,822 bp of sequence that were related to the obligatory endosymbiont, Buchnera aphidicola, as well as sequences that suggest the presence of Hamiltonella defensa, a facultative endosymbiont. Conclusions and Significance Molecular resources for an invasive, non-model aphid species were generated. Additionally, the power of next-generation sequencing to uncover endosymbionts was demonstrated. The resources presented here will complement ongoing molecular studies within the Aphididae, including the pea aphid whole genome, lead to better understanding of aphid adaptation and evolution, and help provide novel targets for soybean aphid control. PMID:20614011

  8. Molecular divergence and species delimitation of the cultivated oyster mushrooms: integration of IGS1 and ITS.

    PubMed

    Avin, Farhat Ahmadi; Bhassu, Subha; Tan, Yee Shin; Shahbazi, Pedram; Vikineswary, Sabaratnam

    2014-01-01

    Identification of edible mushrooms particularly Pleurotus genus has been restricted due to various obstacles. The present study attempted to use the combination of two variable regions of IGS1 and ITS for classifying the economically cultivated Pleurotus species. Integration of the two regions proved a high ability that not only could clearly distinguish the species but also served sufficient intraspecies variation. Phylogenetic tree (IGS1+ITS) showed seven distinct clades, each clade belonging to a separate species group. Moreover, the species differentiation was tested by AMOVA and the results were reconfirmed by presenting appropriate amounts of divergence (91.82% among and 8.18% within the species). In spite of achieving a proper classification of species by combination of IGS1 and ITS sequences, the phylogenetic tree showed the misclassification of the species of P. nebrodensis and P. eryngii var. ferulae with other strains of P. eryngii. However, the constructed median joining (MJ) network could not only differentiate between these species but also offer a profound perception of the species' evolutionary process. Eventually, due to the sufficient variation among and within species, distinct sequences, simple amplification, and location between ideal conserved ribosomal genes, the integration of IGS1 and ITS sequences is recommended as a desirable DNA barcode. PMID:24587752

  9. Molecular Divergence and Species Delimitation of the Cultivated Oyster Mushrooms: Integration of IGS1 and ITS

    PubMed Central

    Bhassu, Subha; Tan, Yee Shin; Vikineswary, Sabaratnam

    2014-01-01

    Identification of edible mushrooms particularly Pleurotus genus has been restricted due to various obstacles. The present study attempted to use the combination of two variable regions of IGS1 and ITS for classifying the economically cultivated Pleurotus species. Integration of the two regions proved a high ability that not only could clearly distinguish the species but also served sufficient intraspecies variation. Phylogenetic tree (IGS1 + ITS) showed seven distinct clades, each clade belonging to a separate species group. Moreover, the species differentiation was tested by AMOVA and the results were reconfirmed by presenting appropriate amounts of divergence (91.82% among and 8.18% within the species). In spite of achieving a proper classification of species by combination of IGS1 and ITS sequences, the phylogenetic tree showed the misclassification of the species of P. nebrodensis and P. eryngii var. ferulae with other strains of P. eryngii. However, the constructed median joining (MJ) network could not only differentiate between these species but also offer a profound perception of the species' evolutionary process. Eventually, due to the sufficient variation among and within species, distinct sequences, simple amplification, and location between ideal conserved ribosomal genes, the integration of IGS1 and ITS sequences is recommended as a desirable DNA barcode. PMID:24587752

  10. Prevalence and molecular characterization of Sarcocystis species in water buffaloes (Bubalus bubalus) in Egypt.

    PubMed

    Ashmawy, Karam I; Abu-Akkada, Somaia S; Ghashir, Mohamed Bn

    2014-12-01

    The present study was planned to investigate the prevalence of Sarcocystis spp. among slaughtered water buffaloes (Bubalus bubalis) at Alexandria province, Egypt. Three hundred blood samples were collected from slaughtered buffaloes (5-7 years old). Two techniques were used to evaluate the seroprevalence of Sarcocystis spp., enzyme-linked immunosorbent assay (ELISA) and indirect haemagglutination assay (IHA). It was revealed that 203 (67.6 %) and 191 (63.6 %) of the tested serum samples were seropositive to Sarcocystis spp. by ELISA and IHA, respectively. The results of sensitivity and specificity of IHA relative to ELISA were 94 and 100 %, respectively. For molecular characterization of inter- and intra-species genetic polymorphism within Egyptian isolates of Sarcocystis spp. of water buffaloes, polymerase chain reaction (PCR) and polymerase chain reaction-restriction length polymorphisms (PCR-RFLPs) were performed on four macroscopic isolates. The isolates represented two different geographical regions of Egypt, Alexandria and Assuit provinces. Alexandria isolates (large and small-sized cyst of the same host) and Assuit isolates (large and small-sized cyst of the same host) were used. The 18S rDNA of the macroscopic cysts were characterized, in tandem, by four restriction endonucleases, RsaI, MboI, SspI and DraI. RsaI and MboI enzymes did not show any restriction sites for all isolates, leaving the amplified fragments without cutting. SspI showed two fragments in Alexandria and Assuit small-sized isolates cut by the enzyme at 600-700-bp fragments, while Alexandria and Assuit large-sized cysts amplicons were not digested by this enzyme. The fourth enzyme, DraI, cut the PCR product of Alexandria large-sized cysts into two fragments (420-780 bp), while Assuit large-sized amplicon was not cut. It could be concluded that there was a far distance between the two local isolates (small and large sized), but there were no differences between the large-sized isolates. PMID

  11. A strategy for solubilizing delipidated apolipoprotein with lysophosphatidylcholine and reconstitution with phosphatidylcholine

    SciTech Connect

    Kawooya, J.K.; Wells, M.A.; Law, J.H. )

    1989-08-08

    The apolipoproteins of insect lipophorin were dissociated in guanidinium chloride and isolated by gel permeation chromatography. Over 98% of the total lipid in lipophorin was associated with apolipophorin I (apoLp-I), thus suggesting this apolipoprotein to be the lipid binding component of the particle. ApoLp-I was delipidated with ethanol/ether and solubilized in buffer that contained radioactive lysophosphatidylcholine (({sup 3}H)LPC) above the critical micellar concentration. Sonic irradiation of radioactive phosphatidylcholine (({sup 14}C)PC) with ({sup 3}H)LPC-solubilized apoLp-I at a molar ratio of 318 resulted in reconstituted lipophorin I (RLp-I). ({sup 3}H)LPC was bound to fatty acid free bovine serum albumin and was separated from RLp-I by density gradient ultracentrifugation and gel permeation chromatography. Negatively stained RLp-I particles were quasispherical with an average radius of 55{angstrom}, and their overall morphology and secondary structure were similar to those of native hemolymph lipophorin. The RLp-I particle had a {rho} = 1.137 g/mL, a M{sub r} {approx} 5.2 x 10{sup 5}, and a ({sup 14}C)PC:apoLp-I molar ratio of 308. From the compositional analysis, molecular size, trypsinization, and lipolysis with phospholipase A{sub 2}, the authors concluded that each RLp-I particle contained one molecule of apoLp-I and a monomolecular layer of ({sup 14}C)PC. When injected into the hemolymph of adult moths in vivo, RLp-I was loaded with lipid, as judged by a decrease in its density both in the presence and in the absence of adipokinetic hormone. The similarities in morphology and immunology of RLp-I and native lipophorin, together with the ability of RLp-I to load lipid, suggest that reconstituted lipophorins may serve as models to probe lipophorin structure and function.

  12. An approximate model and empirical energy function for solute interactions with a water-phosphatidylcholine interface.

