Sample records for earwig anisolabis maritima

  1. Progressive Provisioning by the Females of the Earwig, Anisolabis maritima, Increases the Survival Rate of the Young

    PubMed Central

    Suzuki, Seizi

    2010-01-01

    Provisioning the young is an important form of insect parental care and is believed to improve the survival and growth of the young. Anisolabis maritima Bonelli (Dermaptera: Anisolabididae) is a cosmopolitan species of earwig that shows sub-social behavior in which the females tend clutches of eggs in soil burrows. The defensive and provisioning behaviors of these females were examined in this study. When disturbed, maternal individuals abandoned the nest less than non-maternal individuals. Females brought food to the nest after their eggs hatched, and the survival of the nymphs was increased by provisioning. Even when mothers were removed, providing food to the nymphs increased survival as well as when the nymphs were provisioned by the mother. These results show that A. maritima mothers provision the nymphs and that this provisioning improves their survival. PMID:21062141

  2. Morphological characterization of the antennal sensilla of t he earwig Anisolabis maritima (Dermaptera: Carcinophoridae) with reference to their probable functions

    PubMed Central

    Al-Dosary, Mona Mohammed

    2009-01-01

    The earwig, Anisolabis maritima (Dermaptera: Carcinophoridae), is one of the most significant insects in KSA because, it was recorded in Saudi Arabia as a beneficial predator on eggs and newly hatched larvae of the red palm weevil, Rhyncophorus ferrugineus. We examined the external morphology of the antennal sensilla of males and females of A. maritima using scanning electron microscopy (SEM). The filiform antennae of A. maritima were of the conventional type comprising a basal scape, pedicle and a long, thread-like flagellum, which was composed of 12 flagellomeres of males and 16 flagellomeres of females. Six morphologically unique sensillar types were found and described on the antennae of males and females of A. maritima. Of those identified, there were three types of porous trichoid sensilla (long, curved and arcuate), and two types of basiconic sensilla (short and curved), and one type of aporous trichoid sensilla. The shape, external morphology and array of sensilla on the antennae of males and females of A. maritima were similar. PMID:23961038

  3. Earwigs

    E-print Network

    Mott, Dale; Jackman, John A.

    2004-08-06

    will not solve the prob- lem of earwigs entering the building and should be used only as a supplement to outdoor efforts. Boric acid or aerosol insecticides labeled for indoor use are effective when used around baseboards, carpet edges, door and window frames...

  4. Asymmetric forceps increase fighting success among males of similar size in the maritime earwig

    PubMed Central

    Munoz, Nicole E.; Zink, Andrew G.

    2012-01-01

    Extreme asymmetric morphologies are hypothesized to serve an adaptive function that counteracts sexual selection for symmetry. However direct tests of function for asymmetries are lacking, particularly in the context of animal weapons. The weapon of the maritime earwig, Anisolabis maritima, exhibits sizeable variation in the extent of directional asymmetry within and across body sizes, making it an ideal candidate for investigating the function of asymmetry. In this study, we characterized the extent of weapon asymmetry, characterized the manner in which asymmetric weapons are used in contests, staged dyadic contests between males of different size classes and analyzed the correlates of fighting success. In contests between large males, larger individuals won more fights and emerged as the dominant male. In contests between small males, however, weapon asymmetry was more influential in predicting overall fighting success than body size. This result reveals an advantage of asymmetric weaponry among males that are below the mean size in the population. A forceps manipulation experiment suggests that asymmetry may be an indirect, correlate of a morphologically independent factor that affects fighting ability. PMID:22984320

  5. Multifunctional weaponry: the chemical defenses of earwigs.

    PubMed

    Gasch, Tina; Schott, Matthias; Wehrenfennig, Christoph; Düring, Rolf-Alexander; Vilcinskas, Andreas

    2013-12-01

    Earwigs protect themselves against predators using pincer-like cerci and/or malodorous exudates secreted from abdominal glands. Little is known about the chemistry of these secretions and their potential functions. However, because earwigs live in aggregations and overwinter in soil, they are exposed to high microbial loads throughout their lifecycle, and we therefore hypothesized that the secretions are used not only to deter predators but also to combat pathogens and parasites in their environment. We analyzed the defensive secretions of the European earwig Forficula auricularia, the short-winged earwig Apterygida media and the woodland earwig Chelidurella guentheri by gas chromatography-mass spectrometry. The secretions of all three species contained 2-methyl-1,4-benzoquinone and 2-ethyl-1,4-benzoquinone, whereas A. media also produced 2,3-dimethyl-1,4-benzoquinone and 2-ethyl-3-methyl-1,4-benzoquinone. The latter has not been identified in the exudates of insects before. The composition and/or quantity of these components were species-specific and partially sex-specific. All secretions showed antimicrobial activity against Gram-positive and Gram-negative bacteria as well as two entomopathogenic fungi. Furthermore, the secretion of F. auricularia displayed nematicidal activity against Caenorhabditis elegans. Our data support the hypothesis that earwig secretions are multifunctional, serving both to deter predators and sanitize the microenvironment. PMID:24090659

  6. New mid-Cretaceous earwigs in amber from Myanmar (Dermaptera)

    E-print Network

    Engel, Michael S.; Grimaldi, David A.

    2014-01-29

    and interspecific relationships in Der- maptera. Oecologia 96(3): 360–364. Shepard, M., V. Waddill, & W. Kloft. 1973. Biology of the predaceous earwig Labidura riparia (Dermaptera: Labiduridae). Annals of the Entomological Society of America 66(4): 837–841. Shi, G...

  7. Management strategies in apple orchards influence earwig community.

    PubMed

    Malagnoux, Laure; Marliac, Gaëlle; Simon, Sylvaine; Rault, Magali; Capowiez, Yvan

    2015-04-01

    Our aim was to assess whether different apple orchard management strategies (low-input, organic, Integrated Pest Management (IPM)) would have an effect on earwigs, which are important natural enemies of apple pests. These commercial orchards were as well compared to abandoned orchards. The density of Forficula auricularia and Forficula pubescens was studied for three years in 74 orchards around Avignon. The pesticide usage, some orchard characteristics and two small-scale landscape parameters were characterized. Pesticide use was significantly different between low-input, organic and IPM orchards with particularly significant differences in the number of insecticide applications (2.2, 4.9 and 9.2 respectively). Pesticide use had a much stronger impact on earwig community than other characteristics. F. auricularia density was significantly lower in IPM orchards (0.47 individuals per tree) compared to organic, low-input and abandoned orchards (3.1, 4.5 and 1.6 individuals per tree, respectively). F. pubescens was almost absent from IPM orchards and its abundance was higher in abandoned or low-input orchards compared to organic orchards (1.5 and 2.8 vs 0.8 individuals per tree). The percentage of F. pubescens in the earwig community decreased from abandoned (52%) to low-input (40%), organic (15%) and IPM orchards (0.5%). These results were confirmed by LD50 assays showing that for the two pesticides causing mortality close to normal application rates (chlorpyrifos-ethyl and acetamiprid), F. pubescens was significantly more sensitive than F. auricularia. Since earwigs are also easy to capture and identify, they may be useful to estimate the effects of management strategies and their modification in pome fruit orchards. PMID:25577700

  8. The chemical defense in larvae of the earwig Forficula auricularia.

    PubMed

    Gasch, Tina; Vilcinskas, Andreas

    2014-08-01

    Larvae of the European earwig, Forficula auricularia, possess a paired pygidial gland with yet unknown content and function. We used gas chromatography-mass spectrometry to analyze the larval secretions revealing the presence of 2-methyl-1,4-benzoquinone, 2-ethyl-1,4-benzoquinone, n-tridecane and n-pentadecane. Based on our recent discovery that the morphologically-distinct abdominal glands of adult earwigs produce secretions with antibacterial, antifungal and nematicidal activity, we propose that the pygidial glands mediate chemical defenses in the larvae. We next considered whether the defensive functions of larval secretions include repellent activity against sympatric predators. Therefore, we tested the effects of larval secretions on foraging workers of the ant species Myrmica rubra, the actively hunting spiders Anyphaena accentuata and Philodromus aureolus and the net-hunting spider Pholcus phalangioides in laboratory feeding assays. The secretion is released in response to ant attacks, and discourages feeding in M. rubra, however, it does not discourage feeding in spiders. Our results suggest that earwigs use different glands during ontogenesis to produce secretions that play roles in chemical defense against predators such as ants. PMID:24879968

  9. Detecting aphid predation by earwigs in organic citrus orchards using molecular markers.

    PubMed

    Romeu-Dalmau, C; Piñol, J; Agustí, N

    2012-10-01

    Aphids (Hemiptera: Aphidoidea) can damage citrus trees via direct damage to leaves and flowers or via the indirect transmission of viruses. Predators such as the European earwig, Forficula auricularia Linnaeus (Dermaptera: Forficulidae), may assist in keeping aphid populations under control in citrus orchards. Group-specific primers were developed to detect aphid DNA in earwigs, in order to determine earwig predation rates in aphids in Mediterranean organic citrus trees. These primers were designed in accordance with the alignment of comparable sequences of aphids and earwigs, and they amplified a 224 bp fragment of the mitochondrial cytochrome c oxidase subunit I (COI) region. Following the consumption of three to five Aphis spiraecola Patch, aphid DNA was still detectable in 50% of earwigs one day after the ingestion. When predation was evaluated in the field, aphid DNA was detected in earwigs in May, June and July but not in April and August. The most interesting result is that of May, when aphid abundance was very low but 30% of the earwigs tested positive for aphid DNA. This finding suggests that earwigs are important aphid predators in citrus orchards, as they probably alter aphid dynamics as a result of early seasonal pressure on this pest. PMID:22414267

  10. European Earwig, Forficula auricularia L. (Dermaptera: Forficulidae) at the Hanford Reach National Monument, Washington State

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The European earwig, Forficula auricularia L., was surveyed using pitfall traps at three sites at the Hanford Reach National Monument in south central Washington state. Pitfall traps were collected weekly from April 2002 through April 2003. The earwig was consistently taken during all months of the...

  11. Beta maritima: the Origin of Beets

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Along the undisturbed shores, especially of the Mediterranean Sea and the European North Atlantic Ocean, is a widespread plant called Beta maritima (Beta vulgaris subspecies maritima) by the botanists, or more commonly sea beet. Nothing for the inexperienced observer's eye distinguishes it from surr...

  12. Phylogeny of earwigs (Insecta: Dermaptera) based on molecular and morphological evidence: reconsidering the classification of Dermaptera

    Microsoft Academic Search

    KARL J. J ARVIS; F ABIAN H AAS

    2004-01-01

    Dermaptera (earwigs) is a cosmopolitan order of insects, the phyloge- netic relationships of which are poorly understood. The phylogeny of Dermaptera was inferred from large subunit ribosomal (28S), small subunit ribosomal (18S), histone-3 (H3) nuclear DNA sequences, and forty-three morphological characters. Sequence data were collected for thirty-two earwig exemplar taxa representing eight families in two suborders: Hemimeridae (suborder Hemimerina); Pygidicra-

  13. New earwigs in mid-Cretaceous amber from Myanmar (Dermaptera, Neodermaptera)

    PubMed Central

    Engel, Michael S.

    2011-01-01

    Abstract Two new earwigs (Dermaptera) recently discovered in mid-Cretaceous (latest Albian) amber from Myanmar are described and figured. Astreptolabis ethirosomatia gen. et sp. n. is represented by a peculiar pygidicranoid female, assigned to a new subfamily, Astreptolabidinae subfam. n., and differs from other protodermapterans in the structure of the head, pronotum, tegmina, and cercal forceps. Tytthodiplatys mecynocercus gen. et sp. n. is a distinctive form of first-instar nymph of the Diplatyidae, the earliest record for this basal earwig family. The taxon can be distinguished from other Early Cretaceous nymphs by the structure of the head, antennae, legs, and most notably its filamentous and annulate cerci. The character affinities of these taxa among Neodermaptera are generally discussed as is the identity of an enigmatic ‘earwig-like’ species from the Jurassic of China. PMID:22259272

  14. Transitional fossil earwigs - a missing link in Dermaptera evolution

    PubMed Central

    2010-01-01

    Background The Dermaptera belongs to a group of winged insects of uncertain relationship within Polyneoptera, which has expanded anal region and adds numerous anal veins in the hind wing. Evolutional history and origin of Dermaptera have been in contention. Results In this paper, we report two new fossil earwigs in a new family of Bellodermatidae fam. nov. The fossils were collected from the Jiulongshan Formation (Middle Jurassic) in Inner Mongolia, northeast China. This new family, characterized by an unexpected combination of primitive and derived characters, is bridging the missing link between suborders of Archidermaptera and Eodermaptera. Phylogenetic analyses support the new family to be a new clade at the base of previously defined Eodermaptera and to be a stem group of (Eodermaptera+Neodermaptera). Conclusion Evolutional history and origin of Dermaptera have been in contention, with dramatically different viewpoints by contemporary authors. It is suggested that the oldest Dermaptera might possibly be traced back to the Late Triassic-Early Jurassic and they had divided into Archidermaptera and (Eodermaptera+Neodermaptera) in the Middle Jurassic. PMID:21062504

  15. UNCORRECTED PROOF A phylogeny of earwigs (Insecta: Dermaptera) based on molecular and morphological evidence: reconsidering the classification of Dermaptera

    Microsoft Academic Search

    KARL J. J ARVIS; F ABIAN H AAS

    Dermaptera (earwigs) is a cosmopolitan order of insects, the phyloge- netic relationships of which are poorly understood. The phylogeny of Dermaptera was inferred from large subunit ribosomal (28S), small subunit ribosomal (18S), histone-3 (H3) nuclear DNA sequences, and forty-three morphological characters. Sequence data were collected for thirty-two earwig exemplar taxa representing eight families in two suborders: Hemimeridae (suborder Hemimerina); Pygidicra-

  16. Novel inositol catabolic pathway in Thermotoga maritima.

    PubMed

    Rodionova, Irina A; Leyn, Semen A; Burkart, Michael D; Boucher, Nathalie; Noll, Kenneth M; Osterman, Andrei L; Rodionov, Dmitry A

    2013-08-01

    myo-inositol (MI) is a key sugar alcohol component of various metabolites, e.g. phosphatidylinositol-based phospholipids that are abundant in animal and plant cells. The seven-step pathway of MI degradation was previously characterized in various soil bacteria including Bacillus subtilis. Through a combination of bioinformatics and experimental techniques we identified a novel variant of the MI catabolic pathway in the marine hyperthermophilic bacterium Thermotoga maritima. By using in vitro biochemical assays with purified recombinant proteins we characterized four inositol catabolic enzymes encoded in the TM0412-TM0416 chromosomal gene cluster. The novel catabolic pathway in T.?maritima starts as the conventional route using the myo-inositol dehydrogenase IolG followed by three novel reactions. The first 2-keto-myo-inositol intermediate is oxidized by another, previously unknown NAD-dependent dehydrogenase TM0412 (named IolM), and a yet unidentified product of this reaction is further hydrolysed by TM0413 (IolN) to form 5-keto-l-gluconate. The fourth step involves epimerization of 5-keto-l-gluconate to d-tagaturonate by TM0416 (IolO). T.?maritima is unable to grow on myo-inositol as a single carbon source. The determined in vitro specificity of the InoEFGK (TM0418-TM0421) transporter to myo-inositol-phosphate suggests that the novel pathway in Thermotoga utilizes a phosphorylated derivative of inositol. PMID:23441918

  17. De Novo Transcriptome Hybrid Assembly and Validation in the European Earwig (Dermaptera, Forficula auricularia)

    PubMed Central

    Pichon, Samuel; Arbore, Roberto; Kühn-Bühlmann, Simone; Kölliker, Mathias; Walser, Jean-Claude

    2014-01-01

    Background The European earwig (Forficula auricularia) is an established system for studies of sexual selection, social interactions and the evolution of parental care. Despite its scientific interest, little knowledge exists about the species at the genomic level, limiting the scope of molecular studies and expression analyses of genes of interest. To overcome these limitations, we sequenced and validated the transcriptome of the European earwig. Methodology and Principal Findings To obtain a comprehensive transcriptome, we sequenced mRNA from various tissues and developmental stages of female and male earwigs using Roche 454 pyrosequencing and Illumina HiSeq. The reads were de novo assembled independently and screened for possible microbial contamination and repeated elements. The remaining contigs were combined into a hybrid assembly and clustered to reduce redundancy. A comparison with the eukaryotic core gene dataset indicates that we sequenced a substantial part of the earwig transcriptome with a low level of fragmentation. In addition, a comparative analysis revealed that more than 8,800 contigs of the hybrid assembly show significant similarity to insect-specific proteins and those were assigned for Gene Ontology terms. Finally, we established a quantitative PCR test for expression stability using commonly used housekeeping genes and applied the method to five homologs of known sex-biased genes of the honeybee. The qPCR pilot study confirmed sex specific expression and also revealed significant expression differences between the brain and antenna tissue samples. Conclusions By employing two different sequencing approaches and including samples obtained from different tissues, developmental stages, and sexes, we were able to assemble a comprehensive transcriptome of F. auricularia. The transcriptome presented here offers new opportunities to study the molecular bases and evolution of parental care and sociality in arthropods. PMID:24722757

  18. When the Body Hides the Ancestry: Phylogeny of Morphologically Modified Epizoic Earwigs Based on Molecular Evidence

    PubMed Central

    Kocarek, Petr; John, Vaclav; Hulva, Pavel

    2013-01-01

    Here, we present a study regarding the phylogenetic positions of two enigmatic earwig lineages whose unique phenotypic traits evolved in connection with ectoparasitic relationships with mammals. Extant earwigs (Dermaptera) have traditionally been divided into three suborders: the Hemimerina, Arixeniina, and Forficulina. While the Forficulina are typical, well-known, free-living earwigs, the Hemimerina and Arixeniina are unusual epizoic groups living on molossid bats (Arixeniina) or murid rodents (Hemimerina). The monophyly of both epizoic lineages is well established, but their relationship to the remainder of the Dermaptera is controversial because of their extremely modified morphology with paedomorphic features. We present phylogenetic analyses that include molecular data (18S and 28S ribosomal DNA and histone-3) for both Arixeniina and Hemimerina for the first time. This data set enabled us to apply a rigorous cladistics approach and to test competing hypotheses that were previously scattered in the literature. Our results demonstrate that Arixeniidae and Hemimeridae belong in the dermapteran suborder Neodermaptera, infraorder Epidermaptera, and superfamily Forficuloidea. The results support the sister group relationships of Arixeniidae+Chelisochidae and Hemimeridae+Forficulidae. This study demonstrates the potential for rapid and substantial macroevolutionary changes at the morphological level as related to adaptive evolution, in this case linked to the utilization of a novel trophic niche based on an epizoic life strategy. Our results also indicate that the evolutionary consequences of the transition to an ectoparazitic mode of living, which is extremely rare in earwigs, have biased previous morphology-based hypotheses regarding the phylogeny of this insect group. PMID:23826171

  19. Advanced morphology and behaviour of extinct earwig-like cockroaches (Blattida: Fuziidae fam. nov.)

    NASA Astrophysics Data System (ADS)

    Vršanský, Peter; Liang, Jun-Hui; Ren, Dong

    2009-12-01

    We describe the extinct cockroach family Fuziidae fam. nov., represented by Fuzia dadao gen. et sp. nov. from the ?Bathonian (168 Ma) Middle Jurassic sediments of Daohugou, Inner Mongolia, China. Males are characterized by unique, long and narrow bodies with a notch on forceps of earwig-like cerci, which attaches to the long external ovipositor during courtship. In a combination with the presence of male tergal glands, it appears the most advanced form of reproduction in the nearly 300 Myr history of long external ovipositor-bearing cockroaches. Its advanced morphology significantly supports attribution of living and fossil cockroaches within a single order Blattida.

  20. Phytologia (December 2007) 89(3) 263 JUNIPERUS MARITIMA, THE SEASIDE JUNIPER, A NEW

    E-print Network

    Adams, Robert P.

    Phytologia (December 2007) 89(3) 263 JUNIPERUS MARITIMA, THE SEASIDE JUNIPER, A NEW SPECIES FROM as well as morphology and ecology, a new cryptic species, Juniperus maritima, from the Puget Sound region WORDS: Juniperus maritima, Puget Sound, J. scopulorum, J. virginiana, cryptic species, terpenoids, nr

  1. The Complete Mitochondrial Genome of the Geophilomorph Centipede Strigamia maritima.

    PubMed

    Robertson, Helen E; Lapraz, François; Rhodes, Adelaide C; Telford, Maximilian J

    2015-01-01

    Strigamia maritima (Myriapoda; Chilopoda) is a species from the soil-living order of geophilomorph centipedes. The Geophilomorpha is the most speciose order of centipedes with over a 1000 species described. They are notable for their large number of appendage bearing segments and are being used as a laboratory model to study the embryological process of segmentation within the myriapods. Using a scaffold derived from the recently published genome of Strigamia maritima that contained multiple mitochondrial protein-coding genes, here we report the complete mitochondrial genome of Strigamia, the first from any geophilomorph centipede. The mitochondrial genome of S. maritima is a circular molecule of 14,938 base pairs, within which we could identify the typical mitochondrial genome complement of 13 protein-coding genes and 2 ribosomal RNA genes. Sequences resembling 16 of the 22 transfer RNA genes typical of metazoan mitochondrial genomes could be identified, many of which have clear deviations from the standard 'cloverleaf' secondary structures of tRNA. Phylogenetic trees derived from the concatenated alignment of protein-coding genes of S. maritima and >50 other metazoans were unable to resolve the Myriapoda as monophyletic, but did support a monophyletic group of chilopods: Strigamia was resolved as the sister group of the scolopendromorph Scolopocryptos sp. and these two (Geophilomorpha and Scolopendromorpha), along with the Lithobiomorpha, formed a monophyletic group the Pleurostigmomorpha. Gene order within the S. maritima mitochondrial genome is unique compared to any other arthropod or metazoan mitochondrial genome to which it has been compared. The highly unusual organisation of the mitochondrial genome of Strigamia maritima is in striking contrast with the conservatively evolving nuclear genome: sampling of more members of this order of centipedes will be required to see whether this unusual organization is typical of the Geophilomorpha or results from a more recent reorganisation in the lineage leading to Strigamia. PMID:25794168

  2. The Complete Mitochondrial Genome of the Geophilomorph Centipede Strigamia maritima

    PubMed Central

    Rhodes, Adelaide C.; Telford, Maximilian J.

    2015-01-01

    Strigamia maritima (Myriapoda; Chilopoda) is a species from the soil-living order of geophilomorph centipedes. The Geophilomorpha is the most speciose order of centipedes with over a 1000 species described. They are notable for their large number of appendage bearing segments and are being used as a laboratory model to study the embryological process of segmentation within the myriapods. Using a scaffold derived from the recently published genome of Strigamia maritima that contained multiple mitochondrial protein-coding genes, here we report the complete mitochondrial genome of Strigamia, the first from any geophilomorph centipede. The mitochondrial genome of S. maritima is a circular molecule of 14,938 base pairs, within which we could identify the typical mitochondrial genome complement of 13 protein-coding genes and 2 ribosomal RNA genes. Sequences resembling 16 of the 22 transfer RNA genes typical of metazoan mitochondrial genomes could be identified, many of which have clear deviations from the standard ‘cloverleaf’ secondary structures of tRNA. Phylogenetic trees derived from the concatenated alignment of protein-coding genes of S. maritima and >50 other metazoans were unable to resolve the Myriapoda as monophyletic, but did support a monophyletic group of chilopods: Strigamia was resolved as the sister group of the scolopendromorph Scolopocryptos sp. and these two (Geophilomorpha and Scolopendromorpha), along with the Lithobiomorpha, formed a monophyletic group the Pleurostigmomorpha. Gene order within the S. maritima mitochondrial genome is unique compared to any other arthropod or metazoan mitochondrial genome to which it has been compared. The highly unusual organisation of the mitochondrial genome of Strigamia maritima is in striking contrast with the conservatively evolving nuclear genome: sampling of more members of this order of centipedes will be required to see whether this unusual organization is typical of the Geophilomorpha or results from a more recent reorganisation in the lineage leading to Strigamia. PMID:25794168

  3. The earliest earwigs in amber (Dermaptera): A new genus and species from the Early Cretaceous of Lebanon

    E-print Network

    Engel, Michael S.; Ortega-Blanco, Jaime; Azar, Dany

    2011-07-01

    , while photomicrographs were prepared using a Nikon D1x digital camera attached to an Infi nity K-2 long-distance micro- scopic lens. Geological setting Th e fossiliferous amber outcrop of Hammana occurs at a locality named Hammana- Mdeyrij... Neodermaptera Engel, 2003 Rhadinolabis Engel, Ortega-Blanco & Azar gen.n. Type species Rhadinolabis phoenicica Engel, Ortega-Blanco & Azar sp.n. Diagnosis Small earwigs (ca. 3 mm); somewhat dorsoventrally compressed, with scattered setae...

  4. ROOT-EXUDED OXYGEN IN THE AQUATIC ANGIOSPERM 'RUPPIA MARITIMA'

    EPA Science Inventory

    The potential impact of oxygen from roots on the source of inorganic nitrogen for Ruppia maritima L. (Potamogetonales) was investigated in laboratory experiments. Roots released oxygen at an average rate of 2 to 3 micrograms O2 (mg dry wt)/hr. A distinctive oxygenated zone with a...

  5. Sagina maritima Don (Caryophyllaceae) and other halophytes in London

    Microsoft Academic Search

    J. A. EDGINGTON

    Sagina maritima has been recorded at three sites by the River Thames near central London, much further from the open sea than elsewhere in Britain. Other halophytes occur nearby. Hydrological data and other records suggest that saline water carrying seeds or other propagules penetrated far upstream during periods of unusually low freshwater river flow. These are the first records of

  6. Population dynamics of Glaux maritima (L.) along a distributional cline

    Microsoft Academic Search

    L. Jerling

    1988-01-01

    Population fluctuations ofGlaux maritima, along a transect on a Baltle sea shore meadow, were recorded between 1979 and 1983. A bimodal distribution in numbers along the transect reflects the variation in factors regulating numbers: The two maintenance systems of the species, vegetative propagation and sexual reproduction play different roles. Vegetative propagation is fast and responds quickly to variations in the

  7. Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima

    PubMed Central

    Rodionov, Dmitry A.; Rodionova, Irina A.; Li, Xiaoqing; Ravcheev, Dmitry A.; Tarasova, Yekaterina; Portnoy, Vasiliy A.; Zengler, Karsten; Osterman, Andrei L.

    2013-01-01

    Hyperthermophilic bacteria from the Thermotogales lineage can produce hydrogen by fermenting a wide range of carbohydrates. Previous experimental studies identified a large fraction of genes committed to carbohydrate degradation and utilization in the model bacterium Thermotoga maritima. Knowledge of these genes enabled comprehensive reconstruction of biochemical pathways comprising the carbohydrate utilization network. However, transcriptional factors (TFs) and regulatory mechanisms driving this network remained largely unknown. Here, we used an integrated approach based on comparative analysis of genomic and transcriptomic data for the reconstruction of the carbohydrate utilization regulatory networks in 11 Thermotogales genomes. We identified DNA-binding motifs and regulons for 19 orthologous TFs in the Thermotogales. The inferred regulatory network in T. maritima contains 181 genes encoding TFs, sugar catabolic enzymes and ABC-family transporters. In contrast to many previously described bacteria, a transcriptional regulation strategy of Thermotoga does not employ global regulatory factors. The reconstructed regulatory network in T. maritima was validated by gene expression profiling on a panel of mono- and disaccharides and by in vitro DNA-binding assays. The observed upregulation of genes involved in catabolism of pectin, trehalose, cellobiose, arabinose, rhamnose, xylose, glucose, galactose, and ribose showed a strong correlation with the UxaR, TreR, BglR, CelR, AraR, RhaR, XylR, GluR, GalR, and RbsR regulons. Ultimately, this study elucidated the transcriptional regulatory network and mechanisms controlling expression of carbohydrate utilization genes in T. maritima. In addition to improving the functional annotations of associated transporters and catabolic enzymes, this research provides novel insights into the evolution of regulatory networks in Thermotogales. PMID:23986752

  8. Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima.

    PubMed

    Rodionov, Dmitry A; Rodionova, Irina A; Li, Xiaoqing; Ravcheev, Dmitry A; Tarasova, Yekaterina; Portnoy, Vasiliy A; Zengler, Karsten; Osterman, Andrei L

    2013-01-01

    Hyperthermophilic bacteria from the Thermotogales lineage can produce hydrogen by fermenting a wide range of carbohydrates. Previous experimental studies identified a large fraction of genes committed to carbohydrate degradation and utilization in the model bacterium Thermotoga maritima. Knowledge of these genes enabled comprehensive reconstruction of biochemical pathways comprising the carbohydrate utilization network. However, transcriptional factors (TFs) and regulatory mechanisms driving this network remained largely unknown. Here, we used an integrated approach based on comparative analysis of genomic and transcriptomic data for the reconstruction of the carbohydrate utilization regulatory networks in 11 Thermotogales genomes. We identified DNA-binding motifs and regulons for 19 orthologous TFs in the Thermotogales. The inferred regulatory network in T. maritima contains 181 genes encoding TFs, sugar catabolic enzymes and ABC-family transporters. In contrast to many previously described bacteria, a transcriptional regulation strategy of Thermotoga does not employ global regulatory factors. The reconstructed regulatory network in T. maritima was validated by gene expression profiling on a panel of mono- and disaccharides and by in vitro DNA-binding assays. The observed upregulation of genes involved in catabolism of pectin, trehalose, cellobiose, arabinose, rhamnose, xylose, glucose, galactose, and ribose showed a strong correlation with the UxaR, TreR, BglR, CelR, AraR, RhaR, XylR, GluR, GalR, and RbsR regulons. Ultimately, this study elucidated the transcriptional regulatory network and mechanisms controlling expression of carbohydrate utilization genes in T. maritima. In addition to improving the functional annotations of associated transporters and catabolic enzymes, this research provides novel insights into the evolution of regulatory networks in Thermotogales. PMID:23986752

  9. Chromones and flavanones from artemisia campestris subsp. maritima

    Microsoft Academic Search

    João M. J. Vasconcelos; Artur M. S. Silva; José A. S. Cavaleiro

    1998-01-01

    From the acetone extract of Artemisia campestris subsp. maritima six flavanones, two chromones and the coumarin scopoletin were isolated. 5-Hydroxy-7-methoxychromone and 5,7-dimethoxychromone are new compounds, while the flavanone eriodictyol-7,3?-dimethyl ether is reported for the first time in this species. The structures were elucidated by 1D and 2D NMR techniques. The unequivocal assignments of carbon resonances, mainly made by using 1D

  10. Humic substances in estuarine soils colonized by Spartina maritima

    NASA Astrophysics Data System (ADS)

    Santín, Cristina; González-Pérez, Martha; Otero, Xosé Luis; Ángel Álvarez, Miguel; Macías, Felipe

    2009-03-01

    This study characterizes humic substances (HS) from two soils colonized by Spartina maritima at different physiographical positions in estuarine environments on the north-western coast of the Iberian Peninsula: the Villaviciosa site, a stand close to the main tidal channel, and the Ortigueira site, located in the low salt marsh. Humic and fulvic acids were extracted from the soils and characterized qualitatively by the following spectroscopic techniques: Fourier transform infrared spectroscopy, fluorescence spectroscopy and solid-state 13C nuclear magnetic resonance. The characterized HS showed a predominance of low humified compounds with a high proportion of aliphatic components and a low degree of aromaticity. The HS composition differed substantially between sites. In the Villaviciosa soil, the large amount of nonpolar aliphatic components and the very low degree of aromaticity may indicate a significant contribution of marine organic matter and/or microbial material to the HS. However, in the HS from the Ortigueira soil, the higher proportion of polysaccharides together with the presence of lignin-derived compounds may indicate greater inputs of vascular plant material. The ?13C isotopic composition of the bulk soils highlights the large input of Spartina maritima debris to the Ortigueira site, whereas in the Villaviciosa site, organic contributions from this C4 vascular plant were not so evident. The results indicate that in these soils colonized by Spartina maritima, physiographical position has an important effect on the composition of soil HS and, therefore, must be considered in the study of organic matter characteristics in such estuarine environments.

  11. NUTRITIONAL REQUIREMENTS OF THE SUBMERGED ANGIO-SPERM 'RUPPIA MARITIMA' IN ALGAE-FREE CULTURE

    EPA Science Inventory

    Ruppia maritima has the potential to become a model laboratory organism for studies with submerged aquatic vascular plants. The present study demonstrated that algae-free R. maritima grew well in a defined medium without sediment. Growth was a linear response to photon flux densi...

  12. The Genome Organization of Thermotoga maritima Reflects Its Lifestyle

    SciTech Connect

    Latif, Haythem; Lerman, Joshua A.; Portnoy, Vasiliy A.; Tarasova, Yekaterina; Nagarajan, Harish; Rutledge, Alexandra C.; Smith, Richard D.; Adkins, Joshua N.; Lee, Dae-Hee; Qiu, Yu; Zengler, Karsten

    2013-04-25

    Recent studies have revealed that microbial genomes have many more organizational features than previously thought. Here, an integrated approach utilizing multiple ‘omics’ datasets and bioinformatics tools is established that elucidates genomic features spanning various levels of cellular organization. This methodology produces gene annotation improvements and includes the definition of transcription units. These enhancements to the annotation enable identification of a set of genetic elements instrumental to gene expression and regulation including promoters, ribosome binding sites (RBSs) and untranslated regions (UTRs). This was applied to characterize the genome organization of Thermotoga maritima—a phylogenetically deep-branching, hyperthermophilic bacterium with a small 1.86 Mb genome. Analysis derived from this multiomics approach in combination with bioinformatics tools demonstrate that the genome organization of T. maritima reflects its lifestyle, both with respect to its extreme growth temperature and compact genome. Comparative analysis of genome features suggests that thermodynamic limitations on binding kinetics for RNA polymerase and the ribosome necessitate increased sequence conservation of promoters and RBSs. Thus, restricting the sequences capable of initiating transcription and translation. Furthermore, this organism has uncharacteristically short 5’UTRs (11-17 nucleotides), which reduce the potential for 5’UTR regulatory interactions. The short intergenic distances in the T. maritima genome (5 bp on average) leave little space for regulation through transcription factor binding. The net effect of these constraints, temperature and genomic space, is a reduced ability to tune gene expression. This effect is readily apparent in global gene expression patterns, which show a high fraction of genes expressed independent of growth state with a tight, linear mRNA/protein correlation (Pearson r = 0.62, p < 2.2 x 10-16 t-test). This methodology for characterizing the genome organization is applicable to any culturable bacteria, and as similar studies are completed in diverse taxa, comparative analysis of genome features may provide insights into microbial evolution.

  13. Microsatellite marker development for the coastal dune shrub Prunus maritima (Rosaceae)1

    PubMed Central

    Badgley, Emily M.; Grubisha, Lisa C.; Roland, Anna K.; Connolly, Bryan A.; Klooster, Matthew R.

    2015-01-01

    • Premise of the study: Microsatellite primers were developed in the beach plum, Prunus maritima, to investigate the genetic composition of remaining populations in need of conservation and, in future studies, to determine its relation to P. maritima var. gravesii. • Methods and Results: Fourteen primer pairs were identified and tested in four populations throughout the species’ geographic range. Of these 14 loci, 12 were shown to be polymorphic among a total of 60 P. maritima individuals sampled (15 individuals sampled from four populations). Among the polymorphic loci, the number of alleles ranged from two to 10 and observed heterozygosity of loci ranged from 0.07 to 0.93 among specimens tested. • Conclusions: These microsatellites will be useful in evaluating the population genetic composition of P. maritima and in developing approaches for further conservation and management of this species within the endangered coastal dune ecosystem of the northeastern United States. PMID:25699222

  14. Development and characterization of nineteen polymorphic microsatellite loci from seaside alder, Alnus maritima

    Microsoft Academic Search

    Stacey L. Lance; Kenneth L. Jones; Cris Hagen; Travis C. Glenn; J. Matthew Jones; J. Phil Gibson

    2009-01-01

    We isolated and characterized 19 microsatellite loci from the endangered seaside alder, Alnus maritima. Loci were screened in 24 individuals of A. maritima and four individuals of its congener the hazel alder, A. serrulata. The number of alleles per locus ranged from 2 to 6, observed heterozygosity ranged from 0 to 0.952, and the probability\\u000a of identity values ranged from

  15. Characterization of the Earwig, Doru lineare, as a Predator of Larvae of the Fall Armyworm, Spodoptera frugiperda: A Functional Response Study

    PubMed Central

    Sueldo, Mabel Romero; Bruzzone, Octavio A.; Virla, Eduardo G.

    2010-01-01

    Spodoptera frugiperda Smith (Lepidoptera: Noctuidae) is considered as the most important pest of maize in almost all tropical America. In Argentina, the earwig Doru lineare Eschscholtz (Dermaptera: Forficulidae) has been observed preying on S. frugiperda egg masses in corn crops, but no data about its potential role as a biocontrol agent of this pest have been provided. The predation efficiency of D. lineare on newly emerged S. frugiperda larva was evaluated through a laboratory functional response study. D. lineare showed type II functional response to S. frugiperda larval density, and disc equation estimations of searching efficiency and handling time were (a) = 0.374 and (t) = 182.9 s, respectively. Earwig satiation occurred at 39.4 S. frugiperda larvae. PMID:20575739

  16. A seascape genetic analysis reveals strong biogeographical structuring driven by contrasting processes in the polyploid saltmarsh species Puccinellia maritima and Triglochin maritima.

    PubMed

    Rouger, R; Jump, A S

    2014-07-01

    Little is known about the processes shaping population structure in saltmarshes. It is expected that the sea should act as a powerful agent of dispersal. Yet, in contrast, import of external propagules into a saltmarsh is thought to be small. To determine the level of connectivity between saltmarsh ecosystems at a macro-geographical scale, we characterized and compared the population structure of two polyploid saltmarsh species, Puccinellia maritima and Triglochin maritima based on a seascape genetics approach. A discriminant analysis of principal components highlighted a genetic structure for both species arranged according to a regional pattern. Subsequent analysis based on isolation-by-distance and isolation-by-resistance frameworks indicated a strong role of coastal sediment transport processes in delimiting regional structure in P. maritima, while additional overland propagule dispersal was indicated for T. maritima. The identification and comparison of regional genetic structure and likely determining factors presented here allows us to understand the biogeographical units along the UK coast, between which barriers to connectivity occur not only at the species level but at the ecosystem scale. This information is valuable in plant conservation and community ecology and in the management and restoration of saltmarsh ecosystems. PMID:24862943

  17. Diversity and versatility of the Thermotoga maritima sugar kinome.

    PubMed

    Rodionova, Irina A; Yang, Chen; Li, Xiaoqing; Kurnasov, Oleg V; Best, Aaron A; Osterman, Andrei L; Rodionov, Dmitry A

    2012-10-01

    Sugar phosphorylation is an indispensable committed step in a large variety of sugar catabolic pathways, which are major suppliers of carbon and energy in heterotrophic species. Specialized sugar kinases that are indispensable for most of these pathways can be utilized as signature enzymes for the reconstruction of carbohydrate utilization machinery from microbial genomic and metagenomic data. Sugar kinases occur in several structurally distinct families with various partially overlapping as well as yet unknown substrate specificities that often cannot be accurately assigned by homology-based techniques. A subsystems-based metabolic reconstruction combined with the analysis of genome context and followed by experimental testing of predicted gene functions is a powerful approach of functional gene annotation. Here we applied this integrated approach for functional mapping of all sugar kinases constituting an extensive and diverse sugar kinome in the thermophilic bacterium Thermotoga maritima. Substrate preferences of 14 kinases mainly from the FGGY and PfkB families were inferred by bioinformatics analysis and biochemically characterized by screening with a panel of 45 different carbohydrates. Most of the analyzed enzymes displayed narrow substrate preferences corresponding to their predicted physiological roles in their respective catabolic pathways. The observed consistency supports the choice of kinases as signature enzymes for genomics-based identification and reconstruction of sugar utilization pathways. Use of the integrated genomic and experimental approach greatly speeds up the identification of the biochemical function of unknown proteins and improves the quality of reconstructed pathways. PMID:22885293

  18. Morphological and molecular characterization of Mermis nigrescens Dujardin, (Nematoda: Mermithidae) parasitizing the introduced European earwig (Dermaptera: Forficulidae) in New Zealand.

    PubMed

    Presswell, B; Evans, S; Poulin, R; Jorge, F

    2015-05-01

    Parasitic nematodes of the family Mermithidae were found to be infecting the introduced European earwig Forficula auricularia (Dermaptera: Forficulidae) in Dunedin, South Island, New Zealand. Adult females were later collected from various garden plants while depositing eggs. These mermithid specimens were identified morphologically as Mermis nigrescens Dujardin, 1842. A genetic distance of 0.7% between these specimens and a M. nigrescens isolate from Canada (18S rRNA gene), suggests that they have diverged genetically, but there are currently no available comparable sequences for the European M. nigrescens. Two additional nuclear fragments were also amplified, the 28S rRNA and the ribosomal DNA first internal transcribed spacer (ITS1), providing a basis for future studies. Bearing in mind the morphological similarity with other reported M. nigrescens and the lack of sequence data from other parts of the world, we retain the name M. nigrescens, and suggest that the species may be found to represent a complex of cryptic species when more worldwide data are available. Herein, we present a brief description of the post-parasitic worms and adult females, along with an inferred phylogeny using 18S rRNA gene sequences. PMID:24503193

  19. EFFECTS OF SALINITY AND BOTTOM SUBSTRATE COMPOSITION ON THE GROWTH AND PROLIFERATION OF WIDGEONGRASS ( RUPPIA MARITIMA )

    EPA Science Inventory

    The preliminary work for these experiments has been conducted, and the data will be collected during the next 6-8 months. We will collect R. maritima samples from different environments along the Gulf Coast and compare the genetic diversity using the ITRS reg...

  20. The salt marsh vegetation at Vinjekilen, Bamble, SE Norway, with special reference to the Puccinellietum maritimae

    Microsoft Academic Search

    Odd Vevle

    1985-01-01

    In the proposed nature reserve Vinjekile the vegetation types have been studied by means of transects and vegetation samples. The transects have been levelled, their altitudes related to the National Zero Altitude, NN54. The study area, ca 5 ha, constitutes a bay where a small brook built a delta. Puccinellia maritima was found dominating in different zones from-8 to 40

  1. Seed Germination of Triglochin Maritima as Influenced by Salinity and Dormancy Relieving Compounds

    Microsoft Academic Search

    M. A. Khan; I. A. Ungar

    2001-01-01

    Triglochin maritima had only 40 % germination in distilled water, but germination was substantially enhanced when seeds were exposed to ethephon, fusicoccin, proline, kinetin, and thiourea. Also, the effect of low salinity on germination was alleviated by fusicoccin, kinetin, nitrate and thiourea, whereas, the reduction in germination at high salinity was partially countered by ethephon, kinetin, thiourea and nitrate.

  2. The aquatic vascular plant Ruppia maritima as an indicator organisms for contaminated sediments

    SciTech Connect

    Tagliabue, M.D.; Thursby, G.B. [Science Applications International Corporation, Narragansett, RI (United States); Walker, H.A. [Environmental Protection Agency, Narragansett, RI (United States); Johnston, R.K.

    1994-12-31

    An ongoing estuarine ecological risk assessment case study for the Portsmouth Naval Shipyard in the Great Bay (Kittery, ME, Portsmouth, NH) has been the catalyst for continued methods development with a rooted aquatic plant for a sediment toxicity test. A test using the aquatic vascular plant Ruppia maritima would be similar in it`s utility to the Algal (Champia parvula) Reproduction Test, an accepted, short term test (US EPA Short term Methods for Estimating the Chronic Toxicity of Effluents and Receiving Waters to Marine and Estuarine Organisms). Laboratory studies were conducted to evaluate effects of lead, the primary site contaminant on R. maritima in the Great Bay. Morphology and life cycle of R. maritima are similar to that of the aquatic vascular plant Zostra marina which comprises up to 46% of the Great Bay habitat (Short 1992). R. maritima`s reduced size makes it a practical laboratory organism and Ruppia`s effects may offer useful insights into potential effects on Zostra or other aquatic vascular plants. Presently rooted vascular plants are not found in the site of concern (Clark Cove). This can be contributed to either of two factors; the physical parameters of the site, i.e., a depositional zone or the chemical parameters, i.e., metals contamination, specifically lead. Exposure of bedded and nonbedded plants occurred over a four day and ten day period using lead sulfate. Concentrations for bedded exposures were as follows, 0.3, 0.5, 0.8, 1.0 simultaneously extracted metal/acid volatile sulfide (SEM/AVS) molar ratios, and 0.1, 1.0, 10.0 and 100.0mg/l Pb for water only exposures. Some reduction in cumulative leaf growth was observed in the site samples as well as the spiked samples as compared to site controls. Results of this study and associated research which focuses on the further development of the Ruppia test methods will be presented.

  3. Micromonospora maritima sp. nov., isolated from mangrove soil.

    PubMed

    Songsumanus, Apakorn; Tanasupawat, Somboon; Igarashi, Yasuhiro; Kudo, Takuji

    2013-02-01

    Strain D10-9-5(T) was isolated from mangrove soil in Samut Sakhon province, Thailand. A polyphasic approach was used to determine the taxonomic position of the strain. The strain presented single rough spores on substrate mycelium and no aerial mycelium. Chemotaxonomic data supported the assignment of strain D10-9-5(T) to the genus Micromonospora based on the presence of meso-diaminopimelic acid and glycolyl muramic acid in the peptidoglycan, ribose, mannose, galactose, xylose and glucose as whole-cell sugars, MK-10(H(4)) (14.8?%), MK-10(H(6)) (46.7?%) and MK-10(H(8)) (27.5?%) as the predominant isoprenoid quinones, iso-C(15?:?0) (17.9?%), anteiso-C(17?:?0) (14.6?%), iso-C(17?:?0) (9.6?%), C(17?:?0) (8.0?%), iso-C(16?:?0) (7.7?%) and C(17?:?1)?8c (7.0?%) as the major cellular fatty acids, and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides and phosphatidylethanolamine as the predominant phospholipids in the cell wall. The 16S rRNA gene sequence and phylogenetic analysis showed that strain D10-9-5 was closely related to Micromonospora marina JCM 12870(T) (99.6?%), Micromonospora coxensis JCM 13248 (T) (99.4?%), Micromonospora aurantiaca JCM 10878(T) (99.3?%), Micromonospora humi JCM15292(T) (99.3?%), Micromonospora halophytica JCM 3125(T) (99.1%) and Micromonospora chalcea JCM 3031(T) (99.1?%). Strain D10-9-5(T) could be clearly distinguished from related members of the genus Micromonospora by its physiological and biochemical characteristics as well as its phylogenetic position and level of DNA-DNA relatedness. Therefore, the strain represents a novel species for which the name Micromonospora maritima sp. nov. is proposed; the type strain is D10-9-5(T) (?=?JCM 17013(T)?=?NBRC 108767(T)?=?PCU 322(T)?=?TISTR 2000(T)). PMID:22523171

  4. Chemical composition of the essential oil of Jacobaea maritima (L.) Pelser & Meijden and Jacobaea maritima subsp. bicolor (Willd.) B. Nord. & Greuter (Asteraceae) collected wild in Croatia and Sicily, respectively.

    PubMed

    Maggio, Antonella; Venditti, Alessandro; Senatore, Felice; Bruno, Maurizio; Formisano, Carmen

    2015-05-01

    In this study, the chemical compositions of the essential oils from aerial parts (JmA) and radices (JmR) of Jacobaea maritima (L.) Pelser & Meijden, collected in Croatia, and of Jacobaea maritima subsp. bicolor (Willd.) B. Nord. & Greuter, collected in Sicily, were evaluated by using gas chromatography and gas chromatography-mass spectrometry. The main components of the essential oil from J. maritima, both in JmA and JmR, were pentacosane (15.7%), heptacosane (13.1%) and nonacosane (8.1%) whereas the essential oil from J. maritima subsp. bicolor was characterised by the presence of hexadecanoic acid (14.6%), caryophyllene oxide (9.3%) and hexahydrofarnesylacetone (6.5%). The comparison of the essential oil with other studied oils of the genus Jacobaea is discussed. PMID:25533422

  5. Using a toxicity test with Ruppia maritima (Linnaeus) to assess the effects of Roundup.

    PubMed

    Castro, Aline de Jesus Veloso; Colares, Ioni Gonçalves; Franco, Teresa Cristina Rodrigues Dos Santos; Cutrim, Marco Valerio Jansen; Luvizotto-Santos, Ricardo

    2015-02-28

    Glyphosate, the active ingredient in Monsanto's broad-spectrum herbicide Roundup, consists of one of the most used pesticides worldwide, but its effects on the marine flora are still not well understood. Were examined Roundup toxic effects on Ruppia maritima specimens collected from Jansen Lagoon (São Luís, MA, Brazil) and acclimatized under laboratory conditions. The numbers of new and dead leaves, the root and leaf length, the chlorophyll a content, and the weight of R. maritima branches were determined before and after exposure to different Roundup concentrations for seven days. High concentrations caused a significant lethal effect. In addition, significant changes were observed in the wet and dry weights, the number and length of the leaves, and the chlorophyll a content. Leaf elongation was observed in the branches exposed to low concentrations, and this change was likely activated as a compensatory mechanism. The results indicate that high concentrations of this herbicide may compromise estuarine flora. PMID:25455815

  6. Complete genome sequence of Hippea maritima type strain (MH2T)

    SciTech Connect

    Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Lu, Megan [Los Alamos National Laboratory (LANL); Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute

    2011-01-01

    Hippea maritima (Miroshnichenko et al. 1999) is the type species of the genus Hippea, which belongs to the family Desulfurellaceae within the class Deltaproteobacteria. The anaerobic, moderately thermophilic marine sulfur-reducer was first isolated from shallow-water hot vents in Matipur Harbor, Papua New Guinea. H. maritima was of interest for genome se- quencing because of its isolated phylogenetic location, as a distant next neighbor of the ge- nus Desulfurella. Strain MH2T is the first type strain from the order Desulfurellales with a com- pletely sequenced genome. The 1,694,430 bp long linear genome with its 1,723 protein- coding and 57 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  7. Substrate specificity of ribose-5-phosphate isomerases from Clostridium difficile and Thermotoga maritima.

    PubMed

    Yeom, Soo-Jin; Kim, Bi-Na; Park, Chang-Su; Oh, Deok-Kun

    2010-06-01

    The activity of ribose-5-phosphate isomerases (RpiB) from Clostridium difficile for D-ribose isomerization was optimal at pH 7.5 and 40 degrees C, while that from Thermotoga maritima for L-talose isomerization was optimal at pH 8.0 and 70 degrees C. C. difficile RpiB exhibited activity only with aldose substrates possessing hydroxyl groups oriented in the right-handed configuration (Fischer projections) at the C2 and C3 positions, such as D-ribose, D-allose, L-talose, L-lyxose, D-gulose, and L-mannose. In contrast, T. maritima RpiB displayed activity only with aldose substrates possessing hydroxyl groups configured the same direction at the C2, C3, and C4 positions, such as the D- and L-forms of ribose, talose, and allose. PMID:20155483

  8. Structures of and Interactions Between Domains of Trigger Factor from Thermotoga maritima

    SciTech Connect

    Martinez-Hackert,E.; Hendrickson, W.

    2007-01-01

    Trigger factor (TF) is a eubacterial chaperone that associates with ribosomes at the peptide-exit tunnel and also occurs in excess free in the cytosol. TF is a three-domain protein that appears to exist in a dynamic equilibrium of oligomerization states and interdomain conformations. X-ray crystallography and chemical cross-linking were used to study the roles of the N- and C-terminal domains of Thermotoga maritima TF in TF oligomerization and chaperone activity. The structural conservation of both the N- and C-terminal TF domains was unambiguously established. The biochemical and crystallographic data reveal a tendency for these domains to partake in diverse and apparently nonspecific protein-protein interactions. It is found that the T. maritima and Escherichia coli TF surfaces lack evident exposed hydrophobic patches. Taken together, these data suggest that TF chaperones could interact with nascent proteins via hydrophilic surfaces.

  9. Outbreeding and Inbreeding in a Zinc-Lead Mine Population of Armeria maritima

    Microsoft Academic Search

    C. Lefèbvre

    1973-01-01

    ANTONOVICS1 and Lefèbvre2 have shown that self-fertility occurs in zinc-lead mine populations of normally incompatible species (Agrostis tenuis, Anthoxanthum odoratum, Armeria maritima). In Agrostis and Anthoxanthum1 this change to inbreeding is suggested to be an adaptation to reduce gene flow from plants growing adjacent to the mine that do not tolerate metals. In Armeria2 there is no surrounding non-tolerant population

  10. Reactivation of methionine synthase from Thermotoga maritima (TM0268) requires the downstream gene product TM0269.

    PubMed

    Huang, Sha; Romanchuk, Gail; Pattridge, Katherine; Lesley, Scott A; Wilson, Ian A; Matthews, Rowena G; Ludwig, Martha

    2007-08-01

    The crystal structure of the Thermotoga maritima gene product TM0269, determined as part of genome-wide structural coverage of T. maritima by the Joint Center for Structural Genomics, revealed structural homology with the fourth module of the cobalamin-dependent methionine synthase (MetH) from Escherichia coli, despite the lack of significant sequence homology. The gene specifying TM0269 lies in close proximity to another gene, TM0268, which shows sequence homology with the first three modules of E. coli MetH. The fourth module of E. coli MetH is required for reductive remethylation of the cob(II)alamin form of the cofactor and binds the methyl donor for this reactivation, S-adenosylmethionine (AdoMet). Measurements of the rates of methionine formation in the presence and absence of TM0269 and AdoMet demonstrate that both TM0269 and AdoMet are required for reactivation of the inactive cob(II)alamin form of TM0268. These activity measurements confirm the structure-based assignment of the function of the TM0269 gene product. In the presence of TM0269, AdoMet, and reductants, the measured activity of T. maritima MetH is maximal near 80 degrees C, where the specific activity of the purified protein is approximately 15% of that of E. coli methionine synthase (MetH) at 37 degrees C. Comparisons of the structures and sequences of TM0269 and the reactivation domain of E. coli MetH suggest that AdoMet may be bound somewhat differently by the homologous proteins. However, the conformation of a hairpin that is critical for cobalamin binding in E. coli MetH, which constitutes an essential structural element, is retained in the T. maritima reactivation protein despite striking divergence of the sequences. PMID:17656578

  11. Reactivation of methionine synthase from Thermotoga maritima (TM0268) requires the downstream gene product TM0269

    PubMed Central

    Huang, Sha; Romanchuk, Gail; Pattridge, Katherine; Lesley, Scott A.; Wilson, Ian A.; Matthews, Rowena G.; Ludwig, Martha

    2007-01-01

    The crystal structure of the Thermotoga maritima gene product TM0269, determined as part of genome-wide structural coverage of T. maritima by the Joint Center for Structural Genomics, revealed structural homology with the fourth module of the cobalamin-dependent methionine synthase (MetH) from Escherichia coli, despite the lack of significant sequence homology. The gene specifying TM0269 lies in close proximity to another gene, TM0268, which shows sequence homology with the first three modules of E. coli MetH. The fourth module of E. coli MetH is required for reductive remethylation of the cob(II)alamin form of the cofactor and binds the methyl donor for this reactivation, S-adenosylmethionine (AdoMet). Measurements of the rates of methionine formation in the presence and absence of TM0269 and AdoMet demonstrate that both TM0269 and AdoMet are required for reactivation of the inactive cob(II)alamin form of TM0268. These activity measurements confirm the structure-based assignment of the function of the TM0269 gene product. In the presence of TM0269, AdoMet, and reductants, the measured activity of T. maritima MetH is maximal near 80°C, where the specific activity of the purified protein is ?15% of that of E. coli methionine synthase (MetH) at 37°C. Comparisons of the structures and sequences of TM0269 and the reactivation domain of E. coli MetH suggest that AdoMet may be bound somewhat differently by the homologous proteins. However, the conformation of a hairpin that is critical for cobalamin binding in E. coli MetH, which constitutes an essential structural element, is retained in the T. maritima reactivation protein despite striking divergence of the sequences. PMID:17656578

  12. JUNIPERUS MARITIMA, THE SEASIDE JUNIPER, A NEW SPECIES FROM PUGET SOUND, NORTH AMERICA

    Microsoft Academic Search

    Robert P. Adams

    Based on analyses of terpenoids, nrDNA and trnC-D SNPs as well as morphology and ecology, a new cryptic species, Juniperus maritima, from the Puget Sound region is recognized. The species, previously included in J. scopulorum, is characterized by having seed cones that mature in one year (14-16 months), seeds usually exserted from the cone, obtuse scale leaf tips, usually reniform

  13. Biosynthesis of Cyanogenic Glucosides in Triglochin maritima and the Involvement of Cytochrome P450 Enzymes

    Microsoft Academic Search

    John Strikart Nielsen; Birger Lindberg Møller

    1999-01-01

    The biosynthesis of the two cyanogenic glucosides, taxiphyllin and triglochinin, in Triglochin maritima (seaside arrow grass) has been studied using undialyzed microsomal preparations from flowers and fruits. Tyrosine was converted to p-hydroxymandelonitrile with Vmax and Km values of 36 nmol mg?1 g?1 fresh weight and 0.14 mM, respectively. p-Hydroxyphenylacetaldoxime and p-hydroxyphenylacetonitrile accumulated as intermediates in the reaction mixtures. Using radiolabeled

  14. Properties of recombinant Strep -tagged and untagged hyperthermophilic D-arabitol dehydrogenase from Thermotoga maritima

    Microsoft Academic Search

    Verena Kallnik; Christian Schultz; Paul Schweiger; Uwe Deppenmeier

    2011-01-01

    The first hyperthermophilic d-arabitol dehydrogenase from Thermotoga maritima was heterologously purified from Escherichia coli. The protein was purified with and without a Strep-tag. The enzyme exclusively catalyzed the NAD(H)-dependent oxidoreduction of d-arabitol, d-xylitol, d-ribulose, or d-xylulose. A twofold increase of catalytic rates was observed upon addition of Mg2+ or K+. Interestingly, only the tag-less protein was thermostable, retaining 90% of

  15. The aquatic vascular plant Ruppia maritima as an indicator organism for contaminated sediments

    SciTech Connect

    Tagliabue, M.D.; Thursby, G.B.; Walker, H.A. [Environmental Protection Agency, Narragansett, RI (United States); Johnston, R.K.

    1995-12-31

    An ongoing estuarine ecological risk assessment case study for the Portsmouth Naval Shipyard in the Great Bay Estuary (New Hampshire, Maine) was the catalyst to continue development a rooted aquatic plant sediment toxicity test. Laboratory studies were conducted to evaluate effects of lead, the primary site contaminant on R. maritima in the Great Bay. Although the aquatic vascular plant Zostra marina comprises up to 46% of the Great Bay subtidal habitat, R. maritima`s much smaller size makes it a more practical laboratory organism. Effects on Ruppia may offer useful insights into potential effects on Zostra or other aquatic vascular plants. Presently rooted vascular plants are not found in Clark Cove located adjacent to a landfill disposal site on the shipyard. The absence of rooted vegetation can be contributed to, physical parameters of the site (turbidity, grain size, texture) or chemical parameters (heavy metal/Pb contamination, redox potential). Exposure of bedded and nonbedded plants occurred over a four day and ten day period using lead sulfate. Concentrations for bedded exposures were as follows, 0.3, 0.5, 0.8, 1.0 simultaneously extracted metal/acid volatile sulfide (SEM/AVS) molar ratios, and 0.1, 1.0, 10.0 and 100.0mg/l Pb for water only exposures. Reduction in cumulative leaf growth was observed for the Clark Cove sediments as well as the spiked sediments as compared to reference sediments.

  16. DNA protection by histone-like protein HU from the hyperthermophilic eubacterium Thermotoga maritima

    PubMed Central

    Mukherjee, Anirban; Sokunbi, Abimbola O.; Grove, Anne

    2008-01-01

    In mesophilic prokaryotes, the DNA-binding protein HU participates in nucleoid organization as well as in regulation of DNA-dependent processes. Little is known about nucleoid organization in thermophilic eubacteria. We show here that HU from the hyperthermophilic eubacterium Thermotoga maritima HU bends DNA and constrains negative DNA supercoils in the presence of topoisomerase I. However, while binding to a single site occludes ?35 bp, association of T. maritima HU with DNA of sufficient length to accommodate multiple protomers results in an apparent shorter occluded site size. Such complexes consist of ordered arrays of protomers, as revealed by the periodicity of DNase I cleavage. Association of TmHU with plasmid DNA yields a complex that is remarkably resistant to DNase I-mediated degradation. TmHU is the only member of this protein family capable of occluding a 35 bp nonspecific site in duplex DNA; we propose that this property allows TmHU to form exceedingly stable associations in which DNA flanking the kinks is sandwiched between adjacent proteins. We suggest that T. maritima HU serves an architectural function when associating with a single 35 bp site, but generates a very stable and compact aggregate at higher protein concentrations that organizes and protects the genomic DNA. PMID:18515342

  17. Complexes of Thermotoga maritima S-adenosylmethionine decarboxylase provide insights into substrate specificity

    SciTech Connect

    Bale, Shridhar; Baba, Kavita; McCloskey, Diane E.; Pegg, Anthony E.; Ealick, Steven E.

    2010-06-25

    The polyamines putrescine, spermidine and spermine are ubiquitous aliphatic cations and are essential for cellular growth and differentiation. S-Adenosylmethionine decarboxylase (AdoMetDC) is a critical pyruvoyl-dependent enzyme in the polyamine-biosynthetic pathway. The crystal structures of AdoMetDC from humans and plants and of the AdoMetDC proenzyme from Thermotoga maritima have been obtained previously. Here, the crystal structures of activated T. maritima AdoMetDC (TmAdoMetDC) and of its complexes with S-adenosylmethionine methyl ester and 5{prime}-deoxy-5{prime}-dimethylthioadenosine are reported. The results demonstrate for the first time that TmAdoMetDC autoprocesses without the need for additional factors and that the enzyme contains two complete active sites, both of which use residues from both chains of the homodimer. The complexes provide insights into the substrate specificity and ligand binding of AdoMetDC in prokaryotes. The conservation of the ligand-binding mode and the active-site residues between human and T. maritima AdoMetDC provides insight into the evolution of AdoMetDC.

  18. Ecophysiological response of Crambe maritima to airborne and soil-borne salinity

    PubMed Central

    de Vos, Arjen C.; Broekman, Rob; Groot, Maartje P.; Rozema, Jelte

    2010-01-01

    Background and Aims There is a need to evaluate the salt tolerance of plant species that can be cultivated as crops under saline conditions. Crambe maritima is a coastal plant, usually occurring on the driftline, with potential use as a vegetable crop. The aim of this experiment was to determine the growth response of Crambe maritima to various levels of airborne and soil-borne salinity and the ecophysiological mechanisms underlying these responses. Methods In the greenhouse, plants were exposed to salt spray (400 mm NaCl) as well as to various levels of root-zone salinity (RZS) of 0, 50, 100, 200 and 300 mm NaCl during 40 d. The salt tolerance of Crambe maritima was assessed by the relative growth rate (RGR) and its components. To study possible salinity effects on the tissue and cellular level, the leaf succulence, tissue Na+ concentrations, Na+ : K+ ratio, net K+/Na+ selectivity, N, P, K+, Ca2+, Mg2+, proline, soluble sugar concentrations, osmotic potential, total phenolics and antioxidant capacity were measured. Key Results Salt spray did not affect the RGR of Crambe maritima. However, leaf thickness and leaf succulence increased with salt spray. Root zone salinities up to 100 mm NaCl did not affect growth. However, at 200 mm NaCl RZS the RGR was reduced by 41 % compared with the control and by 56 % at 300 mm NaCl RZS. The reduced RGR with increasing RZS was largely due to the reduced specific leaf area, which was caused by increased leaf succulence as well as by increased leaf dry matter content. No changes in unit leaf rate were observed but increased RZS resulted in increased Na+ and proline concentrations, reduced K+, Ca2+ and Mg2+ concentrations, lower osmotic potential and increased antioxidant capacity. Proline concentrations of the leaves correlated strongly (r = 0·95) with RZS concentrations and not with plant growth. Conclusions Based on its growth response, Crambe maritima can be classified as a salt spray tolerant plant that is sensitive to root zone salinities exceeding 100 mm NaCl. PMID:20354071

  19. Structural insight into the low affinity between Thermotoga maritima CheA and CheB compared to their Escherichia coli / Salmonella typhimurium counterparts

    PubMed Central

    Park, SangYoun; Crane, Brian R.

    2011-01-01

    CheA-mediated CheB phosphorylation and the subsequent CheB-mediated demethylation of the chemoreceptors are important steps required for the bacterial chemotactic adaptation response. Although Escherichia coli CheB has been reported to interact with CheA competitively against CheY, we have observed that Thermotoga maritima CheB has no detectable CheA-binding. By determining the CheY-like domain crystal structure of T. maritima CheB, and comparing against the T. maritima CheY and Salmonella typhimurium CheB structures, we propose that the two consecutive glutamates in the ?4/?4 loop of T. maritima CheB that is absent in T. maritima CheY and in E. coli / S. typhimurium CheB may be one factor contributing to the low CheA affinity. PMID:21816169

  20. Scouting contaminated estuaries: heavy metal resistant and plant growth promoting rhizobacteria in the native metal rhizoaccumulator Spartina maritima.

    PubMed

    Mesa, J; Mateos-Naranjo, E; Caviedes, M A; Redondo-Gómez, S; Pajuelo, E; Rodríguez-Llorente, I D

    2015-01-15

    Spartina maritima is a native endangered heavy metal rhizoaccumulator cordgrass naturally growing in southwest coasts of Spain, where is used as a biotool to rehabilitate degraded salt marshes. Fifteen bacterial strains were isolated from the rhizosphere of S. maritima growing in the estuary of the Tinto River, one of the most polluted areas in the world. A high proportion of bacteria were resistant towards several heavy metals. They also exhibited multiple plant growth promoting (PGP) properties, in the absence and the presence of Cu. Bacillus methylotrophicus SMT38, Bacillusaryabhattai SMT48, B. aryabhattai SMT50 and Bacilluslicheniformis SMT51 were selected as the best performing strains. In a gnobiotic assay, inoculation of Medicago sativa seeds with the selected isolates induced higher root elongation. The inoculation of S. maritima with these indigenous metal-resistant PGP rhizobacteria could be an efficient method to increase plant adaptation and growth in contaminated estuaries during restoration programs. PMID:25467875

  1. The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima

    PubMed Central

    Chipman, Ariel D.; Ferrier, David E. K.; Brena, Carlo; Qu, Jiaxin; Hughes, Daniel S. T.; Schröder, Reinhard; Torres-Oliva, Montserrat; Znassi, Nadia; Jiang, Huaiyang; Almeida, Francisca C.; Alonso, Claudio R.; Apostolou, Zivkos; Aqrawi, Peshtewani; Arthur, Wallace; Barna, Jennifer C. J.; Blankenburg, Kerstin P.; Brites, Daniela; Capella-Gutiérrez, Salvador; Coyle, Marcus; Dearden, Peter K.; Du Pasquier, Louis; Duncan, Elizabeth J.; Ebert, Dieter; Eibner, Cornelius; Erikson, Galina; Evans, Peter D.; Extavour, Cassandra G.; Francisco, Liezl; Gabaldón, Toni; Gillis, William J.; Goodwin-Horn, Elizabeth A.; Green, Jack E.; Griffiths-Jones, Sam; Grimmelikhuijzen, Cornelis J. P.; Gubbala, Sai; Guigó, Roderic; Han, Yi; Hauser, Frank; Havlak, Paul; Hayden, Luke; Helbing, Sophie; Holder, Michael; Hui, Jerome H. L.; Hunn, Julia P.; Hunnekuhl, Vera S.; Jackson, LaRonda; Javaid, Mehwish; Jhangiani, Shalini N.; Jiggins, Francis M.; Jones, Tamsin E.; Kaiser, Tobias S.; Kalra, Divya; Kenny, Nathan J.; Korchina, Viktoriya; Kovar, Christie L.; Kraus, F. Bernhard; Lapraz, François; Lee, Sandra L.; Lv, Jie; Mandapat, Christigale; Manning, Gerard; Mariotti, Marco; Mata, Robert; Mathew, Tittu; Neumann, Tobias; Newsham, Irene; Ngo, Dinh N.; Ninova, Maria; Okwuonu, Geoffrey; Ongeri, Fiona; Palmer, William J.; Patil, Shobha; Patraquim, Pedro; Pham, Christopher; Pu, Ling-Ling; Putman, Nicholas H.; Rabouille, Catherine; Ramos, Olivia Mendivil; Rhodes, Adelaide C.; Robertson, Helen E.; Robertson, Hugh M.; Ronshaugen, Matthew; Rozas, Julio; Saada, Nehad; Sánchez-Gracia, Alejandro; Scherer, Steven E.; Schurko, Andrew M.; Siggens, Kenneth W.; Simmons, DeNard; Stief, Anna; Stolle, Eckart; Telford, Maximilian J.; Tessmar-Raible, Kristin; Thornton, Rebecca; van der Zee, Maurijn; von Haeseler, Arndt; Williams, James M.; Willis, Judith H.; Wu, Yuanqing; Zou, Xiaoyan; Lawson, Daniel; Muzny, Donna M.; Worley, Kim C.; Gibbs, Richard A.; Akam, Michael; Richards, Stephen

    2014-01-01

    Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history. PMID:25423365

  2. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.

    PubMed

    Chipman, Ariel D; Ferrier, David E K; Brena, Carlo; Qu, Jiaxin; Hughes, Daniel S T; Schröder, Reinhard; Torres-Oliva, Montserrat; Znassi, Nadia; Jiang, Huaiyang; Almeida, Francisca C; Alonso, Claudio R; Apostolou, Zivkos; Aqrawi, Peshtewani; Arthur, Wallace; Barna, Jennifer C J; Blankenburg, Kerstin P; Brites, Daniela; Capella-Gutiérrez, Salvador; Coyle, Marcus; Dearden, Peter K; Du Pasquier, Louis; Duncan, Elizabeth J; Ebert, Dieter; Eibner, Cornelius; Erikson, Galina; Evans, Peter D; Extavour, Cassandra G; Francisco, Liezl; Gabaldón, Toni; Gillis, William J; Goodwin-Horn, Elizabeth A; Green, Jack E; Griffiths-Jones, Sam; Grimmelikhuijzen, Cornelis J P; Gubbala, Sai; Guigó, Roderic; Han, Yi; Hauser, Frank; Havlak, Paul; Hayden, Luke; Helbing, Sophie; Holder, Michael; Hui, Jerome H L; Hunn, Julia P; Hunnekuhl, Vera S; Jackson, LaRonda; Javaid, Mehwish; Jhangiani, Shalini N; Jiggins, Francis M; Jones, Tamsin E; Kaiser, Tobias S; Kalra, Divya; Kenny, Nathan J; Korchina, Viktoriya; Kovar, Christie L; Kraus, F Bernhard; Lapraz, François; Lee, Sandra L; Lv, Jie; Mandapat, Christigale; Manning, Gerard; Mariotti, Marco; Mata, Robert; Mathew, Tittu; Neumann, Tobias; Newsham, Irene; Ngo, Dinh N; Ninova, Maria; Okwuonu, Geoffrey; Ongeri, Fiona; Palmer, William J; Patil, Shobha; Patraquim, Pedro; Pham, Christopher; Pu, Ling-Ling; Putman, Nicholas H; Rabouille, Catherine; Ramos, Olivia Mendivil; Rhodes, Adelaide C; Robertson, Helen E; Robertson, Hugh M; Ronshaugen, Matthew; Rozas, Julio; Saada, Nehad; Sánchez-Gracia, Alejandro; Scherer, Steven E; Schurko, Andrew M; Siggens, Kenneth W; Simmons, DeNard; Stief, Anna; Stolle, Eckart; Telford, Maximilian J; Tessmar-Raible, Kristin; Thornton, Rebecca; van der Zee, Maurijn; von Haeseler, Arndt; Williams, James M; Willis, Judith H; Wu, Yuanqing; Zou, Xiaoyan; Lawson, Daniel; Muzny, Donna M; Worley, Kim C; Gibbs, Richard A; Akam, Michael; Richards, Stephen

    2014-11-01

    Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history. PMID:25423365

  3. Biosynthesis of cyanogenic glucosides in Triglochin maritima and the involvement of cytochrome P450 enzymes.

    PubMed

    Nielsen, J S; Moller, B L

    1999-08-01

    The biosynthesis of the two cyanogenic glucosides, taxiphyllin and triglochinin, in Triglochin maritima (seaside arrow grass) has been studied using undialyzed microsomal preparations from flowers and fruits. Tyrosine was converted to p-hydroxymandelonitrile with V(max) and K(m) values of 36 nmol mg(-1) g(-1) fresh weight and 0.14 mM, respectively. p-Hydroxyphenylacetaldoxime and p-hydroxyphenylacetonitrile accumulated as intermediates in the reaction mixtures. Using radiolabeled tyrosine as substrate, the radiolabel was easily trapped in p-hydroxyphenylacetaldoxime and p-hydroxyphenylacetonitrile when these were added as unlabeled compounds. p-Hydroxyphenylacetaldoxime was the only product obtained using microsomes prepared from green leaves or dialyzed microsomes prepared from flowers and fruits. These data contrast earlier reports (Hösel and Nahrstedt, Arch. Biochem. Biophys. 203, 753-757, 1980; and Cutler et al., J. Biol. Chem. 256, 4253-4258, 1981) where p-hydroxyphenylacetaldoxime was found not to accumulate. All steps in the conversion of tyrosine to p-hydroxymandelonitrile were found to be catalyzed by cytochrome P450 enzymes as documented by photoreversible carbon monoxide inhibition, inhibition by antibodies toward NADPH-cytochrome P450 oxidoreductase, and by cytochrome P450 inhibitors. We hypothesize that cyanogenic glucoside synthesis in T. maritima is catalyzed by multifunctional cytochrome P450 enzymes similar to CYP79A1 and CYP71E1 in Sorghum bicolor except that the homolog to CYP71E1 in T. maritima exhibits a less tight binding of p-hydroxyphenylacetonitrile, thus permitting the release of this intermediate and its conversion into triglochinin. PMID:10415119

  4. The role of Spartina maritima and Sarcocornia fruticosa on trace metals retention in Ria Formosa, Portugal

    NASA Astrophysics Data System (ADS)

    Moreira da Silva, Manuela; Duarte, Duarte; Isidoro, Jorge; Chícharo, Luís

    2013-04-01

    Over the last years, phytoremediation has become an increasingly recognized pathway for contaminant removal from water and shallow soils. Assessing the phytoremediation potential of wetlands is complex due to variable conditions of hydrology, soil/sediment types, plant species diversity, growing season and water chemistry. Physico-chemical properties of wetlands provide many positive attributes for remediating contaminants. Saltmarsh plants can sequestrate and inherently tolerate high metal concentrations found in saltmarsh sediments. An increasing number of studies have been carried out to understand the role of halophyte vegetation on retention, biovailability and remediation of the pollutants in coastal areas (estuaries and lagoons). It is already known that the accumulation capacity and the pattern of metal distribution in the plant tissues vary among plant species, namely monocotyledonous and dicotyledonous, and with sediment characteristics. During the last decades, there has been a large increase in urbanization and industrialization of the area surrounding Ria Formosa. Due to this reality, anthropogenic contaminants, including trace metals, are transported via untreated sewage and agricultural effluents to several parts of the lagoon. The dominant producers are Spartina maritima (Poales: Poaceae) and Sarcocornia fruticosa (Caryophyllales: Chenopodiaceae), appearing in pure stands respectively in the lower and in the upper saltmarshes. The aim of this work was to survey, comparatively, the role of S. maritima and S. fruticosa on minor and trace element (Ag, Cd, Cu, Cr, Mo, Ni, Pb and Zn), contents and distribution amongst sediment and plant tissues. Both S. maritima and S. fruticosa could fix metals from the surrounding belowground environment and accumulate metals, mainly in roots (also in rhizomes in the case of the former). Metal translocation to aerial parts of the plants was, in general, residual.

  5. Chemical composition of essential oils and aromatic waters from different Italian Anthemis maritima populations.

    PubMed

    Ciccarelli, Daniela; Noccioli, Cecilia; Pistelli, Luisa

    2013-09-01

    The chemical composition of the essential oils and aromatic waters isolated from six Italian Anthemis maritima populations was determined by GC-FID and GC/MS analyses. In total, 122 and 100 chemical compounds were identified in the essential oils and the aromatic waters, respectively. The main compound classes represented in the oils were monoterpene hydrocarbons, oxygenated monoterpenes, sesquiterpene hydrocarbons, oxygenated sesquiterpenes, and terpene esters. Multivariate chemometric techniques such as cluster analysis (CA) and principal coordinate analysis (PCO) were used to classify the samples according to the geographical origin. Statistical analysis allowed the attribution of the analyzed populations to different chemotype groups. PMID:24078600

  6. Biophysical probing of Spartina maritima photo-system II changes during prolonged tidal submersion periods.

    PubMed

    Duarte, B; Santos, D; Marques, J C; Caçador, I

    2014-04-01

    Submergence is one of the major constrains affecting wetland plants, with inevitable impacts on their physiology and productivity. Global warming as a driving force of sea level rise, tend to increase the submersion periods duration. Photosynthesis biophysical probing arise as an important tool to understand the energetics underlying plant feedback to these constrains. As in previous studies with Spartina maritima, there was no inhibition of photosynthetic activity in submerged individuals. Comparing both donor and acceptor sides of the PSII, the first was more severely affected during submersion, driven by the inactivation of the OEC with consequent impairment of the ETC. Although this apparent damage in the PSII donor side, the electron transport per active reaction centre was not substantially affected, indicating that this reduction in the electron flow is accompanied by a proportional increase in the number of active reaction centres. These conditions lead to the accumulation of excessive reducing power, source of damaging ROS, counteracted by efficient energy dissipation processes and anti-oxidant enzymatic defences. This way, S. maritima appears as a well-adapted species with an evident photochemical plasticity towards submersion, allowing it to maintain its photosynthetic activity even during prolonged submersion periods. PMID:24630362

  7. Anthemis maritima L. in different coastal habitats: A tool to explore plant plasticity

    NASA Astrophysics Data System (ADS)

    Spanò, Carmelina; Balestri, Mirko; Bottega, Stefania; Grilli, Isa; Forino, Laura Maria Costantina; Ciccarelli, Daniela

    2013-09-01

    Anthemis maritima, a plant which has the ability to colonise different stressful coastal environments, sand dunes and rocky cliff ecosystems, exhibits a high degree of leaf trait plasticity. The key parameters are the regulation of stomatal density and size, the succulence index and the specific antioxidant response. With the aim to explore plant plasticity, we analysed various morphological and physiological traits of the leaves of A. maritima populations dwelling in three different coastal areas of Italy. The highest values of stomatal density, leaf thickness, and succulence index were found in plants living in a sub-arid climate, on rocky cliffs, with the highest soil pH and salinity. Although this population exhibited the highest concentration of oxygen reactive species (hydrogen peroxide), it also had the lowest value of lipid peroxidation, an indicator of oxidative stress. Ascorbate was the main protective molecule in this population, while phenols appeared to carry out this role in plants living on soils with the lowest salinity and highest annual rainfall.

  8. The in vitro biosynthesis of taxiphyllin and the channeling of intermediates in Triglochin maritima.

    PubMed

    Cutler, A J; Hösel, W; Sternberg, M; Conn, E E

    1981-05-10

    The in vitro biosynthesis of the cyanogenic glucoside taxiphyllin has recently been demonstrated in Triglochin maritima (Hösel, W., and Nahrstedt, A. (1980) Arch. Biochem. Biophys. 203, 753-757). We have now studied in more detail the multistep conversion of tyrosine into p-hydroxymandelonitrile, the immediate precursor of taxiphyllin, catalyzed by microsomes isolated from dark-grown seedlings. The biosynthetic pathway involves N-hydroxytyrosine, p-hydroxyphenylacetaldoxime, and p-hydroxyphenylacetonitrile. In marked contrast to an analogous pathway in Sorghum bicolor, p-hydroxyphenylacetonitrile is the best substrate for cyanide production (Vmax = 224 nmol/h/g, fresh wt) and the physiological substrate tyrosine is the poorest (Vmax = 18.8 nmol/h/g, fresh wt). The substrates exhibit alkaline pH optima between 7.5 and 9, and all except tyrosine show pronounced substrate inhibition. We have found that p-hydroxyphenylacetonitrile generated in situ from tyrosine is free to equilibrate by diffusion with exogenous material. On the other hand, neither N-hydroxytyrosine nor p-hydroxyphenylacetaldoxime will readily exchange with exogenous intermediates. We consider both N-hydroxytyrosine and p-hydroxyphenylacetaldoxime to be channeled in T. maritima, whereas in S. bicolor N-hydroxytyrosine and p-hydroxyphenylacetonitrile are channeled and the aldoxime is freely exchangeable. PMID:7012151

  9. Chemical composition and biological effects of Artemisia maritima and Artemisia nilagirica essential oils from wild plant of Western Himalaya

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Artemisia species possess pharmacological properties that are used for medical purposes worldwide. In this paper, the essential oils from the aerial parts of A. nilagirica and A. maritima from the western Indian Himalaya region are described. The main compounds analyzed by simultaneous GC/MS and GC/...