    PubMed Central

    Sanders, C R; Schwonek, J P

    1993-01-01

    An empirical model of a liquid crystalline (L alpha phase) phosphatidylcholine (PC) bilayer interface is presented along with a function which calculates the position-dependent energy of associated solutes. The model approximates the interface as a gradual two-step transition, the first step being from an aqueous phase to a phase of reduced polarity, but which maintains a high enough concentration of water and/or polar head group moieties to satisfy the hydrogen bond-forming potential of the solute. The second transition is from the hydrogen bonding/low polarity region to an effectively anhydrous hydrocarbon phase. The "interfacial energies" of solutes within this variable medium are calculated based upon atomic positions and atomic parameters describing general polarity and hydrogen bond donor/acceptor propensities. This function was tested for its ability to reproduce experimental water-solvent partitioning energies and water-bilayer partitioning data. In both cases, the experimental data was reproduced fairly well. Energy minimizations carried out on beta-hexyl glucopyranoside led to identification of a global minimum for the interface-associated glycolipid which exhibited glycosidic torsion angles in agreement with prior results (Hare, B.J., K.P. Howard, and J.H. Prestegard. 1993. Biophys. J. 64:392-398). Molecular dynamics simulations carried out upon this same molecule within the simulated interface led to results which were consistent with a number of experimentally based conclusions from previous work, but failed to quantitatively reproduce an available NMR quadrupolar/dipolar coupling data set (Sanders, C.R., and J.H. Prestegard. 1991. J. Am. Chem. Soc. 113:1987-1996). The proposed model and functions are readily incorporated into computational energy modeling algorithms and may prove useful in future studies of membrane-associated molecules. PMID:8241401

  13. EMERGING MOLECULAR COMPUTATIONAL APPROACHES FOR CROSS-SPECIES EXTRAPOLATIONS: A WORKSHOP SUMMARY

    EPA Science Inventory

    Advances in molecular technology have led to the elucidation of full genomic sequences of several multicellular organisms, ranging from nematodes to man. The related molecular field of proteomics and metabolomics are now beginning to advance rapidly as well. In addition, advances...

  14. Molecular evolution of the clustered MMIC-3 multigene family of Gossypium species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Uniqueness, content, localization, and defense-related features of the root-knot nematode resistance-associated MIC-3 supergene cluster in the genus Gossypium are all of interest for molecular evolutionary studies of duplicate supergenes in allopolyploids. Here we report molecular evolutionary rates...

  15. Molecular Evolution of Clustered MIC-3 (Meloidogyne Induced Cotton -3) Multigene Family of Gossypium Species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Uniqueness, content, localization, and defense-related features of the root-knot nematode resistance-associated MIC-3 multigene cluster in the genus Gossypium are all of interest for molecular evolutionary studies of duplicate genes in allopolyploids. Here we report molecular evolutionary rates of t...

  16. Structure and Function of Phosphatidylcholine transfer protein (PC-TP)/StarD2

    SciTech Connect

    Kanno,K.; Wu, M.; Scapa, E.; Roderick, S.; Cohen, D.

    2007-01-01

    Phosphatidylcholine transfer protein (PC-TP) is a highly specific soluble lipid binding protein that transfers phosphatidylcholine between membranes in vitro. PC-TP is a member of the steroidogenic acute regulatory protein-related transfer (START) domain superfamily. Although its biochemical properties and structure are well characterized, the functions of PC-TP in vivo remain incompletely understood. Studies of mice with homozygous disruption of the Pctp gene have largely refuted the hypotheses that this protein participates in the hepatocellular selection and transport of biliary phospholipids, in the production of lung surfactant, in leukotriene biosynthesis and in cellular phosphatidylcholine metabolism. Nevertheless, Pctp-/- mice exhibit interesting defects in lipid homeostasis, the understanding of which should elucidate the biological functions of PC-TP.

  17. Synthesis and Biological Evaluation of Novel Phosphatidylcholine Analogues Containing Monoterpene Acids as Potent Antiproliferative Agents

    PubMed Central

    Gliszczyńska, Anna; Niezgoda, Natalia; Gładkowski, Witold; Czarnecka, Marta; Świtalska, Marta; Wietrzyk, Joanna

    2016-01-01

    The synthesis of novel phosphatidylcholines with geranic and citronellic acids in sn-1 and sn-2 positions is described. The structured phospholipids were obtained in high yields (59–87%) and evaluated in vitro for their cytotoxic activity against several cancer cell lines of different origin: MV4-11, A-549, MCF-7, LOVO, LOVO/DX, HepG2 and also towards non-cancer cell line BALB/3T3 (normal mice fibroblasts). The phosphatidylcholines modified with monoterpene acid showed a significantly higher antiproliferative activity than free monoterpene acids. The highest activity was observed for the terpene-phospholipids containing the isoprenoid acids in sn-1 position of phosphatidylcholine and palmitic acid in sn-2. PMID:27310666

  18. Morphological and molecular analyses support the existence of host-specific Peronospora species infecting Chenopodium.

    PubMed

    Choi, Young-Joon; Denchev, Cvetomir M; Shin, Hyeon-Dong

    2008-03-01

    About 20 species of Peronospora have been reported to cause downy mildew on Chenopodium, but, particularly in plant pathology literature, only one species, P. farinosa, is considered to be involved. We performed sequence analysis of the ITS rDNA to reveal the phylogenetic relationships of Peronospora specimens from five species of Chenopodium, viz. C. album, C. ambrosioides, C. bonus-henricus, C. hybridum, and C. polyspermum. The five clades corresponded to particular Chenopodium species, and showed a high level of sequence divergence. Differences in the morphology of the conidia and ultimate branchlets also supported the separation of the five groups at the host species level. These results suggest that the names P. variabilis, P. boni-henrici, P. chenopodii, and P. chenopodii-polyspermi should be used for the four downy mildew pathogens specific to C. album, C. bonus-henricus, C. hybridum, and C. polyspermum, respectively. The Peronospora on C. ambrosioides was found to be an independent species. PMID:18270803

  19. Are all species of Pseudorhabdosynochus strictly host specific? A molecular study.

    PubMed

    Schoelinck, Charlotte; Cruaud, Corinne; Justine, Jean-Lou

    2012-06-01

    Species of the diplectanid monogenean genus Pseudorhabdosynochus are strictly host-specific (specialist), with the exception of P. cyanopodus, which was reported in New Caledonia, South Pacific, from two host species, Epinephelus cyanopodus and E. chlorostigma. We sequenced the COI gene of both host fish species and of their monogeneans. Morphological identification and pairwise distances showed that the two fish species were distinct (difference 6.1-6.6%), but that their monogeneans were not (difference 0-1.5%). A morphological study of sclerotised parts showed that specimens of P. cyanopodus are similar in both fish. Most species of groupers and their associated Pseudorhabdosynochus species are from warm surface waters, but the two groupers E. cyanopodus and E. chlorostigma are usually caught in deep-sea on the outer slope of the coral reef. This suggests that acquisition of a less strict host specificity is an adaptation of P. cyanopodus to deep-sea hosts. PMID:22326703

  20. Morphological and molecular evidence of three species of pikes Esox spp. (Actinopterygii, Esocidae) in France, including the description of a new species.

    PubMed

    Denys, Gaël Pierre Julien; Dettai, Agnès; Persat, Henri; Hautecœur, Mélyne; Keith, Philippe

    2014-09-01

    This integrative taxonomy study of French pikes compares morphological characters and molecular sequence data (mitochondrial COI and nuclear Plagl2 genes). In addition to the expected E. lucius, DNA sequences and morphology both support a new species in France, E. aquitanicus sp. nov. from the Charente to the Adour drainages. It is characterized by a color pattern of sides with narrow 1-1.5-scale-wide oblique vertical bands, conferring it a marbled coat, a snout only 0.9 times larger than the postorbital length, an anal fin basis 1.1-1.2 times larger than the caudal peduncle length, 101 to 121 lateral scales, 53 to 57 vertebrae, as well as 24 diagnostic sites in the COI gene and 3 in the Plagl2 gene. Partial COI sequences (131 bp) from modern and historical specimens indicate also the presence of E. cisalpinus and E. lucius during the 19th century in Lake Geneva. Morphological and molecular data points to a possible hybridization between E. lucius with both other local pike species, representing a risk for them. Their endangerment status should be evaluated rapidly in order to take conservation measures. PMID:25242691

  1. Activation of Phosphatidylcholine-Specific Phospholipase C in Breast and Ovarian Cancer: Impact on MRS-Detected Choline Metabolic Profile and Perspectives for Targeted Therapy

    PubMed Central

    Podo, Franca; Paris, Luisa; Cecchetti, Serena; Spadaro, Francesca; Abalsamo, Laura; Ramoni, Carlo; Ricci, Alessandro; Pisanu, Maria Elena; Sardanelli, Francesco; Canese, Rossella; Iorio, Egidio