  10. Ferulic acid excretion as a marker of consumption of a French maritime pine ( Pinus maritima) bark extract

    Microsoft Academic Search

    Fabio Virgili; George Pagana; Louise Bourne; Gerald Rimbach; Fausta Natella; Catherine Rice-Evans; Lester Packer

    2000-01-01

    French maritime pine (Pinus maritima) bark extract (PBE) is a polyphenol-rich food supplement patented under the name of Pycnogenol and known to have strong antioxidant activity and different beneficial effects on human health. Although its biological properties have begun to be extensively studied both in vitro, in laboratory animals and more recently in humans, little is known about its bioavailability.

  11. Antioxidant activity and biologic properties of a procyanidin-rich extract from pine ( pinus maritima) bark, pycnogenol

    Microsoft Academic Search

    L Packer; G Rimbach; F Virgili

    1999-01-01

    There is growing interest in the biologic activities of plant extracts such as that obtained from the bark of the French maritime pine Pinus maritima, Pycnogenol. Pycnogenol (PYC) is a standardized extract composed of a mixture of flavonoids, mainly procyandins and phenolic acids. Studies indicate that PYC components are highly bioavailable. Uniquely PYC displays greater biologic effects as a mixture

  12. Structure of an essential GTPase, YsxC, from Thermotoga maritima

    PubMed Central

    Chan, Kwok-Ho; Wong, Kam-Bo

    2011-01-01

    YsxC belongs to the YihA family of TRAFAC class GTPases. The protein is involved in the biogenesis of ribosomes and is essential for the survival of a wide range of bacteria. Here, crystal structures of YsxC from Thermotoga maritima and its complex with GDP were determined at maximal resolutions of 2.3 and 1.9?Å, respectively. Major structural differences are observed in the switch I region, which is disordered in the apo form but exists in both an ‘open’ and a ‘closed’ conformation in the GDP-bound state. A comparison with the structure of the GMPPNP–YsxC complex from Bacillus subtilis provides insights into the mechanism of conformational change in the switch I and II regions upon hydrolysis of GTP. PMID:21636901

  13. Aspects on the Biosynthesis of the Cyanogenic Glucoside Triglochinin in Triglochin maritima1.

    PubMed

    Nahrstedt, A; Kant, J D; Hösel, W

    1984-10-01

    The incorporation of L-[U- (14)C]phenylalanine, L-[U- (14)C]tyrosine and [U- (14)C]4-hydroxyphenylacetonitrile into triglochinin and taxiphyllin, the latter a possible precursor of the former, was studied in seedlings of TRIGLOCHIN MARITIMA L. The nitrile was by far the best substrate; incorporation of the amino acids was poor. Environmental factors such as light and humidity act differently on production of both compounds which also show a wide variation in individual seedlings. Quantitative evaluation of the specific activities indicate that taxiphyllin cannot be regarded as a precursor of triglochinin and that the two compounds are probably synthesized by two, at least mainly independent, pathways. PMID:17340339

  14. High phenotypic plasticity of Suaeda maritima observed under hypoxic conditions in relation to its physiological basis

    PubMed Central

    Wetson, Anne M.; Zörb, Christian; John, Elizabeth A.; Flowers, Timothy J.

    2012-01-01

    Background and Aims Phenotypic plasticity, the potential of specific traits of a genotype to respond to different environmental conditions, is an important adaptive mechanism for minimizing potentially adverse effects of environmental fluctuations in space and time. Suaeda maritima shows morphologically different forms on high and low areas of the same salt marsh. Our aims were to examine whether these phenotypic differences occurred as a result of plastic responses to the environment. Soil redox state, indicative of oxygen supply, was examined as a factor causing the observed morphological and physiological differences. Methods Reciprocal transplantation of seedlings was carried out between high and low marsh sites on a salt marsh and in simulated tidal-flow tanks in a glasshouse. Plants from the same seed source were grown in aerated or hypoxic solution, and roots were assayed for lactate dehydrogenase (LDH) and alcohol dehydrogenase, and changes in their proteome. Key Results Transplanted (away) seedlings and those that remained in their home position developed the morphology characteristic of the home or away site. Shoot Na+, Cl? and K+ concentrations were significantly different in plants in the high and low marsh sites, but with no significant difference between home and away plants at each site. High LDH activity in roots of plants grown in aeration and in hypoxia indicated pre-adaptation to fluctuating root aeration and could be a factor in the phenotypic plasticity and growth of S. maritima over the full tidal range of the salt marsh environment. Twenty-six proteins were upregulated under hypoxic conditions. Conclusions Plasticity of morphological traits for growth form at extremes of the soil oxygenation spectrum of the tidal salt marsh did not correlate with the lack of physiological plasticity in the constitutively high LDH found in the roots. PMID:22316572

  15. Proteomic and metabolic profiles of Cakile maritima Scop. Sea Rocket grown in the presence of cadmium.

    PubMed

    Taamalli, Manel; D'Alessandro, Angelo; Marrocco, Cristina; Gevi, Federica; Timperio, Anna Maria; Zolla, Lello

    2015-03-17

    Recent physiological reports have documented how Cakile maritima Scop. Sea Rocket could accumulate high doses of Cd without altering its physiological parameters. In the present study, we performed an integrated proteomics (2DE) and metabolomics (HPLC-MS) investigation to determine the molecular mechanisms underlying cadmium (Cd) tolerance of this halophyte. Peculiar features were observed: (i) up-regulation of thiol compound anabolism, including glutathione and phytochelatin homeostasis, which allows an intracellular chelation of Cd and its compartmentalization into vacuole by a significant up-regulation of vacuolar transporters; (ii) up-regulation of the PPP and Calvin cycle (both at the enzyme and metabolite level), which utterly promoted the maintenance of NADPH/NADP(+) homeostasis, other than the accumulation of triose-phosphates (serving as anabolic intermediates for triacylglycerol biosynthesis) and the glyoxylate precursor phosphoglycolate, to promote photorespiration and consequently CO2 release. An up-regulation of carbonic anhydrase was also observed. This halophyte is also correlated with a highly efficient antioxidant system, especially a high up-regulation of SOD1, resulting more efficient in coping with heavy metals stress than common plants. Interestingly, exposure to high Cd concentrations partly affected photosystem integrity and metabolic activity, through the up-regulation of enzymes from the Calvin cycle and glutathione-ascorbate homeostasis and PAP3 which stabilizes thylakoid membrane structures. In addition, up-regulation of Peptidyl-prolyl isomerase CYP38 increases stability and biogenesis of PSII. Finally, metabolomics results confirmed proteomics and previous physiological evidence, also suggesting that osmoprotectants, betaine and proline, together with plant hormones, methyl jasmonate and salicylic acid, might be involved in mediating responses to Cd-induced stress. Taken together, these peculiar features confirm that Cakile maritima Scop. Sea Rocket seemed to be naturally equipped to withstand even high doses of Cd pollution. PMID:25639878

  16. Several Archaeal Homologs of Putative Oligopeptide-Binding Proteins Encoded by Thermotoga maritima Bind Sugars†

    PubMed Central

    Nanavati, Dhaval M.; Thirangoon, Kamolwan; Noll, Kenneth M.

    2006-01-01

    The hyperthermophilic bacterium Thermotoga maritima has shared many genes with archaea through horizontal gene transfer. Several of these encode putative oligopeptide ATP binding cassette (ABC) transporters. We sought to test the hypothesis that these transporters actually transport sugars by measuring the substrate affinities of their encoded substrate-binding proteins (SBPs). This information will increase our understanding of the selective pressures that allowed this organism to retain these archaeal homologs. By measuring changes in intrinsic fluorescence of these SBPs in response to exposure to various sugars, we found that five of the eight proteins examined bind to sugars. We could not identify the ligands of the SBPs TM0460, TM1150, and TM1199. The ligands for the archaeal SBPs are TM0031 (BglE), the ?-glucosides cellobiose and laminaribiose; TM0071 (XloE), xylobiose and xylotriose; TM0300 (GloE), large glucose oligosaccharides represented by xyloglucans; TM1223 (ManE), ?-1,4-mannobiose; and TM1226 (ManD), ?-1,4-mannobiose, ?-1,4-mannotriose, ?-1,4-mannotetraose, ?-1,4-galactosyl mannobiose, and cellobiose. For comparison, seven bacterial putative sugar-binding proteins were examined and ligands for three (TM0595, TM0810, and TM1855) were not identified. The ligands for these bacterial SBPs are TM0114 (XylE), xylose; TM0418 (InoE), myo-inositol; TM0432 (AguE), ?-1,4-digalactouronic acid; and TM0958 (RbsB), ribose. We found that T. maritima does not grow on several complex polypeptide mixtures as sole sources of carbon and nitrogen, so it is unlikely that these archaeal ABC transporters are used primarily for oligopeptide transport. Since these SBPs bind oligosaccharides with micromolar to nanomolar affinities, we propose that they are used primarily for oligosaccharide transport. PMID:16461685

  17. Population genetic diversity and structure within and among disjunct populations of Alnus maritima (seaside alder) using microsatellites

    Microsoft Academic Search

    James M. Jones; J. Phil Gibson

    2011-01-01

    Small, isolated populations are prone to genetic drift and high levels of inbreeding that can threaten their long-term survival.\\u000a Alnus maritima persists exclusively in three groups of small, highly disjunct, regional populations in the Delmarva Peninsula, Georgia,\\u000a and Oklahoma. Trees in the three regions are recognized as separate subspecies. Microsatellite markers were used to measure\\u000a fine-scale population genetic diversity and

  18. Electron spin resonance study of free radicals formed from a procyanidin-rich pine ( Pinus maritima) bark extract, pycnogenol

    Microsoft Academic Search

    Qiong Guo; Baolu Zhao; Lester Packer

    1999-01-01

    The free radical generated from the oxidation of a French maritima pine bark extract Pycnogenol (PYC), by the horseradish peroxidase (HRP)–hydrogen peroxide (H2O2) system at pH 7.4–10.0 was studied using electron spin resonance (ESR) spectrometer. The formation rate of the PYC radical (aH = 0.92G; g = 2.0055) was dependent on the PYC and HRP concentrations and pH; the lifetime

  19. Diverse substrate recognition mechanism revealed by Thermotoga maritima Cel5A structures in complex with cellotetraose, cellobiose and mannotriose

    Microsoft Academic Search

    Tzu-Hui Wu; Chun-Hsiang Huang; Tzu-Ping Ko; Hui-Lin Lai; Yanhe Ma; Chun-Chi Chen; Ya-Shan Cheng; Je-Ruei Liu; Rey-Ting Guo

    The hyperthermophilic endoglucanase Cel5A from Thermotoga maritima can find applications in lignocellulosic biofuel production, because it catalyzes the hydrolysis of glucan- and mannan-based polysaccharides. Here, we report the crystal structures in apo-form and in complex with three ligands, cellotetraose, cellobiose and mannotriose, at 1.29Å to 2.40Å resolution. The open carbohydrate-binding cavity which can accommodate oligosaccharide substrates with extensively branched chains

  20. Interacting infl uence of cold stratifi cation treatment and osmotic potential on seed germination of Triglochin maritima L

    Microsoft Academic Search

    Gederts Ievinsh

    2007-01-01

    Th e eff ect of cold stratifi cation treatment and isoosmotic NaCl and polyethyleneglycol (PEG) concentrations on germination of Triglochin maritima seeds was assessed. Th e highest (400 mM) NaCl concentration caused a signifi cant decrease in germination percentage and no germination was observed at the two highest (64 and 128 mM) PEG concentrations. Th e large diff erence in

  1. First record and characterization of a powdery mildew on a member of the Juncaginaceae: Leveillula taurica on Triglochin maritima

    Microsoft Academic Search

    Dean A. Glawe; Frank M. Dugan; Yajuan Liu; Jack D. Rogers

    2005-01-01

    The powdery mildew fungus Leveillula taurica (Erysiphales) is reported for the first time from the monocot Triglochin maritima (Juncaginaceae), a widespread salt marsh plant that causes economic losses because of its high toxicity to young livestock.\\u000a This is the first report of an erysiphaceous fungus on a member of the Juncaginaceae. Morphological data, obtained by light\\u000a and scanning electron microscopy,

  2. In vitro studies of the submerged angiosperm Ruppia maritima : Auxin and cytokinin effects on plant growth and development

    Microsoft Academic Search

    E. W. Koch; M. J. Durako

    1991-01-01

    Axenic tissue cultures ofRuppia maritima L. were established and propagated clonally in vitro from terminal rhizome segments collected from Tampa Bay, Florida, USA. Cultures were maintained in a base medium consisting of synthetic seawater supplemented with half-strength Murashige and Skoog salts and 1% sucrose at pH 5.6. The effects of five cytokins [6-furfurylaminopurine (kinetin), 6-benzylaminopurine (BAP), 2-isopentyladenine (2iP), 6-(4-hydroxy-3-methyl-but-2-enylamino) purine

  3. Iron-sulfur cluster biosynthesis. Thermatoga maritima IscU is a structured iron-sulfur cluster assembly protein.

    PubMed

    Mansy, Sheref S; Wu, Gong; Surerus, Kristene K; Cowan, J A

    2002-06-14

    Genetic evidence has indicated that Isc proteins play an important role in iron-sulfur cluster biogenesis. In particular, IscU is believed to serve as a scaffold for the assembly of a nascent iron-sulfur cluster that is subsequently delivered to target iron-sulfur apoproteins. We report the characterization of an IscU from Thermatoga maritima, an evolutionarily ancient hyperthermophilic bacterium. The stabilizing influence of a D40A substitution allowed characterization of the holoprotein. Mössbauer (delta = 0.29 +/- 0.03 mm/s, DeltaE(Q) = 0.58 +/- 0.03 mm/s), UV-visible absorption, and circular dichroism studies of the D40A protein show that T. maritima IscU coordinates a [2Fe-2S]2+ cluster. Thermal denaturation experiments demonstrate that T. maritima IscU is a thermally stable protein with a thermally unstable cluster. This is also the first IscU type domain that is demonstrated to possess a high degree of secondary and tertiary structure. CD spectra indicate 36.7% alpha-helix, 13.1% antiparallel beta-sheet, 11.3% parallel beta-sheet, 20.2% beta-turn, and 19.1% other at 20 degrees C, with negligible spectral change observed at 70 degrees C. Cluster coordination also has no effect on the secondary structure of the protein. The dispersion of signals in 1H-15N heteronuclear single quantum correlation NMR spectra of wild type and D40A IscU supports the presence of significant tertiary structure for the apoprotein, consistent with a scaffolding role, and is in marked contrast to other low molecular weight Fe-S proteins where cofactor coordination is found to be necessary for proper protein folding. Consistent with the observed sequence homology and proposed conservation of function for IscU-type proteins, we demonstrate T. maritima IscU-mediated reconstitution of human apoferredoxin. PMID:11934893

  4. Tagaturonate-fructuronate epimerase UxaE, a novel enzyme in the hexuronate catabolic network in Thermotoga maritima.

    PubMed

    Rodionova, Irina A; Scott, David A; Grishin, Nick V; Osterman, Andrei L; Rodionov, Dmitry A

    2012-11-01

    Thermotoga maritima is a marine hyperthermophilic microorganism that degrades a wide range of simple and complex carbohydrates including pectin and produces fermentative hydrogen at high yield. Galacturonate and glucuronate, two abundant hexuronic acids in pectin and xylan, respectively, are catabolized via committed metabolic pathways to supply carbon and energy for a variety of microorganisms. By a combination of bioinformatics and experimental techniques we identified a novel enzyme family (named UxaE) catalysing a previously unknown reaction in the hexuronic acid catabolic pathway, epimerization of tagaturonate to fructuronate. The enzymatic activity of the purified recombinant tagaturonate epimerase from T.?maritima was directly confirmed and kinetically characterized. Its function was also confirmed by genetic complementation of the growth of the Escherichia coli uxaB knockout mutant strain on galacturonate. An inferred novel galacturonate to mannonate catabolic pathway in T.?maritima was reconstituted in vitro using a mixture of recombinant purified enzymes UxaE, UxaC and UxuB. Members of the newly identified UxaE family were identified in ~50 phylogenetically diverse heterotrophic bacteria from aquatic and soil environments. The genomic context of respective genes and reconstruction of associated pathways suggest that UxaE enzymatic and biological function remains conserved in all of these species. PMID:22925190

  5. Characterization of two genes encoding metal tolerance proteins from Beta vulgaris subspecies maritima that confers manganese tolerance in yeast.

    PubMed

    Erbasol, Isil; Bozdag, Gonensin Ozan; Koc, Ahmet; Pedas, Pai; Karakaya, Huseyin Caglar

    2013-10-01

    Manganese (Mn(2+)) is an essential micronutrient in plants. However increased Mn(2+) levels are toxic to plant cells. Metal tolerance proteins (MTPs), member of cation diffusion facilitator protein (CDF) family, have important roles in metal homeostatis in different plant species and catalyse efflux of excess metal ions. In this study, we identified and characterized two MTP genes from Beta vulgaris spp. maritima (B. v. ssp. maritima). Overexpression of these two genes provided Mn tolerance in yeast cells. Sequence analyses displayed BmMTP10 and BmMTP11 as members of the Mn-CDF family. Functional analyses of these proteins indicated that they are specific to Mn(2+) with a role in reducing excess cellular Mn(2+) levels when expressed in yeast. GFP-fusion constructs of both proteins localized to the Golgi apparatus as a punctuated pattern. Finally, Q-RT-PCR results showed that BmMTP10 expression was induced threefold in response to the excess Mn(2+) treatment. On the other hand BmMTP11 expression was not affected in response to excess Mn(2+) levels. Thus, our results suggest that the BmMTP10 and BmMTP11 proteins from B. v. ssp. maritima have non-redundant functions in terms of Mn(2+) detoxification with a similar in planta localization and function as the Arabidopsis Mn-CDF homolog AtMTP11 and this conservation shows the evolutionary importance of these vesicular proteins in heavy metal homeostatis among plant species. PMID:23864431

  6. Structural insights into the mechanism of the PLP synthase holoenzyme from Thermotoga maritima.

    PubMed

    Zein, Fairuz; Zhang, Yan; Kang, You-Na; Burns, Kristin; Begley, Tadhg P; Ealick, Steven E

    2006-12-12

    Pyridoxal 5'-phosphate (PLP) is the biologically active form of vitamin B6 and is an important cofactor for several of the enzymes involved in the metabolism of amine-containing natural products such as amino acids and amino sugars. The PLP synthase holoenzyme consists of two subunits: YaaD catalyzes the condensation of ribulose 5-phosphate, glyceraldehyde-3-phosphate, and ammonia, and YaaE catalyzes the production of ammonia from glutamine. Here we describe the structure of the PLP synthase complex (YaaD-YaaE) from Thermotoga maritima at 2.9 A resolution. This complex consists of a core of 12 YaaD monomers with 12 noninteracting YaaE monomers attached to the core. Compared with the previously published structure of PdxS (a YaaD ortholog in Geobacillus stearothermophilus), the N-terminus (1-18), which includes helix alpha0, the beta2-alpha2 loop (46-56), which includes new helix alpha2a, and the C-terminus (270-280) of YaaD are ordered in the complex but disordered in PdxS. A ribulose 5-phosphate is bound to YaaD via an imine with Lys82. Previous studies have demonstrated a similar imine at Lys149 and not at Lys81 (equivalent to Lys150 and Lys82 in T. maritima) for the Bacillus subtilis enzyme suggesting the possibility that two separate sites on YaaD are involved in PLP formation. A phosphate from the crystallization solution is found bound to YaaD and also serves as a marker for a possible second active site. An ammonia channel that connects the active site of YaaE with the ribulose 5-phosphate binding site was identified. This channel is similar to one found in imidazole glycerol phosphate synthase; however, when the beta-barrels of the two complexes are superimposed, the glutaminase domains are rotated by about 180 degrees with respect to each other. PMID:17144654

  7. Cloning and expression of cytochrome P450 enzymes catalyzing the conversion of tyrosine to p-hydroxyphenylacetaldoxime in the biosynthesis of cyanogenic glucosides in Triglochin maritima.

    PubMed

    Nielsen, J S; Møller, B L

    2000-04-01

    Two cDNA clones encoding cytochrome P450 enzymes belonging to the CYP79 family have been isolated from Triglochin maritima. The two proteins show 94% sequence identity and have been designated CYP79E1 and CYP79E2. Heterologous expression of the native and the truncated forms of the two clones in Escherichia coli demonstrated that both encode multifunctional N-hydroxylases catalyzing the conversion of tyrosine to p-hydroxyphenylacetaldoxime in the biosynthesis of the two cyanogenic glucosides taxiphyllin and triglochinin in T. maritima. This renders CYP79E functionally identical to CYP79A1 from Sorghum bicolor, and unambiguously demonstrates that cyanogenic glucoside biosynthesis in T. maritima and S. bicolor is catalyzed by analogous enzyme systems with p-hydroxyphenylacetaldoxime as a free intermediate. This is in contrast to earlier reports stipulating p-hydroxyphenylacetonitrile as the only free intermediate in T. maritima. L-3,4-Dihydroxyphenyl[3-(14)C]Ala (DOPA) was not metabolized by CYP79E1, indicating that hydroxylation of the phenol ring at the meta position, as required for triglochinin formation, takes place at a later stage. In S. bicolor, CYP71E1 catalyzes the subsequent conversion of p-hydroxyphenylacetaldoxime to p-hydroxymandelonitrile. When CYP79E1 from T. maritima was reconstituted with CYP71E1 and NADPH-cytochrome P450 oxidoreductase from S. bicolor, efficient conversion of tyrosine to p-hydroxymandelonitrile was observed. PMID:10759528

  8. Cloning and Expression of Cytochrome P450 Enzymes Catalyzing the Conversion of Tyrosine to p-Hydroxyphenylacetaldoxime in the Biosynthesis of Cyanogenic Glucosides in Triglochin maritima1

    PubMed Central

    Nielsen, John Strikart; Møller, Birger Lindberg

    2000-01-01

    Two cDNA clones encoding cytochrome P450 enzymes belonging to the CYP79 family have been isolated from Triglochin maritima. The two proteins show 94% sequence identity and have been designated CYP79E1 and CYP79E2. Heterologous expression of the native and the truncated forms of the two clones in Escherichia coli demonstrated that both encode multifunctional N-hydroxylases catalyzing the conversion of tyrosine to p-hydroxyphenylacetaldoxime in the biosynthesis of the two cyanogenic glucosides taxiphyllin and triglochinin in T. maritima. This renders CYP79E functionally identical to CYP79A1 from Sorghum bicolor, and unambiguously demonstrates that cyanogenic glucoside biosynthesis in T. maritima and S. bicolor is catalyzed by analogous enzyme systems with p-hydroxyphenylacetaldoxime as a free intermediate. This is in contrast to earlier reports stipulating p-hydroxyphenylacetonitrile as the only free intermediate in T. maritima. l-3,4-Dihydroxyphenyl[3-14C]Ala (DOPA) was not metabolized by CYP79E1, indicating that hydroxylation of the phenol ring at the meta position, as required for triglochinin formation, takes place at a later stage. In S. bicolor, CYP71E1 catalyzes the subsequent conversion of p-hydroxyphenylacetaldoxime to p-hydroxymandelonitrile. When CYP79E1 from T. maritima was reconstituted with CYP71E1 and NADPH-cytochrome P450 oxidoreductase from S. bicolor, efficient conversion of tyrosine to p-hydroxymandelonitrile was observed. PMID:10759528

  9. Tryptophan-scanning mutagenesis of the ligand binding pocket in Thermotoga maritima arginine-binding protein.

    PubMed

    Deacon, Lindsay J; Billones, Hilbert; Galyean, Anne A; Donaldson, Teraya; Pennacchio, Anna; Iozzino, Luisa; D'Auria, Sabato; Dattelbaum, Jonathan D

    2014-04-01

    The Thermotoga maritima arginine binding protein (TmArgBP) is a member of the periplasmic binding protein superfamily. As a highly thermostable protein, TmArgBP has been investigated for the potential to serve as a protein scaffold for the development of fluorescent protein biosensors. To establish a relationship between structural dynamics and ligand binding capabilities, we constructed single tryptophan mutants to probe the arginine binding pocket. Trp residues placed around the binding pocket reveal a strong dependence on fluorescence emission of the protein with arginine for all but one of the mutants. Using these data, we calculated dissociation constants of 1.9-3.3 ?M for arginine. Stern-Volmer quenching analysis demonstrated that the protein undergoes a large conformational change upon ligand binding, which is a common feature of this protein superfamily. While still active at room temperature, time-resolved intensity and anisotropy decay data suggest that the protein exists as a highly rigid structure under these conditions. Interestingly, TmArgBP exists as a dimer at room temperature in both the presence and absence of arginine, as determined by asymmetric flow field flow fractionation (AF4) and supported by native gel-electrophoresis and time-resolved anisotropy. Our data on dynamics and stability will contribute to our understanding of hyperthermophilic proteins and their potential biotechnological applications. PMID:24370478

  10. Germ cells of the centipede Strigamia maritima are specified early in embryonic development

    PubMed Central

    Green, Jack E.; Akam, Michael

    2014-01-01

    We provide the first systematic description of germ cell development with molecular markers in a myriapod, the centipede Strigamia maritima. By examining the expression of Strigamia vasa and nanos orthologues, we find that the primordial germ cells are specified from at least the blastoderm stage. This is a much earlier embryonic stage than previously described for centipedes, or any other member of the Myriapoda. Using these genes as markers, and taking advantage of the developmental synchrony of Strigamia embryos within single clutches, we are able to track the development of the germ cells throughout embryogenesis. We find that the germ cells accumulate at the blastopore; that the cells do not internalize through the hindgut, but rather through the closing blastopore; and that the cells undergo a long-range migration to the embryonic gonad. This is the first evidence for primordial germ cells displaying these behaviours in any myriapod. The myriapods are a phylogenetically important group in the arthropod radiation for which relatively little developmental data is currently available. Our study provides valuable comparative data that complements the growing number of studies in insects, crustaceans and chelicerates, and is important for the correct reconstruction of ancestral states and a fuller understanding of how germ cell development has evolved in different arthropod lineages. PMID:24930702

  11. Bioconversion of Stemodia maritima diterpenes and derivatives by Cunninghamella echinulata var. elegans and Phanerochaete chrysosporium.

    PubMed

    Lamm, Andrew S; Reynolds, William F; Reese, Paul B

    2006-06-01

    Stemodane and stemarane diterpenes isolated from the plant Stemodia maritima and their dimethylcarbamate derivatives were fed to growing cultures of the fungi Cunninghamella echinulata var. elegans ATCC 8688a and Phanerochaete chrysosporium ATCC 24725. C. echinulata transformed stemodin (1) to its 7alpha-hydroxy- (2), 7beta-hydroxy- (3) and 3beta-hydroxy- (4) analogues. 2alpha-(N,N-Dimethylcarbamoxy)-13-hydroxystemodane (6) gave 2alpha-(N,N-dimethylcarbamoxy)-6alpha,13-dihydroxystemodane (7) and 2alpha-(N,N-dimethylcarbamoxy)-7alpha,13-dihydroxystemodane (8). Stemodinone (9) yielded 14-hydroxy-(10) and 7beta-hydroxy- (11) congeners along with 1, 2 and 3. Stemarin (13) was converted to the hitherto unreported 6alpha,13-dihydroxystemaran-19-oic acid (18). 19-(N,N-Dimethylcarbamoxy)-13-hydroxystemarane (14) yielded 13-hydroxystemaran-19-oic acid (17) along with the two metabolites: 19-(N,N-dimethylcarbamoxy)-2beta,13-dihydroxystemarane (15) and 19-(N,N-dimethylcarbamoxy)-2beta,8,13-trihydroxystemarane (16). P. chrysosporium converted 1 into 3, 4 and 2alpha,11beta,13-trihydroxystemodane (5). The dimethylcarbamate (6) was not transformed by this microorganism. Stemodinone (9) was hydroxylated at C-19 to give 12. Both stemarin (13) and its dimethylcarbamate (14) were recovered unchanged after incubation with Phanerochaete. PMID:16725164

  12. Improving thermal stability of thermophilic l-threonine aldolase from Thermotoga maritima.

    PubMed

    Wieteska, Lukasz; Ionov, Maksim; Szemraj, Janusz; Feller, Claudia; Kolinski, Andrzej; Gront, Dominik

    2015-04-10

    Threonine aldolase (TA) catalyzes a reversible reaction, in which threonine is decomposed into glycine and acetaldehyde. The same enzyme can be used to catalyze aldol reaction between glycine and a variety of aromatic and aliphatic aldehydes, thus creating various alpha-amino-alcohols. Therefore, TA is a very promising enzyme that could be used to prepare biologically active compounds or building blocks for pharmaceutical industry. Rational design was applied to thermophilic TA from Thermotoga maritima to improve thermal stability by the incorporation of salt and disulfide bridges between subunits in the functional tetramer. An activity assay together with CD analysis and Western-blot detection was used to evaluate mutants. Except one, each of the designed mutants preserved activity toward the natural substrate. One of the 10 proposed single point mutants, P56C, displayed significantly enhanced stability compared to the wild type (WT). Its initial activity was not affected and persisted longer than WT, proportionally to increased stability. Additionally one of the mutants, W86E, displayed enhanced activity, with stability similar to WT. Higher activity may be explained by a subtle change in active site availability. Salt bridge formation between glutamic acid at position 86 and arginine at position 120 in the neighboring chain may be responsible for the slight shift of the chain fragment, thus creating wider access to the active site both for the substrate and PLP. PMID:25701680

  13. Grass shrimp (Palaemonetes spp.) play a pivotal trophic role in enhancing Ruppia maritima.

    PubMed

    McCall, Donna Drury; Rakocinski, Chet F

    2007-03-01

    Coupled trophic-engineer interactions are potentially important for maintaining habitat function and ecosystem services. As ephemeral submerged aquatic vegetation (SAV), Ruppia maritima has a short well-defined growth-senescence cycle and should benefit from any ecological interaction that enhances its physical condition and longevity. Grass shrimp (Palaemonetes spp.) are abundant facultative grazers of epiphytic algae and conveyors of nutrients in tidal marsh and SAV habitats. Grass shrimp addition consistently enhanced Ruppia biomass and shoot density in a series of three field experiments conducted in Grand Bay National Estuarine Research Reserve, Mississippi, USA. In two experiments, epiphyte grazing by grass shrimp enhanced Ruppia by inhibiting die-back during the mid- and latter stages of the Ruppia life cycle. Despite a nonsignificant epiphyte grazing effect, grass shrimp also enhanced Ruppia during its early growth stage in a third experiment. In that experiment, nutrient addition also significantly increased epiphyte biomass. Grass shrimp may have fostered the early growth of Ruppia through direct deposition of feces to the sediment in the third experiment. Grass shrimp play a pivotal trophic role in the maintenance of Ruppia through context-dependent interactions involving stage of the SAV life cycle, season, and nutrient limitation. PMID:17503590

  14. Comprehensive phylogenetic analyses of the Ruppia maritima complex focusing on taxa from the Mediterranean.

    PubMed

    Ito, Yu; Ohi-Toma, Tetsuo; Murata, Jin; Tanaka, Norio

    2013-11-01

    Recent molecular phylogenetic studies reported high diversity of Ruppia species in the Mediterranean. Multiple taxa, including apparent endemics, are known from that region, however, they have thus far not been exposed to phylogenetic analyses aimed at studying their relationships to taxa from other parts of the world. Here we present a comprehensive phylogenetic analyses of the R. maritima complex using data sets composed of DNA sequences of the plastid genome, the multi-copy nuclear ITS region, and the low-copy nuclear phyB gene with a primary focus on the Mediterranean representatives of the complex. As a result, a new lineage, "Drepanensis", was identified as the seventh entity of the complex. This lineage is endemic to the Mediterranean. The accessions included in the former "Tetraploid" entity were reclassified into two entities: an Asia-Australia-Europe disjunct "Tetraploid_?" with a paternal "Diploid" origin, and a European "Tetraploid_?" originating from a maternal "Drepanensis" lineage. Another entity, "Tetraploid_?", is likely to have been originated as a result of chloroplast capture through backcrossing hybridization between paternal "Tetraploid_?" and maternal "Tetraploid_?". Additional discovery of multiple tetraploidizations as well as hybridization and chloroplast capture at the tetraploid level indicated that hybridization has been a significant factor in the diversification of Ruppia. PMID:23728988

  15. Flow cytometry and GISH reveal mixed ploidy populations and Spartina nonaploids with genomes of S. alterniflora and S. maritima origin

    PubMed Central

    Renny-Byfield, Simon; Ainouche, Malika; Leitch, Ilia J.; Lim, K. Yoong; Le Comber, Steven C.; Leitch, Andrew R.

    2010-01-01

    Background The genus Spartina exhibits extensive hybridization and includes classic examples of recent speciation by allopolyploidy. In the UK there are two hexaploid species, S. maritima and S. alterniflora, as well as the homoploid hybrid S. × townsendii (2n = 60) and a derived allododecaploid S. anglica (2n = 120, 122, 124); the latter two are considered to have originated in Hythe, southern England at the end of the 19th century. Methods Genomic in situ hybridization (GISH) and flow cytometry were used to characterize the genomic composition and distribution of these species and their ploidy levels at Eling Marchwood and Hythe, both near Southampton, southern England. Key Results GISH identified approx. 60 chromosomes each of S. maritima and S. alterniflora origin in S. anglica and 62 chromosomes from S. alterniflora and 30 chromosomes from S. maritima in a nonaploid individual from Eling Marchwood, UK. GISH and flow cytometry also revealed that most (94 %) individuals examined at Hythe were hexaploid (the remaining two individuals (6 %) were dodedcaploid; n = 34), whereas hexaploid (approx. 36 % of plants), nonaploid (approx. 27 %) and dodecaploid (approx. 36 %) individuals were found at Eling Marchwood (n = 22). Conclusions Nonaploid individuals indicate the potential for introgression between hexaploid and dodecaploid species, complicating the picture of polyploid-induced speciation within the genus. Despite the aggressive ecological habit of S. anglica, it has not out-competed S. × townsendii at Hythe (homoploid hybrids at a frequency of 94 %, n = 34), despite >100 years of coexistence. The success of GISH opens up the potential for future studies of polyploid-induced genome restructuring in this genus. PMID:20150197

  16. Purification and characterization of a novel thermostable 4-alpha-glucanotransferase of Thermotoga maritima cloned in Escherichia coli.

    PubMed

    Liebl, W; Feil, R; Gabelsberger, J; Kellermann, J; Schleifer, K H

    1992-07-01

    Maltodextrin glycosyltransferase (4-alpha-glucanotransferase) of the extremely thermophilic ancestral bacterium Thermotoga maritima has been purified from an Escherichia coli clone expressing the corresponding T. maritima MSB8 chromosomal gene. T. maritima 4-alpha-glucanotransferase, an approximately 53-kDa monomeric enzyme, is the most thermophilic glycosyltransferase described to date. It retained more than 90% of its maximum activity at temperatures from 55 degrees C up to 80 degrees C. The proposed action modus is the transfer of 1,4-alpha-glucanosyl chains, thus resulting in the disproportionation of 1,4-alpha-glucans. It converted soluble starch, amylopectin, and amylose, thereby changing the iodine staining properties of these substrates. The addition of low-molecular-mass malto-oligosaccharides, which act as glucanosyl acceptor molecules, enhanced the reaction and resulted in the formation of a series of linear maltohomologues from two to more than nine glucose units in size. Use of either of the malto-oligosaccharides maltotetraose, maltopentaose, maltohexaose, or maltoheptaose as sole substrate also yielded linear maltohomologues. On the other hand, maltose and maltotriose were not disproportionated by 4-alpha-glucanotransferase, although both were good acceptors for glucanosyl transfer. Glucose did not function as an acceptor in transfer reactions. Glucose also never appeared as a reaction product. The chain length of glucanosyl segments transferred ranged from two to probably far more than six glucose residues. Comparison of the N-terminal amino acid sequence of 4-alpha-glucanotransferase with other published protein sequences revealed significant similarity to sequences near the N-termini of various eucaryotic maltases and bacterial cyclodextrin glycosyltransferases, suggesting its relatedness on the molecular level with other starch- and maltodextrin-converting enzymes. PMID:1628664

  17. A Unique ?-1,2-Mannosyltransferase of Thermotoga maritima That Uses Di-myo-Inositol Phosphate as the Mannosyl Acceptor?

    PubMed Central

    Rodrigues, Marta V.; Borges, Nuno; Almeida, Carla P.; Lamosa, Pedro; Santos, Helena

    2009-01-01

    In addition to di-myo-inositol-1,3?-phosphate (DIP), a compatible solute widespread in hyperthermophiles, the organic solute pool of Thermotoga maritima comprises 2-(O-?-d-mannosyl)-di-myo-inositol-1,3?-phosphate (MDIP) and 2-(O-?-d-mannosyl-1,2-O-?-d-mannosyl)-di-myo-inositol-1,3?-phosphate (MMDIP), two newly identified ?-1,2-mannosides. In cells grown under heat stress, MDIP was the major solute, accounting for 43% of the total pool; MMDIP and DIP accumulated to similar levels, each corresponding to 11.5% of the total pool. The synthesis of MDIP involved the transfer of the mannosyl group from GDP-mannose to DIP in a single-step reaction catalyzed by MDIP synthase. This enzyme used MDIP as an acceptor of a second mannose residue, yielding the di-mannosylated compound. Minor amounts of the tri-mannosylated form were also detected. With a genomic approach, putative genes for MDIP synthase were identified in the genome of T. maritima, and the assignment was confirmed by functional expression in Escherichia coli. Genes with significant sequence identity were found only in the genomes of Thermotoga spp., Aquifex aeolicus, and Archaeoglobus profundus. MDIP synthase of T. maritima had maximal activity at 95°C and apparent Km values of 16 mM and 0.7 mM for DIP and GDP-mannose, respectively. The stereochemistry of MDIP was characterized by isotopic labeling and nuclear magnetic resonance (NMR): DIP selectively labeled with carbon 13 at position C1 of the l-inositol moiety was synthesized and used as a substrate for MDIP synthase. This ?-1,2-mannosyltransferase is unrelated to known glycosyltransferases, and within the domain Bacteria, it is restricted to members of the two deepest lineages, i.e., the Thermotogales and the Aquificales. To our knowledge, this is the first ?-1,2-mannosyltransferase characterized thus far. PMID:19648237

  18. Structure of an essential bacterial protein YeaZ (TM0874) from Thermotoga maritima at 2.5?Å resolution

    PubMed Central

    Xu, Qingping; McMullan, Daniel; Jaroszewski, Lukasz; Krishna, S. Sri; Elsliger, Marc-André; Yeh, Andrew P.; Abdubek, Polat; Astakhova, Tamara; Axelrod, Herbert L.; Carlton, Dennis; Chiu, Hsiu-Ju; Clayton, Thomas; Duan, Lian; Feuerhelm, Julie; Grant, Joanna; Han, Gye Won; Jin, Kevin K.; Klock, Heath E.; Knuth, Mark W.; Miller, Mitchell D.; Morse, Andrew T.; Nigoghossian, Edward; Okach, Linda; Oommachen, Silvya; Paulsen, Jessica; Reyes, Ron; Rife, Christopher L.; van den Bedem, Henry; Hodgson, Keith O.; Wooley, John; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.

    2010-01-01

    YeaZ is involved in a protein network that is essential for bacteria. The crystal structure of YeaZ from Thermotoga maritima was determined to 2.5?Å resolution. Although this protein belongs to a family of ancient actin-like ATPases, it appears that it has lost the ability to bind ATP since it lacks some key structural features that are important for interaction with ATP. A conserved surface was identified, supporting its role in the formation of protein complexes. PMID:20944216

  19. An evaluation of genetic fidelity of encapsulated microshoots of the medicinal plant: Cineraria maritima following six months of storage

    Microsoft Academic Search

    Vikas Srivastava; Shamshad A. Khan; Suchitra Banerjee

    2009-01-01

    Regrowth of encapsulated microshoots, using alginate encapsulation, of Cineraria maritima reached 82.35% following 6 months of storage. Amongst developing plantlets, 33.33% exhibited formation of multiple shoots\\u000a at the onset of regrowth and 11.76% demonstrated simultaneous formation of shoots and roots. Healthy root formation was observed\\u000a in plantlets following 2 weeks of their transfer to half-strength Murashige and Skoog medium containing 1.0 mg l?1 ?-naphthalene

  20. NMR characterisation of inulin-type fructooligosaccharides as the major water-soluble carbohydrates from Matricaria maritima (L.).