    2016-01-01

    Elucidation of molecular mechanisms underlying the aberrant phosphatidylcholine cycle in cancer cells plays in favor of the use of metabolic imaging in oncology and opens the way for designing new targeted therapies. The anomalous choline metabolic profile detected in cancer by magnetic resonance spectroscopy and spectroscopic imaging provides molecular signatures of tumor progression and response to therapy. The increased level of intracellular phosphocholine (PCho) typically detected in cancer cells is mainly attributed to upregulation of choline kinase, responsible for choline phosphorylation in the biosynthetic Kennedy pathway, but can also be partly produced by activation of phosphatidylcholine-specific phospholipase C (PC-PLC). This hydrolytic enzyme, known for implications in bacterial infection and in plant survival to hostile environmental conditions, is reported to be activated in mitogen- and oncogene-induced phosphatidylcholine cycles in mammalian cells, with effects on cell signaling, cell cycle regulation, and cell proliferation. Recent investigations showed that PC-PLC activation could account for 20–50% of the intracellular PCho production in ovarian and breast cancer cells of different subtypes. Enzyme activation was associated with PC-PLC protein overexpression and subcellular redistribution in these cancer cells compared with non-tumoral counterparts. Moreover, PC-PLC coimmunoprecipitated with the human epidermal growth factor receptor-2 (HER2) and EGFR in HER2-overexpressing breast and ovarian cancer cells, while pharmacological PC-PLC inhibition resulted into long-lasting HER2 downregulation, retarded receptor re-expression on plasma membrane and antiproliferative effects. This body of evidence points to PC-PLC as a potential target for newly designed therapies, whose effects can be preclinically and clinically monitored by metabolic imaging methods. PMID:27532027

  2. Activation of Phosphatidylcholine-Specific Phospholipase C in Breast and Ovarian Cancer: Impact on MRS-Detected Choline Metabolic Profile and Perspectives for Targeted Therapy.

    PubMed

    Podo, Franca; Paris, Luisa; Cecchetti, Serena; Spadaro, Francesca; Abalsamo, Laura; Ramoni, Carlo; Ricci, Alessandro; Pisanu, Maria Elena; Sardanelli, Francesco; Canese, Rossella; Iorio, Egidio

    2016-01-01

    Elucidation of molecular mechanisms underlying the aberrant phosphatidylcholine cycle in cancer cells plays in favor of the use of metabolic imaging in oncology and opens the way for designing new targeted therapies. The anomalous choline metabolic profile detected in cancer by magnetic resonance spectroscopy and spectroscopic imaging provides molecular signatures of tumor progression and response to therapy. The increased level of intracellular phosphocholine (PCho) typically detected in cancer cells is mainly attributed to upregulation of choline kinase, responsible for choline phosphorylation in the biosynthetic Kennedy pathway, but can also be partly produced by activation of phosphatidylcholine-specific phospholipase C (PC-PLC). This hydrolytic enzyme, known for implications in bacterial infection and in plant survival to hostile environmental conditions, is reported to be activated in mitogen- and oncogene-induced phosphatidylcholine cycles in mammalian cells, with effects on cell signaling, cell cycle regulation, and cell proliferation. Recent investigations showed that PC-PLC activation could account for 20-50% of the intracellular PCho production in ovarian and breast cancer cells of different subtypes. Enzyme activation was associated with PC-PLC protein overexpression and subcellular redistribution in these cancer cells compared with non-tumoral counterparts. Moreover, PC-PLC coimmunoprecipitated with the human epidermal growth factor receptor-2 (HER2) and EGFR in HER2-overexpressing breast and ovarian cancer cells, while pharmacological PC-PLC inhibition resulted into long-lasting HER2 downregulation, retarded receptor re-expression on plasma membrane and antiproliferative effects. This body of evidence points to PC-PLC as a potential target for newly designed therapies, whose effects can be preclinically and clinically monitored by metabolic imaging methods. PMID:27532027

  3. Molecular phylogenetics, species diversity, and biogeography of the Andean lizards of the genus Proctoporus (Squamata: Gymnophthalmidae).

    PubMed

    Goicoechea, Noemí; Padial, José M; Chaparro, Juan C; Castroviejo-Fisher, Santiago; De la Riva, Ignacio

    2012-12-01

    The family Gymnophthalmidae comprises ca. 220 described species of Neotropical lizards distributed from southern Mexico to Argentina. It includes 36 genera, among them Proctoporus, which contains six currently recognized species occurring across the yungas forests and wet montane grasslands of the Amazonian versant of the Andes from central Peru to central Bolivia. Here, we investigate the phylogenetic relationships and species limits of Proctoporus and closely related taxa by analyzing 2121 base pairs of mitochondrial (12S, 16S, and ND4) and nuclear (c-mos) genes. Our taxon sampling of 92 terminals includes all currently recognized species of Proctoporus and 15 additional species representing the most closely related groups to the genus. Maximum parsimony, maximum likelihood and Bayesian phylogenetic analyses recovered a congruent, fully resolved, and strongly supported hypothesis of relationships that challenges previous phylogenetic hypotheses and classifications, and biogeographic scenarios. Our main results are: (i) discovery of a strongly supported clade that includes all species of Proctoporus and within which are nested the monotypic Opipeuter xestus (a genus that we consider a junior synonym of Proctoporus), and two species of Euspondylus, that are therefore transferred to Proctoporus; (ii) the paraphyly of Proctoporus bolivianus with respect to P. subsolanus, which is proposed as a junior synonym of P. bolivianus; (iii) the detection of seven divergent and reciprocally monophyletic lineages (five of them previously assigned to P. bolivianus) that are considered confirmed candidate species, which implies that more candidate species are awaiting formal description and naming than currently recognized species in the genus; (iv) rejection of the hypothesis that Proctoporus diversified following a south to north pattern parallel to the elevation of the Andes; (v) species diversity in Proctoporus is the result of in situ diversification through vicariance in

  4. Comparison of molecular species identification for North Sea calanoid copepods (Crustacea) using proteome fingerprints and DNA sequences.

    PubMed

    Laakmann, S; Gerdts, G; Erler, R; Knebelsberger, T; Martínez Arbizu, P; Raupach, M J

    2013-09-01

    Calanoid copepods play an important role in the pelagic ecosystem making them subject to various taxonomic and ecological studies, as well as indicators for detecting changes in the marine habitat. For all these investigations, valid identification, mainly of sibling and cryptic species as well as early life history stages, represents a central issue. In this study, we compare species identification methods for pelagic calanoid copepod species from the North Sea and adjacent regions in a total of 333 specimens. Morphologically identified specimens were analysed on the basis of nucleotide sequences (i.e. partial mitochondrial cytochrome c oxidase subunit I (COI) and complete 18S rDNA) and on proteome fingerprints using the technology of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). On all three molecular approaches, all specimens were classified to species level indicated by low intraspecific and high interspecific variability. Sequence divergences in both markers revealed a second Pseudocalanus species for the southern North Sea identified as Pseudocalanus moultoni by COI sequence comparisons to GenBank. Proteome fingerprints were valid for species clusters irrespective of high intraspecific variability, including significant differences between early developmental stages and adults. There was no effect of sampling region or time; thus, trophic effect, when analysing the whole organisms, was observed in species-specific protein mass spectra, underlining the power of this tool in the application on metazoan species identification. Because of less sample preparation steps, we recommend proteomic fingerprinting using the MALDI-TOF MS as an alternative or supplementary approach for rapid, cost-effective species identification. PMID:23848968

  5. Phylogeny of Laniarius: molecular data reveal L. liberatus synonymous with L. erlangeri and "plumage coloration" as unreliable morphological characters for defining species and species groups.

    PubMed

    Nguembock, Billy; Fjeldså, Jon; Couloux, Arnaud; Pasquet, Eric

    2008-08-01

    Laniarius is one of the larger genera within the avian bush-shrike radiation, the family Malaconotidae. Fairly homogenous by size and shape but highly variable by colours, these have been classified mainly on basis of plumage colours. In the present study, which is the first taxon-dense analysis of the genus Laniarius based on molecular sequence data (nuclear BRM15 intron-15, and mitochondrial ND2 and ATPase6 genes), we investigate interrelationships between 16 species and 34 subspecies of Laniarius. Altogether 2094bp were aligned and subjected to maximum likelihood and Bayesian inference analyses. Results strongly support the monophyly of Laniarius, and place it close to Chlorophoneus, but without outlining a precise sister-group. In a generally well-resolved phylogeny of Laniarius, L. leucorhynchus and L. atrococcineus constitute deep branches and the remaining species form five clades which are not concordant with previously defined superspecies. The black and white boubous belong to two different clades. L. aethiopicus appears polyphyletic and our results support the resurrection of Laniarius major, Laniarius erlangeri and Laniarius sublacteus. We also find that L. liberatus, described in 1991 based on the only known live individual, is identified as an unusual colour morph from L. erlangeri. The black boubous are not monophyletic; L. funebris and L. leucorhynchus appear as isolated species whereas L. poensis and L. fuelleborni are sister-taxa. We recovered the polyphyly of crimson boubous and new hypotheses on their relationships have been generated. Overall, the variation in pigments and patterns does not follow phylogenetic lineages. The plumage coloration could be thoroughly subject to modification and it could not reflect exactly colour plumages of the parents. From then on, the plumage coloration appears as an unreliable morphological character for defining species and species groups. PMID:18514549

  6. Phosphatidylinositol induces fluid phase formation and packing defects in phosphatidylcholine model membranes

    PubMed Central

    Peng, Aaron; Pisal, Dipak S.; Doty, Amy; Balu-Iyer, Sathy V.

    2011-01-01

    Liposomes consisted of phosphatidylinositol (PI) and phosphatidylcholine (PC) have been utilized as delivery vehicle for drugs and proteins. In the present work, we studied the effect of soy PI on physical properties of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) liposomes such as phase state of lipid bilayer, lipid packing and phase properties using multiple orthogonal biophysical techniques. The 6-dodecanoyl-2-dimethylamino naphthalene (Laurdan) fluorescence studies showed that presence of PI induces the formation of fluid phases in DMPC. Differential scanning calorimetry (DSC), temperature dependent fluorescence anisotropy measurements, and generalized polarization values for Laurdan showed that the presence of as low as 10 mol% of PI induces substantial broadening and shift to lower temperature of phase transition of DMPC. The fluorescence emission intensity of DPH labeled, PI containing DMPC lipid bilayer decreased possibly due to deeper penetration of water molecules in lipid bilayer. In order to further delineate the effect of PI on the physico chemical properties of DMPC is due to either significant hydrophobic mismatch between the acyl chains of the DMPC and that of soy PI or due to the inositol head group, we systematically replaced soy PI with PC species of similar acyl chain composition (DPPC and 18:2 (Cis) PC) or with diacylglycerol (DAG) respectively. The anisotropy of PC membrane containing soy PI showed largest fluidity change compared to other compositions. The data suggests that addition of PI alters structure and dynamics of DMPC bilayer in that it promotes deeper water penetration in the bilayer, induces fluid phase characteristics and causes lipid packing defects that involve its inositol head group. PMID:22024173

  7. [Molecular phylogenetic relationships among species in Oxya serville(Orthoptera: Catantopidae) based on random amplified polymorphic DNA(RAPD)].

    PubMed

    Zhang, Jian-Zhen; Ma, En-Bo; Guo, Ya-Ping

    2003-06-01

    The molecular phylogenetic relationships of five species of Oxya Audient-serville including O. chinensis, O. brachyptera, O. agavisa, O. japonica and O. intricata were studied with RAPD. Genomic DNA of forty-one individuals were amplified with eight oligonucleotide (10 mer) primers which were previously selected, the specifical bands occured in all them, a total of 96 clear and reproducible bands (rang from 200-2500 bp) were generated, 95 of which were polymorphic band, the only one band (850 bp) which was amplified with S362 was common to five species of Oxya. The obtaining segments of individual primer were between 8-16, the average was 12. A molecular phylogenetic tree based on was constructed Euclidean distance among five species of rice grasshopper by between-groups linkage method, the result indicated O. chinensis was closely related to O. brachyptera, the genetic relationship of O. japonica and O. agavisa was also close, whereas O. intricata had far phylogenetic relationship with them. The results of dendrogram were consistent with the previous conclusion of morphologic classification and cytotaxonomy, and suggested RAPD was suitable for analysis of phylogenetic relationships among species of Oxya. PMID:12939798

  8. Noninvasive molecular methods to identify live scarab larvae: an example of sympatric pest and nonpest species in New Zealand.

    PubMed

    Lefort, M-C; Boyer, S; Worner, S P; Armstrong, K

    2012-05-01

    Despite the negative impact that many scarab larvae have on agro-ecosystems, very little attention has been paid to their taxonomy. Their often extremely similar morphological characteristics have probably contributed to this impediment, which has also meant that they are very difficult to identify in the field. Molecular methods can overcome this challenge and are particularly useful for the identification of larvae to enable management of pest species occurring sympatrically with nonpest species. However, the invasive collection of DNA samples for such molecular methods is not compatible with subsequent behavioural, developmental or fitness studies. Two noninvasive DNA sampling and DNA analysis methods suitable for the identification of larvae from closely related scarab species were developed here. Using the frass and larval exuviae as sources of DNA, field-collected larvae of Costelytra zealandica (White) and Costelytra brunneum (Broun) (Scarabaeidae: Melolonthinae) were identified by multiplex PCR based on the difference in size of the resulting PCR products. This study also showed that small quantities of frass can be used reliably even 7 days after excretion. This stability of the DNA is of major importance in ecological studies where timeframes rarely allow daily monitoring. The approach developed here is readily transferable to the study of any holometabolous insect species for which morphological identification of larval stages is difficult. PMID:22189059

  9. Beilschmiedia turbinata: A Newly Recognized but Dying Species of Lauraceae from Tropical Asia Based on Morphological and Molecular Data

    PubMed Central

    Liu, Bing; Yang, Yong; Xie, Lei; Zeng, Gang; Ma, Keping

    2013-01-01

    China took great efforts to reforestation, even turned the long-term forest loss into a net gain, but this cannot hide the loss of species diversity due to destruction of primary forests, habitat loss, invasion of alien species, and over exploitation. Here we provide such a case by recording a dying tree species of Lauraceae from the evergreen forests of SE Yunnan of China and adjoining Vietnam. We made field collections and observations for four consecutive years from 2009 to 2012. Phylogenetic analyses were conducted based on a combined dataset from nrITS and plastid trnL-trnF region, rpl16 intron, and psbA-trnH spacer. The results indicate that the Asiatic Beilschmiedia and Syndiclis are reciprocally monophyletic with Endiandra as a sister group, and both morphology and molecular phylogeny clearly suggest that the new species belongs to Beilschmiedia. Thus Beilschmiedia turbinata Bing Liu et Y. Yang is illustrated and described as new to science, color plates, line drawings, distribution map and comparison with related species are provided. This new species is similar to B. yunnanensis in the small and ferruginous-brown tomentose terminal buds, elliptic to oblong-lanceolate and alternate or subopposite leaves bearing the fine veinlet reticulation, but differs from the latter by the smaller flowers, the eglandular stamens of the third whorl, and the large turbinate furfuraceous fruits. PMID:23840756

  10. Molecular phylogenetic relationships of some common sweetlips (Haemulidae: Plectorhynchinae) and the synonyms controversy of two Plectorhinchus species.

    PubMed

    Liang, Rishen; Wang, Chao; Zou, Qing; Zhou, Aiguo; Zhou, Meng

    2016-05-01

    Molecular phylogenetic topologies from 40 individuals of 17 sweetlips were constructed based on the mitochondrial cytochrome b (cyt b) and cytochrome c oxidase subunit I (COI) genes. All phylogenetic results strongly revealed the division of the sweetlips into three morphological distinct groups. Group I: sweetlips with colorful patterns, Group II and Group III: species with uniformly dark patterns. The relationships of those morphologically confused Plectorhinchus species were well-resolved in the phylogenetic results. We also confirmed that the genus Diagramma was placed inside the colorful Plectorhinchus groups, suggesting close relationship of Diagramma within Plectorhinchus. Additionally, we found that two species, P. orientalis and P. vittatus, which were traditionally considered as synonyms for oriental sweetlips, which were suggested to be two distinct species. Sequence divergence also revealed a great genetic variation between P. orientalis and P. vittatus (6.0% in Cyt b and 7.4% in COI), which was largely greater than the species diagnosis divergence value (2%) suggested by Hebert et al. This new finding suggested P. orientalis and P. vittatus might be two distinct species and should not be placed as synonyms. PMID:25484173

  11. Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods

    PubMed Central

    Flynn, Jullien M; Brown, Emily A; Chain, Frédéric J J; MacIsaac, Hugh J; Cristescu, Melania E