    PubMed

    Cérantola, Stéphane; Kervarec, Nelly; Pichon, Roger; Magné, Christian; Bessieres, Marie-Anne; Deslandes, Eric

    2004-10-01

    By use of 1H and 13C NMR spectroscopy including 2D 1H,1H DQF-COSY/TOCSY and 1H,13C HMQC/HMBC experiments, the main water-soluble carbohydrate components extracted from leaves of Matricaria maritima were identified as oligofructans composed of a linear chain of (2-->1)-linked beta-D-fructofuranosyl residues specifying an inulin-type structure. Alpha-D-Glcp-(1-->2)-[beta-D-Fruf-(2-->1)-beta-D-Frucf]n-(2-->1)-beta-D-Fruf. PMID:15388360

  1. Flowering time in wild beet ( Beta vulgaris ssp. maritima) along a latitudinal cline

    NASA Astrophysics Data System (ADS)

    Dijk, Henk Van; Boudry, Pierre; McCombre, Helen; Vernet, Philippe

    The wild beet ( Beta vulgaris ssp. maritima, a perennial species from the Mediterranean and the European Atlantic coasts) shows marked variation in flowering time in terms of both the year of first flowering and flowering date in a given year. Much of this variability is related to latitude. Beta vulgaris plants flower either in the same year as they germinate or in their second year. This is mainly due to differences in their requirement for vernalization, which is determined by a single gene B/b and by quantitative trait loci. The more southern the origin of the plants, the less vernalization is required. Also the B allele, which cancels vernalization requirement completely, has a high frequency in the Mediterranean region, but is completely absent in the northern part of the distribution of this species. We found that flowering date variation in relation to the latitude of origin is maintained under greenhouse conditions but does not follow a simple clinal relationship. From the Mediterranean northwards to the west coast of Brittany, flowering occurs progressively earlier, but from Brittany northwards to south-east England and The Netherlands it is progressively later. A possible explanation for this difference is that in the southern part of the range sensitivity to daylength and warmth control flowering time, whereas further north vernalization requirement is also a key factor. A substantial part of all differences in flowering time was heritable: heritability within populations was measured as 0.33 under greenhouse conditions. The high heritability implies evolutionary change may occur in this character.

  2. Functional and structural characterization of a thermostable acetyl esterase from Thermotoga maritima

    PubMed Central

    Levisson, Mark; Han, Gye Won; Deller, Marc C.; Xu, Qingping; Biely, Peter; Hendriks, Sjon; Ten Eyck, Lynn F.; Flensburg, Claus; Roversi, Pietro; Miller, Mitchell D.; McMullan, Daniel; von Delft, Frank; Kreusch, Andreas; Deacon, Ashley M.; van der Oost, John; Lesley, Scott A.; Elsliger, Marc-André; Kengen, Servé W. M.; Wilson, Ian A.

    2012-01-01

    TM0077 from Thermotoga maritima is a member of the carbohydrate esterase family 7 and is active on a variety of acetylated compounds, including cephalosporin C. TM0077 esterase activity is confined to short-chain acyl esters (C2-C3), and is optimal around 100°C and pH 7.5. The positional specificity of TM0077 was investigated using 4-nitrophenyl-?-D-xylopyranoside monoacetates as substrates in a ?-xylosidase-coupled assay. TM0077 hydrolyzes acetate at positions 2, 3 and 4 with equal efficiency. No activity was detected on xylan or acetylated xylan, which implies that TM0077 is an acetyl esterase and not an acetyl xylan esterase as currently annotated. Selenomethionine-substituted and native structures of TM0077 were determined at 2.1 Å and 2.5 Å resolution, respectively, revealing a classic ?/?-hydrolase fold. TM0077 assembles into a doughnut-shaped hexamer with small tunnels on either side leading to an inner cavity, which contains the six catalytic centers. Structures of TM0077 with covalently bound phenylmethylsulfonyl fluoride (PMSF) and paraoxon were determined to 2.4 Å and 2.1 Å, respectively, and confirmed that both inhibitors bind covalently to the catalytic serine (Ser188). Upon binding of inhibitor, the catalytic serine adopts an altered conformation, as observed in other esterase and lipases, and supports a previously proposed catalytic mechanism in which this Ser hydroxyl rotation prevents reversal of the reaction and allows access of a water molecule for completion of the reaction. PMID:22411095

  3. High frequency Agrobacterium -mediated transformation and plant regeneration via direct shoot formation from leaf explants in Beta vulgaris and Beta maritima

    Microsoft Academic Search

    H. Hisano; Y. Kimoto; H. Hayakawa; J. Takeichi; T. Domae; R. Hashimoto; J. Abe; S. Asano; A. Kanazawa; Y. Shimamoto

    2004-01-01

    We have developed a new procedure for Agrobacterium-mediated transformation of plants in the genus Beta using shoot-base as the material for Agrobacterium infection. The frequency of regeneration from shoot bases was analyzed in seven accessions of sugarbeet ( Beta vulgaris) and two accessions of B. maritima to select materials suitable for obtaining transformed plants. The frequency of transformation of the

  4. Overexpression, crystallization and preliminary X-ray crystallographic analysis of ?-N-acetylglucosaminidase from Thermotoga maritima encoded by the Tm0809 gene

    PubMed Central

    Lee, Hyung Ho; Jung, Sang Taek

    2013-01-01

    ?-N-acetylglucosaminidase (NagA) protein hs a chitin-degrading activity and chitin is one of the most abundant polymers in nature. NagA contains a family 3 glycoside (GH3)-type N-terminal domain and a unique C-terminal domain. The structurally uncharacterized C-terminal domain of NagA may be involved in substrate specificity. To provide a structural basis for the substrate specificity of NagA, structural analysis of NagA from Thermotoga maritima encoded by the Tm0809 gene was initiated. NagA from T. maritima has been overexpressed in Escherichia coli and crystallized at 296?K using ammonium sulfate as a precipitant. Crystals of T. maritima NagA diffracted to 3.80?Å resolution and belonged to the monoclinic space group C2, with unit-cell parameters a = 231.15, b = 133.62, c = 140.88?Å, ? = 89.97°. The crystallization of selenomethionyl-substituted protein is in progress to solve the crystal structure of T. maritima NagA. PMID:23385748

  5. Phylogeographic evidence for the postglacial colonization of the North and Baltic Sea coasts from inland glacial refugia by Triglochin maritima L

    Microsoft Academic Search

    Esther Lambracht; Erik Westberg; Joachim W. Kadereit

    2007-01-01

    We investigated the geographical distribution of genetic variation in 67 individuals of Triglochin maritima from 38 localities across Europe using AFLP markers. Analysis of genetic variation resulted in the recognition of two major genetic groups. Apart from few geographical outliers, these are distributed (1) along the Atlantic coasts of Portugal, Spain and France and (2) in the North Sea area,

  6. Comparison of parasitic hymenoptera captured in malaise traps baited with two flowering plants Lobularia maritima (Brassicales:Brassicaceae) and Spermacoce verticillate (Gentianales:Rubiaceae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Many adult hymenopterous parasitoids feed on floral nectar, and occasionally pollen. However, flowers differ in both accessibility and attractiveness to these insects. Malaise traps, a type of “passive/interception” trap, were baited with potted flowering plants, Lobularia maritima L. (Brassicaceae)...

  7. Putative free radical-scavenging activity of an extract of Cineraria maritima in preventing selenite-induced cataractogenesis in Wistar rat pups

    PubMed Central

    Anitha, Thirugnanasambandhar Sivasubramanian; Muralidharan, Arumugam Ramachandran; Annadurai, Thangaraj; Jesudasan, Christdas Arul Nelson; Thomas, Philip Aloysius

    2013-01-01

    Purpose To investigate the possible free radical-scavenging activity of an extract of Cineraria maritima on selenite-induced cataractous lenses in Wistar rat pups. Methods In the present study, Wistar rat pups were divided into three experimental groups. On P10, Group I (control) rat pups received an intraperitoneal injection of 0.89% saline. Rats in groups II (selenite-challenged, untreated) and III (selenite-challenged, C. maritima treated) received a subcutaneous injection of sodium selenite (19 ?mol/kg bodyweight); Group III rat pups also received an intraperitoneal injection of the extract of C. maritima (350 mg/kg bodyweight) once daily P9–14. Both eyes of each pup were examined from P16 until P30. Cytochemical localization of nitroblue tetrazolium salts and generation of superoxide, hydroxyl, and nitric oxide levels were measured. The expression of the inducible nitric oxide synthase gene was evaluated with reverse transcription-PCR. Immunoblot analysis was also performed to confirm the differential expression of the inducible nitric oxide synthase protein. Results Subcutaneous injection of sodium selenite led to severe oxidative damage in the lenticular tissues, shown by increased formation of formazan crystals, elevated generation of superoxide, hydroxyl, and nitric oxide radicals, and elevated inducible nitric oxide synthase gene and protein expression that possibly contributed to the opacification of the lens and thus cataract formation. When rat pups were treated with intraperitoneal administration of the extract of C. maritima, the generation of free radicals as well as the messenger ribonucleic acid and protein expression of inducible nitric oxide synthase were maintained at near normal levels. Conclusions The data generated by this study suggest that an ethanolic extract of C. maritima possibly prevents cataractogenesis in a rat model by minimizing free radical generation. PMID:24357923

  8. Investigations into the effects of environmental and physical variables on the growth of natural and transplanted populations of Ruppia maritima L. s.l. in the Galveston Bay System, Texas

    E-print Network

    Schubert, William James

    2002-01-01

    The effects of sixteen environmental and physical variables on the growth of six natural populations and on the establishment and growth of transplanted populations of widgeon grass, Ruppia maritima L. s.l., were evaluated in the Galveston Bay...

  9. Crystal structure of a transcriptional regulator TM1030 from Thermotoga maritima solved by an unusual MAD experiment

    PubMed Central

    Koclega, Katarzyna D.; Chruszcz, Maksymilian; Zimmerman, Matthew D.; Cymborowski, Marcin; Evdokimova, Elena; Minor, Wladek

    2007-01-01

    The crystal structure of a putative transcriptional regulator protein TM1030 from Thermotoga maritima, a hyperthermophilic bacterium, was determined by an unusual multi-wavelength anomalous dispersion method at 2.0 Å resolution., in which data from two different crystals and two different beamlines were used. The protein belongs to the tetracycline repressor TetR superfamily. The three-dimensional structure of TM1030 is similar to the structures of proteins that function as multidrug-binding transcriptional repressors, and contains a large solvent-exposed pocket similar to the drug-binding pockets present in those repressors. The asymmetric unit in the crystal structure contains a single protein chain and the two-fold symmetry of the dimer is adopted by the crystal symmetry. The structure described in this paper is an apo-form of TM1030. Although it is known that the protein is significantly overexpressed during heat shock, its detailed function cannot be yet explained. PMID:17588774

  10. Effect of dimerization on the stability and catalytic activity of dihydrofolate reductase from the hyperthermophile Thermotoga maritima.

    PubMed

    Loveridge, E Joel; Rodriguez, Robert J; Swanwick, Richard S; Allemann, Rudolf K

    2009-06-30

    In contrast to all other chromosomally encoded dihydrofolate reductases characterized so far, dihydrofolate reductase (DHFR) from the hyperthermophile Thermotoga maritima forms a highly stable dimer. The dimer interface involves residues whose mobility is important for catalysis in monomeric DHFRs. Here, we report the generation of a variant of DHFR from T. maritima, TmDHFR-V11D, in which a single amino acid replacement was sufficient to favor the monomeric form of the enzyme in the presence of the nondenaturing zwitterionic detergent 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate. The free energy of stabilization of monomeric TmDHFR-V11D was 15 kJ mol(-1) lower than that of the wild-type dimer, while the melting temperature of monomeric TmDHFR-V11D was comparable to that of monomeric DHFR from the thermophile Bacillus stearothermophilus, supporting the hypothesis that oligomerization is required to achieve the thermal stabilities necessary for activity at temperatures optimal for growth of hyperthermophiles. Both the steady-state turnover numbers and rates of hydride transfer were reduced in TmDHFR-V11D. However, a similar reduction of the rate constants was observed in a different variant, TmDHFR-V126E, which remained as a dimer under all experimental conditions used here. Monomeric TmDHFR-V11D had a similar rate of hydride transfer to the dimeric form, but a reduced steady-state turnover rate. Intersubunit motions therefore appear to be less important than correlated motions within individual subunits for TmDHFR-catalyzed hydride transfer, but are critical to the overall progression of the catalytic cycle. Hence, the reduced catalytic activity of TmDHFR relative to the monomeric Escherichia coli enzyme is not caused by rigidity resulting from dimerization, but is a subtle consequence of the sequence and structure of its subunits, which appear to have evolved to allow thermostability at the expense of catalysis. PMID:19453185

  11. Phenological development stages variation versus mercury tolerance, accumulation, and allocation in salt marsh macrophytes Triglochin maritima and Scirpus maritimus prevalent in Ria de Aveiro coastal lagoon (Portugal).

    PubMed

    Anjum, Naser A; Ahmad, Iqbal; Válega, Mónica; Figueira, Etelvina; Duarte, Armando C; Pereira, Eduarda

    2013-06-01

    Efficient and sustainable management of rapidly mounting environmental issues has been the focus of current intensive research. The present study aimed to investigate the impact of plant phenological development stage variation on mercury (Hg) tolerance, accumulation, and allocation in two salt marsh macrophytes Triglochin maritima and Scirpus maritimus prevalent in historically Hg-contaminated Ria de Aveiro coastal lagoon (Portugal). Both plant samples and the sediments vegetated by monospecific stands of T. maritima and S. maritimus were collected from reference (R) and sites with moderate (M) and high (H) Hg contamination in Laranjo bay within Ria de Aveiro lagoon. Hg tolerance, uptake, and allocation in T. maritima and S. maritimus, physico-chemical traits (pH, redox potential, and organic matter content) and Hg concentrations in sediments vegetated by these species were impacted differentially by phenological development stages variation irrespective of the Hg contamination level. In T. maritima, Hg concentration increased with increase in Hg contamination gradient where root displayed significantly higher Hg followed by rhizome and leaf maximally at H. However, in S. maritimus, the highest Hg concentration was perceptible in rhizome followed by root maximally at M. Between the two studied plant species, S. maritimus displayed higher Hg tolerance index (depicted by higher plant dry mass allocated to reproductive stage) and higher available Hg at M (during all growth stages) and H (during senescent stage) when compared to T. maritimus. Both plant species proved to be Hg excluder (low root/rhizome-leaf Hg translocation). Additionally, T. maritima also acted as Hg stabilizer while, S. maritimus as Hg accumulator. It can be inferred from the study that (a) the plant phenological development stage variations significantly influenced plant Hg sensitivity by impacting sediment chemistry, plant growth (in terms of plant dry mass), Hg accumulation, and its subsequent allocation capacity, contingent to Hg contamination gradient; (b) S. maritimus accumulated higher Hg but restricted its translocation to above-ground part using exclusion process at both M and H due to its accelerated growth during Hg-tolerant reproductive/metabolically active phenological development stage greater than its counterpart T. maritima; and (c) the studied salt marsh plants although hailed from the same C3 and monocot group did not necessarily display similar phenotypic plasticity and behavior towards Hg-contaminated scenario during their life cycle. PMID:23184133

  12. Spatial genetic structure in Beta vulgaris subsp. maritima and Beta macrocarpa reveals the effect of contrasting mating system, influence of marine currents, and footprints of postglacial recolonization routes

    PubMed Central

    Leys, Marie; Petit, Eric J; El-Bahloul, Yasmina; Liso, Camille; Fournet, Sylvain; Arnaud, Jean-François

    2014-01-01

    Understanding the factors that contribute to population genetic divergence across a species' range is a long-standing goal in evolutionary biology and ecological genetics. We examined the relative importance of historical and ecological features in shaping the present-day spatial patterns of genetic structure in two related plant species, Beta vulgaris subsp. maritima and Beta macrocarpa. Using nuclear and mitochondrial markers, we surveyed 93 populations from Brittany (France) to Morocco – the southern limit of their species' range distribution. Whereas B. macrocarpa showed a genotypic structure and a high level of genetic differentiation indicative of selfing, the population genetic structure of B. vulgaris subsp. maritima was consistent with an outcrossing mating system. We further showed (1) a strong geographic clustering in coastal B. vulgaris subsp. maritima populations that highlighted the influence of marine currents in shaping different lineages and (2) a peculiar genetic structure of inland B. vulgaris subsp. maritima populations that could indicate the admixture of distinct evolutionary lineages and recent expansions associated with anthropogenic disturbances. Spatial patterns of nuclear diversity and differentiation also supported a stepwise recolonization of Europe from Atlantic-Mediterranean refugia after the last glacial period, with leading-edge expansions. However, cytoplasmic diversity was not impacted by postglacial recolonization: stochastic long-distance seed dispersal mediated by major oceanic currents may mitigate the common patterns of reduced cytoplasmic diversity observed for edge populations. Overall, the patterns we documented here challenge the general view of reduced genetic diversity at the edge of a species' range distribution and provide clues for understanding how life-history and major geographic features interact to shape the distribution of genetic diversity. PMID:24963380

  13. Subcellular concentrations of sugar alcohols and sugars in relation to phloem translocation in Plantago major, Plantago maritima , Prunus persica , and Apium graveolens

    Microsoft Academic Search

    Jan Nadwodnik; Gertrud Lohaus

    2008-01-01

    Sugar and sugar alcohol concentrations were analyzed in subcellular compartments of mesophyll cells, in the apoplast, and\\u000a in the phloem sap of leaves of Plantago major (common plantain), Plantago maritima (sea plantain), Prunus persica (peach) and Apium graveolens (celery). In addition to sucrose, common plantain, sea plantain, and peach also translocated substantial amounts of sorbitol,\\u000a whereas celery translocated mannitol as

  14. Structure-Based Design of Robust Glucose Biosensors using a Thermotoga maritima Periplasmic Glucose-Binding Protein

    SciTech Connect

    Tian,Y.; Cunco, M.; Changela, A.; Hocker, B.; Beese, L.; Hellinga, H.

    2007-01-01

    We report the design and engineering of a robust, reagentless fluorescent glucose biosensor based on the periplasmic glucose-binding protein obtained from Thermotoga maritima (tmGBP). The gene for this protein was cloned from genomic DNA and overexpressed in Escherichia coli, the identity of its cognate sugar was confirmed, ligand binding was studied, and the structure of its glucose complex was solved to 1.7 Angstroms resolution by X-ray crystallography. TmGBP is specific for glucose and exhibits high thermostability (midpoint of thermal denaturation is 119 {+-} 1 C and 144 {+-} 2 C in the absence and presence of 1 mM glucose, respectively). A series of fluorescent conjugates was constructed by coupling single, environmentally sensitive fluorophores to unique cysteines introduced by site-specific mutagenesis at positions predicted to be responsive to ligand-induced conformational changes based on the structure. These conjugates were screened to identify engineered tmGBPs that function as reagentless fluorescent glucose biosensors. The Y13C Cy5 conjugate is bright, gives a large response to glucose over concentration ranges appropriate for in vivo monitoring of blood glucose levels (1-30 mM), and can be immobilized in an orientation-specific manner in microtiter plates to give a reversible response to glucose. The immobilized protein retains its response after long-term storage at room temperature.

  15. X-ray structure of the [FeFe]-hydrogenase maturase HydE from Thermotoga maritima.

    PubMed

    Nicolet, Yvain; Rubach, Jon K; Posewitz, Matthew C; Amara, Patricia; Mathevon, Carole; Atta, Mohamed; Fontecave, Marc; Fontecilla-Camps, Juan C

    2008-07-01

    Maturation of the [FeFe]-hydrogenase active site depends on at least the expression of three gene products called HydE, HydF, and HydG. We have solved the high resolution structure of recombinant, reconstituted S-adenosine-L-methionine-dependent HydE from Thermotoga maritima. Besides the conserved [Fe(4)S(4)] cluster involved in the radical-based reaction, this HydE was reported to have a second [Fe(4)S(4)] cluster coordinated by three Cys residues. However, in our crystals, depending on the reconstitution and soaking conditions, this second cluster is either a [Fe(2)S(2)] center, with water occupying the fourth ligand site or is absent. We have carried out site-directed mutagenesis studies on the related HydE from Clostridium acetobutylicum, along with in silico docking and crystal soaking experiments, to define the active site region and three anion-binding sites inside a large, positive cavity, one of which binds SCN(-) with high affinity. Although the overall triose-phosphate isomerase-barrel structure of HydE is very similar to that of biotin synthase, the residues that line the internal cavity are significantly different in the two enzymes. PMID:18400755

  16. Growth Habit and Mechanical Architecture of the Sand Dune?adapted Climber Clematis flammula var. maritima L.

    PubMed Central

    ISNARD, SANDRINE; ROWE, NICK; SPECK, THOMAS

    2003-01-01

    Clematis flammula var. maritima is a woody lianoid plant that grows on coastal sand dunes in the Mediterranean region. Older perennial stems are present as extensive underground axes. These generate surface growth of shorter?lived stems producing monospecific trellises above the surface of the sand. Despite its sand dune habitat and shortage of host support plants, this variety of Clematis shows mechanical characteristics during growth that are closely comparable with those of scandent woody lianas. A significant decrease in the value of structural Young’s modulus is observed from the aerial trellis?forming shoots (1·619 ± 0·492 GN m–2) to emergent axes (0·855 ± 0·253 GN m–2) and underground woody stems (0·470 ± 0·113 GN m–2). Biomechanical and evelopmental observations indicate that most emergent branches are optimized geometrically and mechanically in relation to their points of emergence from the sand, with increases in structural Young’s modulus and the second moment of area around the surface of the sand. Lianoid plants, physiologically capable of withstanding sand dune environments, might represent acceptable natural or introduced species for dune stabilization and conservation. PMID:12588720

  17. Hyperthermophilic aldolases as biocatalyst for C-C bond formation: rhamnulose 1-phosphate aldolase from Thermotoga maritima.

    PubMed

    Oroz-Guinea, Isabel; Sánchez-Moreno, Israel; Mena, Montaña; García-Junceda, Eduardo

    2015-04-01

    The TM1072 gene from Thermotoga maritima codifies for a putative form of a rhamnulose-1-phosphate aldolase (Rha-1PA Tm). To investigate this enzyme further, its gene was cloned and expressed in Escherichia coli. The purified enzyme was activated by Co(2+) as a divalent metal ion cofactor, instead of Zn(2+) as its E. coli homologue, and exhibited a maximum of activity at 95 °C. Furthermore, the enzyme displayed a high stability against extreme reaction conditions, retaining 90 % of its activity in the presence of 40 % of acetonitrile and showing a half-life greater than 3 h at 115 °C. The kinetic parameters at room temperature (R/T) were also studied; the K M was calculated to be 3.6?±?0.33 mM, while k cat/K M was found to be 0.7?×?10(3) s(-1) M(-1). Given these characteristics, Rha-1PA Tm is an attractive enzyme for use as a biocatalyst for industrial applications, offering intriguing possibilities for practical biocatalysis. PMID:25324130

  18. Diverse substrate recognition mechanism revealed by Thermotoga maritima Cel5A structures in complex with cellotetraose, cellobiose and mannotriose.

    PubMed

    Wu, Tzu-Hui; Huang, Chun-Hsiang; Ko, Tzu-Ping; Lai, Hui-Lin; Ma, Yanhe; Chen, Chun-Chi; Cheng, Ya-Shan; Liu, Je-Ruei; Guo, Rey-Ting

    2011-12-01

    The hyperthermophilic endoglucanase Cel5A from Thermotoga maritima can find applications in lignocellulosic biofuel production, because it catalyzes the hydrolysis of glucan- and mannan-based polysaccharides. Here, we report the crystal structures in apo-form and in complex with three ligands, cellotetraose, cellobiose and mannotriose, at 1.29Å to 2.40Å resolution. The open carbohydrate-binding cavity which can accommodate oligosaccharide substrates with extensively branched chains explained the dual specificity of the enzyme. Combining our structural information and the previous kinetic data, it is suggested that this enzyme prefers ?-glucosyl and ?-mannosyl moieties at the reducing end and uses two conserved catalytic residues, E253 (nucleophile) and E136 (general acid/base), to hydrolyze the glycosidic bonds. Moreover, our results also suggest that the wide spectrum of Tm_Cel5A substrates might be due to the lack of steric hindrance around the C2-hydroxyl group of the glucose or mannose unit from active-site residues. PMID:21839861

  19. Metabolic fate of cardiac glycosides and flavonoids upon fermentation of aqueous sea squill (Drimia maritima L.) extracts.

    PubMed

    Knittel, Diana N; Stintzing, Florian C; Kammerer, Dietmar R

    2015-06-10

    Sea squill (Drimia maritima L.) extracts have been used for centuries for the medical treatment of heart diseases. A procedure for the preparation of Drimia extracts applied for such purposes comprising a fermentation step is described in the German Homoeopathic Pharmacopoeia (GHP). However, little is known about the secondary metabolite profile of such extracts and the fate of these components upon processing and storage. Thus, in the present study sea squill extracts were monitored during fermentation and storage by HPLC-DAD-MS(n) and GC-MS to characterise and quantitate individual cardiac glycosides and phenolic compounds. For this purpose, a previously established HPLC method for the separation and quantitation of pharmacologically relevant cardiac glycosides (bufadienolides) was validated. Within 12 months of storage, total bufadienolide contents decreased by about 50%, which was attributed to microbial and plant enzyme activities. The metabolisation and degradation rates of individual bufadienolide glycosides significantly differed, which was attributed to differing structures of the aglycones. Further degradation of bufadienolide aglycones was also observed. Besides reactions well known from human metabolism studies, dehydration of individual compounds was monitored. Quantitatively predominating flavonoids were also metabolised throughout the fermentation process. The present study provides valuable information about the profile and stability of individual cardiac glycosides and phenolic compounds in fermented Drimia extracts prepared for medical applications, and expands the knowledge of cardiac glycoside conversion upon microbial fermentation. PMID:25841205

  20. Proteomic and physiological responses of the halophyte Cakile maritima to moderate salinity at the germinative and vegetative stages.

    PubMed

    Debez, Ahmed; Braun, Hans-Peter; Pich, Andreas; Taamalli, Wael; Koyro, Hans-Werner; Abdelly, Chedly; Huchzermeyer, Bernhard

    2012-10-22

    Responses of the halophyte Cakile maritima to moderate salinity were addressed at germination and vegetative stages by bringing together proteomics and eco-physiological approaches. 75 mM NaCl-salinity delayed significantly the germination process and decreased slightly the seed germination percentage compared to salt-free conditions. Monitoring the proteome profile between 0 h and 120 h after seed sowing revealed a delay in the degradation of seed storage proteins when germination took place under salinity, which may explain the slower germination rate observed. Of the sixty-seven proteins identified by mass spectrometry, several proteins involved in glycolysis, amino acid metabolism, photosynthesis, and protein folding showed significantly increased abundance during germination. This pattern was less pronounced under salinity. At the vegetative stage, 100mM NaCl-salinity stimulated significantly the plant growth, which was sustained by enhanced leaf expansion, water content, and photosynthetic activity. Comparative proteome analyses of leaf tissue revealed 44 proteins with different abundance changes, most of which being involved in energy metabolism. A specific set of proteins predominantly involved in photosynthesis and respiration showed significantly higher abundance in salt-treated plants. Altogether, combining proteomics with eco-physiological tools provides valuable information, which contributes to improve our understanding in the salt-response of this halophyte during its life cycle. PMID:22940175

  1. Stationary Phase and Nutrient Levels Trigger Transcription of a Genomic Locus Containing a Novel Peptide (TM1316) in the Hyperthermophilic Bacterium Thermotoga maritima

    PubMed Central

    Frock, Andrew D.; Montero, Clemente I.; Blumer-Schuette, Sara E.

    2013-01-01

    The genome of the hyperthermophilic bacterium Thermotoga maritima encodes numerous putative peptides/proteins of 100 amino acids or less. While most of these open reading frames (ORFs) are transcribed during growth, their corresponding physiological roles are largely unknown. The onset of stationary phase in T. maritima was accompanied by significant morphological changes and upregulation of several ORFs located in the TM1298-TM1336 genome locus. This region contains putative HicAB toxin-antitoxin pairs, hypothetical proteins, radical S-adenosylmethionine (SAM) enzymes, and ABC transporters. Of particular note was the TM1315-TM1319 operon, which includes a putative 31-amino-acid peptide (TM1316) that was the most highly transcribed gene in the transcriptome during stationary phase. Antibodies directed against a synthetic version of TM1316 were used to track its production, which correlated closely with transcriptomic data. Immunofluorescence microscopy revealed that TM1316 was localized to the cell envelope and prominent in cell aggregates formed during stationary phase. The only functionally characterized locus with an organization similar to that of TM1315-TM1319 is in Bacillus subtilis, which contains subtilosin A, a cyclic peptide with Cys–to–?-carbon linkages that functions as an antilisterial bacteriocin. While the organization of TM1316 resembled that of the Bacillus peptide (e.g., in its number of amino acids and spacing of Cys residues), preparations containing high levels of TM1316 affected the growth of neither Thermotoga species nor Pyrococcus furiosus, a hyperthermophilic archaeon isolated from the same locale as T. maritima. Several other putative Cys-rich peptides could be identified in the TM1298-TM1336 locus, and while their roles are also unclear, they merit examination as potential antimicrobial agents in hyperthermophilic biotopes. PMID:23974142

  2. Ligands of Thermophilic ABC Transporters Encoded in a Newly Sequenced Genomic Region of Thermotoga maritima MSB8 Screened by Differential Scanning Fluorimetry ? †

    PubMed Central

    Boucher, Nathalie; Noll, Kenneth M.

    2011-01-01

    The chromosome of Thermotoga maritima strain MSB8 was found to have an 8,870-bp region that is not present in its published sequence. The isolate that was sequenced by The Institute for Genomic Research (TIGR) in 1999 is apparently a laboratory variant of the isolate deposited at the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSM 3109) in 1986. This newly sequenced region from the DSMZ culture was located between TM1848 (cbp, cellobiose phosphorylase) and TM1847 (the 3? end of a truncated ROK regulator). The new region contained seven genes: a beta glucosidase gene (bglA), three trehalose ABC transporter genes (treEFG), three xylose ABC transporter genes (xylE2F2K2), and the 5? end of a gene encoding the ROK regulator TM1847. We present a new differential scanning fluorimetry method using a low pH that was necessary to screen potential ligands of these exceptionally thermostable periplasmic substrate-binding proteins. This method showed that trehalose, sucrose, and glucose stabilized TreE, and their binding was confirmed by measuring changes in intrinsic fluorescence upon ligand binding. Binding constants of 0.024 ?M, 0.300 ?M, and 56.78 ?M at 60°C, respectively, were measured. XylE2 ligands were similarly determined and xylose, glucose, and fucose bound with Kd (dissociation constant) values of 0.042 ?M, 0.059 ?M, and 1.436 ?M, respectively. Since there is no discernible phenotypic difference between the TIGR isolate and the DSMZ isolate despite the variance in their genomes, we propose that they be called genomovars: T. maritima MSB8 genomovar TIGR and T. maritima MSB8 genomovar DSM 3109, respectively. PMID:21764944

  3. Improved Activity of a Thermophilic Cellulase, Cel5A, from Thermotoga maritima on Ionic Liquid Pretreated Switchgrass

    PubMed Central

    Chen, Zhiwei; Pereira, Jose H.; Liu, Hanbin; Tran, Huu M.; Hsu, Nathan S. Y.; Dibble, Dean; Singh, Seema; Adams, Paul D.; Sapra, Rajat; Hadi, Masood Z.; Simmons, Blake A.; Sale, Kenneth L.

    2013-01-01

    Ionic liquid pretreatment of biomass has been shown to greatly reduce the recalcitrance of lignocellulosic biomass, resulting in improved sugar yields after enzymatic saccharification. However, even under these improved saccharification conditions the cost of enzymes still represents a significant proportion of the total cost of producing sugars and ultimately fuels from lignocellulosic biomass. Much of the high cost of enzymes is due to the low catalytic efficiency and stability of lignocellulolytic enzymes, especially cellulases, under conditions that include high temperatures and the presence of residual pretreatment chemicals, such as acids, organic solvents, bases, or ionic liquids. Improving the efficiency of the saccharification process on ionic liquid pretreated biomass will facilitate reduced enzyme loading and cost. Thermophilic cellulases have been shown to be stable and active in ionic liquids but their activity is typically at lower levels. Cel5A_Tma, a thermophilic endoglucanase from Thermotoga maritima, is highly active on cellulosic substrates and is stable in ionic liquid environments. Here, our motivation was to engineer mutants of Cel5A_Tma with higher activity on 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]) pretreated biomass. We developed a robotic platform to screen a random mutagenesis library of Cel5A_Tma. Twelve mutants with 25–42% improvement in specific activity on carboxymethyl cellulose and up to 30% improvement on ionic-liquid pretreated switchgrass were successfully isolated and characterized from a library of twenty thousand variants. Interestingly, most of the mutations in the improved variants are located distally to the active site on the protein surface and are not directly involved with substrate binding. PMID:24244549

  4. Improved activity of a thermophilic cellulase, Cel5A, from Thermotoga maritima on ionic liquid pretreated switchgrass.

    PubMed

    Chen, Zhiwei; Pereira, Jose H; Liu, Hanbin; Tran, Huu M; Hsu, Nathan S Y; Dibble, Dean; Singh, Seema; Adams, Paul D; Sapra, Rajat; Hadi, Masood Z; Simmons, Blake A; Sale, Kenneth L

    2013-01-01

    Ionic liquid pretreatment of biomass has been shown to greatly reduce the recalcitrance of lignocellulosic biomass, resulting in improved sugar yields after enzymatic saccharification. However, even under these improved saccharification conditions the cost of enzymes still represents a significant proportion of the total cost of producing sugars and ultimately fuels from lignocellulosic biomass. Much of the high cost of enzymes is due to the low catalytic efficiency and stability of lignocellulolytic enzymes, especially cellulases, under conditions that include high temperatures and the presence of residual pretreatment chemicals, such as acids, organic solvents, bases, or ionic liquids. Improving the efficiency of the saccharification process on ionic liquid pretreated biomass will facilitate reduced enzyme loading and cost. Thermophilic cellulases have been shown to be stable and active in ionic liquids but their activity is typically at lower levels. Cel5A_Tma, a thermophilic endoglucanase from Thermotoga maritima, is highly active on cellulosic substrates and is stable in ionic liquid environments. Here, our motivation was to engineer mutants of Cel5A_Tma with higher activity on 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]) pretreated biomass. We developed a robotic platform to screen a random mutagenesis library of Cel5A_Tma. Twelve mutants with 25-42% improvement in specific activity on carboxymethyl cellulose and up to 30% improvement on ionic-liquid pretreated switchgrass were successfully isolated and characterized from a library of twenty thousand variants. Interestingly, most of the mutations in the improved variants are located distally to the active site on the protein surface and are not directly involved with substrate binding. PMID:24244549

  5. Crystal structure of octaprenyl pyrophosphate synthase from hyperthermophilic Thermotoga maritima and mechanism of product chain length determination.

    PubMed

    Guo, Rey-Ting; Kuo, Chih-Jung; Chou, Chia-Cheng; Ko, Tzu-Ping; Shr, Hui-Lin; Liang, Po-Huang; Wang, Andrew H-J

    2004-02-01

    Octaprenyl pyrophosphate synthase (OPPs) catalyzes consecutive condensation reactions of farnesyl pyrophosphate (FPP) with isopentenyl pyrophosphate (IPP) to generate C40 octaprenyl pyrophosphate (OPP), which constitutes the side chain of bacterial ubiquinone or menaquinone. In this study, the first structure of long chain C40-OPPs from Thermotoga maritima has been determined to 2.28-A resolution. OPPs is composed entirely of alpha-helices joined by connecting loops and is arranged with nine core helices around a large central cavity. An elongated hydrophobic tunnel between D and F alpha-helices contains two DDXXD motifs on the top for substrate binding and is occupied at the bottom with two large residues Phe-52 and Phe-132. The products of the mutant F132A OPPs are predominantly C50, longer than the C40 synthesized by the wild-type and F52A mutant OPPs, suggesting that Phe-132 is the key residue for determining the product chain length. Ala-76 and Ser-77 located close to the FPP binding site and Val-73 positioned further down the tunnel were individually mutated to larger amino acids. A76Y and S77F mainly produce C20 indicating that the mutated large residues in the vicinity of the FPP site limit the substrate chain elongation. Ala-76 is the fifth amino acid upstream from the first DDXXD motif on helix D of OPPs, and its corresponding amino acid in FPPs is Tyr. In contrast, V73Y mutation led to additional accumulation of C30 intermediate. The new structure of the trans-type OPPs, together with the recently determined cis-type UPPs, significantly extends our understanding on the biosynthesis of long chain polyprenyl molecules. PMID:14617622

  6. Crystal Structure of Butyrate Kinase 2 from Thermotoga maritima, a Member of the ASKHA Superfamily of Phosphotransferases

    SciTech Connect

    Diao, Jiasheng; Hasson, Miriam S.; (Purdue)

    2009-04-01

    The enzymatic transfer of phosphoryl groups is central to the control of many cellular processes. One of the phosphoryl transfer mechanisms, that of acetate kinase, is not completely understood. Besides better understanding of the mechanism of acetate kinase, knowledge of the structure of butyrate kinase 2 (Buk2) will aid in the interpretation of active-site structure and provide information on the structural basis of substrate specificity. The gene buk2 from Thermotoga maritima encodes a member of the ASKHA (acetate and sugar kinases/heat shock cognate/actin) superfamily of phosphotransferases. The encoded protein Buk2 catalyzes the phosphorylation of butyrate and isobutyrate. We have determined the 2.5-{angstrom} crystal structure of Buk2 complexed with ({beta},{gamma}-methylene) adenosine 5'-triphosphate. Buk2 folds like an open-shelled clam, with each of the two domains representing one of the two shells. In the open active-site cleft between the N- and C-terminal domains, the active-site residues consist of two histidines, two arginines, and a cluster of hydrophobic residues. The ATP binding region of Buk2 in the C-terminal domain consists of abundant glycines for nucleotide binding, and the ATP binding motif is similar to those of other members of the ASKHA superfamily. The enzyme exists as an octamer, in which four disulfide bonds form between intermolecular cysteines. Sequence alignment and structure superposition identify the simplicity of the monomeric Buk2 structure, a probable substrate binding site, the key residues in catalyzing phosphoryl transfer, and the substrate specificity differences among Buk2, acetate, and propionate kinases. The possible enzyme mechanisms are discussed.

  7. Kinetics of ATP and TNP-ATP binding to the active site of CheA from Thermotoga maritima.

    PubMed

    Eaton, Anna K; Stewart, Richard C

    2010-07-13

    The mechanism of nucleotide binding to the active site of Thermotoga maritima CheA was investigated using stopped-flow fluorescence experiments that monitored binding of ATP and TNP-ATP to the catalytic domain (P4) of CheA that had been engineered to include a tryptophan residue as a fluorescent reporter group at the active site (P4(F487W)). Rapid decreases in protein intrinsic fluorescence and increases in TNP-ATP fluorescence were observed during binding reactions, and time courses were analyzed to define the kinetic mechanisms for ATP and TNP-ATP binding. This analysis indicated that binding of ATP(Mg(2+)) to P4(F487W) involves a single reversible step with a k(on) of 0.92 +/- 0.09 microM(-1) s(-1), a k(off) of 1.9 +/- 0.4 s(-1), and a K(d) of 1.5-2.1 microM (all values determined at 4 degrees C). Binding of TNP-ATP(Mg(2+)) to P4(F487W) involves a more complicated mechanism, requiring at least three sequential steps. Computer simulations and nonlinear regression analysis were used to estimate the rate constants of the forward and reverse reactions for each of the three steps in the reaction scheme [Formula: see text] Similar analysis indicated that an alternative reaction scheme, involving a rate-limiting conformational change in P4 prior to TNP-ATP binding, did an equally good job of accounting for all of the kinetics results:[Formula: see text] In both models, steps 2 and 3 have slow reversal rates that contribute to the high affinity of the active site for TNP-ATP (K(d) = 0.015 microM). These results highlight the dramatic effect of the TNP moieties on CheA-nucleotide interactions, and they provide the first detailed information about the kinetic mechanism underlying interaction of a protein histidine kinase with this tight-binding inhibitor. PMID:20565117

  8. Crystal structures of CheY from Thermotoga maritima do not support conventional explanations for the structural basis of enhanced thermostability.

    PubMed Central

    Usher, K. C.; de la Cruz, A. F.; Dahlquist, F. W.; Swanson, R. V.; Simon, M. I.; Remington, S. J.