    2015-01-01

    Metabarcoding has the potential to become a rapid, sensitive, and effective approach for identifying species in complex environmental samples. Accurate molecular identification of species depends on the ability to generate operational taxonomic units (OTUs) that correspond to biological species. Due to the sometimes enormous estimates of biodiversity using this method, there is a great need to test the efficacy of data analysis methods used to derive OTUs. Here, we evaluate the performance of various methods for clustering length variable 18S amplicons from complex samples into OTUs using a mock community and a natural community of zooplankton species. We compare analytic procedures consisting of a combination of (1) stringent and relaxed data filtering, (2) singleton sequences included and removed, (3) three commonly used clustering algorithms (mothur, UCLUST, and UPARSE), and (4) three methods of treating alignment gaps when calculating sequence divergence. Depending on the combination of methods used, the number of OTUs varied by nearly two orders of magnitude for the mock community (60–5068 OTUs) and three orders of magnitude for the natural community (22–22191 OTUs). The use of relaxed filtering and the inclusion of singletons greatly inflated OTU numbers without increasing the ability to recover species. Our results also suggest that the method used to treat gaps when calculating sequence divergence can have a great impact on the number of OTUs. Our findings are particularly relevant to studies that cover taxonomically diverse species and employ markers such as rRNA genes in which length variation is extensive. PMID:26078860

  12. Use of Molecular Diagnostic Tools for the Identification of Species Responsible for Snakebite in Nepal: A Pilot Study

    PubMed Central

    Sharma, Sanjib Kumar; Kuch, Ulrich; Höde, Patrick; Bruhse, Laura; Pandey, Deb P.; Ghimire, Anup; Chappuis, François; Alirol, Emilie

    2016-01-01

    Snakebite is an important medical emergency in rural Nepal. Correct identification of the biting species is crucial for clinicians to choose appropriate treatment and anticipate complications. This is particularly important for neurotoxic envenoming which, depending on the snake species involved, may not respond to available antivenoms. Adequate species identification tools are lacking. This study used a combination of morphological and molecular approaches (PCR-aided DNA sequencing from swabs of bite sites) to determine the contribution of venomous and non-venomous species to the snakebite burden in southern Nepal. Out of 749 patients admitted with a history of snakebite to one of three study centres, the biting species could be identified in 194 (25.9%). Out of these, 87 had been bitten by a venomous snake, most commonly the Indian spectacled cobra (Naja naja; n = 42) and the common krait (Bungarus caeruleus; n = 22). When both morphological identification and PCR/sequencing results were available, a 100% agreement was noted. The probability of a positive PCR result was significantly lower among patients who had used inadequate “first aid” measures (e.g. tourniquets or local application of remedies). This study is the first to report the use of forensic genetics methods for snake species identification in a prospective clinical study. If high diagnostic accuracy is confirmed in larger cohorts, this method will be a very useful reference diagnostic tool for epidemiological investigations and clinical studies. PMID:27105074

  13. Beilschmiedia turbinata: a newly recognized but dying species of Lauraceae from tropical Asia based on morphological and molecular data.

    PubMed

    Liu, Bing; Yang, Yong; Xie, Lei; Zeng, Gang; Ma, Keping

    2013-01-01

    China took great efforts to reforestation, even turned the long-term forest loss into a net gain, but this cannot hide the loss of species diversity due to destruction of primary forests, habitat loss, invasion of alien species, and over exploitation. Here we provide such a case by recording a dying tree species of Lauraceae from the evergreen forests of SE Yunnan of China and adjoining Vietnam. We made field collections and observations for four consecutive years from 2009 to 2012. Phylogenetic analyses were conducted based on a combined dataset from nrITS and plastid trnL-trnF region, rpl16 intron, and psbA-trnH spacer. The results indicate that the Asiatic Beilschmiedia and Syndiclis are reciprocally monophyletic with Endiandra as a sister group, and both morphology and molecular phylogeny clearly suggest that the new species belongs to Beilschmiedia. Thus Beilschmiedia turbinata Bing Liu et Y. Yang is illustrated and described as new to science, color plates, line drawings, distribution map and comparison with related species are provided. This new species is similar to B. yunnanensis in the small and ferruginous-brown tomentose terminal buds, elliptic to oblong-lanceolate and alternate or subopposite leaves bearing the fine veinlet reticulation, but differs from the latter by the smaller flowers, the eglandular stamens of the third whorl, and the large turbinate furfuraceous fruits. PMID:23840756

  14. Use of Molecular Diagnostic Tools for the Identification of Species Responsible for Snakebite in Nepal: A Pilot Study.

    PubMed

    Sharma, Sanjib Kumar; Kuch, Ulrich; Höde, Patrick; Bruhse, Laura; Pandey, Deb P; Ghimire, Anup; Chappuis, François; Alirol, Emilie

    2016-04-01

    Snakebite is an important medical emergency in rural Nepal. Correct identification of the biting species is crucial for clinicians to choose appropriate treatment and anticipate complications. This is particularly important for neurotoxic envenoming which, depending on the snake species involved, may not respond to available antivenoms. Adequate species identification tools are lacking. This study used a combination of morphological and molecular approaches (PCR-aided DNA sequencing from swabs of bite sites) to determine the contribution of venomous and non-venomous species to the snakebite burden in southern Nepal. Out of 749 patients admitted with a history of snakebite to one of three study centres, the biting species could be identified in 194 (25.9%). Out of these, 87 had been bitten by a venomous snake, most commonly the Indian spectacled cobra (Naja naja; n = 42) and the common krait (Bungarus caeruleus; n = 22). When both morphological identification and PCR/sequencing results were available, a 100% agreement was noted. The probability of a positive PCR result was significantly lower among patients who had used inadequate "first aid" measures (e.g. tourniquets or local application of remedies). This study is the first to report the use of forensic genetics methods for snake species identification in a prospective clinical study. If high diagnostic accuracy is confirmed in larger cohorts, this method will be a very useful reference diagnostic tool for epidemiological investigations and clinical studies. PMID:27105074

  15. Molecular characterization of constitutive heterochromatin in three species of Trypoxylon (Hymenoptera: Crabronidae: Trypoxylini) by CMA3/DAPI staining

    PubMed Central

    Menezes, Rodolpho Santos Telles; Carvalho, Antonio Freire; Silva, Janisete Gomes; Costa, Marco Antonio

    2011-01-01

    Abstract Previous cytogenetic analyses in Trypoxylon Latreille, 1796 have been basically restricted to C-banding. In the present study, base-specific CMA3 and DAPI fluorochrome staining were used to characterize the constitutive heterochromatin in three Trypoxylon species. The heterochromatin was GC-rich in all the species studied; however, in Trypoxylon nitidum F. Smith, 1856the molecular composition of the heterochromatinwasdifferent among chromosome pairs. Conversely, the euchromatin was AT-rich in the three species. These results suggest high conservatism in the euchromatic regions as opposed to the heterochromatic regions that have a high rate of changes. In this study, we report the karyotype of Trypoxylon rugifrons F. Smith, 1873which has the lowest chromosome number in the genus and other characteristics of the likely ancestral Trypoxylon karyotype. PMID:24260620

  16. Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species

    PubMed Central

    Gupta, Radhey S; Lorenzini, Emily

    2007-01-01

    Background The Bacteroidetes and Chlorobi species constitute two main groups of the Bacteria that are closely related in phylogenetic trees. The Bacteroidetes species are widely distributed and include many important periodontal pathogens. In contrast, all Chlorobi are anoxygenic obligate photoautotrophs. Very few (or no) biochemical or molecular characteristics are known that are distinctive characteristics of these bacteria, or are commonly shared by them. Results Systematic blast searches were performed on each open reading frame in the genomes of Porphyromonas gingivalis W83, Bacteroides fragilis YCH46, B. thetaiotaomicron VPI-5482, Gramella forsetii KT0803, Chlorobium luteolum (formerly Pelodictyon luteolum) DSM 273 and Chlorobaculum tepidum (formerly Chlorobium tepidum) TLS to search for proteins that are uniquely present in either all or certain subgroups of Bacteroidetes and Chlorobi. These studies have identified > 600 proteins for which homologues are not found in other organisms. This includes 27 and 51 proteins that are specific for most of the sequenced Bacteroidetes and Chlorobi genomes, respectively; 52 and 38 proteins that are limited to species from the Bacteroidales and Flavobacteriales orders, respectively, and 5 proteins that are common to species from these two orders; 185 proteins that are specific for the Bacteroides genus. Additionally, 6 proteins that are uniquely shared by species from the Bacteroidetes and Chlorobi phyla (one of them also present in the Fibrobacteres) have also been identified. This work also describes two large conserved inserts in DNA polymerase III (DnaE) and alanyl-tRNA synthetase that are distinctive characteristics of the Chlorobi species and a 3 aa deletion in ClpB chaperone that is mainly found in various Bacteroidales, Flavobacteriales and Flexebacteraceae, but generally not found in the homologs from other organisms. Phylogenetic analyses of the Bacteroidetes and Chlorobi species is also reported based on

  17. Molecular phylogeny of the Puerto Rican Lepidocyrtus and Pseudosinella (Hexapoda: Collembola), a validation of Yoshii's "color pattern species".

    PubMed

    Soto-Adames, Felipe N

    2002-10-01

    Color pattern was one of the most important characters used to diagnose species in the genus Lepidocyrtus until the introduction of chaetotaxy to Collembola taxonomy. Chaetotaxy confirmed most species diagnoses based only on color patterns, but a number of populations with distinct pigmentation patterns have been found to be identical in all other morphological characters. The absence of individuals showing intermediate color patterns prompted Yoshii to suggest that, despite chaetotaxic identity, populations with distinct color forms represent valid species (implying reproductive isolation and therefore biological species) in what he designated as "color pattern species." In Puerto Rico Lepidocyrtus biphasis, L. dispar, and L. caprilesi show a remarkable variation in pigmentation and as a group include 11 different color forms. Here I present a phylogenetic analysis of the cytochrome oxidase I gene (COI) in 17 species of Lepidocyrtus and Pseudosinella, including 11 species and 10 color forms of Puerto Rican Lepidocyrtus, to test Yoshii's color pattern species concept. The analysis shows large genetic distances between species defined based on morphology alone (morphospecies) and between most color variants within morphospecies. The most often used calibration for the COI molecular clock (2.3% sequence divergence per million years) suggests that morphospecies diverged between 20 and 25 million years before present while color forms within morphospecies diverged between 8 and 19 million years ago. This indicates that changes in climate and sea levels during the Pleistocene were irrelevant to the speciation process in the Puerto Rican Lepidocyrtus. Examination of the genetic variation, phylogenetic relationships, and collection data in light of the biological and phylogenetic species concepts supports the hypothesis that most populations of morphospecies differing only in color pattern are distinct species, thus validating Yoshii's color pattern species concept. As a

  18. Methylmercury-induced toxicity is mediated by enhanced intracellular calcium through activation of phosphatidylcholine-specific phospholipase C

    SciTech Connect

    Kang, Mi Sun; Jeong, Ju Yeon; Seo, Ji Heui; Jeon, Hyung Jun; Jung, Kwang Mook; Chin, Mi-Reyoung; Moon, Chang-Kiu; Bonventre, Joseph V.; Jung, Sung Yun; Kim, Dae Kyong . E-mail: proteinlab@hanmail.net

    2006-10-15

    Methylmercury (MeHg) is a ubiquitous environmental toxicant to which humans can be exposed by ingestion of contaminated food. MeHg has been suggested to exert its toxicity through its high reactivity to thiols, generation of arachidonic acid and reactive oxygen species (ROS), and elevation of free intracellular Ca{sup 2+} levels ([Ca{sup 2+}]{sub i}). However, the precise mechanism has not been fully defined. Here we show that phosphatidylcholine-specific phospholipase C (PC-PLC) is a critical pathway for MeHg-induced toxicity in MDCK cells. D609, an inhibitor of PC-PLC, significantly reversed the toxicity in a time- and dose-dependent manner with concomitant inhibition of the diacylglycerol (DAG) generation and the phosphatidylcholine (PC)-breakdown. MeHg activated the group IV cytosolic phospholipase A{sub 2} (cPLA{sub 2}) and acidic form of sphingomyelinase (A-SMase) downstream of PC-PLC, but these enzymes as well as protein kinase C (PKC) were not linked to the toxicity by MeHg. Furthermore, MeHg produced ROS, which did not affect the toxicity. Addition of EGTA to culture media resulted in partial decrease of [Ca{sup 2+}]{sub i} and partially blocked the toxicity. In contrast, when the cells were treated with MeHg in the presence of Ca{sup 2+} in the culture media, D609 completely prevented cell death with parallel decrease in [Ca{sup 2+}]{sub i}. Our results demonstrated that MeHg-induced toxicity was linked to elevation of [Ca{sup 2+}]{sub i} through activation of PC-PLC, but not attributable to the signaling pathways such as cPLA{sub 2}, A-SMase, and PKC, or to the generation of ROS.

  19. Species relationships in the genus Agrostis based on flow cytometry and MITE-display molecular markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    It is estimated that there are between 150 and 200 species of Agrostis, and interspecific hybridization is a proven method for improving cultivated Agrostis species. The pool of publicly available Agrostis germplasm, available through the National Plant Germplasm System (NPGS), represents 17% of th...

  20. Global molecular surveillance provides a framework for understanding diversity within the Fusarium graminearum species complex

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Members of the Fusarium graminearum species complex (FGSC) are responsible for diseases of a variety of cereal crops worldwide. These species also are a significant food-safety concern because they contaminate grain with trichothecene mycotoxins that inhibit eukaryotic protein synthesis and can modu...

  1. Molecular Systematics of Threatened Seed Plant Species Endemic in the Caribbean Islands

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A review of available Caribbean Island red-lists species (CR and EN categories based on the IUCN guidelines from 2001, and E category established according to the IUCN guidelines from 1980) is presented. A database of at least 1,300 endemic species that are either Critically Endangered or Endangered...

  2. New molecular markers for fungal phylogenetics: Two genes for species level systematics in the Sordariomycetes (Ascomycota)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although significant progress has been made resolving deep branches of the fungal tree of life in recent works, many fungal systematists are interested in species-level questions to both define species and to assess fungal biodiversity. Fungal genome sequences are a useful resource to systematic bio...

  3. Molecular characterization of diversity and relationships within and among seven cultivated species of Prunus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Analysis of genetic variability and differentiation within and among seven cultivated species and seven wild species of Prunus using amplified fragment length polymorphism revealed four well-supported groups corresponding to the four sections Amygdalus, Armeniaca, Cerasus and Prunophora described wi...

  4. Two New Species of Liuixalus (Rhacophoridae, Anura): Evidence from Morphological and Molecular Analyses

    PubMed Central

    Jiang, Ke; Cai, Bo; Xie, Feng; Jiang, Jianping; Murphy, Robert W.; Li, Jia-Tang; Wang, Yuezhao

    2015-01-01

    Due to small body sizes, superficial similarities in morphologies, and obscure activity behaviors, the phylogeny and taxonomy of species in the genus Liuixalus were very troublesome. Some species might comprise a complex of cryptic species. To investigate the species of group, we constructed the matrilineal genealogy of the genus using 16s rRNA mitochondrial DNA sequences. Analyses recovered six well supported matrilines that involved L. romeri, L. ocellatus, L. hainanus, L. calcarius, Liuixalus shiwandashan sp. nov. and Liuixalus jinxiuensis sp. nov., though the historical relationships among them remained unresolved. Currently, Liuixalus included 4 species, distributed eastwards from northern Vietnam to Hong Kong, China. Based on genealogical and morphological distinctiveness, we described Liuixalus jinxiuensis sp. nov. from the type locality Mt. Dayao, Jinxiu, China and Liuixalus shiwandashan sp. nov. from the type locality Mt. Shiwanda, China. A combination of morphological measurements, genetic, bioacoustic and osteological analysis was served to diagnose the new taxa. PMID:26305377

  5. Molecular detection of Rickettsia, Coxiella and Rickettsiella DNA in three native Australian tick species.

    PubMed

    Vilcins, Inger-Marie E; Old, Julie M; Deane, Elizabeth

    2009-11-01

    Three Australian native animal species yielded 60 samples composed of three indigenous ticks. Hosts included twelve koalas, two echidnas and one wombat from Victoria, and ticks were of the species Ixodes tasmani (n = 42), Bothriocroton concolor (n = 8) and B. auruginans (n = 10), respectively. PCR screening and sequencing detected a species of Coxiella, sharing closest sequence identity to C. burnetii (>98%), in all B. auruginans, as well as a species of Rickettsia, matching closest to R. massiliae, in 70% of the same samples. A genotype sharing closest similarity to Rickettsia bellii (>99%) was identified in three female B. concolor collected from one of the echidnas. Three samples of I. tasmani, taken from three koalas, yielded different genotypes of Rickettsiella. These results represent the first detection of the three genera in each tick species and identify a high level of previously undetected bacterial diversity in Australian ticks. PMID:19296229