    1998-01-01

    The crystal structure of CheY protein from Thermotoga maritima has been determined in four crystal forms with and without Mg++ bound, at up to 1.9 A resolution. Structural comparisons with CheY from Escherichia coli shows substantial similarity in their folds, with some concerted changes propagating away from the active site that suggest how phosphorylated CheY, a signal transduction protein in bacterial chemotaxis, is recognized by its targets. A highly conserved segment of the protein (the "y-turn loop," residues 55-61), previously suggested to be a rigid recognition determinant, is for the first time seen in two alternative conformations in the different crystal structures. Although CheY from Thermotoga has much higher thermal stability than its mesophilic counterparts, comparison of structural features previously proposed to enhance thermostability such as hydrogen bonds, ion pairs, compactness, and hydrophobic surface burial would not suggest it to be so. PMID:9521117

  9. Phylogenetic depth of S10 and spc operons: cloning and sequencing of a ribosomal protein gene cluster from the extremely thermophilic bacterium Thermotoga maritima.

    PubMed Central

    Sanangelantoni, A M; Bocchetta, M; Cammarano, P; Tiboni, O

    1994-01-01

    A segment of Thermotoga maritima DNA spanning 6,613 bp downstream from the gene tuf for elongation factor Tu was sequenced by use of a chromosome walking strategy. The sequenced region comprised a string of 14 tightly linked open reading frames (ORFs) starting 50 bp downstream from tuf. The first 11 ORFs were identified as homologs of ribosomal protein genes rps10, rpl3, rpl4, rpl23, rpl2, rps19, rpl22, rps3, rpl16, rpl29, and rps17 (which in Escherichia coli constitute the S10 operon, in that order); the last three ORFs were homologous to genes rpl14, rpl24, and rpl5 (which in E. coli constitute the three promoter-proximal genes of the spectinomycin operon). The 14-gene string was preceded by putative -35 and -10 promoter sequences situated 5' to gene rps10, within the 50-bp spacing between genes tuf and rps10; the same region exhibited a potential transcription termination signal for the upstream gene cluster (having tuf as the last gene) but displayed also the potential for formation of a hairpin loop hindering the terminator; this suggests that transcription of rps10 and downstream genes may start farther upstream. The similar organization of the sequenced rp genes in the deepest-branching bacterial phyla (T. maritima) and among Archaea has been interpreted as indicating that the S10-spc gene arrangement existed in the (last) common ancestor. The phylogenetic depth of the Thermotoga lineage was probed by use of r proteins as marker molecules: in all except one case (S3), Proteobacteria or the gram-positive bacteria, and not the genus Thermotoga, were the deepest-branching lineage; in only two cases, however, was the inferred branching order substantiated by bootstrap analysis. PMID:8002596

  10. Fungal decontamination and enhancement of shelf life of edible split beans of wild legume Canavalia maritima by the electron beam irradiation

    NASA Astrophysics Data System (ADS)

    Supriya, P.; Sridhar, K. R.; Ganesh, S.

    2014-03-01

    Ripened split beans of the coastal sand dune wild legume Canavalia maritima serve as one of the traditional nutritional sources of the coastal dwellers in Southwest coast of India. Nine fungi were isolated from the unirradiated dry beans by plating on the potato dextrose agar medium. Toxigenic fungus Aspergillus niger showed the highest incidence (33-50%) followed by Aspergillus flavus (14-20%) and Penicillium chrysogenum (7-13%). Unirradiated dry beans and irradiated dry beans with electron beam doses 2.5, 5, 10 and 15 kGy were monitored for occurrence of fungal species and their incidence during 0, 3 and 6 months storage period under laboratory conditions. Irradiation resulted in dose-dependent decrease in fungal species (5-7, 4-6, 3-6 and 0 on irradiation at 0, 2.5, 5 and 10 or 15 kGy, respectively) as well as incidence (80-99, 19-46, 13-21 and 0%, respectively). Although aflatoxins (B1 and B2) were found below detectable level (<2 ng/g) in 0, 3 and 6 months stored unirradiated and irradiated beans (2.5 and 5 kGy), they were not present in beans irradiated with 10 and 15 kGy. In spite of occurrence of toxigenic fungus Aspergillus ochraceus in unirradiated and irradiated beans (2.5 and 5 kGy) stored for 3 and 6 months, the beans were devoid of ochratoxin-A. Electron beam irradiation dose 10 kGy could be recommended for fungal decontamination and improvement of shelf life of C. maritima ripened dry split beans.

  11. Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae)

    PubMed Central

    Ferreira de Carvalho, J; Poulain, J; Da Silva, C; Wincker, P; Michon-Coudouel, S; Dheilly, A; Naquin, D; Boutte, J; Salmon, A; Ainouche, M

    2013-01-01

    Spartina species have a critical ecological role in salt marshes and represent an excellent system to investigate recurrent polyploid speciation. Using the 454 GS-FLX pyrosequencer, we assembled and annotated the first reference transcriptome (from roots and leaves) for two related hexaploid Spartina species that hybridize in Western Europe, the East American invasive Spartina alterniflora and the Euro-African S. maritima. The de novo read assembly generated 38?478 consensus sequences and 99% found an annotation using Poaceae databases, representing a total of 16?753 non-redundant genes. Spartina expressed sequence tags were mapped onto the Sorghum bicolor genome, where they were distributed among the subtelomeric arms of the 10 S. bicolor chromosomes, with high gene density correlation. Normalization of the complementary DNA library improved the number of annotated genes. Ecologically relevant genes were identified among GO biological function categories in salt and heavy metal stress response, C4 photosynthesis and in lignin and cellulose metabolism. Expression of some of these genes had been found to be altered by hybridization and genome duplication in a previous microarray-based study in Spartina. As these species are hexaploid, up to three duplicated homoeologs may be expected per locus. When analyzing sequence polymorphism at four different loci in S. maritima and S. alterniflora, we found up to four haplotypes per locus, suggesting the presence of two expressed homoeologous sequences with one or two allelic variants each. This reference transcriptome will allow analysis of specific Spartina genes of ecological or evolutionary interest, estimation of homoeologous gene expression variation using RNA-seq and further gene expression evolution analyses in natural populations. PMID:23149455

  12. Structural Analysis of Semi-specific Oligosaccharide Recognition by a Cellulose-binding Protein of Thermotoga maritima Reveals Adaptations for Functional Diversification of the Oligopeptide Periplasmic Binding Protein Fold*

    PubMed Central

    Cuneo, Matthew J.; Beese, Lorena S.; Hellinga, Homme W.

    2009-01-01

    Periplasmic binding proteins (PBPs) constitute a protein superfamily that binds a wide variety of ligands. In prokaryotes, PBPs function as receptors for ATP-binding cassette or tripartite ATP-independent transporters and chemotaxis systems. In many instances, PBPs bind their cognate ligands with exquisite specificity, distinguishing, for example, between sugar epimers or structurally similar anions. By contrast, oligopeptide-binding proteins bind their ligands through interactions with the peptide backbone but do not distinguish between different side chains. The extremophile Thermotoga maritima possesses a remarkable array of carbohydrate-processing metabolic systems, including the hydrolysis of cellulosic polymers. Here, we present the crystal structure of a T. maritima cellobiose-binding protein (tm0031) that is homologous to oligopeptide-binding proteins. T. maritima cellobiose-binding protein binds a variety of lengths of ?(1?4)-linked glucose oligomers, ranging from two rings (cellobiose) to five (cellopentaose). The structure reveals that binding is semi-specific. The disaccharide at the nonreducing end binds specifically; the other rings are located in a large solvent-filled groove, where the reducing end makes several contacts with the protein, thereby imposing an upper limit of the oligosaccharides that are recognized. Semi-specific recognition, in which a molecular class rather than individual species is selected, provides an efficient solution for the uptake of complex mixtures. PMID:19801540

  13. Structural Analysis of Semi-specific Oligosaccharide Recognition by a Cellulose-binding Protein of Thermotoga maritima Reveals Adaptations for Functional Diversification of the Oligopeptide Periplasmic Binding Protein Fold

    SciTech Connect

    Cuneo, Matthew J.; Beese, Lorena S.; Hellinga, Homme W.; (Duke)

    2010-05-25

    Periplasmic binding proteins (PBPs) constitute a protein superfamily that binds a wide variety of ligands. In prokaryotes, PBPs function as receptors for ATP-binding cassette or tripartite ATP-independent transporters and chemotaxis systems. In many instances, PBPs bind their cognate ligands with exquisite specificity, distinguishing, for example, between sugar epimers or structurally similar anions. By contrast, oligopeptide-binding proteins bind their ligands through interactions with the peptide backbone but do not distinguish between different side chains. The extremophile Thermotoga maritima possesses a remarkable array of carbohydrate-processing metabolic systems, including the hydrolysis of cellulosic polymers. Here, we present the crystal structure of a T. maritima cellobiose-binding protein (tm0031) that is homologous to oligopeptide-binding proteins. T. maritima cellobiose-binding protein binds a variety of lengths of {beta}(1 {yields} 4)-linked glucose oligomers, ranging from two rings (cellobiose) to five (cellopentaose). The structure reveals that binding is semi-specific. The disaccharide at the nonreducing end binds specifically; the other rings are located in a large solvent-filled groove, where the reducing end makes several contacts with the protein, thereby imposing an upper limit of the oligosaccharides that are recognized. Semi-specific recognition, in which a molecular class rather than individual species is selected, provides an efficient solution for the uptake of complex mixtures.

  14. Subcellular concentrations of sugar alcohols and sugars in relation to phloem translocation in Plantago major, Plantago maritima, Prunus persica, and Apium graveolens

    PubMed Central

    Nadwodnik, Jan

    2008-01-01

    Sugar and sugar alcohol concentrations were analyzed in subcellular compartments of mesophyll cells, in the apoplast, and in the phloem sap of leaves of Plantago major (common plantain), Plantago maritima (sea plantain), Prunus persica (peach) and Apium graveolens (celery). In addition to sucrose, common plantain, sea plantain, and peach also translocated substantial amounts of sorbitol, whereas celery translocated mannitol as well. Sucrose was always present in vacuole and cytosol of mesophyll cells, whereas sorbitol and mannitol were found in vacuole, stroma, and cytosol in all cases except for sea plantain. The concentration of sorbitol, mannitol and sucrose in phloem sap was 2- to 40-fold higher than that in the cytosol of mesophyll cells. Apoplastic carbohydrate concentrations in all species tested were in the low millimolar range versus high millimolar concentrations in symplastic compartments. Therefore, the concentration ratios between the apoplast and the phloem were very strong, ranging between 20- to 100-fold for sorbitol and mannitol, and between 200- and 2000-fold for sucrose. The woody species, peach, showed the smallest concentration ratios between the cytosol of mesophyll cells and the phloem as well as between the apoplast and the phloem, suggesting a mixture of apoplastic and symplastic phloem loading, in contrast to the herbal plant species (common plantain, sea plantain, celery) which likely exhibit an active loading mode for sorbitol and mannitol as well as sucrose from the apoplast into the phloem. PMID:18188589

  15. Manipulation of the tuf gene provides clues to the localization of sequence element(s) involved in the thermal stability of Thermotoga maritima elongation factor Tu.

    PubMed

    Sanangelantoni, A M; Cammarano, P; Tiboni, O

    1996-09-01

    Truncated versions of the tuf gene for elongation factor Tu (EF-Tu; 400 aa) from the hyperthermophilic bacterium Thermotoga maritima have been produced by progressive 3'-->5' trimming. The truncated genes have been expressed in Escherichia coli and the thermal stability of the gene products has been assayed by monitoring their GDP-binding capacity after preheating the cell-free extracts at various temperatures (65-95 degrees C). One of the truncated proteins, corresponding to the nucleotide-binding domain (G domain; aa 1-200) appears to be only slightly less stable than the full-length EF-Tu. Replacement of the first 90 N-terminal residues of both the full-length Thermotoga EF-Tu and the isolated G domain with the corresponding sequence of the mesophilic bacterium E. coli, drastically destabilizes both the complete and the truncated protein, indicating that sequence element(s) that are crucial for the attainment of a thermally stable conformation of the Thermotoga EF-Tu lie well within the initial portion of the G domain between residues 1 and 90. The relevant residues defy identification, however, as no amino acid preferences, or exclusive sequence element(s), appear to distinguish the N-terminal region of the thermophilic proteins from those of mesophilic counterparts. It is suggested that the thermal stability of Thermotoga EF-Tu is critically dependent upon unique tertiary structural interactions involving certain N-terminal residues of the molecule. PMID:8828220

  16. Differences between the rhizosphere microbiome of Beta vulgaris ssp. maritima—ancestor of all beet crops—and modern sugar beets

    PubMed Central

    Zachow, Christin; Müller, Henry; Tilcher, Ralf; Berg, Gabriele

    2014-01-01

    The structure and function of the plant microbiome is driven by plant species and prevailing environmental conditions. Effectuated by breeding efforts, modern crops diverge genetically and phenotypically from their wild relatives but little is known about consequences for the associated microbiota. Therefore, we studied bacterial rhizosphere communities associated with the wild beet B. vulgaris ssp. maritima grown in their natural habitat soil from coastal drift lines (CS) and modern sugar beets (Beta vulgaris ssp. vulgaris) cultivated in CS and potting soil (PS) under greenhouse conditions. Analysis of 16S rRNA gene fingerprints and pyrosequencing-based amplicon libraries revealed plant genotype- and soil-specific microbiomes. Wild beet plants harbor distinct operational taxonomic units (OTUs) and a more diverse bacterial community than the domesticated sugar beet plants. Although the rhizospheres of both plant genotypes were dominated by Proteobacteria and Planctomycetes, 37.5% of dominant OTUs were additionally detected in the wild beet rhizosphere. Analysis of the cultivable fraction confirmed these plant genotype-specific differences at functional level. The proportion of isolates displayed in vitro activity against phytopathogens was lower for wild beet (?45.8%) than for sugar beet (?57.5%). Conversely, active isolates from the wild beet exhibited stronger ability to cope with abiotic stresses. From all samples, active isolates of Stenotrophomonas rhizophila were frequently identified. In addition, soil type-specific impacts on the composition of bacterial communities were found: Acidobacteria, Chloroflexi, and Planctomycetes were only detected in plants cultivated in CS; whereas Bacteroidetes and Proteobacteria dominated in PS. Overall, in comparison to modern sugar beets, wild beets were associated with taxonomically and functionally distinct microbiomes. PMID:25206350

  17. Isolation and cloning of Omp alpha, a coiled-coil protein spanning the periplasmic space of the ancestral eubacterium Thermotoga maritima.

    PubMed Central

    Engel, A M; Cejka, Z; Lupas, A; Lottspeich, F; Baumeister, W

    1992-01-01

    We have discovered a new oligomeric protein component associated with the outer membrane of the ancestral eubacterium Thermotoga maritima. In electron micrographs, the protein, Omp alpha, appears as a rod-shaped spacer that spans the periplasm, connecting the outer membrane to the inner cell body. Purification, biochemical characterization and sequencing of Omp alpha suggest that it is a homodimer composed of two subunits of 380 amino acids with a calculated M(r) of 43,000 and a pI of 4.54. The sequence of the omp alpha gene indicates a tripartite organization of the protein with a globular NH2-terminal domain of 64 residues followed by a putative coiled-coil segment of 300 residues and a COOH-terminal, membrane-spanning segment. The predicted length of the coiled-coil segment (45 nm) correlates closely with the spacing between the inner and outer membranes. Despite sequence similarity to a large number of coiled-coil proteins and high scores in a coiled-coil prediction algorithm, the sequence of the central rod-shaped domain of Omp alpha does not have the typical 3.5 periodicity of coiled-coil proteins but rather has a periodicity of 3.58 residues. Such a periodicity was also found in the central domain of staphylococcal M protein and beta-giardin and might be indicative of a subclass of fibrous proteins with packing interactions that are distinct from the ones seen in other two-stranded coiled-coils. Images PMID:1330536

  18. Crystal structure of Thermotoga maritima TM0439: implications for the mechanism of bacterial GntR transcription regulators with Zn2+-binding FCD domains

    SciTech Connect

    Zheng, Meiying; Cooper, David; Grossoehmerb, Nickolas; Yu, Minmin; Hung, Li-Wei; Cieslik, Murcin; Derewendaro, Urszula; Lesley, Scott; Wilson, Ian; Giedrocb, David; Derewenda, Zygmunt

    2009-06-06

    The GntR superfamily of dimeric transcription factors, with more than 6200 members encoded in bacterial genomes, are characterized by N-terminal winged helix (WH) DNA-binding domains and diverse C-terminal, regulatory domains, which provide a basis for the classification of the constituent families. The largest of these families, FadR, contains nearly 3000 proteins with all a-helical regulatory domains classified into two related Pfam families: FadR{_}C and FCD. Only two crystal structures of the FadR family members, i.e. the E. coli FadR protein and the LldR from C. glutamicum, have been described to date in literature. Here we describe the crystal structure of TM0439, a GntR regulator with an FCD domain, found in the Thermotoga maritima genome. The FCD domain is similar to that of the LldR regulator, and contains a buried metal binding site. Using atomic absorption spectroscopy and Trp fluorescence, we show that the recombinant protein contains bound Ni{sup 2+} ions, but it is able to bind Zn{sup 2+} with K{sub D} < 70 nM . We conclude that Zn{sup 2+} is the likely physiological metal, where it may perform either or both structural and regulatory roles. Finally, we compare the TM0439 structure to two other FadR family structures recently deposited by Structural Genomics consortia. The results call for a revision in the classification of the FadR family of transcription factors.

  19. Contrasting effects of ecosystem engineering by the cordgrass Spartina maritima and the sandprawn Callianassa kraussi in a marine-dominated lagoon

    NASA Astrophysics Data System (ADS)

    Pillay, D.; Branch, G. M.; Dawson, J.; Henry, D.

    2011-01-01

    Ecosystem engineering by plants and animals significantly influences community structure and the physico-chemical characteristics of marine habitats. In this paper we document the contrasting effects of ecosystem engineering by the cordgrass Spartina maritima and the burrowing sandprawn Callianassa kraussi on physico-chemical characteristics, microflora, macrofaunal community structure and morphological attributes in the high shore intertidal sandflats of Langebaan Lagoon, a marine-dominated system on the west coast of South Africa. Comparisons were made at six sites in the lagoon within Spartina and Callianassa beds, and in a "bare zone" of sandflat between these two habitats that lacks both sandprawns and cordgrass. Sediments in Spartina habitats were consolidated by the root-shoot systems of the cordgrass, leading to low sediment penetrability, while sediments in beds of C. kraussi were more penetrable, primarily due to the destabilising effects of sandprawn bioturbation. Sediments in the "bare zone" had intermediate to low values of penetrability. Sediment organic content was lowest in bare zones and greatest in Spartina beds, while sediment chl- a levels were greatest on bare sand, but were progressively reduced in the Spartina and Callianassa beds. These differences among habitats induced by ecosystem engineering in turn affected the macrofauna. Community structure was different between all three habitats sampled, with species richness being surprisingly greater in Callianassa beds than either the bare zone or Spartina beds. In general, the binding of surface sediments by the root systems of Spartina favoured rigid-bodied, surface-dwelling and tube-building species, while the destabilising effect of bioturbation by C. kraussi favoured burrowing species. The contrasting effects of these ecosystem engineers suggest that they play important roles in increasing habitat heterogeneity. Importantly, the role of bioturbation by C. kraussi in enhancing macrofaunal richness was unexpected. By loosening sediments, reducing anoxia and enhancing organic content, C. kraussi may engineer these high shore habitats to ameliorate environmental stresses or increase food availability.

  20. Structural and biochemical characterization of the ?-N-acetylglucosaminidase from Thermotoga maritima: Toward rationalization of mechanistic knowledge in the GH73 family.

    PubMed

    Lipski, Alexandra; Hervé, Mireille; Lombard, Vincent; Nurizzo, Didier; Mengin-Lecreulx, Dominique; Bourne, Yves; Vincent, Florence

    2015-03-01

    Members of the GH73 glycosidase family cleave the ?-1,4-glycosidic bond between the N-acetylglucosaminyl (GlcNAc) and N-acetylmuramyl (MurNAc) moieties in bacterial peptidoglycan. A catalytic mechanism has been proposed for members FlgJ, Auto, AcmA and Atl(WM) and the structural analysis of FlgJ and Auto revealed a conserved ?/? fold reminiscent of the distantly related GH23 lysozyme. Comparison of the active site residues reveals variability in the nature of the catalytic general base suggesting two distinct catalytic mechanisms: an inverting mechanism involving two distant glutamate residues and a substrate-assisted mechanism involving anchimeric assistance by the C2-acetamido group of the GlcNAc moiety. Herein, we present the biochemical characterization and crystal structure of TM0633 from the hyperthermophilic bacterium Thermotoga maritima. TM0633 adopts the ?/? fold of the family and displays ?-N-acetylglucosaminidase activity on intact peptidoglycan sacculi. Site-directed mutagenesis identifies Glu34, Glu65 and Tyr118 as important residues for catalysis. A thorough bioinformatic analysis of the GH73 sequences identified five phylogenetic clusters. TM0633, FlgJ and Auto belong to a group of three clusters that conserve two carboxylate residues involved in a classical inverting acid-base mechanism. Members of the other two clusters lack a conserved catalytic general base supporting a substrate-assisted mechanism. Molecular modeling of representative members from each cluster suggests that variability in length of the ?-hairpin region above the active site confers ligand-binding specificity and modulates the catalytic mechanisms within the GH73 family. PMID:25344445

  1. Role of N-terminal extension of Bacillus stearothermophilus RNase H2 and C-terminal extension of Thermotoga maritima RNase H2.

    PubMed

    Permanasari, Etin-Diah; Angkawidjaja, Clement; Koga, Yuichi; Kanaya, Shigenori

    2013-10-01

    Bacillus stearothermophilus RNase H2 (BstRNH2) and Thermotoga maritima RNase H2 (TmaRNH2) have N-terminal and C-terminal extensions, respectively, as compared with Aquifex aeolicus RNase H2 (AaeRNH2). To analyze the role of these extensions, BstRNH2 and TmaRNH2 without these extensions were constructed, and their biochemical properties were compared with those of their intact partners and AaeRNH2. The far-UV CD spectra of all proteins were similar, suggesting that the protein structure is not significantly altered by removal of these extensions. However, both the junction ribonuclease and RNase H activities of BstRNH2 and TmaRNH2, as well as their substrate-binding affinities, were considerably decreased by removal of these extensions. The stability of BstRNH2 and TmaRNH2 was also decreased by removal of these extensions. The activity, substrate binding affinity and stability of TmaRNH2 without the C-terminal 46 residues were partly restored by the attachment of the N-terminal extension of BstRNH2. These results suggest that the N-terminal extension of BstRNH2 functions as a substrate-binding domain and stabilizes the RNase H domain. Because the C-terminal extension of TmaRNH2 assumes a helix hairpin structure and does not make direct contact with the substrate, this extension is probably required to make the conformation of the substrate-binding site functional. AaeRNH2 showed comparable junction ribonuclease activity to those of BstRNH2 and TmaRNH2, and was more stable than these proteins, indicating that bacterial RNases H2 do not always require an N-terminal or C-terminal extension to increase activity, substrate-binding affinity, and/or stability. PMID:23937561

  2. Post-translational Modification of Ribosomal Proteins: Structural and Functional Characterization of RimO from Thermotoga maritima, a Radical S-adenosylmethionine methylthiotransferase

    SciTech Connect

    Arragain, S.; Latour, J; Forouhar, F; Neely, H; Montelione, G; Hunt, J; Mulliez, E; Fontecave, M; Atta, M; et al.

    2010-01-01

    Post-translational modifications of ribosomal proteins are important for the accuracy of the decoding machinery. A recent in vivo study has shown that the rimO gene is involved in generation of the 3-methylthio derivative of residue Asp-89 in ribosomal protein S12 (Anton, B. P., Saleh, L., Benner, J. S., Raleigh, E. A., Kasif, S., and Roberts, R. J. (2008) Proc. Natl. Acad. Sci. U. S. A. 105, 1826-1831). This reaction is formally identical to that catalyzed by MiaB on the C2 of adenosine 37 near the anticodon of several tRNAs. We present spectroscopic evidence that Thermotoga maritima RimO, like MiaB, contains two [4Fe-4S] centers, one presumably bound to three invariant cysteines in the central radical S-adenosylmethionine (AdoMet) domain and the other to three invariant cysteines in the N-terminal UPF0004 domain. We demonstrate that holo-RimO can specifically methylthiolate the aspartate residue of a 20-mer peptide derived from S12, yielding a mixture of mono- and bismethylthio derivatives. Finally, we present the 2.0 {angstrom} crystal structure of the central radical AdoMet and the C-terminal TRAM (tRNA methyltransferase 2 and MiaB) domains in apo-RimO. Although the core of the open triose-phosphate isomerase (TIM) barrel of the radical AdoMet domain was conserved, RimO showed differences in domain organization compared with other radical AdoMet enzymes. The unusually acidic TRAM domain, likely to bind the basic S12 protein, is located at the distal edge of the radical AdoMet domain. The basic S12 protein substrate is likely to bind RimO through interactions with both the TRAM domain and the concave surface of the incomplete TIM barrel. These biophysical results provide a foundation for understanding the mechanism of methylthioation by radical AdoMet enzymes in the MiaB/RimO family.

  3. Post-translational Modification of Ribosomal Proteins - Structural and Functional Characterization of RimO from Thermotoga Maritima, A Radiacal S-Adenosylmethionine Methylthiotransferase

    SciTech Connect

    Arragain, S.; Garcia-Serres, R; Blondin, G; Douki, T; Clemancey, M; Latour, J; Forouhar, F; Neely, H; Montelione, G; et. al.

    2010-01-01

    Post-translational modifications of ribosomal proteins are important for the accuracy of the decoding machinery. A recent in vivo study has shown that the rimO gene is involved in generation of the 3-methylthio derivative of residue Asp-89 in ribosomal protein S12 (Anton, B. P., Saleh, L., Benner, J. S., Raleigh, E. A., Kasif, S., and Roberts, R. J. (2008) Proc. Natl. Acad. Sci. U. S. A. 105, 1826-1831). This reaction is formally identical to that catalyzed by MiaB on the C2 of adenosine 37 near the anticodon of several tRNAs. We present spectroscopic evidence that Thermotoga maritima RimO, like MiaB, contains two [4Fe-4S] centers, one presumably bound to three invariant cysteines in the central radical S-adenosylmethionine (AdoMet) domain and the other to three invariant cysteines in the N-terminal UPF0004 domain. We demonstrate that holo-RimO can specifically methylthiolate the aspartate residue of a 20-mer peptide derived from S12, yielding a mixture of mono- and bismethylthio derivatives. Finally, we present the 2.0 {angstrom} crystal structure of the central radical AdoMet and the C-terminal TRAM (tRNA methyltransferase 2 and MiaB) domains in apo-RimO. Although the core of the open triose-phosphate isomerase (TIM) barrel of the radical AdoMet domain was conserved, RimO showed differences in domain organization compared with other radical AdoMet enzymes. The unusually acidic TRAM domain, likely to bind the basic S12 protein, is located at the distal edge of the radical AdoMet domain. The basic S12 protein substrate is likely to bind RimO through interactions with both the TRAM domain and the concave surface of the incomplete TIM barrel. These biophysical results provide a foundation for understanding the mechanism of methylthioation by radical AdoMet enzymes in the MiaB/RimO family.

  4. A Loose Domain Swapping Organization Confers a Remarkable Stability to the Dimeric Structure of the Arginine Binding Protein from Thermotoga maritima

    PubMed Central

    Ruggiero, Alessia; Dattelbaum, Jonathan D.; Staiano, Maria; Berisio, Rita; D'Auria, Sabato; Vitagliano, Luigi

    2014-01-01

    The arginine binding protein from Thermatoga maritima (TmArgBP), a substrate binding protein (SBP) involved in the ABC system of solute transport, presents a number of remarkable properties. These include an extraordinary stability to temperature and chemical denaturants and the tendency to form multimeric structures, an uncommon feature among SBPs involved in solute transport. Here we report a biophysical and structural characterization of the TmArgBP dimer. Our data indicate that the dimer of the protein is endowed with a remarkable stability since its full dissociation requires high temperature as well as SDS and urea at high concentrations. In order to elucidate the atomic level structural properties of this intriguing protein, we determined the crystallographic structures of the apo and the arginine-bound forms of TmArgBP using MAD and SAD methods, respectively. The comparison of the liganded and unliganded models demonstrates that TmArgBP tertiary structure undergoes a very large structural re-organization upon arginine binding. This transition follows the Venus Fly-trap mechanism, although the entity of the re-organization observed in TmArgBP is larger than that observed in homologous proteins. Intriguingly, TmArgBP dimerizes through the swapping of the C-terminal helix. This dimer is stabilized exclusively by the interactions established by the swapping helix. Therefore, the TmArgBP dimer combines a high level of stability and conformational freedom. The structure of the TmArgBP dimer represents an uncommon example of large tertiary structure variations amplified at quaternary structure level by domain swapping. Although the biological relevance of the dimer needs further assessments, molecular modelling suggests that the two TmArgBP subunits may simultaneously interact with two distinct ABC transporters. Moreover, the present protein structures provide some clues about the determinants of the extraordinary stability of the biomolecule. The availability of an accurate 3D model represents a powerful tool for the design of new TmArgBP suited for biotechnological applications. PMID:24832102

  5. Female choice and manipulations of forceps size and symmetry in the earwig Forficula auricularia L

    Microsoft Academic Search

    JOSEPH L. TOMKINS; LEIGH W. SIMMONS

    1998-01-01

    The size and asymmetry of male secondary sexual traits are believed to convey reliable information to females concerning the quality of potential mates. Experimental manipulations of male sexual traits provide a powerful approach to the study of preference evolution. Nevertheless, the majority of studies rely on correlational evidence for selection acting on secondary sexual traits. Here we report that in

  6. 75 FR 35990 - Endangered and Threatened Wildlife and Plants; Listing the Flying Earwig Hawaiian Damselfly and...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-24

    ...Devick 1991, p. 190; Englund 1999, p. 226; Staples and Cowie 2001, p. 32; Brasher...Brasher 2003, p. 1054; Englund 1999, p. 226; Englund and Polhemus 2001; Englund 2004...landslides, or prolonged drought (Jones et al. 1984, p. 209). For example, Polhemus...

  7. Germ cells of the centipede Strigamia maritima are specified early in embryonic development

    E-print Network

    Green, Jack E.; Akam, Michael

    2014-06-12

    annotation of the Strigamia genome (Chipman et al., submitted). The names and Ensembl IDs of this set are provided in Supplementary Table 1. We designed gene-specific primers for 8 of these putative germ line markers and amplified PCR products from embryonic... cDNA. The amplified fragments were cloned into pGEM-T Easy vector (Promega). The names, Ensembl IDs and primer sequences used for this set of 8 genes are provided in Supplementary Table 1. We screened these 8 possible germ line markers by examining...

  8. Uniformity of the nuclear and chloroplast genomes of Spartina maritima (Poaceae), a salt-marsh

    E-print Network

    Alvarez, Nadir

    DNA. The results reveal an extremely low level of genetic variation in this species: only one nuclear spread both naturally and as a result of artificial plantations to become a particularly invasive species on different continents (Thompson, 1991; Gue´ne´gou and Levasseur, 1993; Gray and Raybould, 1997). Recent

  9. Formylglycinamide Ribonucleotide Amidotransferase from Thermotoga maritima: Structural Insights into Complex Formation

    E-print Network

    Morar, Mariya

    In the fourth step of the purine biosynthetic pathway, formyl glycinamide ribonucleotide (FGAR) amidotransferase, also known as PurL, catalyzes the conversion of FGAR, ATP, and glutamine to formyl glycinamidine ribonucleotide ...

  10. Genetic structure and gene flow in Beta vulgaris subspecies maritima along the Atlantic coast of France

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Locating and quantifying genetic variation within crop wild relatives is an ongoing activity of gene banks tasked with ex situ conservation. Without detailed information about the population genetics of a species geography often serves as a reasonable proxy for differentiation. With this in mind, ...

  11. Waterbird impacts on widgeongrass Ruppia maritima in a Mediterranean wetland: comparing bird groups and seasonal effects

    E-print Network

    Green, Andy J.

    allowed us to exclude flamingos or all waterbirds from 3)/3 m plots within the ponds and compare them cycle with varying bird densities. Flamingos and wildfowl (ducks and coot) had significant negative higher in all-bird exclosures than in controls or flamingo exclosures. Presence and biomass

  12. Biology and ecology of the earwig, Doru taeniata (Dohrn) and evaluation as a predator of Spodoptera frugiperda attacking corn and sorghum in Honduras

    E-print Network

    Jones, Robert Wallace

    1985-01-01

    and Greene 1974, Martin et al. 1980). Yield loss estimates for S. ~f' d d g \\ '* d gh t 11 tbllhd. C artificially infested with up to 20 second instar larvae per plant at different growth stages failed to produce yield loss (Morrill and Greene 1974). Gelt... and Peairs, working in Mexico, reported average yield losses flygd t S. . ~f'd GC t t 1. 1911 'td' Ad 1990) S g'fi t yi ld 1 lt d h S. ~f' d gg artificially placed on 20 and 100X of corn plants at the mid-whorl stage in Indiana (Cruz and Turpin 1983...

  13. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima

    E-print Network

    Chipman, Ariel D.; Ferrier, David E. K.; Brena, Carlo; Qu, Jiaxin; Hughes, Daniel S. T.; Schröder, Reinhard; Torres-­Oliva, Montserrat; Znassi, Nadia; Jiang, Huaiyang; Almeida, Francisca C.; Alonso, Claudio R.; Apostolou, Zivkos; Aqrawi, Peshtewani; Arthur, Wallace; Barna, Jennifer C. J.; Blankenburg, Kerstin P.; Brites, Daniela; Capella-Gutiérrez, Salvador; Coyle, Marcus; Dearden, Peter K.; Du Pasquier, Louis; Duncan, Elizabeth J.; Ebert, Dieter; Eibner, Cornelius; Erikson, Galina; Evans, Peter D.; Extavour, Cassandra G.; Francisco, Liezl; Gabaldón, Toni; Gillis, William J.; Goodwin-­Horn, Elizabeth A.; Green, Jack E.; Griffiths-­Jones, Sam; Grimmelikhuijzen, Cornelis J. P.; Gubbala, Sai; Guigó, Roderic; Han, Yi; Hauser, Frank; Havlak, Paul; Hayden, Luke; Helbing, Sophie; Holder, Michael; Hui, Jerome H. L.; Hunn, Julia P.; Hunnekuhl, Vera S.; Jackson, LaRonda; Javaid, Mehwish; Jhangiani, Shalini N.; Jiggins, Francis M.; Jones, Tamsin E.; Kaiser, Tobias S.; Kalra, Divya; Kenny, Nathan J.; Korchina, Viktoriya; Kovar, Christie L.; Kraus, F. Bernhard; Lapraz, François; Lee, Sandra L.; Lv, Jie; Mandapat, Christigale; Manning, Gerard; Mariotti, Marco; Mata, Sandra; Mathew, Tittu; Neumann, Tobias; Newsham, Irene; Ngo, Dinh N.; Ninova, Maria; Okwuonu, Geoffrey; Ongeri, Fiona; Palmer, William J.; Patil, Shobha; Patraquim, Pedro; Pham, Christopher; Pu, Ling?Ling; Putman, Nicholas H.; Rabouille, Catherine; Ramos, Olivia Mendivil; Rhodes, Adelaide C.; Robertson, Helen E.; Robertson, Hugh M.; Ronshaugen, Matthew; Rozas, Julio; Saada, Nehad; Sánchez-­Gracia, Alejandro; Scherer, Steven E.; Schurko, Andrew M.; Siggens, Kenneth W.; Simmons, DeNard; Stief, Anna; Stolle, Eckart; Telford, Maximilian J.; Tessmar-­ Raible, Kristin; Thornton, Rebecca; van der Zee, Maurijn; von Haeseler, Arndt; Williams, James M.; Willis, Judith H.; Wu, Yuanqing; Zou, Xiaoyan; Lawson, Daniel; Muzny, Donna M.; Worley, Kim C.; Gibbs, Richard A.; Akam, Michael; Richards, Stephen

    2014-01-01

    .    Putative  cuticular  proteins    A  defining  characteristic  of  arthropods  is  an  exoskeleton  with  chitin  and  cuticular  proteins  as  the  primary  components.  Although  several  families  of...  ~64  amino  acid  residues  and  shown  to  be  necessary  and  sufficient  for  binding  to  chitin  [80].  No  clear  instances  of  the  Rebers  and  Riddiford  (RR)  consensus  have  been...

  14. Cytotoxic and Antimicrobial Constituents of the Bark of Diospyros maritima Collected in Two Geographical Locations in Indonesia

    E-print Network

    Falkinham, Joseph

    a new naphthoquinone derivative, (4S)-shinanolone (5), and a new natural product coumarin, 7,8-dimethoxy diverse secondary metabolites, including alkanol ester,7 aliphatic lactone,8 benzenoid,9 coumarin,2

  15. Adaptation in perennial coastal plants-with particular reference to heritable variation in Puccinellia maritima and Ammophila arenaria

    Microsoft Academic Search

    A. J. Gray

    1985-01-01

    Perennial species invading the early stages of primary successions face constant, and often rapid, change in their biotic and abiotic environment. The relative abilities of different species to adapt to this change is reflected in the zonation patterns which characterize coastal vegetation. Variation in those species with wide ecological amplitudes, particularly in populations near the boundary of the realized niche,

  16. Arabidopsis thaliana Rubisco small subunit transit peptide increases the accumulation of Thermotoga maritima endoglucanase Cel5A in chloroplasts of transgenic tobacco plants.

    PubMed

    Kim, Suyeon; Lee, Dae-Seok; Choi, In Seong; Ahn, Sung-Ju; Kim, Yong-Hwan; Bae, Hyeun-Jong

    2010-06-01

    Over the past decade various approaches have been used to increase the expression level of recombinant proteins in plants. One successful approach has been to target proteins to specific subcellular sites/compartments of plant cells, such as the chloroplast. In the study reported here, hyperthermostable endoglucanase Cel5A was targeted into the chloroplasts of tobacco plants via the N-terminal transit peptide of nuclear-encoded plastid proteins. The expression levels of Cel5A transgenic lines were then determined using three distinct transit peptides, namely, the light-harvesting chlorophyll a/b-binding protein (CAB), Rubisco small subunit (RS), and Rubisco activase (RA). RS:Cel5A transgenic lines produced highly stable active enzymes, and the protein accumulation of these transgenic lines was up to 5.2% of the total soluble protein in the crude leaf extract, remaining stable throughout the life cycle of the tobacco plant. Transmission election microscopy analysis showed that efficient targeting of Cel5A protein was under the control of the transit peptide. PMID:19851881

  17. Cloning and Expression of Cytochrome P450 Enzymes Catalyzing the Conversion of Tyrosine to p-Hydroxyphenylacetaldoxime in the Biosynthesis of Cyanogenic Glucosides in Triglochin maritima

    Microsoft Academic Search

    John Strikart Nielsen; Birger Lindberg Møller

    2000-01-01

    Two cDNA clones encoding cytochrome P450 enzymes belong- ing to the CYP79 family have been isolated from Triglochin mari- tima. The two proteins show 94% sequence identity and have been designated CYP79E1 and CYP79E2. Heterologous expression of the native and the truncated forms of the two clones in Escherichia coli demonstrated that both encode multifunctional N-hydroxylases cat- alyzing the conversion

  18. Effects of seed ingestion and herbivory by waterfowl on seedling establishment: a field experiment with wigeongrass Ruppia maritima in Doñana, south-west Spain

    Microsoft Academic Search

    Jordi Figuerola; Andy J. Green

    2004-01-01

    The ingestion of seeds by vertebrates usually affects the viability and\\/or germination rate of seeds. Increases in germination rate following passage through the vertebrate gut have often been assumed to be favourable for seedling survival and plant fitness, but this assumption has never been tested experimentally. Given that numbers of herbivorous waterfowl are higher in winter in Mediterranean wetlands, herbivory

  19. 121J. Biosci. | vol. 25 | No. 2 | June 2000 | 121124 | Indian Academy of Sciences How asymmetrical before it's asymmetrical?

    E-print Network

    Borges, Renee M

    of the genome to buffer development against environmental stressors (Swaddle 1999). It is supposed to provide has occurred in organisms ranging from earwigs, to birds, deer and humans (reviewed in Møller

  20. Bell Pettigrew Museum of Natural History

    E-print Network

    Brierley, Andrew

    -dwelling herbivores and carnivores (e.g. many beetles and ants), scavengers (e.g. earwigs, houseflies and cockroaches.g. black-fly larvae) and benthic scavengers (e.g. caddis , and mayfly nymphs). Classification within

  1. Family, Home & Garden Education Center practical solutions to everyday questions

    E-print Network

    New Hampshire, University of

    . Description and life cycle The adult European earwig is reddish brown and resembles certain beetles. Unlike they may damage dahlias, zinnias, butterfly bush, lettuce, strawberry, celery, potatoes and seedling beans

  2. 77 FR 60237 - Endangered and Threatened Wildlife and Plants; Removal of the Valley Elderberry Longhorn Beetle...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-02

    ...at all, constitutes a significant threat to the beetle. The European earwig (Forficula auricularia) is a scavenger and omnivore that is often found on elderberry shrubs, and may feed opportunistically on exposed valley elderberry longhorn beetle...