  6. Two New Species of Liuixalus (Rhacophoridae, Anura): Evidence from Morphological and Molecular Analyses.

    PubMed

    Qin, Shaobo; Mo, Yunming; Jiang, Ke; Cai, Bo; Xie, Feng; Jiang, Jianping; Murphy, Robert W; Li, Jia-Tang; Wang, Yuezhao

    2015-01-01

    Due to small body sizes, superficial similarities in morphologies, and obscure activity behaviors, the phylogeny and taxonomy of species in the genus Liuixalus were very troublesome. Some species might comprise a complex of cryptic species. To investigate the species of group, we constructed the matrilineal genealogy of the genus using 16s rRNA mitochondrial DNA sequences. Analyses recovered six well supported matrilines that involved L. romeri, L. ocellatus, L. hainanus, L. calcarius, Liuixalus shiwandashan sp. nov. and Liuixalus jinxiuensis sp. nov., though the historical relationships among them remained unresolved. Currently, Liuixalus included 4 species, distributed eastwards from northern Vietnam to Hong Kong, China. Based on genealogical and morphological distinctiveness, we described Liuixalus jinxiuensis sp. nov. from the type locality Mt. Dayao, Jinxiu, China and Liuixalus shiwandashan sp. nov. from the type locality Mt. Shiwanda, China. A combination of morphological measurements, genetic, bioacoustic and osteological analysis was served to diagnose the new taxa. PMID:26305377

  7. Thermodynamic, thermomechanical, and structural properties of a hydrated asymmetric phosphatidylcholine.

    PubMed Central

    Zhu, T; Caffrey, M

    1993-01-01

    1-Behenyl-2-lauryl-sn-glycero-3-phosphocholine (22/12 PC) belongs to a unique group of phospholipids in which the molecule has one acyl chain almost twice as long as the other. The temperature-composition phase diagram for this lipid in the range of 25-65 degrees C, and 0 to 84.3% (w/w) water has been constructed by using the isoplethal method in the heating direction and x-ray diffraction for phase identification and structure characterization. At water contents between 10.3 and 34% (w/w) and at temperatures below 43 degrees C, a single mixed interdigitated lamellar gel phase (Lm beta, [symbol: see text]) of the type described by Hui et al. (1984. Biochemistry. 23:5570-5577) and McIntosh et al. (1984. Biochemistry. 23:4038-4044) was found. A second phase consisting of bulk aqueous solution coexists with the Lm beta phase at hydration levels above 34% (w/w) water in the temperature range between 25 and 43 degrees C. Above 43 degrees C, a partially interdigitated lamellar liquid crystalline (Lp alpha) phase ([symbol: see text]) is seen in the water concentration range extending from 0 to 84.3% (w/w). The pure Lp alpha phase is found below 43% (w/w) water, while coexistence of the Lp alpha phase and the bulk aqueous solution is observed above this water concentration which marks the hydration boundary. Interestingly, the latter boundary for both Lm beta and Lp alpha phases is nearly vertical in the temperature range studied. Furthermore, the lamellar chain-melting transition temperature appears to be relatively insensitive to hydration in the range 0-85% (w/w) water. We have confirmed the identify of the Lm beta phase by constructing a 5.7-A resolution electron density profile on oriented samples by the swelling method. Temperature-induced chain melting effects an increase in lipid bilayer thickness suggesting that the Lp alpha phase has chains packed in the partially as opposed to the mixed interdigitated configuration. Unlike the symmetric phosphatidylcholines a

  8. Molecular taxonomy provides new insights into anopheles species of the neotropical arribalzagia series.

    PubMed

    Gómez, Giovan F; Bickersmith, Sara A; González, Ranulfo; Conn, Jan E; Correa, Margarita M

    2015-01-01

    Phylogenetic analysis of partial mitochondrial cytochrome oxidase c subunit I (COI) and nuclear internal transcribed spacer 2 (ITS2) sequences were used to evaluate initial identification and to investigate phylogenetic relationships of seven Anopheles morphospecies of the Arribalzagia Series from Colombia. Phylogenetic trees recovered highly supported clades for An. punctimaculas.s., An. calderoni, An. malefactor s.l., An. neomaculipalpus, An. apicimacula s.l., An. mattogrossensis and An. peryassui. This study provides the first molecular confirmation of An. malefactorfrom Colombia and discovered conflicting patterns of divergence for the molecular markers among specimens from northeast and northern Colombia suggesting the presence of two previously unrecognized Molecular Operational Taxonomic Units (MOTUs). Furthermore, two highly differentiated An. apicimacula MOTUs previously found in Panama were detected. Overall, the combined molecular dataset facilitated the detection of known and new Colombian evolutionary lineages, and constitutes the baseline for future research on their bionomics, ecology and potential role as malaria vectors. PMID:25774795

  9. Molecular markers and conservation of plant species in Latin America: the case of Phaedranassa viridflora (Amaryllidaceae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellites are molecular markers with great potential for investigating genetic structure of populations. This information is valuable for generating effective conservation plans. We studied the endemic and endangered Phaedranassa viridiflora (Amaryllidaceae) to show the utility of microsatelli...

  10. Molecular Taxonomy Provides New Insights into Anopheles Species of the Neotropical Arribalzagia Series

    PubMed Central

    Gómez, Giovan F.; Bickersmith, Sara A.; González, Ranulfo; Conn, Jan E.; Correa, Margarita M.

    2015-01-01

    Phylogenetic analysis of partial mitochondrial cytochrome oxidase c subunit I (COI) and nuclear internal transcribed spacer 2 (ITS2) sequences were used to evaluate initial identification and to investigate phylogenetic relationships of seven Anopheles morphospecies of the Arribalzagia Series from Colombia. Phylogenetic trees recovered highly supported clades for An. punctimaculas.s., An. calderoni, An. malefactor s.l., An. neomaculipalpus, An. apicimacula s.l., An. mattogrossensis and An. peryassui. This study provides the first molecular confirmation of An. malefactorfrom Colombia and discovered conflicting patterns of divergence for the molecular markers among specimens from northeast and northern Colombia suggesting the presence of two previously unrecognized Molecular Operational Taxonomic Units (MOTUs). Furthermore, two highly differentiated An. apicimacula MOTUs previously found in Panama were detected. Overall, the combined molecular dataset facilitated the detection of known and new Colombian evolutionary lineages, and constitutes the baseline for future research on their bionomics, ecology and potential role as malaria vectors. PMID:25774795

  11. Gas-Phase Molecular Dynamics: High Resolution Spectroscopy and Collision Dynamics of Transient Species

    SciTech Connect

    Hall G. E.; Goncharov, V.

    2012-05-29

    This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. Chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry are investigated by high resolution spectroscopic tools. Production, reaction, and energy transfer processes are investigated by transient, double resonance, polarization and saturation spectroscopies, with an emphasis on technique development and connection with theory, as well as specific molecular properties.

  12. Gas-Phase Molecular Dynamics: High Resolution Spectroscopy and Collision Dynamics of Transient Species

    SciTech Connect

    Hall, G.E.

    2011-05-31

    This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. Chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry are investigated by high resolution spectroscopic tools. Production, reaction, and energy transfer processes are investigated by transient, double resonance, polarization and saturation spectroscopies, with an emphasis on technique development and connection with theory, as well as specific molecular properties.