  3. A comparative study of the tolerance of salt marsh plants to manganese

    Microsoft Academic Search

    A. Cooper

    1984-01-01

    Summary Salicornia europaea, Puccinellia maritima, Triglochin maritima, Aster tripolium, Plantago maritima, Armeria maritima, Juncus gerardii andFestuca rubra, collected as seed from a salt marsh at Portaferry, County Down, were grown on saline (340 mM NaCl) and non saline nutrient solutions at five concentrations of manganese sulphate (0.025–10.0 mM). After an eight week growing period, shoot and root yields and the

  4. Phytologia (April 2010) 92(1)68 DISCOVERY AND SNPS ANALYSES OF POPULATIONS OF

    E-print Network

    Adams, Robert P.

    Phytologia (April 2010) 92(1)68 DISCOVERY AND SNPS ANALYSES OF POPULATIONS OF JUNIPERUS MARITIMA 98368 ABSTRACT Trees from two populations of Juniperus commonly identified as J. scopulorum growing of a Pleistocene refugium for J. maritima. Phytologia 92(1): 68-81 (April, 2010). KEY WORDS: Juniperus maritima, J

  5. Aquatic macrophyte and animal communities in a recently restored brackish marsh: possible influences of restoration design and the invasive plant species Myriophyllum spicatum

    E-print Network

    Bell, Michael Thomas

    2012-07-16

    Growth inhibition of R. maritima by M. spicatum ............................ 27 5 Mean relative change in biomass of R. maritima in aquariums with differing amounts R. maritima biomass added. ..... 28 6 Mean fauna (fish and invertebrate... twenty stations of all fishes and invertebrates collected from the marsh in four sampling periods from August 2009 through May 2010 ............................................. 29 3 Discriminant function analysis (DF1) and densities...

  6. BULLETIN OF MARINE SCIENCE, 77(3): 453458, 2005 453Bulletin of Marine Science

    E-print Network

    Durako, Michael J.

    , rather than temperature, is the prime factor in ecotypic variation in R. maritima seed germination ON SEED GERMINATION IN RUPPIA MARITIMA FROM FLORIDA BAY A. E. Kahn and M. J. Durako Ruppia maritima L to require recruitment via seed germination in this species (Kantrud, 1991). Germination in Ruppia spp

  7. Vegetation dynamics and plant species interactions under grazed and ungrazed conditions in a western European salt marsh

    NASA Astrophysics Data System (ADS)

    Tessier, Marc; Vivier, Jean-Paul; Ouin, Annie; Gloaguen, Jean-Claude; Lefeuvre, Jean-Claude

    2003-05-01

    Experiments in exclosures were conducted on a salt marsh in a macrotidal system in western France. The aim of this study was threefold: (1) to compare vegetation dynamics over a period of 8 years in grazed and ungrazed conditions (2) to investigate the response of annual species to grazing duration during seedling establishment (3) to test the effect of an increase in soil nitrogen availability after cessation of grazing on interactions between Suaeda maritima and Puccinellia maritima. In grazed conditions, during all the survey, vegetation was dominated by a short P. maritima sward with the annual Salicornia europaea in the lower and middle marshes. However, after cessation of grazing in 1994, a homogeneous matrix of the forb Halimione portulacoides, quickly replaced P. maritima in the well drained lower marsh. At the middle marsh level, fine sediment and poor drainage maintained P. maritima while the annual S. maritima which tolerates taller and denser vegetation replaced S. europaea. Elymus pungens cover was limited till 2000 but its rising in 2001 let expect its dominance in the future. While P. maritima abundance remained high, spring abundance of annual species such as S. europaea and S. maritima globally decreased with sheep grazing duration on the salt marsh between February and June. Experiments with monocultures of P. maritima and S. maritima demonstrated that nitrogen was a limiting factor on the salt marsh. In a mixed community, a moderate application of nitrogen (15 g N m -2 year -1 as NH 4-NO 3) promoted growth of P. maritima and limited the biomass of S. maritima, but growth of the latter was enhanced by a high application of nitrogen (30 g N m -2 year -1). An increase in the abundance of annuals such as S. maritima on the salt marsh is discussed.

  8. Spring staging in Brent Geese Branta bernicla : feeding constraints and the impact of diet on the accumulation of body reserves

    Microsoft Academic Search

    Jouke Prop; Charlotte Deerenberg

    1991-01-01

    The diet composition of Brent Geese Branta bernicla on a salt-marsh was quantified. Puccinellia maritima was the principal food species, while Plantago maritima and Triglochin maritima were less commonly taken. Festuca rubra only acted as a substitute for Puccinellia when production of the latter species dropped. The metabolizable energy of the food plants ranged from 5 to 11 kJ·g-1. By

  9. Mulch and Moisture Pests and Occasional Invaders

    NSDL National Science Digital Library

    0000-00-00

    Tutorials on houshold pests. Each tutorial has 50 questions; incorrect answers lead to additional information. Covers booklice, plaster beetles, centipedes, millipedes, amphipods, earwigs, pillbugs, sowbugs, fungus gnats, springtails, silverfish, scorpions, thrips, crickets and plaster bagworm. Requires Windows. $15. Easy to use once loaded on hard drive. Some of the pests depicted are largely restricted to the Deep South. Part number SW 161.

  10. University of Basel Master Projects in Basel, May 2010

    E-print Network

    Kölliker, Mathias

    in collaboration with FiBL Frick and Agroscope Changins-Wädenswil on the role of earwigs in control of pest species where fungi spores and bacteria are abundant. The care for clutches of eggs is the most widespread form and investigate the behavioural and chemical mechanisms by which females counter infections of their eggs

  11. Epilogue to Special Issue on Developmental Robotics: Can Experiments with Machines Inform Theory in Infant Development?

    ERIC Educational Resources Information Center

    Prince, Christopher G.

    2008-01-01

    Developmental robotics has forwarded a range of models of development and behaviours. With the variety of systems that have been created, and with some of these approximating prominent human behaviours (e.g. joint attention, word learning, imitation), one may argue that developmental robotics has started to go past robotic models of earwigs

  12. Ecological Entomology (2008), DOI: 10.1111/j.1365-2311.2008.01022.x 2008 The Author

    E-print Network

    Knell, Rob

    al., 2005; Cook & Bean, 2006). Whereas the analysis of what might be termed simple allometries has, including the horns of beetles, the forceps of earwigs, and the heads of certain castes of ant. 2. Non, the alternative mating tactics displayed by many species of beetle are widely associated with dimorphisms in horn

  13. MATERNAL BEHAVIOUR AND THE EVOLUTION OF CHEMICAL SIGNALLING BY OFFSPRING IN THE

    E-print Network

    Amrhein, Valentin

    sans conflit. Flore Mas 2009 #12;iv SUMMARY Parental care provided to current offspring such as food regulate reproductive physiology (i.e. hormones). Therefore I decided for my thesis to explore the possible. In a first experiment, I manipulated the nutritional condition (low-food, LF, versus high-food, HF) of earwig

  14. Insects did it first: a micropatterned adhesive tape for robotic applications

    Microsoft Academic Search

    Stanislav N Gorb; Mitali Sinha; Andrei Peressadko; Kathryn A Daltorio; Roger D Quinn

    2007-01-01

    Based on the structural and experimental studies of more than 300 insect species from different lineages, we have developed and characterized a bioinspired polymer material with the ability of multiple glue-free bonding and debonding. The material surface is covered with a pattern of microstructures, which resembles the geometry of tenent hairs previously described from the feet of flies, beetles, earwigs

  15. Host-parasite relationship between colonial terns and bacteria is modified by a mutualism with a plant with antibacterial defenses.

    PubMed

    Møller, Anders Pape; Flensted-Jensen, Einar; Mardal, Willy; Soler, J J

    2013-09-01

    Predator-prey and host-parasite interactions and mutualisms are common and may have profound effects on ecosystems. Here we analyze the parasitic and mutualistic associations between three groups of organisms: the plant Artemisia maritima, bacteria, and a colonial seabird (the sandwich tern Sterna sandvicensis) that breeds in dense colonies covered in feces produced by both adults and chicks. A disproportionately large fraction of colonies of the sandwich tern in Denmark were located in patches covered by A. maritima. This association was specific for the densely colonial sandwich tern, but was not present for four other sympatric species of terns that breed in much less dense colonies. A. maritima reduced the abundance of pathogenic Staphylococcus on chicken eggshells in a field experiment. Recruitment by sandwich terns breeding in patches of A. maritima was 18 % higher than for sandwich terns breeding in the absence of A. maritima. A. maritima benefitted from the association with sandwich terns due to the supply of nutrients from feces and uneaten food lost by young. These findings are consistent with sandwich terns exploiting the association with A. maritima and its antimicrobial properties to improve their reproductive success, while sandwich terns and A. maritima are involved in a mutualistic interaction. PMID:23404068

  16. Aquatic macrophytes in saline lakes of the Canadian prairies

    Microsoft Academic Search

    U. Theodore Hammer; J. Michael Heseltine

    1988-01-01

    Vascular macrophyte species richness decreases with increasing salinity. Only three species of submerged plants (Potamogeton pectinatus, Ruppia maritima, R. occidentalis) tolerate hypersaline waters (>50 g l-1, total of ionic constituents). Eight emergent species occur in more saline habitats but only five (Scirpus maritimus var. paludosus, Distichlisstricta, Puccinellia nuttalliana, Scirpus americanus, Triglochin maritima) occur commonly over a range of saline lakes

  17. Determinants of phylogeographic structure: a comparative study of seven coastal flowering plant species across their European range

    Microsoft Academic Search

    J. W. KADEREIT; E. WESTBERG

    We here synthesize our own mostly published work on the phylogeographic structure of seven flowering plant species (Cakile maritima, Calystegia sold- anella, Eryngium maritimum, Salsola kali, Halimione portulacoides, Triglochin maritima and Crithmum maritimum) widely distributed along the European coasts. Three categories of factors were identified to determine phylogeographic structure and are illustrated with examples. These are 1) historical abiotic factors

  18. Competition and herbivory during salt marsh succession: the importance of forb growth strategy

    Microsoft Academic Search

    Carsten F. Dormann; Rene Van Der Wal; Jan P. Bakker

    2000-01-01

    Summary 1 Despite much debate about their importance, only a few field studies have evalu- ated the intensity of competition and herbivory. 2 Artemisia maritima, Atriplex portulacoides and Plantago maritima, three plant species which are common in European temperate salt marshes, were transplanted into diÄerent successional stages (15, 30 and 45 years old) of a temperate salt marsh. Biomass of

  19. EFFECT OF SOIL SALINITY ON THE LIPID COMPOSITION OF HALOPHYTE PLANTS FROM THE SAND BAR OF POMORIE

    Microsoft Academic Search

    A. Ivanova; J. Nechev; K. Stefanov

    2006-01-01

    Summary. Seven samples of halophyte plants (Bassia hirsuta Aschers, Euphorbia peplis L., Salicornia europeae L., Calystegia soldanella, Calystegia sepium, Stachys maritima Gonan and Suaeda maritima Dumort,) were collected from a sand bar near the town of Pomorie (Bulgaria). The soil salinity ranged between 650 and 850 mg salts in 100 g soil. For com- parison, two other samples from the

  20. Eur. J. Biochem. 268, 25272539 (2001) q FEBS 2001 Solution NMR structure of the cold-shock protein from the

    E-print Network

    Schuler, Ben

    2001-01-01

    structure of TmCsp from Thermotoga maritima, the hyperthermophilic member of this class of proteins that the thermostability of TmCsp is based on the peripheral ion cluster around the side chain of R2. Keywords: cold hyperthermophilic member of this family has been cloned from Thermotoga maritima (TmCsp); its sequence

  1. Entry Number: 1 GL A NEW HONEY BEE THREAT-THE PARASITIZING PHORID FLY APOCEPHALUS BOREALIS

    E-print Network

    . maritima as a model system, I have quantitated the characteristics that lead to male reproductive success between intra- and intersexual selection helps determine a male's optimal reproductive strategy. Using A

  2. Experiments to examine transplant procedures on the seagrass Halodule beaudettei

    E-print Network

    Land, Frederick Joseph

    2007-09-17

    light treatments with shoal-grass, widgeongrass (Ruppia maritima), star grass (Halophila engelmannii), and turtlegrass (Thalassia testudinum), with survival and growth occurring in the high light treatment and decline and death occurring in the low light...

  3. Variation in ecogeographical traits of pecan cultivars and provenances

    E-print Network

    Sagaram, Madhulika

    2009-05-15

    maritima (Marsh.) Muhl. ex Nutt. (Schrader and Graves, 2000), Chamaecyparis thyoides (L.) B.S.P. (Jull et al., 1999), Maackia 3 amurensis Rupr. (Pai and Graves, 1995), Platanus occidentalis L. (Shoemake, 1996; Shoemake and Arnold, 1997) and Pinus...

  4. Managing Insects and Related Pests of Roses

    E-print Network

    Drees, Bastiaan M.; Pemberton, Brent; Cole, Charles L.

    1999-07-12

    -Step Method Do-It- Yourself Fire Ant Control); Figure 4. A thrips. Figure 3. A spider mite. n White grubs (see L-1131, White Grubs in Texas Turfgrass); n Snails and slugs (see L-1737, Snails and Slugs); n Centipedes and millipedes (see L-1747, Centipedes... carbaryl (5%), Greenlight Bug & Snail Bait armyworms, crickets, earwigs, for use in lawns, metaldehyde (1%) grasshoppers, sowbugs, pillbugs, flowerbeds, ornamental snails, slugs and home vegetable gardens diazinon (4.2%), Fertilome Triple-Action aphids...

  5. Which insect species numerically respond to allochthonous inputs?

    PubMed

    Sugiura, Shinji; Ikeda, Hiroshi

    2013-08-01

    Herons (Ardeidae) frequently breed in inland forests and provide organic material in the form of carcasses of prey (that they drop) and chicks (that die) to the forest floor. Such allochthonous inputs of organic materials are known to increase arthropod populations in forests. However, the exact species that show numerical responses to allochthonous inputs in heron breeding colonies remains unclear. Very few studies have clarified which factors determine numerical responses in individual species. We used pitfall and baited traps to compare the densities of arthropods between forest patches in heron breeding colonies (five sites) and areas outside of colonies (five sites) in central Japan. The density of all arthropods was not significantly different between colonies and non-colony areas. However, significant differences between colonies and non-colony areas were found in four arthropod groups. Earwigs (Dermaptera: Anisolabididae), hister beetles (Coleoptera: Histeridae), and carrion beetles (Coleoptera: Silphidae) were more abundant in colonies, while ants (Hymenoptera: Formicidae) were less abundant in colonies. We detected numerical responses to heron breeding in two earwig, one histerid, five silphid, and one ant species. Chick and prey carcasses from herons may have directly led to increases in consumer populations such as earwigs, histerids, and silphids in colonies, while microenvironmental changes caused by heron breeding may have reduced ant abundance. In the Silphidae, five species showed numerical responses to allochthonous inputs, and the other two species did not. Numerical responses in individual species may have been determined by life history traits such as reproductive behaviour. PMID:23780624

  6. Which insect species numerically respond to allochthonous inputs?

    NASA Astrophysics Data System (ADS)

    Sugiura, Shinji; Ikeda, Hiroshi

    2013-08-01

    Herons (Ardeidae) frequently breed in inland forests and provide organic material in the form of carcasses of prey (that they drop) and chicks (that die) to the forest floor. Such allochthonous inputs of organic materials are known to increase arthropod populations in forests. However, the exact species that show numerical responses to allochthonous inputs in heron breeding colonies remains unclear. Very few studies have clarified which factors determine numerical responses in individual species. We used pitfall and baited traps to compare the densities of arthropods between forest patches in heron breeding colonies (five sites) and areas outside of colonies (five sites) in central Japan. The density of all arthropods was not significantly different between colonies and non-colony areas. However, significant differences between colonies and non-colony areas were found in four arthropod groups. Earwigs (Dermaptera: Anisolabididae), hister beetles (Coleoptera: Histeridae), and carrion beetles (Coleoptera: Silphidae) were more abundant in colonies, while ants (Hymenoptera: Formicidae) were less abundant in colonies. We detected numerical responses to heron breeding in two earwig, one histerid, five silphid, and one ant species. Chick and prey carcasses from herons may have directly led to increases in consumer populations such as earwigs, histerids, and silphids in colonies, while microenvironmental changes caused by heron breeding may have reduced ant abundance. In the Silphidae, five species showed numerical responses to allochthonous inputs, and the other two species did not. Numerical responses in individual species may have been determined by life history traits such as reproductive behaviour.

  7. Native plant restoration combats environmental change: development of carbon and nitrogen sequestration capacity using small cordgrass in European salt marshes.

    PubMed

    Curado, Guillermo; Rubio-Casal, Alfredo E; Figueroa, Enrique; Grewell, Brenda J; Castillo, Jesús M

    2013-10-01

    Restoration of salt marshes is critical in the context of climate change and eutrophication of coastal waters because their vegetation and sediments may act as carbon and nitrogen sinks. Our primary objectives were to quantify carbon (C) and nitrogen (N) stocks and sequestration rates in restored marshes dominated by Spartina maritima to provide support for restoration and management strategies that may offset negative aspects of eutrophication and climate change in estuarine ecosystems. Sediment C content was between ca. 13 mg C g(-1)and sediment N content was ca. 1.8 mg N g(-1). The highest C content for S. maritima was recorded in leaves and stems (ca. 420 mg C g(-1)) and the lowest in roots (361?±?4 mg C g(-1)). S. maritima also concentrated more N in its leaves (31?±?1 mg N g(-1)) than in other organs. C stock in the restored marshes was 29.6 t C ha(-1); ca. 16 % was stored in S. maritima tissues. N stock was 3.6 t N ha(-1), with 8.3 % stored in S. maritima. Our results showed that the S. maritima restored marshes, 2.5 years after planting, were sequestering atmospheric C and, therefore, provide some mitigation for global warming. Stands are also capturing nitrogen and reducing eutrophication. The concentrations of C and N contents in sediments, and cordgrass relative cover of 62 %, and low below-ground biomass (BGB) suggest restored marshes can sequester more C and N. S. maritima plantations in low marshes replace bare sediments and invasive populations of exotic Spartina densiflora and increase the C and N sequestration capacity of the marsh by increasing biomass production and accumulation. PMID:23591677

  8. Sugar Transport and Metabolism in Thermotoga

    SciTech Connect

    Noll, Kenneth M.; Romano, Antonio H.

    2003-02-11

    The work conducted under this grant demonstrated that the hyperthermophilic bacterium Thermotoga neapolitana carries out glucose and lactose transport in a sodium-dependent manner and that energization of anaerobic cells is required to observe transport. We also demonstrated that Thermotoga maritima carries out maltose and glucose transport using periplasmic sugar binding proteins. We began defining patterns of expression of genes encoding sugar transport and catabolic functions in both T. maritima and T. neapolitana. We began a collaborative effort to identify all the genes regulated at the transcriptional level in response to sugars substrates. These funds also allowed us to begin an examination of the functions of several periplasmic substrate binding proteins encoded in the genome of T. maritima.

  9. Effects of thermoperiod on recovery of seed germination of halophytes from saline conditions.

    PubMed

    Khan, M; Ungar, I

    1997-02-01

    Recovery of seed germination from NaCl salinity of desert shrubs (Haloxylon recurvum and Suaeda fruticosa, and the herbs Zygophyllum simplex and Triglochin maritima was studied under various thermoperiods. The percentage of ungerminated seeds that recovered when they were transferred to distilled water varied significantly with variation in species and thermoperiods. Zygophyllum simplex had little recovery from all NaCl concentrations in all thermoperiods. Haloxylon recurvum, S. fruticosa, and T. maritima showed substantial recovery. Percentage recovery was highest in S. fruticosa, followed by T. maritima, and H. recurvum. Thermoperiodic effects varied with the species investigated. There was little thermoperodic effect on the percentage recovery of S. fruticosa, except in the higher salinity treatment at higher thermoperiods. Variation in thermoperiod appears to play an important role in recovery of germination of halophytes from salt stress when seeds are transferred to distilled water. PMID:21712207

  10. Were the original eubacteria thermophiles?

    NASA Technical Reports Server (NTRS)

    Achenbach-Richter, L.; Gupta, R.; Stetter, K. O.; Woese, C. R.; Johnson, P. C. (Principal Investigator)

    1987-01-01

    Thermotoga maritima is one of the more unusual eubacteria: It is highly thermophilic, growing at temperatures higher than any other eubacterium; its cell wall appears to have a unique structure and its lipids a unique composition; and the organism is surrounded by a loose-fitting sheath of unknown function. Its phenotypic uniqueness is matched by its phylogenetic position; Thermotoga maritima represents the deepest known branching in the eubacterial line of descent, as measured by ribosomal RNA sequence comparisons. T. maritima also represents the most slowly evolving of eubacterial lineages. The fact that the two deepest branchings in the eubacterial line of descent (the other, the green non-sulfur bacteria and relatives, i.e. Chloroflexus, Thermomicrobium, etc.) are both basically thermophilic and slowly evolving, strongly suggests that all eubacteria have ultimately arisen from a thermophilic ancestor.

  11. Cues of maternal condition influence offspring selfishness.

    PubMed

    Wong, Janine W Y; Lucas, Christophe; Kölliker, Mathias

    2014-01-01

    The evolution of parent-offspring communication was mostly studied from the perspective of parents responding to begging signals conveying information about offspring condition. Parents should respond to begging because of the differential fitness returns obtained from their investment in offspring that differ in condition. For analogous reasons, offspring should adjust their behavior to cues/signals of parental condition: parents that differ in condition pay differential costs of care and, hence, should provide different amounts of food. In this study, we experimentally tested in the European earwig (Forficula auricularia) if cues of maternal condition affect offspring behavior in terms of sibling cannibalism. We experimentally manipulated female condition by providing them with different amounts of food, kept nymph condition constant, allowed for nymph exposure to chemical maternal cues over extended time, quantified nymph survival (deaths being due to cannibalism) and extracted and analyzed the females' cuticular hydrocarbons (CHC). Nymph survival was significantly affected by chemical cues of maternal condition, and this effect depended on the timing of breeding. Cues of poor maternal condition enhanced nymph survival in early broods, but reduced nymph survival in late broods, and vice versa for cues of good condition. Furthermore, female condition affected the quantitative composition of their CHC profile which in turn predicted nymph survival patterns. Thus, earwig offspring are sensitive to chemical cues of maternal condition and nymphs from early and late broods show opposite reactions to the same chemical cues. Together with former evidence on maternal sensitivities to condition-dependent nymph chemical cues, our study shows context-dependent reciprocal information exchange about condition between earwig mothers and their offspring, potentially mediated by cuticular hydrocarbons. PMID:24498046

  12. Cues of Maternal Condition Influence Offspring Selfishness

    PubMed Central

    Wong, Janine W. Y.; Lucas, Christophe; Kölliker, Mathias

    2014-01-01

    The evolution of parent-offspring communication was mostly studied from the perspective of parents responding to begging signals conveying information about offspring condition. Parents should respond to begging because of the differential fitness returns obtained from their investment in offspring that differ in condition. For analogous reasons, offspring should adjust their behavior to cues/signals of parental condition: parents that differ in condition pay differential costs of care and, hence, should provide different amounts of food. In this study, we experimentally tested in the European earwig (Forficula auricularia) if cues of maternal condition affect offspring behavior in terms of sibling cannibalism. We experimentally manipulated female condition by providing them with different amounts of food, kept nymph condition constant, allowed for nymph exposure to chemical maternal cues over extended time, quantified nymph survival (deaths being due to cannibalism) and extracted and analyzed the females’ cuticular hydrocarbons (CHC). Nymph survival was significantly affected by chemical cues of maternal condition, and this effect depended on the timing of breeding. Cues of poor maternal condition enhanced nymph survival in early broods, but reduced nymph survival in late broods, and vice versa for cues of good condition. Furthermore, female condition affected the quantitative composition of their CHC profile which in turn predicted nymph survival patterns. Thus, earwig offspring are sensitive to chemical cues of maternal condition and nymphs from early and late broods show opposite reactions to the same chemical cues. Together with former evidence on maternal sensitivities to condition-dependent nymph chemical cues, our study shows context-dependent reciprocal information exchange about condition between earwig mothers and their offspring, potentially mediated by cuticular hydrocarbons. PMID:24498046

  13. Seasonal changes in the food habits of the Great-tailed Grackle, Cassidix mexicanus

    E-print Network

    Davis, Walter Ragland

    1970-01-01

    in the early morning just after leaving the roost, and ate the crickets that rems. ined. De rrna pt. e ra Earwigs of the family Labiduzidae were present in the stomachs of an immature fernale and s. n immature male ts. ken during November. Each sarr pie... maneuverability might make it d!fficu]t for adult males to capture rapidly mo~ing insects such as crickets and grasshoppers. Accepting these observe. tions and speculations, s. model of the feeding behavior of Great-tailed Grackles can be sugges ted...

  14. Diary of an Examiner

    E-print Network

    Macfarlane, Alan

    2013-08-13

    ’, ‘Analyze and dissect the physical anthropology of the soul’, ‘What has anthropology learnt from the social organization of earwigs’ or whatever. It would be fun if one or more examples of such humour (much wittier than the examples above) still exist... member of the Board for three or four minutes as if they were reading proofs of an article. They can get a sense of the parts and the whole, mark small trivial corrections to spelling, grammar and other matters which can be dealt with by the Examiner...

  15. Piper kelleyi, a hotspot of ecological interactions and a new species from Ecuador and Peru

    PubMed Central

    Tepe, Eric. J.; Rodríguez-Castañeda, Genoveva; Glassmire, Andrea E.; Dyer, Lee A.

    2014-01-01

    Abstract We describe Piper kelleyi sp. nov., a new species from the eastern Andes of Ecuador and Peru, named in honor of Dr. Walter Almond Kelley. Piper kelleyi is a member of the Macrostachys clade of the genus Piper and supports a rich community of generalist and specialist herbivores, their predators and parasitoids, as well as commensalistic earwigs, and mutualistic ants. This new species was recognized as part of an ecological study of phytochemically mediated relationships between plants, herbivores, predators, and parasitoids. Compared to over 100 other Piper species surveyed, Piper kelleyi supports the largest community of specialist herbivores and parasitoids observed to date. PMID:24596490

  16. Piper kelleyi, a hotspot of ecological interactions and a new species from Ecuador and Peru.

    PubMed

    Tepe, Eric J; Rodríguez-Castañeda, Genoveva; Glassmire, Andrea E; Dyer, Lee A

    2014-01-01

    We describe Piper kelleyi sp. nov., a new species from the eastern Andes of Ecuador and Peru, named in honor of Dr. Walter Almond Kelley. Piper kelleyi is a member of the Macrostachys clade of the genus Piper and supports a rich community of generalist and specialist herbivores, their predators and parasitoids, as well as commensalistic earwigs, and mutualistic ants. This new species was recognized as part of an ecological study of phytochemically mediated relationships between plants, herbivores, predators, and parasitoids. Compared to over 100 other Piper species surveyed, Piper kelleyi supports the largest community of specialist herbivores and parasitoids observed to date. PMID:24596490

  17. The role of proline accumulation in halophytes.

    PubMed

    Stewart, G R; Lee, J A

    1974-01-01

    It is shown that in the majority of higher plant halophytes examined proline is the major component of the amino acid pool in plants collected from the field. In Triglochin maritima L. free proline can represent 10-20% of the shoot dry weight. Under non-saline conditions proline levels are low and increase as the salinity is raised. Comparisons of inland and coastal populations of Ameria maritima Willd. suggest that the capacity to accumulate proline is correlated with salt tolerance. It is suggested that proline functions as a source of solute for intracellular osmotic adjustments under saline conditions. PMID:24442703

  18. Effect of some insecticides on acetylcholinesterase from beneficial insects: Coccinella septempunctata, Chrysoperla carnea and Forficula auricularia.

    PubMed

    Bozsik, Andras; Francis, Frédéric; Gaspar, Charles; Haubruge, Eric

    2002-01-01

    In vitro enzyme activity of head homogenates from adults of Coccinella septempunctata, Chrysoperla carnea and Forficula auricularia originated from different habitats in Belgium (wheat, barley, rye, set-aside fields and experimental orchard, uncultivated area) were investigated in presence of insecticide active ingredients. Using the procedure of Ellman, I50 (M) and Ki (M-1 min-1) values were established. The beneficial insects showed the least susceptibility to diazinon and the differences between their measured values were not remarkable. Paraoxon was extremely toxic to the AChE of F. auricularia but Ch. carnea and C. septempunctata were similarly more tolerant to this organophosphate. In the case of malaoxon earwig and green lacewing AChEs were much more sensitive than AChE of the ladybird beetle. Measuring the carbaryl inhibition, F. auricularia was the least tolerant. The susceptibility of ladybird AChE differed highly from that of both species. According to the measured values, the green lacewing was less tolerant than the ladybird beetle but more tolerant compared with the common earwig. Summarizing our biochemical results, the order of susceptibility of beneficial insects to insecticides investigated was the following F. auricularia > Ch. carnea > C. septempunctata. PMID:12696436

  19. Evidence for preferential depths of metal retention in roots of salt marsh plants

    Microsoft Academic Search

    Miguel Caetano; Carlos Vale; Rute Cesário; Nuno Fonseca

    2008-01-01

    Depth variation (2-cm resolution) of Fe, Mn, Zn, Cr, Ni, Cu, As and Cd concentrations were determined in belowground biomass of Spartina maritima and Sarcocornia fruticosa and in sediments between roots from two marshes in Tagus (Rosário) and Guadiana (Castro Marim) estuaries in Portugal with different anthropogenic pressures. Levels of metals were also determined in aboveground plant parts. Metal concentrations

  20. NOTICE OF RELEASE OF SUGARBEET GERMPLASM LINES CN12 AND CN72

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sugarbeet germplasm lines CN12 and CN72 were officially released on 02/28/05. These releases are multigerm, random-mated populations that segregate for resistance to sugarbeet cyst nematode from the wild species Beta vulgaris subsp. maritima. Cyst nematode is one of the most damaging pests of suga...

  1. The effects of floral understoreys on parasitism of leafrollers (Lepidoptera: Tortricidae) on apples in New Zealand

    Microsoft Academic Search

    N. A. Irvin; S. L. Scarratt; S. D. Wratten; C. M. Frampton; R. B. Chapman; J. M. Tylianakis

    2006-01-01

    Field and laboratory experiments on the conservation biocontrol of lepidop- teran leafroller pests were carried out in apples at Lincoln, New Zealand. 2 Apple understoreys were planted with replicated treatments of alyssum (Lobularia maritima), phacelia (Phacelia tanacetifolia) and buckwheat (Fagopyrum esculentum). 3 Rates of parasitism of experimentally released larvae of the light-brown apple moth, Epiphyas postvittana (Walker) (Lepidoptera: Tortricidae), by

  2. Molecular and Morpho-Physiological Characterization of Sea, Ruderal and Cultivated Beets

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Beta vulgaris genetic resources are essential for broadening genetic base of sugar beet and developing cultivars adapted to adverse environmental conditions. Wild beets (sea beets, B. vulgaris spp. maritima and their naturalized introgressions with cultivated beets known as ruderal beets) harbor su...

  3. Chromatographic fingerprint analysis of Pycnogenol® dietary supplements

    Technology Transfer Automated Retrieval System (TEKTRAN)

    French maritime bark (Pinus maritima) has been widely used as an herbal remedy for various degenerative diseases. A standardized bark extract is available that complies with its USP monograph and is derived from Pinus pinaster, Ait. (Pycnogenol®, Horphag Research Ltd., UK). The method specified in...

  4. The seed oils of some species of the family Cruciferae

    Microsoft Academic Search

    V. S. Dolya; E. N. Shkurupii; T. V. Podzolkova; N. A. Kaminskii

    1973-01-01

    Summary  The physicochemical properties of the oils of the seeds of seven plants of the family Cruciferae —Cakile maritima, Sisymbrium altissimum, Sisymbrium Loeselii, Descurainia Sophia, Erysimum cheiranthoides, Brassica amoracioides andCrambe pontica — have been studied and their fatty acid compositions have been determined. The results obtained showed no marked differences\\u000a from those given in the literature.

  5. 78 FR 62560 - Endangered and Threatened Wildlife and Plants; Endangered Status for Agave eggersiana and...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-22

    ...diameter. Fruit is a bright red berry with many seeds...250 or more species of trees and shrubs of tropical...fruit is a one-seeded, red drupe about 0.2 in...Pilosocereus royenii (Royen's tree, Suriana maritima (bay cedar), Bursera...

  6. Coping with low nutrient availability and inundation: root growth responses of three halophytic grass species from different elevations along a flooding gradient

    Microsoft Academic Search

    Tjeerd J. Bouma; Bas P. Koutstaal; Michel van Dongen; Kai L. Nielsen

    2001-01-01

    We describe the responses of three halophytic grass species that dominate the low (Spartina anglica), middle (Puccinellia maritima) and high (Elymus pycnanthus) parts of a salt marsh, to soil conditions that are believed to favour contrasting root-growth strategies. Our hypotheses were: (1) individual lateral root length is enhanced by N limitations in the soil but restricted by oxygen limitations, (2)

  7. The 5 Leader of Precursor tRNAAsp Bound to the Bacillus subtilis RNase P

    E-print Network

    Walter, Nils G.

    -resolution X-ray crystal structures of RNase P RNA from Thermotoga maritima (6) and Bacillus stearothermophilusThe 5 Leader of Precursor tRNAAsp Bound to the Bacillus subtilis RNase P Holoenzyme Has an Extended Bacillus subtilis comprises a large RNA component (130 kDa, P RNA) and a small protein subunit (14 kDa, P

  8. Effects of Thermoperiod on Recovery of Seed Germination of Halophytes from Saline Conditions

    Microsoft Academic Search

    M. Ajmal Khan; Irwin A. Ungar

    1997-01-01

    Recovery of seed germination from NaCl salinity of desert shrubs (Haloxylon recurvum and Suaeda fruticosa, and the herbs Zygophyllum simplex and Triglochin maritima was studied under various thermoperiods. The percentage of unger- minated seeds that recovered when they were transferred to distilled water varied significantly with variation in species and thermoperiods. Zygophyllum simplex had little recovery from all NaCl concentrations

  9. The role of proline accumulation in halophytes

    Microsoft Academic Search

    G. R. Stewart; J. A. Lee

    1974-01-01

    It is shown that in the majority of higher plant halophytes examined proline is the major component of the amino acid pool in plants collected from the field. In Triglochin maritima L. free proline can represent 10–20% of the shoot dry weight. Under non-saline conditions proline levels are low and increase as the salinity is raised. Comparisons of inland and

  10. Accumulation, distribution and cellular partitioning of mercury in several halophytes of a contaminated salt marsh

    Microsoft Academic Search

    Rita Castro; Sofia Pereira; Ana Lima; Sofia Corticeiro; Mónica Válega; Eduarda Pereira; Armando Duarte; Etelvina Figueira

    2009-01-01

    This work evaluates the role of a plant community in mercury (Hg) stabilization and mobility in a contaminated Portuguese salt marsh. With this aim, the distribution of Hg in below and aboveground tissues, as well as the metal partitioning between cellular fractions (soluble and insoluble) in four different species (Triglochin maritima L., Juncus maritimus Lam, Sarcocornia perennis (Miller) A.J. Scott,

  11. Heavy metal uptake by marsh plants in hydroponic solution cultures

    Microsoft Academic Search

    C. R. Lee; T. C. Sturgis; M. C. Landin

    1981-01-01

    Eight marsh plants were grown in chemically controlled hydroponic solutions containing three concentrations of heavy metals to evaluate the ability of each plant species to take up and accumulate heavy metals. The marsh plants studited were Cyperus esculentus, Scirpus validus, Spartina patens, Scirpus robustus, Distichiis spicata, Triglochin maritima, Spartina alterniflora, and Spartina foliosa. These species represented freshwater, brackish water, and

  12. I sanden på stranden - svampar längs Laholmsbunktens dyner

    Microsoft Academic Search

    KILL PERSSON; HÅKAN PLEIJEL

    The macrofungi of the coastal sand dunes of the southernmost part of the county of Halland were studied. A number of typical sand fungi were found, including Phallus hadriani, Crinipellis scabellum, Mycena chlorantha, Inocybe maritima, Geoglossum arenarium, Geoglossum cookeia- num, Geopora arenicola and Psathyrella ammophila. In the southern part of the area the sand has a considerable content of lime.

  13. Competition between endoparasitic nematodes and effect on biomass of Ammophila arenaria (marram grass) as affected by timing of inoculation and plant age

    Microsoft Academic Search

    E. Pernilla Brinkman; Henk Duyts; Wim H. van der Putten

    2005-01-01

    We studied the effects of intra- and interspecific competition on the abundance of endoparasitic nematodes and assessed the consequences for biomass production of the natural dune grass Ammophila arenaria. Pratylenchus penetrans was limited by intraspecific competition and it suppressed the abundance of Heterodera arenaria, whilst the interaction between H. arenaria and Meloidogyne maritima was neutral. Pratylenchus penetrans and H. arenaria

  14. Two new species of Isochrysis with remarks on the genus Ruttnera

    Microsoft Academic Search

    C. Billard; P. Gayral

    1972-01-01

    Two marine strains of Chrysophyceae have been studied with the aid of light and electron microscopy. The benthic stages show definite similarities with two marine Gloeochrysis spp. (G. maritima and G. litoralis) described by Anand (1937), but the swarmers do not agree with the definition of this genus. The reason why they also cannot be assigned to the genus Ruttnera

  15. Comparative dispersal effectiveness of wigeongrass seeds by waterfowl wintewring in south-west Spain: quantitative and qualitative aspects

    Microsoft Academic Search

    Jordi Figuerola; Andy J. Green; L. Santamaría

    2002-01-01

    The effectiveness of a seed disperser depends on the quantity of seed dispersed and the quality of dispersal provided to each seed. Relationships between the quantity and quality components and their dependence on characteristics of the dispersers remain largely uninvestigated. 2 The effectiveness of different waterfowl species at dispersing seeds of Ruppia maritima was evaluated in a wetland in south-west

  16. Ingestion, enzymatic digestion and absorption of particles derived from different vegetal sources by the cockle Cerastoderma edule

    Microsoft Academic Search

    U. Arambalza; M. B. Urrutia; E. Navarro; I. Ibarrola

    2010-01-01

    Ingestion, enzymatic digestion and absorption of particulate detrital matter derived from six different vegetal sources by the common cockle Cerastoderma edule was analyzed in a series of seasonal experiments performed in March, May and October 2005. Two green macroalgae: Ulva lactuca and Enteromorpha sp; two vascular plants: Spartina maritima and Juncus maritimus, the red macroalgae Gracilaria gracilis; and the microalgae

  17. Nitrogen resorption from senescing leaves of three salt marsh plant species

    Microsoft Academic Search

    P. Cartaxana; F. Catarino

    2002-01-01

    Seasonalvariation in leaf nitrogen of mature green and senescent leaves and nitrogenresorption efficiency in three plants (Spartina maritima, Halimioneportulacoides and Arthrocnemum perenne) of aTagus estuary salt marsh are reported. Total nitrogen concentrations in greenand senescent leaves were higher during winter (December and March). Soilinorganic nitrogen availability showed an opposite pattern with higherconcentrations during summer (June and September) when total leaf

  18. FtsZ From Escherichia coli, Azotobacter vinelandii, and Thermotoga

    E-print Network

    Erickson, Harold P.

    FtsZ From Escherichia coli, Azotobacter vinelandii, and Thermotoga maritima--Quantitation, GTP and Azotobacter vinelandii and expressed the proteins (TmFtsZ and AzFtsZ) in Escherichia coli. We compared as well, as Escherichia coli FtsZ (EcFtsZ) can assemble in vitro into protofilament sheets with a lattice

  19. A field experiment investigating the effects of olive husk and cow manure on heavy metal availability in a contaminated calcareous soil from Murcia (Spain)

    Microsoft Academic Search

    R. Clemente; C. Paredes; M. P. Bernal

    2007-01-01

    The transfer of heavy metals from the former sites of mining activity in La Unión (Murcia) to the nearby agricultural soils is a serious environmental risk. The effect of two organic wastes, used as soil amendments, on the bioavailability of heavy metals in an agricultural soil and on their accumulation in Beta vulgaris L. var. Nomonta and Beta maritima L.

  20. Changes in Microbial Biomass Parameters of a Heavy Metal-Contaminated Calcareous Soil during a Field Remediation Experiment

    Microsoft Academic Search

    R. Clemente; C. de la Fuente; R. Moral; M. P. Bernal

    2007-01-01

    Soil microbial biomass parameters give useful information about the restoration degree and quality of contaminated soils. These pa- rameters were studied in a field experiment where the effect of two organic amendments on the bioavailability of heavy metals in an agri- cultural soil and on their accumulation in Beta vulgaris and Beta maritima was assessed. The soil was a calcareous

  1. Crystal Structure of the MJ0490 Gene Product of the Hyperthermophilic Archaebacterium Methanococcus

    E-print Network

    Suh, Se Won

    been supported by activity assays. The cofactor preference is explained by the presence of a glycine, which is conserved in MDHs but not in LDHs. The enzymatic assay showed that the MJ0490 protein possesses dehydrogenase; TmLDH, LDH from Thermotoga maritima; BlLDH, LDH from Bi®dobacterium longum; BsLDH, LDH from

  2. Losses and gains to the Scottish Flora

    Microsoft Academic Search

    Michael M. Scott

    1990-01-01

    Several examples are discussed of plants which have been exterminated from or introduced to Scotland as a result of human activities, and an attempt is made to draw lessons from these case histories. Four rare or threatened Scottish plants, Homogyne alpina, Mertensia maritima, Primula scotica, and Pteridium aquilinum ssy. latiusculum are considered to illustrate future plant conservation imperatives. Threats to

  3. The importance of salt-marsh wetness for seed exploitation by dabbling ducks Anas sp

    Microsoft Academic Search

    Ole R. Therkildsen; Thomas Bregnballe

    2006-01-01

    The relationship between the inundation of a salt marsh in southeast Denmark not subject to lunar tides and the availability and predation of seeds of the annuals Salicornia spp. and Suada maritima by autumn staging dabbling ducks was studied by carrying out exclosure experiments over the course of 2 years. There was a marked difference in the wetness of the salt

  4. Manuel d'tude et de gestion des oiseaux et de leurs habitats en zones ctires, 2012 321 Prendre en compte les surfaces rellement exploitables

    E-print Network

    Paris-Sud XI, Université de

    (Mahéo, 2000-2005), hors Bécasseau violet Calidris maritima et Tourne- pierre à collier Arenaria interpres, s'alimentant surtout en substrat dur. Les superfi- cies exondées ont été estimées heure par heure

  5. Effects on shorebird numbers of disturbance, the loss of a roost site and its replacement by an artificial island at Hartlepool, Cleveland

    Microsoft Academic Search

    Niall H. K. Burton; Peter R. Evans; M. Andrew Robinson

    1996-01-01

    Hartlepool West Harbour contains nationally important high water roosts for wintering shorebirds, including purple sandpipers Calidris maritima, turnstones Arenaria interpres and knots Calidris canutus. Redevelopment of the site, starting in summer 1991, replaced the dilapidated stone pier used formerly as the main roost site with a new pier and an island built specially for the birds. Maximum numbers of turnstone,

  6. Gene Transfer & Hybridization Studies in Hyperthermophilic Species

    SciTech Connect

    Nelson, Karen E.

    2005-10-14

    A. ABSTRACT The importance of lateral gene transfer (LGT) in the evolution of microbial species has become increasingly evident with each completed microbial genome sequence. Most significantly, the genome of Thermotoga maritima MSB8, a hyperthermophilic bacterium isolated by Karl Stetter and workers from Vulcano Italy in 1986, and sequenced at The Institute for Genomic Research (TIGR) in Rockville Maryland in 1999, revealed extensive LGT between % . this bacterium and members of the archaeal domain (in particular Archaeoglobus fulgidus, and Pyracoccus frcriosus species). Based on whole genome comparisons, it was estimated that 24% of the genetic information in this organism was acquired by genetic exchange with archaeal species, Independent analyses including periodicity analysis of the T. maritimu genomic DNA sequence, phylogenetic reconstruction based on genes that appear archaeal-like, and codon and amino acid usage, have provided additional evidence for LGT between T. maritima and the archaea. More recently, DiRuggiero and workers have identified a very recent LGT event between two genera of hyperthermophilic archaea, where a nearly identical DNA fragment of 16 kb in length flanked by insertion sequence (IS) elements, exists. Undoubtedly, additional examples of LGT will be identified as more microbial genomes are completed. For the present moment however, the genome sequence of T. maritima and other hyperthermophiles including P. furiosus, Pyrococcus horikoshii, Pyrococcus abyssi, A. fulgidus, and Aquifex aeolicus, have significantly increased out awareness of evolution being a web of life rather than a tree of life, as suggested by single gene phylogenies. In this proposal, we will aim to determine the extent of LGT across the hyperthemophiles, employing iY maritima as the model organism. A variety of biochemical techniques and phylogenetic reconstructions will allow for a detailed and thorough characterization of the extent of LGT in this species. The complete characterization of LGT in i? maritima will also allow for the identification of both false positive and false negative cases of LGT that have been described or overlooked respectively.

  7. Beneficial Insects

    NSDL National Science Digital Library

    0000-00-00

    Tutorials on insect predators that feed on insect and mite pests. Each tutorial has 50 questions; incorrect answers lead to additional information. Covers brown lacewings, ambush bugs, dragonflies, damselflies, paper wasps, earwigs, long-legged flies, predaceous mites, damsel bugs, minute pirate bug, tiger beetles, tachnid flies, parasitic nematodes, entomopathogenic fungi and viruses. Requires Windows. SOme illustrations may be most apporopriate for the southern U.S. A couple of the questions have rather arbitrary answers; in general, the tutorials are well constructed and the information is accurate. Requires Windows operating system; program must be downloaded to the comptuer's hard drive, but once loaded is easy to launch and use. $15. Part number SW 154.

  8. Embryos of the Viviparous Dermapteran, Arixenia esau Develop Sequentially in Two Compartments: Terminal Ovarian Follicles and the Uterus

    PubMed Central

    Tworzydlo, Waclaw; Kisiel, Elzbieta; Bilinski, Szczepan M.

    2013-01-01

    Three main reproductive strategies have been described among insects: most common oviparity, ovoviviparity and viviparity. In the latter strategy, the embryonic development takes place within the body of the mother which provides gas exchange and nutrients for embryos. Here we present the results of histological and EM analyses of the female reproductive system of the viviparous earwig, Arixenia esau, focusing on all the modifications related to the viviparity. We show that in the studied species the embryonic development consists of two “physiological phases” that take place in two clearly disparate compartments, i.e. the terminal ovarian follicle and the uterus. In both compartments the embryos are associated with synthetically active epithelial cells. We suggest that these cells are involved in the nourishment of the embryo. Our results indicate that viviparity in arixeniids is more complex than previously considered. We propose the new term “pseudoplacento-uterotrophic viviparity” for this unique two-phase reproductive strategy. PMID:23667700

  9. Determination of substrate specificities against ?-glucosidase A (BglA) from Thermotoga maritime: a molecular docking approach.

    PubMed

    Rajoka, Muhammad Ibrahim; Idrees, Sobia; Ashfaq, Usman Ali; Ehsan, Beenish; Haq, Asma

    2015-01-28

    Thermostable enzymes derived from Thermotoga maritima have attracted worldwide interest for their potential industrial applications. Structural analysis and docking studies were preformed on T. maritima ?-glucosidase enzyme with cellobiose and pNP-linked substrates. The 3D structure of the thermostable ?-glucosidase was downloaded from the Protein Data Bank database. Substrates were downloaded from the PubCehm database and were minimized using MOE software. Docking of BglA and substrates was carried out using MOE software. After analyzing docked enzyme/substrate complexes, it was found that Glu residues were mainly involved in the reaction, and other important residues such as Asn, Ser, Tyr, Trp, and His were involved in hydrogen bonding with pNP-linked substrates. By determining the substrate recognition pattern, a more suitable ?-glucosidase enzyme could be developed, enhancing its industrial potential. PMID:25179901

  10. The Late-Weichselian Flora of the Isle of Man.

    PubMed

    Dickson, C A; Dickson, J H; Mitchell, G F

    1970-03-26

    The last glacial deposits of the Ballaugh-Kirkmichael area in the north-east of the Isle of Man have been investigated by analysis of pollen and macroscopic fossils and by radiocarbon dating. Assemblages totalling over 160 taxa of vascular plants and mosses have been recorded from strata referred to Late-Weichselian zones I, II and III. Among the most noteworthy species are 46 not now living on the island; these include Dianthus deltoides, Juncus balticus, Lychnis viscaria, Ranunculus hyperboreus, Sibbaldia procumbens, Meesia tristicha, Helodium blandowii and Polytrichum norvegicum. The vegetation comprised a great diversity of communities of open, largely calcareous grassland, snow beds, mires both base-rich and base-poor, flushes, freshwater, inundated flats and calcareous dunes. Saline conditions are indicated by Glaux maritima and Triglochin maritima. Trees were represented only by Betula and the taller shrubs by Juniperus and Salix. PMID:22408824

  11. A variable-temperature direct electrochemical study of metalloproteins from hyperthermophilic microorganisms involves in hydrogen production from pyruvate

    SciTech Connect

    Smith, E.T.; Blamey, J.; Zhou, Z.Z.; Adams, M.W.W. [Univ. of Georgia, Athens, GA (United States)

    1995-05-30

    The hyperthomophilic bacterium Thermotoga maritima and the hyperthermolic archaeon Pyrococcus furiosus grow optimally at 80{degrees} and 100{degrees}C, respectively, by the fermentation of carbohydrates to organic acids, CO{sub 2}, and H{sub 2}. Pyruvate is a major source of reductant for H{sub 2} production during fermentation, and pyruvate ferredoxin oxidoreductase (POR), a 4Fe-type ferredoxin, and hydrogenase have been previously purified from both species. P. furiosus utilizes copper-iron-containing POR and a nickel-iron-containing hydrogenase, whereas the POR of T. maritima lacks copper and its hydrogenase lacks nickel. For all four enzymes and for the two ferredoxins, we have determined their reproduction potentials (E{degrees}` and, where possible, thermodynamic parameters associated with electron transfer {Delta}S{degrees} and {Delta}H{degrees}), using differential pulse voltammetry at temperatures ranging from 25 to 95{degrees}C. 55 refs., 7 fig., 2 tabs.

  12. Large methyl halide emissions from south Texas salt marshes

    NASA Astrophysics Data System (ADS)

    Rhew, R. C.; Whelan, M. E.; Min, D.-H.

    2014-06-01

    Coastal salt marshes are natural sources of methyl chloride (CH3Cl) and methyl bromide (CH3Br) to the atmosphere, but measured emission rates vary widely by geography. Here we report large methyl halide fluxes from subtropical salt marshes of south Texas. Sites with the halophytic plant, Batis maritima, emitted methyl halides at rates that are orders of magnitude greater than sites containing other vascular plants or macroalgae. B. maritima emissions were generally highest at midday; however, diurnal variability was more pronounced for CH3Br than CH3Cl, and surprisingly high nighttime CH3Cl fluxes were observed in July. Seasonal and intra-site variability were large, even taking into account biomass differences. Overall, these subtropical salt marsh sites show much higher emission rates than temperate salt marshes at similar times of the year, supporting the contention that low-latitude salt marshes are significant sources of CH3Cl and CH3Br.

  13. Large methyl halide emissions from south Texas salt marshes

    NASA Astrophysics Data System (ADS)

    Rhew, R. C.; Whelan, M. E.; Min, D.-H.

    2014-11-01

    Coastal salt marshes are natural sources of methyl chloride (CH3Cl) and methyl bromide (CH3Br) to the atmosphere, but measured emission rates vary widely by geography. Here we report large methyl halide fluxes from subtropical salt marshes of south Texas. Sites with the halophytic plant, Batis maritima, emitted methyl halides at rates that are orders of magnitude greater than sites containing other vascular plants or macroalgae. B. maritima emissions were generally highest at midday; however, diurnal variability was more pronounced for CH3Br than CH3Cl, and surprisingly high nighttime CH3Cl fluxes were observed in July. Seasonal and intra-site variability were large, even taking into account biomass differences. Overall, these subtropical salt marsh sites show much higher emission rates than temperate salt marshes at similar times of the year, supporting the contention that low-latitude salt marshes are significant sources of CH3Cl and CH3Br.

  14. Effect of habitat quality on diet flexibility in Barbary macaques.

    PubMed

    Ménard, Nelly; Motsch, Peggy; Delahaye, Alexia; Saintvanne, Alice; Le Flohic, Guillaume; Dupé, Sandrine; Vallet, Dominique; Qarro, Mohamed; Tattou, Mohamed Ibn; Pierre, Jean-Sébastien

    2014-07-01

    Barbary macaques live in extreme temperate environments characterized by strongly seasonal resource availability. They are mainly terrestrial while foraging, harvesting food from the herbaceous layer. These monkeys are threatened mainly because of anthropogenic habitat degradation. We studied the adaptive capacities of wild groups of Barbary macaques that lived in different cedar forests undergoing varying extents of grazing pressure from domestic livestock. In all three sites, diet varied seasonally. Heavy grazing led to a significant decrease in herbaceous production and species richness. As a consequence, the monkeys' diet in this poor habitat showed a decreased plant species richness. Moreover, it incorporated fewer above-ground herbaceous resources, and a greater proportion of subterranean resources (especially hypogeous fungi and subterranean invertebrates such as earthworms, eggs and adults of earwigs, and ant's larvae) than the diet of monkeys inhabiting ungrazed forest. Cedar bark, cedar strobiles, earthworms, and earwigs were part of the monkeys' diet only in grazed forest. Monkeys in heavily grazed forest compensated for a lack of herbaceous foods by eating subterranean foods preferentially to tree and shrub products. The foods they consumed take longer to harvest and process than the seeds or leaves consumed by Barbary macaques in less heavily grazed forest habitats. Our results suggest that monkeys do differ in their diets according to the degree of habitat change induced by human activities. They also highlight the dietary flexibility of Barbary macaques as a key element that allows them to cope with degraded habitats. We later compare the dietary adjustments of Barbary macaques facing environmental change to dietary strategies of other macaques and temperate-zone primates. PMID:24573596

  15. Mobility of Pb in salt marshes recorded by total content and stable isotopic signature

    Microsoft Academic Search

    Miguel Caetano; Nuno Fonseca; Rute Cesário Carlos Vale

    2007-01-01

    Total lead and its stable isotopes were analysed in sediment cores, leaves, stem and roots of Sacorconia fruticosa and Spartina maritima sampled from Tagus (contaminated site) and Guadiana (low anthropogenic pressure) salt marshes. Lead concentration in vegetated sediments from the Tagus marsh largely exceeded the levels in non-vegetated sediments. Depth profiles of 206Pb\\/207Pb and 206Pb\\/208Pb showed a decrease towards the

  16. Capybara ( Hydrochaeris hydrochaeris rodentia: Hydrochaeridae): A mammalian seagrass herbivore

    Microsoft Academic Search

    Joel C. Creed

    2004-01-01

    This note reports an unknown trophic interaction between a mammalian herbivore, the capybara (Hydrochaeris hydrochaeris), and the seagrassRuppia maritima (wigeongrass) and compares the feeding behavior of capybaras to other seagrass grazers. Observations were made in Spring\\u000a 2002 in the Barra Grande, a small, shallow, moderately stratified, bar-built estuary at Ilha Grande, Rio de Janeiro State,\\u000a southeast Brazil. The activities of

  17. Food habits and distribution of wintering canvasbacks, Aythya valisineria , on Chesapeake Bay

    Microsoft Academic Search

    Matthew C. Perry; Francis M. Uhler

    1988-01-01

    Baltic clams (Macoma balthica) were the predominant food items of 323 canvasbacks (Aythya valisineria) collected throughout Chesapeake Bay during 1970–1979. Natural vegetation constituted 4% of the food volume. Widgeongrass\\u000a (Ruppia maritima) and redhead grass (Potamogeton perfoliatus) constituted the greatest percent volume and frequency of occurrence among the plant species, whereas wild celery (Vallisneria americana) constituted only a trace of the

  18. Analysis of DNA polymorphisms in sugar beet ( Beta vulgaris L.) and development of an SNP-based map of expressed genes

    Microsoft Academic Search

    Katharina Schneider; Dagmar Kulosa; Thomas Rosleff Soerensen; Silke Möhring; Martin Heine; Gregor Durstewitz; Andreas Polley; Eberhard Weber; Jamsari; Jens Lein; Uwe Hohmann; Emma Tahiro; Bernd Weisshaar; Britta Schulz; Georg Koch; Christian Jung; Martin Ganal

    2007-01-01

    A panel of 13 sugar beet lines and one genotype each of the Beta vulgaris cultivars red beet and Swiss chard, and B. vulgaris ssp. maritima were used to identify polymorphisms in alignments of genomic DNA sequences derived from 315 EST- and 43 non-coding RFLP-derived\\u000a loci. In sugar beet lines, loci of expressed genes showed an average SNP frequency of

  19. Nectar-carbohydrate production and composition vary in relation to nectary anatomy and location within individual flowers of several species of Brassicaceae

    Microsoft Academic Search

    Arthur R. Davis; Jeffrey D. Pylatuik; Joelle C. Paradis; Nicholas H. Low

    1998-01-01

    .   Nectar-carbohydrate production and composition were investigated by high-performance liquid chromatography and enzymology\\u000a in nine species from five tribes of the Brassicaceae. In six species (Arabidopsis thaliana (L.) Heynh., Brassica napus L., B. rapa L., Lobularia maritima (L.) Desv., Raphanus sativus L., Sinapis arvensis L.) that produced nectar from both lateral nectaries (associated with the short stamens) and median nectaries

  20. Gene Transfer & Hybridization Studies in Hyperthermophilic Species

    Microsoft Academic Search

    Karen E

    2005-01-01

    A. ABSTRACT;\\u000aThe importance of lateral gene transfer (LGT) in the evolution of microbial species has;\\u000abecome increasingly evident with each completed microbial genome sequence. Most;\\u000asignificantly, the genome of Thermotoga maritima MSB8, a hyperthermophilic bacterium;\\u000aisolated by Karl Stetter and workers from Vulcano Italy in 1986, and sequenced at The Institute;\\u000afor Genomic Research (TIGR) in Rockville Maryland in

  1. Sulphide tolerance in coastal halophytes

    Microsoft Academic Search

    D. C. Havill; A. Ingold; J. Pearson

    1985-01-01

    The effect of sulphide on the growth of several species of salt-marsh plants was investigated. Relative growth rates were significantly reduced in two upper-marsh species, Festuca rubra and Atriplex patula, and in the lower-marsh species Puccinellia maritima. However the growth of Salicornia europaea, a species frequently associated with sulphide-containing sediments, was unaffected. In a separate experiment the wide ranging halophyte

  2. Effects of environmental context on the susceptibility of Atriplex patula to attack by herbivorous beetles

    Microsoft Academic Search

    Tatyana A. Rand

    1999-01-01

    The susceptibility of plants to attack by insect herbivores often depends on local environmental conditions. This study documents\\u000a variation in herbivore damage by the chrysomelid beetle Erynephala maritima to the annual forb Atriplex patula in two microhabitats within New England salt marshes: bare patches and dense matrix vegetation. Environmental conditions\\u000a within bare patches differ from those within matrix vegetation in

  3. Heavy metal uptake by selected marsh plant species grown in hydroponic cultures

    Microsoft Academic Search

    C. R. Lee; T. C. Sturgis; M. C. Landin

    1975-01-01

    Eight marsh plant species (Cyperus esculentus, Scirpus validus, Spartina patens, Scirpus robustus, Triglochin maritima, Distichlis spicata, Spartina alterniflora, and Spartina foliosa) were grown under greenhouse conditions in chemically controlled nutrient solutions. Heavy metals (zinc, cadmium, nickel, chromium, and lead) were added to the nutrient solutions at levels of 0, 0.5, and 1.0 mg\\/l. Plant parts (leaves, rhizomes, tubers, and roots)

  4. Stratigraphic and Ecophysical Characterizations of Salt Pools: Dynamic Landforms of the Webhannet Salt Marsh, Wells, ME, USA

    Microsoft Academic Search

    Kristin R. Wilson; Joseph T. Kelley; Arie Croitoru; Michele Dionne; Daniel F. Belknap; Robert Steneck

    2009-01-01

    Salt pools are water-filled depressions common to north-temperate salt marshes. In Wells, ME, USA, cores reveal a unique salt\\u000a pool signature consisting of water-saturated dark-gray mud often containing fragments of Ruppia maritima. Cores through pool sediment reenter salt marsh peat, not tidal flat sediment, demonstrating that most pools are of secondary\\u000a origin. A principal component analysis of attribute data collected

  5. Chromosome Evolution in the Thermotogales: Large-Scale Inversions and Strain Diversification of CRISPR Sequences

    Microsoft Academic Search

    Robert T. DeBoy; Emmanuel F. Mongodin; Joanne B. Emerson; Karen E. Nelson

    2006-01-01

    In the present study, the chromosomes of two members of the Thermotogales were compared. A whole-genome alignment of Thermotoga maritima MSB8 and Thermotoga neapolitana NS-E has revealed numerous large-scale DNA rearrangements, most of which are associated with CRISPR DNA repeats and\\/or tRNA genes. These DNA rearrangements do not include the putative origin of DNA replication but move within the same

  6. Abundance of wigeongrass during winter and use by herbivorous waterbirds in a texas coastal marsh

    Microsoft Academic Search

    Kevin M. Hartke; Kevin H. Kriegel; G. Matt Nelson; M. Todd Merendino

    2009-01-01

    Wigeongrass (Ruppia maritima), a submerged aquatic plant inhabiting estuarine wetlands, is an important winter food for waterbirds along the Texas Gulf\\u000a Coast. We examined availability of wigeongrass at Mad Island Wildlife Management Area, Texas, USA by estimating aboveground\\u000a biomass from October through January, 1998–1999 and 2001–2002. We also used an exclosure experiment to determine the extent\\u000a to which herbivory by

  7. The Structure of a Bacterial DUF199\\/WhiA Protein: Domestication of an Invasive Endonuclease

    Microsoft Academic Search

    Brett K. Kaiser; Matthew C. Clifton; Betty W. Shen; Barry L. Stoddard

    2009-01-01

    SUMMARY Proteins of the DUF199 family, present in all Gram- positive bacteria and best characterized by the WhiA sporulation control factor in Streptomyces coelicolor, are thought to act as genetic regulators. The crystal structure of the DUF199\\/WhiA protein from Thermatoga maritima demonstrates that these proteins possess a bipartite structure, in which a degenerate N-terminal LAGLIDADG homing endo- nuclease (LHE) scaffold

  8. Estimating the contribution of Spartina anglica biomass to salt-marsh sediments using compound specific stable carbon isotope measurements

    Microsoft Academic Search

    Ian D. Bull; Pim F. van Bergen; Roland Bol; Sue Brown; Andrew R. Gledhill; Alan J. Gray; Douglas D. Harkness; Simon E. Woodbury; Richard P. Evershed

    1999-01-01

    Compound specific ?13C analyses were used to determine the relative input of a C4 temperate grass (Spartina anglica) to primary biomass in a salt-marsh sediment. Lipid distributions revealed a C32n-alkanol homologue as a characteristically dominant component of Spartina anglica whilst the cohabiting C3 species, Puccinellia maritima, exhibited a C26 maximum. The C32n-alkanol component was used to create an isotopic mixing

  9. Correlation between thermostability and stability of glycosidases in ionic liquid

    Microsoft Academic Search

    Salim Ferdjani; Marina Ionita; Bimalendu Roy; Michel Dion; Zeineddine Djeghaba; Claude Rabiller; Charles Tellier

    2011-01-01

    The activity and stability of a ?-glycosidase (Thermus thermophilus) and two ?-galactosidases (Thermotoga maritima and Bacillus stearothermophilus) were studied in different hydrophilic ionic liquid (IL)\\/water ratios. For the ILs used, the glycosidases showed the best\\u000a stability and activity in 1,3-dimethylimidazolium methyl sulfate [MMIM][MeSO4] and 1,2,3-trimethylimidazolium methyl sulfate [TMIM][MeSO4]. A close correlation was observed between the thermostability of the enzymes and

  10. Selenium Levels in Biota from Irrigation Drainwater Impoundments in the San Joaquin Valley, California

    Microsoft Academic Search

    Douglas A. Barnum; David S. Gilmer

    1988-01-01

    Waterfowl, fish, invertebrates, and plants were collected from impoundments used for evaporating subsurface irrigation drainwater in Kings and Kern counties, California. Specimens were analyzed for trace elements with emphasis on selenium. Dry weight concentrations of total selenium ranged from 2.5 to 17 ?g\\/g in wigeongrass, Ruppia maritima; 7.6 to 30 ?g\\/g in water boatmen, Corixidae; 12 to 40 ?\\/g in

  11. Accumulation, distribution and cellular partitioning of mercury in several halophytes of a contaminated salt marsh.

    PubMed

    Castro, Rita; Pereira, Sofia; Lima, Ana; Corticeiro, Sofia; Válega, Mónica; Pereira, Eduarda; Duarte, Armando; Figueira, Etelvina

    2009-09-01

    This work evaluates the role of a plant community in mercury (Hg) stabilization and mobility in a contaminated Portuguese salt marsh. With this aim, the distribution of Hg in below and aboveground tissues, as well as the metal partitioning between cellular fractions (soluble and insoluble) in four different species (Triglochin maritima L., Juncus maritimus Lam, Sarcocornia perennis (Miller) A.J. Scott, and Halimione portulacoides (L.) Aellen) was assessed. Mercury accumulation, translocation and compartmentation between organs and cellular fractions were related to the plant species. Results showed that the degree of Hg absorption and retention was influenced both by environmental parameters and metal translocation/partitioning strategies. Different plant species presented different allocation patterns, with marked differences between monocots (T. maritima and J. maritimus) and dicots (S. perennis, H. portulacoides). Overall, the two monocots, in particular T. maritima showed higher Hg retention in the belowground organs whereas the dicots, particularly S. perennis presented a more pronounced translocation to the aboveground tissues. Considering cellular Hg partitioning, all species showed a higher Hg binding to cell walls and membranes rather than in the soluble fractions. This strategy can be related to the high degree of tolerance observed in the studied species. These results indicate that the composition of salt marsh plant communities can be very important in dictating the Hg mobility within the marsh ecosystem and in the rest of the aquatic system as well as providing important insights to future phytoremediation approaches in Hg contaminated salt marshes. PMID:19595432

  12. Biosynthesis of cyanogenic glucosides: in vitro analysis of the glucosylation step.

    PubMed

    Hösel, W; Schiel, O

    1984-02-15

    The last step in the biosynthesis of cyanogenic glucosides, the glucosylation of the cyanohydrin intermediate, has been investigated in detail using Triglochin maritima seedlings. The glucosyltransferase activity is not associated with membranes and appears to be a "soluble" enzyme. The cyanohydrin intermediate, which is formed by hydroxylation of 4-hydroxyphenylacetonitrile by a membrane-bound enzyme, is free to equilibrate in the presence of the glucosyltransferase and UDPG, because it can be trapped very efficiently. This indicates that this intermediate is not channeled (unlike some of the other intermediates), although it is probably the most labile of all of them. The glucosyltransferase of T. maritima responsible for the glucosylation of the cyanohydrin was separated from another glucosyltransferase, which used 4-hydroxybenzylalcohol as a substrate, and purified over 200-fold. It catalyzed the glucose transfer from UDPG to only 4-hydroxymandelonitrile and 3,4-dihydroxymandelonitrile, giving rise to the respective cyanogenic glucosides. Although the activities with these two substrates behaved differently in certain respects (e.g., extent of inactivation during purification and difference in activation by higher salt concentrations), most of the data acquired favor the view that only one enzyme in T. maritima is responsible for the glucosylation of both substrates. PMID:6230992

  13. Screening of common Plantago species in Hungary for bioactive molecules and antioxidant activity.

    PubMed

    Gonda, S; Tóth, L; Parizsa, P; Nyitrai, M; Vasas, G

    2010-01-01

    Five species of Plantago genus, namely P. lanceolata, P. major, P. media, P. altissima and P. maritima were screened for iridoid content (CE-MEKC), total caffeoyl phenylethanoid glycoside (CPG) content and antioxidant activity (CUPRAC assay). The five species could be distinguished by TLC pattern analysis in a single run in a system commonly used for quality management of P. lanceolata leaves, as shown by cluster analysis of major bands; with the exception, that P. altissima and P. lanceolata did not show enough pattern difference to be fully separated. P. maritima was shown to have the highest antioxidant capacity (0.42 ?mol ascorbic acid equivalent (AAE)/g DW), and the highest level of CPGs (4.29%). P. altissima was shown to be chemically indistinguishable from P. lanceolata with repsect to iridoid content (aucubin 0.55 ± 0.04%, 0.68 ± 0.23%, catalpol 0.66 ± 0.13% and 0.89 ± 0.22%, respectively), CPG content (2.40 ± 0.38% and 2.54 ± 0.56%, respectively) and antioxidant capacity (0.2206 ± 0.0290 and 0.2428 ± 0.0191 ?mol AAEAC/g DW). The presented data show the potency of medicinal use of Hungarian wild populations of the studied five species, especially in the case of P. maritima, and that P. altissima can be a potential replacement of P. lanceolata in herbal mixtures. PMID:21565762

  14. Mobility of Pb in salt marshes recorded by total content and stable isotopic signature.

    PubMed

    Caetano, Miguel; Fonseca, Nuno; Cesário Carlos Vale, Rute

    2007-07-15

    Total lead and its stable isotopes were analysed in sediment cores, leaves, stem and roots of Sacorconia fruticosa and Spartina maritima sampled from Tagus (contaminated site) and Guadiana (low anthropogenic pressure) salt marshes. Lead concentration in vegetated sediments from the Tagus marsh largely exceeded the levels in non-vegetated sediments. Depth profiles of (206)Pb/(207)Pb and (206)Pb/(208)Pb showed a decrease towards the surface ((206)Pb/(207)Pb=1.160-1.167) as a result of a higher proportion of pollutant Pb components. In contrast, sediments from Guadiana marsh exhibited low Pb concentrations and an uniform isotopic signature ((206)Pb/(207)Pb=1.172+/-0.003) with depth. This suggests a homogeneous mixing of mine-derived particles and pre-industrial sediments with minor inputs of anthropogenic Pb. Lead concentrations in roots of plants from the two marshes were higher than in leaves and stems, indicating limited transfer of Pb to aerial parts. A similar Pb isotopic signature was found in roots and in vegetated sediments, indicating that Pb uptake by plants reflects the input in sediments as determined by a significant anthropogenic contribution of Pb at Tagus and by mineralogical Pb phases at Guadiana. The accumulation in roots from Tagus marsh (max. 2870 microg g(-1) in S. fruticosa and max. 1755 microg g(-1) in S. maritima) clearly points to the dominant role of belowground biomass in the cycling of anthropogenic Pb. The fraction of anthropogenic Pb in belowground biomass was estimated based on the signature of anthropogenic Pb components in sediments ((206)Pb/(207)Pb=1.154). Since no differences exist between Pb signature in roots and upper sediments, the background and anthropogenic levels of Pb in roots were estimated. Interestingly, both background and anthropogenic Pb in roots exhibited a maximum at the same depth, although the proportion of anthropogenic Pb was relatively constant with depth (83+/-4% for S. fruticosa and 74+/-8% for S. maritima). PMID:17320933

  15. Genes for the major structural components of Thermotogales species' togas revealed by proteomic and evolutionary analyses of OmpA and OmpB homologs

    SciTech Connect

    Petrus, Amanda K.; Swithers, Kristen S.; Ranjit, Chaman R.; Wu, Si; Brewer, Heather M.; Gogarten, J Peter; Pasa-Tolic, Ljiljana; Noll, Kenneth M.

    2012-06-29

    The unifying structural characteristic of members of the bacterial order Thermotogales is an unusual cell envelope that includes a loose-fitting sheath around each cell, often called a toga. Only two toga-associated structural proteins have been identified in Thermotoga maritima: the anchor protein OmpA1 (previously termed Omp?) and the porin OmpB (previously termed Omp?). The gene encoding OmpA (ompA1) was assigned in the genome sequence to TM0477, but because no peptide sequence was available for OmpB, its gene (ompB) was not annotated. Here we identify the ompB gene as TM0476, determined by LC/MS/MS analysis of the native OmpB protein purified from T. maritima cells. The purified Omp? had ?-sheet secondary structure as determined by circular dichroism. Analysis of the sequence of ompB product shows it has porin characteristics including a carboxy terminus anchoring motif and a porin-specific amino acid composition. Orthologs of ompB were found in the genomes of some, but not all, Thermotogales. Those without orthologs have putative analogs. Phylogenetic analyses of OmpA1 revealed that each species of the Thermotogales has one to three OmpA homologs. T. maritima has two OmpA homologs, encoded by ompA1(TM0477) and ompA2 (TM1729), both of which were found in the toga protein-enriched cell extracts. These annotations of the genes encoding toga structural proteins will guide future examinations of the structure and function of this unusual lineage-defining cell sheath.

  16. Effects of migratory geese on plant communities of an Alaskan salt marsh

    USGS Publications Warehouse

    Zacheis, A.; Hupp, J.W.; Ruess, R.W.

    2001-01-01

    1. We studied the effects of lesser snow geese (Anser caerulescens caerulescens) and Canada geese (Branta canadensis) on two salt marsh plant communities in Cook Inlet, Alaska, a stopover area used during spring migration. From 1995 to 1997 we compared plant species composition and biomass on plots where geese were excluded from feeding with paired plots where foraging could occur. 2. Foraging intensity was low (650-1930 goose-days km-2) compared to other goose-grazing systems. 3. Canada geese fed mainly on above-ground shoots of Triglochin maritimum, Puccinellia spp. and Carex ramenskii, whereas the majority of the snow goose diet consisted of below-ground tissues of Plantago maritima and Triglochin maritimum. 4. Plant communities responded differently to goose herbivory. In the sedge meadow community, where feeding was primarily on above-ground shoots, there was no effect of grazing on the dominant species Carex ramenskii and Triglochin maritimum. In the herb meadow community, where snow geese fed on Plantago maritima roots and other below-ground tissues, there was a difference in the relative abundance of plant species between treatments. Biomass of Plantago maritima and Potentilla egedii was lower on grazed plots compared with exclosed, whereas biomass of Carex ramenskii was greater on grazed plots. There was no effect of herbivory on total standing crop biomass in either community. The variable effect of herbivory on Carex ramenskii between communities suggests that plant neighbours and competitive interactions are important factors in a species' response to herbivory. In addition, the type of herbivory (above- or below-ground) was important in determining plant community response to herbivory. 5. Litter accumulation was reduced in grazed areas compared with exclosed in both communities. Trampling of the previous year's litter into the soil surface by geese incorporated more litter into soils in grazed areas. 6. This study illustrates that even light herbivore pressure can alter plant communities and affect forage availability.

  17. Prokaryotes in salt marsh sediments of Ria de Aveiro: Effects of halophyte vegetation on abundance and diversity

    NASA Astrophysics Data System (ADS)

    Oliveira, Vanessa; Santos, Ana L.; Aguiar, Claúdia; Santos, Luisa; Salvador, Ângelo C.; Gomes, Newton C. M.; Silva, Helena; Rocha, Sílvia M.; Almeida, Adelaide; Cunha, Ângela

    2012-09-01

    The aim of this study was to investigate the influence of monospecific colonization of sediment stands by Spartina maritima or Halimione portulacoides on benthic prokaryote assemblages in a salt marsh located in Ria de Aveiro (Portugal). The distribution of Bacteria, Archaea and sulfate-reducing bacteria (SRB) in sediments with monospecific plant stands and in unvegetated sediments was characterized by Fluorescence In Situ Hybridization (FISH). Total prokaryote abundance (0.4 × 109-1.7 × 109 cells gdw-1) was highest in sediments from the surface layer. The domain Bacteria comprised approximately 40% of total prokaryote communities with the highest percentages occurring in the surface layer. Archaeal cells corresponded to an average of 25% of total prokaryote population, with higher abundance in the vegetation banks, and displaying homogeneous vertical distribution. The relative abundance of SRB represented approximately 3% of total 4', 6-diamidino-2-phenylindole dihydrochloride (DAPI) stained cells at unvegetated sediment and H. portulacoides stand and 7% at S. maritima stand. Headspace solid-phase microextraction (HS-SPME) combined with Comprehensive Two-Dimensional Gas Chromatography-Time-of-Flight Mass Spectrometry (GC × GC-ToFMS) was used to analyse the volatile and semi-volatile fraction of root exudates. A total of 171 compounds were identified and Principal Component Analysis showed a clear separation between the chemical composition (volatile and semi-volatile organic compounds) of the exudates of the two plants. The patterns of vertical distribution and differences in the proportion of SRB and Archaea in the prokaryote communities developing in sediments colonized by Spartina maritima or Halimione portulacoides suggest the existence of plant-specific interactions between halophyte vegetation and estuarine sediment bacteria in Ria de Aveiro salt marshes, exerted via sediment lithology and root-derived exudates.

  18. Screening seeds of Scottish plants for antibacterial activity.

    PubMed

    Kumarasamy, Yashodharan; Cox, Philip John; Jaspars, Marcel; Nahar, Lutfun; Sarker, Satyajit Dey

    2002-11-01

    Based on ethnopharmacological and taxonomic information, seeds of 21 Scottish plant species from 14 different families were obtained from authentic seed suppliers. Their n-hexane, dichloromethane and methanol extracts were assessed for antibacterial activity against 11 pathogenic bacterial species. Methanol extracts of 11 plant species showed significant antibacterial activity. Malva moschata and Prunus padus were active against five bacterial species, Reseda lutea against four, Centaurium erythraea and Crithmum maritimum against three, Calluna vulgaris against two, and Armeria maritima, Centaurea scabiosa, Daucus carota, Rosa canina and Stellaria holostea against one bacterial species. C. erythraea and P. padus were also active against methicillin resistant Staphylococcus aureus. PMID:12413709

  19. A redescription of Rhysida celeris (Humbert & Saussure, 1870), with a proposal of eight new synonyms (Scolopendromorpha, Scolopendridae, Otostigminae)

    PubMed Central

    Chagas-Júnior, Amazonas

    2013-01-01

    Abstract Seven species of the genus Rhysida Wood, 1862 from Venezuela and one subspecies from Peru described by Manuel Angel González Sponga and Wolfgang Bücherl respectively, are revised. Rhysida caripensis González-Sponga, 2002, Rhysida neoespartana González-Sponga, 2002, Rhysida guayanica González-Sponga, 2002, Rhysida maritima González-Sponga, 2002, Rhysida monaguensis González-Sponga, 2002, Rhysida porlamarensis González-Sponga 2002, Rhysida sucupanensis González-Sponga, 2002 and Rhysida celeris andina Bücherl, 1953 are junior synonyms of Rhysida celeris (Humbert & Saussure, 1870), which is redescribed and illustrated for the first time. Its geographic distribution is updated and a map showing its distribution is presented. PMID:23653497

  20. On salt marsh vegetation in North Korea

    Microsoft Academic Search

    Ji?í Kolbek; Ji?í Dostálek; Ivan Jarolímek; Ivan Ostrý; Li Sek-Ha

    1989-01-01

    The salt marsh vegetation on the west coast of North Korea was studied by the method of the Zürich-Montpellier school. The\\u000a following communities were distinguished:Suaedetum japonicae, Scirpetum iseensis, Artemisietum fukudo, and the following were described as new:Triglochini maritimae-Phragmitetum communis, Artemisio capillaris-Salsoletum komarovii andSalsolo komarovii-Rosetum rugosae. The phytocoenological material was also analysed by means of numerical techniques.\\u000a \\u000a The population density ofSuaeda

  1. Induced Changes in the Amino Acid Profile of Biomphalaria alexandrina Molluscan Host to Schistosoma mansoni Using Sublethal Concentrations of Selected Plant Molluscicides

    NASA Astrophysics Data System (ADS)

    Sanad Soliman, Mahmoud; El-Ansary, Afaf

    Amino acid profiles of control and Solanum nigrum, Ambrosia maritima, Thymelaea hirsute, Sinapis arvensis, Peganum haramala and Callistemon lanceolatus-treated Biomphalaria alexandrina snails were investigated in a trial to correlate the amino acid profile of treated snails to their previously reported molluscicidal and biological effects. Amino acid profiles of the snails were greatly manipulated with the treatment of dry powdered sublethal concentrations of the six studied plant molluscicides. The disturbed amino acid profiles of treated snails were discussed in relation to the decrease in snail's egg laying capacity, reduction of their compatibility for the development of the schistosome larvae and cercarial penetration of mammalian skin.

  2. Remote sensing of biomass of salt marsh vegetation in France

    NASA Technical Reports Server (NTRS)

    Gross, M. F.; Klemas, V.; Levasseur, J. E.

    1988-01-01

    Spectral data (gathered using a hand-held radiometer) and harvest data were collected from four salt marsh vegetation types in Brittany, France, to develop equations predicting live aerial biomass from spectral measurements. Remote sensing estimates of biomass of the general salt marsh community (GSM) and of Spartina alterniflora can be obtained throughout the growing season if separate biomass prediction equations are formulated for different species mixtures (for the GSM) and for different canopy types (for S. alterniflora). Results suggest that remote sensing will not be useful for predicting Halimione portulacoides biomass, but can be used to estimate Puccinellia maritima biomass early in the growing season.