  13. An Integrated Morphological and Molecular Approach to the Description and Systematisation of a Novel Genus and Species of Macrodasyida (Gastrotricha)

    PubMed Central

    Todaro, M. Antonio; Dal Zotto, Matteo; Leasi, Francesca

    2015-01-01

    Background Gastrotricha systematics is in a state of flux mainly due to the conflicts between cladistic studies base on molecular markers and the classical systematisation based on morphological traits. In sandy samples from Thailand, we found numerous macrodasyidan gastrotrichs belonging to an undescribed species of difficult taxonomic affiliation. The abundance and original nature of the specimens prompted us to undertake a deep survey of both morphological and molecular traits aiming at a reliable systematisation of the new taxon. Methodology/Principal Findings Using several microscopical techniques we investigated the external and internal anatomy, including the muscular and nervous systems of the new species. Additional specimens were used to obtain the 18S rRNA gene sequence; molecular data was analysed cladistically in conjunction with data from additional species belonging to the near complete Macrodasyida taxonomic spectrum. Specimens are vermiform, up to 806 μm in total length, and show a well-defined head equipped with peculiar leaf-like sensorial organs and a single-lobed posterior end. The adhesive apparatus includes anterior, ventrolateral, dorsal and posterior tubes. Pharynx is about 1/4 of the total length and shows pores at its posterior 3/4. Adult specimens exhibit maturing eggs and a bulky, muscular caudal organ, but do not show sperm nor the frontal organ. Musculature and nervous system organisation resemble the usual macrodasyidan plan; however, the somatic circular muscles of the intestinal region surround all other muscular components and a third FMRFamide-IR commissure ventral to the pharyngo-intestinal junction appear to be an autoapomorphic traits of the new species. Conclusions/Significance While the anatomical characteristics of the Asian specimens appear so unique to grant the establishment of a new taxon, for which the name Thaidasys tongiorgii gen. et sp. nov. is proposed, the result of phylogenetic analyses based on the 18S r

  14. A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruits

    PubMed Central

    2011-01-01

    Background The nematode Caenorhabditis elegans is a major laboratory model in biology. Only ten Caenorhabditis species were available in culture at the onset of this study. Many of them, like C. elegans, were mostly isolated from artificial compost heaps, and their more natural habitat was unknown. Results Caenorhabditis nematodes were found to be proliferating in rotten fruits, flowers and stems. By collecting a large worldwide set of such samples, 16 new Caenorhabditis species were discovered. We performed mating tests to establish biological species status and found some instances of semi-fertile or sterile hybrid progeny. We established barcodes for all species using ITS2 rDNA sequences. By obtaining sequence data for two rRNA and nine protein-coding genes, we determined the likely phylogenetic relationships among the 26 species in culture. The new species are part of two well-resolved sister clades that we call the Elegans super-group and the Drosophilae super-group. We further scored phenotypic characters such as reproductive mode, mating behavior and male tail morphology, and discuss their congruence with the phylogeny. A small space between rays 2 and 3 evolved once in the stem species of the Elegans super-group; a narrow fan and spiral copulation evolved once in the stem species of C. angaria, C. sp. 8 and C. sp. 12. Several other character changes occurred convergently. For example, hermaphroditism evolved three times independently in C. elegans, C. briggsae and C. sp. 11. Several species can co-occur in the same location or even the same fruit. At the global level, some species have a cosmopolitan distribution: C. briggsae is particularly widespread, while C. elegans and C. remanei are found mostly or exclusively in temperate regions, and C. brenneri and C. sp. 11 exclusively in tropical zones. Other species have limited distributions, for example C. sp. 5 appears to be restricted to China, C. sp. 7 to West Africa and C. sp. 8 to the Eastern United

  15. Root productivity of deciduous and evergreen species identified using a molecular approach

    NASA Astrophysics Data System (ADS)

    Ellsworth, P.; Sternberg, L. O.

    2012-12-01

    The linkage between leaf traits and root structure may explain how plants integrate above and belowground traits into whole plant adaptations to environmental stresses. In dry seasonal forests, the lack of dry season precipitation dries out the relatively nutrient-rich shallow soil, leaving shallow soil water and nutrients inaccessible to uptake until the wet season. In tropical or subtropical seasonal dry forests, deciduousness may allow for the survival of shallow fine roots during the dry season. Losing leaves during the dry season reduces aboveground plant water demand, and a greater proportion of water extracted from deep soil can be used to maintain shallow roots until the wet season. Higher shallow root survival through the dry season than evergreen species means that deciduous species can take advantage of the nutrient pulse associated with the onset of the wet season. To test the above hypothesis, fine roots were collected from soil cores in a seasonally dry forest during the dry season, onset of the wet season, and the wet season and were identified to selected evergreen and deciduous study species. The fine roots of two of the selected species (Lyonia ferruginea and Carya floridana) could be identified from visual characteristics. The other three study species, which were all from the genus Quercus (Q. geminata, Q. myrtifolia, and Q. laevis), were impossible to separate visually. We developed a PCR-based restriction fragment length polymorphism (PCR-RFLP) technique, which provided a quick, simple, low-cost way to identify the species of all fine roots of our study species. We extracted DNA from all roots that were not visually identified, amplified the internal transcribed spacer region (ITS), digested the ITS region with the restriction enzyme TaqαI, and used gel electrophoresis to separate DNA fragments. Using a PCR-RFLP based root identification key that we developed for the species at Archbold Biological Station, all species that could not be

  16. Fish allergy in patients with parvalbumin-specific immunoglobulin E depends on parvalbumin content rather than molecular differences in the protein among fish species.

    PubMed

    Kobayashi, Ayako; Kobayashi, Yukihiro; Shiomi, Kazuo

    2016-10-01

    Allergenic characteristics of purified parvalbumins from different fish species have not been thoroughly investigated. We revealed that purified parvalbumins from nine different fish species have identical IgE-reactivities and high cross-reactivities. We also showed that fish allergenicity is associated with the parvalbumin content of the fish species, rather than species-specific differences in the molecular characteristics of the individual parvalbumin proteins. PMID:27251554

  17. Molecular architecture of Pipistrellus pipistrellus/Pipistrellus pygmaeus complex (Chiroptera: Vespertilionidae): further cryptic species and Mediterranean origin of the divergence.

    PubMed

    Hulva, Pavel; Horácek, Ivan; Strelkov, Petr P; Benda, Petr

    2004-09-01

    Previous genetic analyses have demonstrated that two phonic types of one of the most common European bats, the Common pipistrelle, belong to distinct species, although they are almost identical morphologically (45 kHz Pipistrellus pipistrellus and 55 kHz Pipistrellus pygmaeus). To reconstruct the history of the species complex and explain the codistribution of both forms in Europe and the Mediterranean, we performed phylogenetic analysis based on a 402-bp portion of the cytochrome b gene. Particular attention was paid to the eastern and southern parts of the range where no data were available. We found further distinctive allopatric haplotypes from Libya and Morocco. The difference of about 6-7% described in the Libyan population suggests the occurrence of a new species in the southern Mediterranean. The species status of Moroccan population is also discussed. The phylogeographic patterns obtained and analysis of fossil records support the hypothesis of expansion of both species into Europe from the Mediterranean region during the Holocene. The allopatric speciation model fits our data best. The paleobiographic scenario envisaged is corroborated also by molecular clock estimations and correlations with Late Neogene environmental changes in the Mediterranean region which ended with the Messinian salinity crisis. PMID:15288073

  18. Cytogenetic and Molecular Analyses Reveal a Divergence between Acromyrmex striatus (Roger, 1863) and Other Congeneric Species: Taxonomic Implications

    PubMed Central

    Cristiano, Maykon Passos; Cardoso, Danon Clemes; Fernandes-Salomão, Tânia Maria

    2013-01-01

    The leafcutter ants, which consist of Acromyrmex and Atta genera, are restricted to the New World and they are considered the main herbivores in the neotropics. Cytogenetic studies of leafcutter ants are available for five species of Atta and 14 species of Acromyrmex, both including subspecies. These two ant genera have a constant karyotype with a diploid number of 22 and 38 chromosomes, respectively. The most distinct Acromyrmex species from Brazil is A. striatus, which is restricted to the southern states of Santa Catarina and Rio Grande do Sul. Several cytogenetic and phylogenetic studies have been conducted with ants, but the karyotypic characterization and phylogenetic position of this species relative to leafcutter ants remains unknown. In this study, we report a diploid number of 22 chromosomes for A. striatus. The phylogenetic relationship between A. striatus and other leafcutter ants was estimated based on the four nuclear genes. A. striatus shared the same chromosome number as Atta species and the majority of metacentric chromosomes. Nuclear data generated a phylogenetic tree with a well-supported cluster, where A. striatus formed a different clade from other Acromyrmex spp. This combination of cytogenetic and molecular approaches provided interesting insights into the phylogenetic position of A. striatus among the leafcutter ants and the tribe Attini. PMID:23527267

  19. Molecular Identification of Dendrobium Species (Orchidaceae) Based on the DNA Barcode ITS2 Region and Its Application for Phylogenetic Study

    PubMed Central

    Feng, Shangguo; Jiang, Yan; Wang, Shang; Jiang, Mengying; Chen, Zhe; Ying, Qicai; Wang, Huizhong

    2015-01-01

    The over-collection and habitat destruction of natural Dendrobium populations for their commercial medicinal value has led to these plants being under severe threat of extinction. In addition, many Dendrobium plants are similarly shaped and easily confused during the absence of flowering stages. In the present study, we examined the applic