  3. Parent-offspring conflict and the genetic trade-offs shaping parental investment.

    PubMed

    Kölliker, Mathias; Boos, Stefan; Wong, Janine W Y; Röllin, Lilian; Stucki, Dimitri; Raveh, Shirley; Wu, Min; Meunier, Joël

    2015-01-01

    The genetic conflict between parents and their offspring is a cornerstone of kin selection theory and the gene-centred view of evolution, but whether it actually occurs in natural systems remains an open question. Conflict operates only if parenting is driven by genetic trade-offs between offspring performance and the parent's ability to raise additional offspring, and its expression critically depends on the shape of these trade-offs. Here we investigate the occurrence and nature of genetic conflict in an insect with maternal care, the earwig Forficula auricularia. Specifically, we test for a direct response to experimental selection on female future reproduction and correlated responses in current offspring survival, developmental rate and growth. The results demonstrate genetic trade-offs that differ in shape before and after hatching. Our study not only provides direct evidence for parent-offspring conflict but also highlights that conflict is not inevitable and critically depends on the genetic trade-offs shaping parental investment. PMID:25880586

  4. Insects did it first: a micropatterned adhesive tape for robotic applications.

    PubMed

    Gorb, Stanislav N; Sinha, Mitali; Peressadko, Andrei; Daltorio, Kathryn A; Quinn, Roger D

    2007-12-01

    Based on the structural and experimental studies of more than 300 insect species from different lineages, we have developed and characterized a bioinspired polymer material with the ability of multiple glue-free bonding and debonding. The material surface is covered with a pattern of microstructures, which resembles the geometry of tenent hairs previously described from the feet of flies, beetles, earwigs and other insects. The tape with such a microstructure pattern demonstrates at least two times higher pull-off force per unit apparent contact area compared to the flat polymer. Additionally, the tape is less sensitive to contamination by dust particles than a commercially available pressure-sensitive adhesive tape. Even if the 'insect tape' is contaminated, it can be washed with a soap solution in water, in order to completely recover its adhesive properties. We have successfully applied the tape to the 120 g wall-climbing robot Mini-Whegs. Furthermore, the tape can be used for multiple adhering of objects to glass surfaces or as a protective tape for sensitive glass surfaces of optical quality. Another area of potential applications is gripping and manipulation of objects with smooth surfaces. PMID:18037721

  5. Diet of western Burrowing Owls wintering in southern Texas

    USGS Publications Warehouse

    Littles, C.J.; Williford, D.; Skoruppa, M.K.; Woodin, M.C.; Hickman, G.C.

    2007-01-01

    Winter diets of the western Burrowing Owl (Athene cunicularia hypugaea) are little known. We determined the diet of western Burrowing Owls wintering in southern Texas by analyzing the contents of 182 pellets collected over four winters (1999-2000, 2001-2002, 2002-2003, and 2003-2004) in three habitat types (agricultural, mainland grassland, and barrier island). Remains of a total of 7476 prey items were recovered, 98% of which were arthropods. Gryllidae (crickets) formed the largest component (50%) of the prey, followed by lepidopteran larvae (13%), beetles (8%), spiders (7%), and earwigs (6%). Although vertebrates, primarily small mammals and birds, represented only 2% of prey items by number, they represented most (71%) of the biomass. Northern pygmy mice (Baiomys taylori) and fulvous harvest mice (Reithrodontomys fulveccens) were the two most frequently consumed vertebrate species. In all habitats, arthropods, especially orthopterans, were the primary prey item by number, whereas vertebrates, primarily small mammals, were the most important by biomass. Greater consumption of arthropods by Burrowing Owls in agricultural areas may be a factor contributing to owl use of these highly altered environments. ?? 2007 The Raptor Research Foundation, Inc.

  6. A chemical signal of offspring quality affects maternal care in a social insect

    PubMed Central

    Mas, Flore; Haynes, Kenneth F.; Kölliker, Mathias

    2009-01-01

    Begging signals of offspring are condition-dependent cues that are usually predicted to display information about the short-term need (i.e. hunger) to which parents respond by allocating more food. However, recent models and experiments have revealed that parents, depending on the species and context, may respond to signals of quality (i.e. offspring reproductive value) rather than need. Despite the critical importance of this distinction for life history and conflict resolution theory, there is still limited knowledge of alternative functions of offspring signals. In this study, we investigated the communication between offspring and caring females of the common earwig, Forficula auricularia, hypothesizing that offspring chemical cues display information about nutritional condition to which females respond in terms of maternal food provisioning. Consistent with the prediction for a signal of quality we found that mothers exposed to chemical cues from well-fed nymphs foraged significantly more and allocated food to more nymphs compared with females exposed to solvent (control) or chemical cues from poorly fed nymphs. Chemical analysis revealed significant differences in the relative quantities of specific cuticular hydrocarbon compounds between treatments. To our knowledge, this study demonstrates for the first time that an offspring chemical signal reflects nutritional quality and influences maternal care. PMID:19439438

  7. Effects of monospecific banks of salt marsh vegetation on sediment bacterial communities.

    PubMed

    Oliveira, Vanessa; Santos, Ana L; Coelho, Francisco; Gomes, Newton C M; Silva, Helena; Almeida, Adelaide; Cunha, Angela

    2010-07-01

    The aim of this study was to understand if two species of salt marsh plants, widely distributed in European estuaries (Spartina maritima and Halimione portulacoides) differently influence the distribution, activity, and metabolic physiology of sediment bacterial communities in monospecific banks, in comparison with uncolonized sediment (control). Microbiological descriptors of abundance and activity were assessed along vertical profiles of sediments. Rates of activity of the extracellular enzymes beta-glucosidase, alpha-glucosidase, aminopeptidase, arylsulfatase, and phosphatase were generally higher in the vegetation banks in relation to control sediments where they were also less variable with depth. This is interpreted as an indirect effect related to supply of plant-derived polymeric substrates for bacterial growth. Parameters related to sediment texture (grain size, percent of fines or water content) showed significant relations with cell abundance or maximum hydrolysis rates, pointing to an indirect effect of plant colonization exerted through the modification of sediment physical properties. The profiles of utilization of sole-carbon-source (Biolog Ecoplates) showed that only the communities from the upper sediment layer of the S. maritima and the H. portulacoides banks exhibit consistent differences in terms of physiological profiles. Bacterial communities in control sediments exhibited the lowest physiological variability between surface and sub-surface communities. The results indicate that microbial colonization and organic matter decomposition are enhanced under the influence of salt marsh plants and confirm that plant coverage is a major determinant of the processes of organic matter recycling in intertidal estuarine sediments. PMID:20495797

  8. Evaluation of a Florida coastal golf complex as a local and watershed source of bioavailable contaminants.

    PubMed

    Lewis, Michael A; Quarles, Robert L; Dantin, Darrin D; Moore, James C

    2004-02-01

    Contaminant fate in coastal areas impacted by golf course runoff is not well understood. This report summarizes trace metal, pesticide and PCB residues for colonized periphyton, Ruppia maritima (widgeon grass), Callinectes sapidus Rathbun (blue crabs) and Crassostrea virginica Gemlin (Eastern oyster) collected from areas adjacent to a Florida golf course complex which receive runoff containing reclaimed municipal wastewater. Concentrations of 19 chlorinated pesticides and 18 PCB congeners were usually below detection in the biota. In contrast, 8 trace metals were commonly detected although concentrations were not usually significantly different for biota collected from reference and non-reference coastal areas. Residue concentrations in decreasing order were typically: zinc, arsenic, copper, chromium, lead, nickel, cadmium and mercury. Mean BCF values for the eight trace metals ranged between 160-57000 (periphyton), 79-11033 (R. maritima), 87-162625 (C. virginica) and 12-9800 (C. sapidus). Most trace metal residues in periphyton colonized adjacent to the golf complex, were either similar to or significantly less than those reported for periphyton colonized in nearby coastal areas impacted by urban stormwater runoff and treated municipal and industrial wastewater discharges. Consequently, the recreational complex does not appear to be a major source of bioavailable contaminants locally nor in the immediate watershed based on results for the selected biota. PMID:14972577

  9. Phylogeny, biogeography and evolution of Triglochin L. (Juncaginaceae) - Morphological diversification is linked to habitat shifts rather than to genetic diversification.

    PubMed

    von Mering, Sabine; Kadereit, Joachim W

    2015-02-01

    A species-level phylogeny is presented for Triglochin, the largest genus of Juncaginaceae (Alismatales) comprising about 30 species of annual and perennial herbs. Triglochin has an almost cosmopolitan distribution with Australia as centre of species diversity. Trans-Atlantic and trans-African disjunctions exist in the genus. Phylogenetic analyses were conducted based on molecular data obtained from nuclear (ITS, internal transcribed spacer) and chloroplast sequence data (psbA-trnH spacer, matK gene). Based on the phylogeny of the group divergence times were estimated and ancestral distribution areas reconstructed. Our data confirm the monophyly of Triglochin and resolve relationships between the major lineages of the genus. The sister group relationship between the Mediterranean/African T. bulbosa complex and the American T. scilloides (formerly Lilaea s.) is strongly supported. This clade is sister to the rest of the genus which contains two main clades. In the first, the widespread T. striata is sister to a clade comprising annual Triglochin species from Australia. The second clade comprises T. palustris as sister to the T. maritima complex, of which the latter is further divided into a Eurasian and an American subclade. Taxonomic diversity in some clades appears to be linked to habitat shifts and is not present in old but ecologically invariable lineages such as the non-monophyletic T. maritima. Diversification in Triglochin began in the Miocene or Oligocene, and most disjunctions in Triglochin were dated to the Miocene. PMID:25450100

  10. Responses of Halophytes to High Salinities and Low Water Potentials 1

    PubMed Central

    Jefferies, Robert L.; Rudmik, Tony; Dillon, Eva M.

    1979-01-01

    The effects of nonsaline polyethylene glycol (PEG)-6000 and saline seawater solutions of comparable osmotic potential on the concentrations of organic solutes and inorganic ions in the tissues of halophytes (Plantago maritima L., Triglochin maritima L., Limonium vulgare Mill., Halimione portulacoides (L.) Aell) have been investigated. Studies were made to determine whether high salinities induce specific ion effects that are absent in plants grown in nonsaline solutions of comparable osmotic potential. Over-all, the responses of each species to the two different treatments (seawater or PEG) are similar; the accumulation of organic solutes (compatible osmotica) in tissues is primarily correlated with a decrease in the osmotic potential of culture solutions. Depending on the species, sorbitol, proline, reducing sugars, quaternary ammonium compounds, and ?-amino nitrogen accumulate in tissues as the water potential of the tissues falls. Within a species there are differences in the concentrations of inorganic ions and organic solutes between roots and shoots of plants grown at high salinities or at high concentrations of PEG. PMID:16661119

  11. Responses of halophytes to high salinities and low water potentials.

    PubMed

    Jefferies, R L; Rudmik, T; Dillon, E M

    1979-12-01

    The effects of nonsaline polyethylene glycol (PEG)-6000 and saline seawater solutions of comparable osmotic potential on the concentrations of organic solutes and inorganic ions in the tissues of halophytes (Plantago maritima L., Triglochin maritima L., Limonium vulgare Mill., Halimione portulacoides (L.) Aell) have been investigated. Studies were made to determine whether high salinities induce specific ion effects that are absent in plants grown in nonsaline solutions of comparable osmotic potential. Over-all, the responses of each species to the two different treatments (seawater or PEG) are similar; the accumulation of organic solutes (compatible osmotica) in tissues is primarily correlated with a decrease in the osmotic potential of culture solutions. Depending on the species, sorbitol, proline, reducing sugars, quaternary ammonium compounds, and alpha-amino nitrogen accumulate in tissues as the water potential of the tissues falls. Within a species there are differences in the concentrations of inorganic ions and organic solutes between roots and shoots of plants grown at high salinities or at high concentrations of PEG. PMID:16661119

  12. Chromosome evolution in the Thermotogales: large-scale inversions and strain diversification of CRISPR sequences.

    PubMed

    DeBoy, Robert T; Mongodin, Emmanuel F; Emerson, Joanne B; Nelson, Karen E

    2006-04-01

    In the present study, the chromosomes of two members of the Thermotogales were compared. A whole-genome alignment of Thermotoga maritima MSB8 and Thermotoga neapolitana NS-E has revealed numerous large-scale DNA rearrangements, most of which are associated with CRISPR DNA repeats and/or tRNA genes. These DNA rearrangements do not include the putative origin of DNA replication but move within the same replichore, i.e., the same replicating half of the chromosome (delimited by the replication origin and terminus). Based on cumulative GC skew analysis, both the T. maritima and T. neapolitana lineages contain one or two major inverted DNA segments. Also, based on PCR amplification and sequence analysis of the DNA joints that are associated with the major rearrangements, the overall chromosome architecture was found to be conserved at most DNA joints for other strains of T. neapolitana. Taken together, the results from this analysis suggest that the observed chromosomal rearrangements in the Thermotogales likely occurred by successive inversions after their divergence from a common ancestor and before strain diversification. Finally, sequence analysis shows that size polymorphisms in the DNA joints associated with CRISPRs can be explained by expansion and possibly contraction of the DNA repeat and spacer unit, providing a tool for discerning the relatedness of strains from different geographic locations. PMID:16547022

  13. Plantain (Plantago L.) species as novel sources of flavonoid antioxidants.

    PubMed

    Beara, Ivana N; Lesjak, Marija M; Jovin, Emilija D; Balog, Kristina J; Anackov, Goran T; Orci?, Dejan Z; Mimica-Duki?, Neda M

    2009-10-14

    To examine the antioxidant properties of methanol extracts of selected Plantago species (P. argentea Chaix., P. holosteum Scop., P. major L., P. maritima L., and P. media L.), various assays that measure free radical scavenging ability were carried out: DPPH, hydroxyl radical, superoxide anion, and nitric oxide scavenger capacity tests, reducing power (FRAP) assay, and Fe(2+)/ascorbate induced lipid peroxidation. In all of the tests extracts showed a potent antioxidant effect compared with BHT, a well-known synthetic antioxidant, and the extract of P. major, accepted as an official remedy. Besides, in examined extracts the total phenolic amount (ranging from 38.43 to 70.97 mg of GAE/g of dw) and the total flavonoid content (5.31-13.10 mg of QE/g of dw) were determined. Furthermore, the presence and content of selected flavonoids (luteolin-7-O-glucoside, apigenin-7-O-glucoside, luteolin, apigenin, rutin, and quercetin) were studied using LC-MS/MS technique. LC-MS/MS analysis showed noticeable qualitative and quantitative differences between the species according to which the examined Plantago species could be regarded as a possible new source of natural antioxidants. In this study three of the species examined, P. maritima, P. argentea, and P. holosteum, have been analyzed for the first time. PMID:19754195

  14. The effects of olive mill waste compost and poultry manure on the availability and plant uptake of nutrients in a highly saline soil.

    PubMed

    Walker, David J; Bernal, M Pilar

    2008-01-01

    The effects of a compost (produced from by-products of the olive oil industry) and a poultry manure on mineral ion solubility and exchangeability in a highly saline agricultural soil (electrical conductivity for a 1:5 soil:water extract=1.85 dS m(-1)) from Murcia (SE Spain) were studied. The organic amendments did not change significantly the soil electrical conductivity or the soluble Na(+), Ca(2+) or Mg(2+). Only soluble K(+) increased, due to the K(+) supplied by the amendments. The cation exchange capacity increased in treated soils, the exchange complex being mainly saturated with Ca(2+), Mg(2+) and K(+). However, Na(+) was not retained in the exchange sites, and the sodium absorption ratio remained low. The compost and manure increased markedly the shoot growth of the salt-tolerant Beta maritima L. (sea beet) and Beta vulgaris L. (sugar beet). For B. maritima, this seemed to be related to decreases in the shoot concentrations of Na(+) and Cl(-) and increases in K(+) and H(2)PO(4)(-). In the case of B. vulgaris, increases in shoot H(2)PO(4)(-) and B and, for manure-treated soil, a decrease in shoot Na(+) may have been involved. Cultivation of tomato (Lycopersicon esculentum Mill. cv. Moneymaker) in the soil used previously for B. vulgaris indicated that the effects of the manure on tissue cation concentrations were longer-lasting than those of the compost. PMID:17275292

  15. Light-dark O2 dynamics in submerged leaves of C3 and C4 halophytes under increased dissolved CO2: clues for saltmarsh response to climate change.

    PubMed

    Duarte, B; Santos, D; Silva, H; Marques, J C; Caçador, I; Sleimi, N

    2014-01-01

    Waterlogging and submergence are the major constraints to which wetland plants are subjected, with inevitable impacts on their physiology and productivity. Global warming and climate change, as driving forces of sea level rise, tend to increase such submersion periods and also modify the carbonate chemistry of the water column due to the increased concentration of CO2 in the atmosphere. In the present work, the underwater O2 fluxes in the leaves of two abundant Mediterranean halophytes were evaluated at different levels of dissolved CO2. Photosynthetic enhancement due to increased dissolved CO2 was confirmed for both Halimione portulacoides and Spartina maritima, probably due to high tissue porosity, formation of leaf gas films and reduction of the oxygenase activity of Rubisco. Enhancement of the photosynthetic rates in H. portulacoides and S. maritima was concomitant with an increase in energy trapping and transfer, mostly due to enhancement of the carboxylation reaction of Rubisco, leading to a reduction of the energy costs for carbon fixation. Transposing these findings to the ecosystem, and assuming increased dissolved CO2 concentration scenarios, the halophyte community displays a new ecosystem function, increasing the water column oxygenation and thus reinforcing their role as principal primary producers of the estuarine system. PMID:25381259

  16. Tagus estuary and Ria de Aveiro salt marsh dynamics and the impact of sea level rise

    NASA Astrophysics Data System (ADS)

    Valentim, J. M.; Vaz, N.; Silva, H.; Duarte, B.; Caçador, I.; Dias, J. M.

    2013-09-01

    Different characteristics of Spartina maritima found in two distinct salt marshes located in different estuaries were analysed through interpretation of their local hydrodynamic patterns, as well as the impact of sea level rise on physical processes and consequently on plant dynamics and salt marshes stability. These salt marshes are situated in two of the most important Portuguese coastal systems, Tagus estuary (Rosário salt marsh) and Ria de Aveiro lagoon (Barra salt marsh), which are dominated by physical processes that induce strong tidal currents. They were monitored during one year and plant and sediment samples of S. maritima were collected quarterly in order to determine the vegetation coverage, above and belowground biomass, organic matter and sediment moisture. Residual circulation, tidal asymmetry and tidal dissipation were determined from numerical modelling results of the MOHID 2D model that was applied to each coastal system, considering the actual sea level and a sea level rise (SLR) scenario. Results suggest that the different characteristics found for Spartina maritima in the Rosário and the Barra salt marshes may be related with the diverse hydrodynamic conditions identified for each salt marsh. Consequently, the exploration of SLR scenario predictions indicates how these salt marshes could evolve in the future, showing that the important changes in these hydrodynamic parameters under climate change context might induce significant modifications in the salt marshes dynamics and stability. SLR scenario could lead to changes in nutrients and sediments patterns around the salt marshes and thus vegetation coverage percentage would be affected. Additionally, as a consequence of flood duration increase, sediment moisture will increase causing a stress condition to plants. Hence, the ratio below/aboveground biomass might increase, becoming critical to plants survival under conditions of accelerated sea level rise. Accordingly, both SLR and expected changes in vegetation coverage percentage in controlling salt marshes evolution have important implications in their stability and consequently in coastal management. These conditions are unlikely to be unique to these salt marshes and it is suggested that similar analyses are replicated for other tidally dominated systems to improve understanding and characterization of their dynamics and stability under climate change context.

  17. Genes for the Major Structural Components of Thermotogales Species’ Togas Revealed by Proteomic and Evolutionary Analyses of OmpA and OmpB Homologs

    SciTech Connect

    Petrus, Amanda K.; Swithers, Kristen S.; Ranjit, Chaman R.; Wu, Si; Brewer, Heather M.; Gogarten, J Peter; Pasa-Tolic, Ljiljana; Noll, Kenneth M.

    2012-06-29

    The unifying structural characteristic of members of the bacterial order Thermotogales is their toga, an unusual cell envelope that includes a loose-fitting sheath around each cell. Only two toga-associated structural proteins have been purified and characterized in Thermotoga maritima: the anchor protein OmpA1 (or Ompa) and the porin OmpB (or Ompb). The gene encoding OmpA1 (ompA1) was cloned and sequenced and later assigned to TM0477 in the genome sequence, but because no peptide sequence was available for OmpB, its gene (ompB) was not annotated. We identified six porin candidates in the genome sequence of T. maritima. Of these candidates, only one, encoded by TM0476, has all the characteristics reported for OmpB and characteristics expected of a porin including predominant b-sheet structure, a carboxy terminus porin anchoring motif, and a porin-specific amino acid composition. We highly enriched a toga fraction of cells for OmpB by sucrose gradient centrifugation and hydroxyapatite chromatography and analyzed it by LC/MS/MS. We found that the only porin candidate that it contained was the TM0476 product. This cell fraction also had b-sheet character as determined by circular dichroism, consistent with its enrichment for OmpB. We conclude that TM0476 encodes OmpB. A phylogenetic analysis of OmpB found orthologs encoded in syntenic locations in the genomes of all but two Thermotogales species. Those without orthologs have putative isofunctional genes in their place. Phylogenetic analyses of OmpA1 revealed that each species of the Thermotogales has one or two OmpA homologs. T. maritima has two OmpA homologs, encoded by ompA1 (TM0477) and ompA2 (TM1729), both of which were found in the toga protein-enriched cell extracts. These annotations of the genes encoding toga structural proteins will guide future examinations of the structure and function of this unusual lineage-defining cell sheath.

  18. Nutrient levels modify saltmarsh responses to increased inundation in different soil types.

    PubMed

    Wong, Joanne X W; Van Colen, Carl; Airoldi, Laura

    2015-03-01

    Saltmarshes have been depleted historically, and cumulative stressors threaten their future persistence. We examined experimentally how nutrient availability (high vs. low) affects the responses of Spartina maritima to increased inundation in two mineral soil types (low vs. medium organic). Increased inundation, one of the effects of accelerated sea level rise, had negative effects on most plant growth parameters, but the magnitude varied with soil and nutrient levels, and between plants from different locations. Average differences between inundation treatments were largest at high nutrient conditions in low organic matter soils. We conclude that saltmarsh vegetation would be more drastically affected by increased inundation in low than in medium organic matter soils, and especially in estuaries already under high nutrient availability. This knowledge enhances the prediction of changes at the foreshore of saltmarshes related to sea level rise, and the development of site-specific conservation strategies. PMID:25594372

  19. Feasibility of using hyperaccumulating plants to bioremediate metal-contaminated soil

    SciTech Connect

    Kelly, R.J. [Dames and Moore, Sydney, New South Wales (Australia); Guerin, T.F. [Minenco Bioremediation Services, Bundoora, Victoria (Australia)

    1995-12-31

    A feasibility study was carried out to determine whether selected plants were capable of hyperaccumulating anthropogenic sources of metals found in soils from three contaminated sites. A trial was conducted using the previously reported hyperaccumulators, Armeria maritima (thrift), Impatiens balsamina (balsam), Alyssum saxatile (gold dust), and the control species, Brassica oleracea (cabbage). Although none of these plants showed any substantial hyperaccumulation of Cu, Zn, Pb, and Cd, it was established that there is an optimum period in the life-cycle of these plants in which the metal concentration reaches a maximum. This period was dependent on the metal, soil, and plant type. The current paper describes the data obtained for Zn and Cu uptake by thrift.

  20. Correlation between thermostability and stability of glycosidases in ionic liquid.

    PubMed

    Ferdjani, Salim; Ionita, Marina; Roy, Bimalendu; Dion, Michel; Djeghaba, Zeineddine; Rabiller, Claude; Tellier, Charles

    2011-06-01

    The activity and stability of a ?-glycosidase (Thermus thermophilus) and two ?-galactosidases (Thermotoga maritima and Bacillus stearothermophilus) were studied in different hydrophilic ionic liquid (IL)/water ratios. For the ILs used, the glycosidases showed the best stability and activity in 1,3-dimethylimidazolium methyl sulfate [MMIM][MeSO(4)] and 1,2,3-trimethylimidazolium methyl sulfate [TMIM][MeSO(4)]. A close correlation was observed between the thermostability of the enzymes and their stability in IL media. At high IL concentration (80%), a time-dependent irreversible denaturing effect was observed on glycosidases while, at lower concentration (<30%), a reversible inactivation affecting mainly the k (cat) was obtained. The results demonstrate that highly thermostable glycosidases are more suitable for biocatalytic reactions in water-miscible ILs. PMID:21331585

  1. Synthesis of carbohydrates in a continuous flow reactor by immobilized phosphatase and aldolase.

    PubMed

    Babich, Lara; Hartog, Aloysius F; van Hemert, Lieke J C; Rutjes, Floris P J T; Wever, Ron

    2012-12-01

    Herein, we report a new flow process with immobilized enzymes to synthesize complex chiral carbohydrate analogues from achiral inexpensive building blocks in a three-step cascade reaction. The first reactor contained immobilized acid phosphatase, which phosphorylated dihydroxyacetone to dihydroxyacetone phosphate using pyrophosphate as the phosphate donor. The second flow reactor contained fructose-1,6-diphosphate aldolase (RAMA, rabbit muscle aldolase) or rhamnulose-1-phosphate aldolase (RhuA from Thermotoga maritima) and acid phosphatase. The immobilized aldolases coupled the formed dihydroxyacetone phosphate to aldehydes, resulting in phosphorylated carbohydrates. A final reactor containing acid phosphatase that dephosphorylated the phosphorylated product yielded the final product. Different aldehydes were used to synthesize carbohydrates on a gram scale. To demonstrate the feasibility of the flow systems, we synthesized 0.6 g of the D-fagomine precursor. By using immobilized aldolase RhuA we were also able to obtain other stereoisomers of the D-fagomine precursor. PMID:23150241

  2. Feeding ecology of waterfowl wintering on evaporation ponds in California

    USGS Publications Warehouse

    Euliss, N.H., Jr.; Jarvis, R.L.; Gilmer, D.S.

    1991-01-01

    We examined the feeding ecology of Northern Pintails (Anas acuta), Northern Shovelers (A. clypeata), and Ruddy Ducks (Oxyura jamaicensis) wintering on drainwater evaporation ponds in California from 1982 through 1984. Pintails primarily consumed midges (Chironomidae) (39.3%) and widegeongrass (Ruppia maritima) nutlets (34.6%). Shovelers and Ruddy Ducks consumed 92.5% and 90.1% animal matter, respectively. Water boatmen (Corixidae) (51.6%), rotifers (Rotatoria) (20.4%), and copepods (Copepoda) (15.2%) were the most important Shoveler foods, and midges (49.7%) and water boatmen (36.0%) were the most important foods of Ruddy Ducks. All three species were opportunistic foragers, shifting their diets seasonally to the most abundant foods given their behavioral and morphological attributes.

  3. Promiscuous Substrate Recognition in Folding and Assembly Activities of the Trigger Factor Chaperone

    PubMed Central

    Martinez-Hackert, Erik; Hendrickson, Wayne A.

    2009-01-01

    SUMMARY Trigger factor (TF) is a molecular chaperone that famously binds to bacterial ribosomes where it contacts emerging nascent chains, but TF is also abundant free in the cytosol where its activity is less well characterized. In vitro studies show that TF promotes protein refolding. We find here that ribosome-free TF stably associates with and rescues from misfolding a large repertoire of full-length proteins. We identify over 170 members of this cytosolic Escherichia coli TF substrate proteome, including ribosomal protein S7. We analyzed the biochemical properties of a TF:S7 complex from Thermotoga maritima and determined its crystal structure. This is the first atomic-level structure of a promiscuous chaperone in complex with a physiological substrate protein. The structure of the complex reveals the molecular basis of substrate recognition by TF, indicates how TF could accelerate protein folding and suggests a role for TF in the biogenesis of protein complexes. PMID:19737520

  4. Intrinsic stability of Brassicaceae plasma membrane in relation to changes in proteins and lipids as a response to salinity.

    PubMed

    Chalbi, Najla; Martínez-Ballesta, M Carmen; Youssef, Nabil Ben; Carvajal, Micaela

    2015-03-01

    Changes in plasma membrane lipids, such as sterols and fatty acids, have been observed as a result of salt stress. These alterations, together with modification of the plasma membrane protein profile, confer changes in the physical properties of the membrane to be taken into account for biotechnological uses. In our experiments, the relationship between lipids and proteins in three different Brassicaceae species differing in salinity tolerance (Brassica oleracea, B. napus and Cakile maritima) and the final plasma membrane stability were studied. The observed changes in the sterol (mainly an increase in sitosterol) and fatty acid composition (increase in RUFA) in each species led to physical adaptation of the plasma membrane to salt stress. The in vitro vesicles stability was higher in the less tolerant (B. oleracea) plants together with low lipoxygenase activity. These results indicate that the proteins/lipids ratio and lipid composition is an important aspect to take into account for the use of natural vesicles in plant biotechnology. PMID:25544590

  5. Wetland plants as indicators of heavy metal contamination.

    PubMed

    Phillips, D P; Human, L R D; Adams, J B

    2015-03-15

    In this study metal accumulating abilities of three emergent macrophytes (Phragmites australis, Typha capensis and Spartina maritima) were investigated in the urbanised Swartkops Estuary. Plants and sediment samples were collected at seven sites along the banks of the main channel and in adjacent canals. Sediments and plant organs were analysed, by means of atomic absorption spectrometry, for four elements (Cd, Cu, Pb, and Zn). Metal concentrations in the sediments of adjacent canals were found to be substantially higher than those at sites along the banks of the estuary. These differences were reflected in the plant organs for Pb and Zn, but not for Cu and Cd. All three species exhibited significantly higher concentrations of metals in their roots. These species are therefore suitable for use as indicators of the presence and level of heavy metal contaminants in estuaries. PMID:25599629

  6. Identification of polyunsaturated fatty acid and diterpenoid biosynthesis pathways from draft genome of Aureispira sp. CCB-QB1.

    PubMed

    Furusawa, Go; Lau, Nyok-Sean; Shu-Chien, Alexander Chong; Jaya-Ram, Annette; Amirul, Al-Ashraf Abdullah

    2015-02-01

    The genus Aureispira consisting of two species, Aureispira marina and Aureispira maritima is an arachidonic acid-producing bacterium and produces secondary metabolites. In this study, we isolated a new Aureispira strain, Aureispira sp. CCB-QB1 from coastal area of Penang, Malaysia and the genome sequence of this strain was determined. The draft genome of this strain is composed of 185 contigs for 7,370,077 bases with 35.6% G+C content and contains 5911 protein-coding genes and 76 RNA genes. Linoleoyl-CoA desaturase, the key gene in arachidonic acid biosynthesis, is present in the genome. It was found that this strain uses mevalonate pathway for the synthesis of geranylgeranyl diphosphate (GGPP), which is precursor of diterpenoid, and novel pathway via futalosine for the synthesis of menaquinones. This is the first draft genome sequence of a member of the genus Aureispira. PMID:25468060

  7. Impacts of oil sands process water on fen plants: implications for plant selection in required reclamation projects.

    PubMed

    Pouliot, Rémy; Rochefort, Line; Graf, Martha D

    2012-08-01

    Fen plant growth in peat contaminated with groundwater discharges of oil sands process water (OSPW) was assessed in a greenhouse over two growing seasons. Three treatments (non-diluted OSPW, diluted OSPW and rainwater) were tested on five vascular plants and four mosses. All vascular plants tested can grow in salinity and naphthenic acids levels currently produced by oil sands activity in northwestern Canada. No stress sign was observed after both seasons. Because of plant characteristics, Carex species (C. atherodes and C. utriculata) and Triglochin maritima would be more useful for rapidly restoring vegetation and creating a new peat-accumulating system. Groundwater discharge of OSPW proved detrimental to mosses under dry conditions and ensuring adequate water levels would be crucial in fen creation following oil sands exploitation. Campylium stellatum would be the best choice to grow in contaminated areas and Bryum pseudotriquetrum might be interesting as it has spontaneously regenerated in all treatments. PMID:22575093

  8. The class III ribonucleotide reductase from Neisseria bacilliformis can utilize thioredoxin as a reductant

    PubMed Central

    Wei, Yifeng; Funk, Michael A.; Rosado, Leonardo A.; Baek, Jiyeon; Drennan, Catherine L.; Stubbe, JoAnne

    2014-01-01

    The class III anaerobic ribonucleotide reductases (RNRs) studied to date couple the reduction of ribonucleotides to deoxynucleotides with the oxidation of formate to CO2. Here we report the cloning and heterologous expression of the Neisseria bacilliformis class III RNR and show that it can catalyze nucleotide reduction using the ubiquitous thioredoxin/thioredoxin reductase/NADPH system. We present a structural model based on a crystal structure of the homologous Thermotoga maritima class III RNR, showing its architecture and the position of conserved residues in the active site. Phylogenetic studies suggest that this form of class III RNR is present in bacteria and archaea that carry out diverse types of anaerobic metabolism. PMID:25157154

  9. Inhibition of acetylcholinesterase by extracts and constituents from Angelica archangelica and Geranium sylvaticum.

    PubMed

    Sigurdsson, Steinthor; Gudbjarnason, Sigmundur

    2007-01-01

    The aim of this study was to explore the acetylcholinesterase (AChE) inhibition of several Icelandic medicinal herbs. Ethanolic extracts of Angelica archangelica seeds and the aerial parts of Geranium sylvaticum proved effective, with IC50 values of 2.20 mg/ml and 3.56 mg/ml, respectively. The activity of imperatorin and xanthotoxin from A. archangelica was measured. Xanthotoxin proved much more potent than imperatorin, with an IC50 value of 155 microg/ml (0.72 mM) but that for imperatorin was above 274 microg/ml (1.01 mM). However, furanocoumarins seem to have a minor part in the total activity of this extract. Synergistic interaction was observed between the extracts of A. archangelica and G. sylvaticum. Several medicinal herbs (Achillea millefolium, Filipendula ulmaria, Thymus praecox and Matricaria maritima) did not show AChE inhibitory activity. PMID:18069242

  10. Taxonomic synopsis of invasive and native Spartina (Poaceae, Chloridoideae) in the Pacific Northwest (British Columbia, Washington and Oregon), including the first report of Spartina ×townsendii for British Columbia, Canada.

    PubMed

    Saarela, Jeffery M

    2012-01-01

    Five species of the grass genus Spartina are invading salt marshes along the Pacific coast of North America, of which three have been documented in British Columbia, Canada, in only the last decade. A taxonomic synopsis of the two native (Spartina gracilis, Spartina pectinata) and five introduced Spartina taxa (Spartina anglica, Spartina alterniflora, Spartina densiflora, Spartina patens, Spartina ×townsendii) in the Pacific Northwest is presented to facilitate their identification, including nomenclature, a new taxonomic key, new descriptions for a subset of taxa, and representative specimens. Spartina ×townsendii is newly reported for the flora of British Columbia. The non-coastal species Spartina pectinata is reported from an urban site in British Columbia, the first confirmed report of the taxon for the province. Lectotypes are newly designated for Spartina anglica C.E. Hubb., Spartina maritima subvar. fallax St.-Yves, and Spartina cynosuroides f. major St.-Yves. PMID:22461730

  11. Promiscuous Substrate Recognition in Folding and Assembly Activities of the Trigger Factor Chaperone

    SciTech Connect

    Martinez-Hackert, E.; Hendrickson, W

    2009-01-01

    Trigger factor (TF) is a molecular chaperone that binds to bacterial ribosomes where it contacts emerging nascent chains, but TF is also abundant free in the cytosol where its activity is less well characterized. In vitro studies show that TF promotes protein refolding. We find here that ribosome-free TF stably associates with and rescues from misfolding a large repertoire of full-length proteins. We identify over 170 members of this cytosolic Escherichia coli TF substrate proteome, including ribosomal protein S7. We analyzed the biochemical properties of a TF:S7 complex from Thermotoga maritima and determined its crystal structure. Thereby, we obtained an atomic-level picture of a promiscuous chaperone in complex with a physiological substrate protein. The structure of the complex reveals the molecular basis of substrate recognition by TF, indicates how TF could accelerate protein folding, and suggests a role for TF in the biogenesis of protein complexes.

  12. Biohydrogenesis in the Thermotogales

    SciTech Connect

    Kelly, Robert M [North Carolina State University

    2014-12-13

    The production and consumption of molecular hydrogen drives the physiology and bioenergetics of many microorganisms in hydrothermal environments. As such, the potential of these microorganisms as model systems to probe fundamental issues related to biohydrogen production merits consideration. It is important to understand how carbon/energy sources relate to the disposition of reducing power and, ultimately, the formation of molecular hydrogen by high temperature microorganisms. This project focused on bacteria in the thermophilic order Thermotogales, fermentative anaerobes that produce H2 from simple and complex carbohydrates. The major thrusts of the project are summarized in the Objectives listed below: OBJECTIVE 1: Examine the regulation of substrate catabolic proteins and pathways as this relates to carbon partitioning, disposition of reducing power, and H2 generation in Thermotoga maritima. OBJECTIVE 2: Apply classical genetics and develop molecular genetic tools for Thermotoga species to dissect catabolic and regulatory pathways related to sugar metabolism and H2 evolution. OBJECTIVE 3: Thermotogales biodiversity arises from adaptive specialization that expands on a conserved minimal genome; physiological characterization of selected novel traits will be done to expand understanding of biohydrogenesis. Four species within the genus Thermotoga were examined to understand similarities and differences in the mechanisms by which simple and complex carbohydrates were utilized and converted to molecular hydrogen. Although the core genome of these four species represented 75% of open reading frames (ORFs), there were significant differences in carbohydrate utilization patterns. New ABC transporters were identified within the Thermotogales through genomic and biochemical analysis. Molecular genetics tools were developed to examine Thermotoga maritima physiology. Cell lines were created in which both H2 and acetate levels were elevated on a per cell basis relative to the wild type, while lactate remained undetectable. Genome resequencing indicated that the primary genetic target for these phenotypic changes was the ATP binding component of a maltose ABC transporter. High temperature anaerobic [14C]-maltose transport assays demonstrated maltose uptake was reduced in the H2 overproducing cell lines. This suggested normal rates of maltose transport in the wild type organism lead to a metabolic imbalance that limited H2 synthesis. The microbial ecology of T. maritima was examined through functional genomics experiments. Under low nutrient conditions, T. maritima was observed to produce a range of putative peptides, some of which were related to ?-carbon cyclic peptides produced by Bacillus subtilus. Finally, the role of ‘toga’ in these novel microorganisms was shown to involve association with insoluble growth substrates. The ‘toga’ distends from the cytoplasmic membrane-enclosed portion of the cells as they enter the late exponential/stationary phase of growth. Some of the genes encoding toga-associated proteins were up-regulated during this phase of growth and the distension is caused by continued growth of the toga, and not shrinkage of the cytoplasmic aspect of the cells. This increase in cell surface area may have selective value to provide a larger anchor for polysaccharide hydrolytic enzymes during a time of nutritional stress. This project led to many interesting insights about the Thermotogales that have both scientific and technological implications. Ongoing work will leverage these developments to further elucidate many interesting features of these novel microorganisms.

  13. The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construction

    NASA Technical Reports Server (NTRS)

    Weisburg, W. G.; Giovannoni, S. J.; Woese, C. R.

    1989-01-01

    Through comparative analysis of 16S ribosomal RNA sequences, it can be shown that two seemingly dissimilar types of eubacteria Deinococcus and the ubiquitous hot spring organism Thermus are distantly but specifically related to one another. This confirms an earlier report based upon 16S rRNA oligonucleotide cataloging studies (Hensel et al., 1986). Their two lineages form a distinctive grouping within the eubacteria that deserved the taxonomic status of a phylum. The (partial) sequence of T. aquaticus rRNA appears relatively close to those of other thermophilic eubacteria. e.g. Thermotoga maritima and Thermomicrobium roseum. However, this closeness does not reflect a true evolutionary closeness; rather it is due to a "thermophilic convergence", the result of unusually high G+C composition in the rRNAs of thermophilic bacteria. Unless such compositional biases are taken into account, the branching order and root of phylogenetic trees can be incorrectly inferred.

  14. POLYPEPTIDE AND POLYSACCHARIDE PROCESSING IN HYPERTHERMOPHILIC MICROORGANISMS

    SciTech Connect

    KELLY, ROBERT M.

    2008-12-22

    This project focused on the microbial physiology and biochemistry of heterotrophic hyperthermophiles with respect to mechanisms by which these organisms process polypeptides and polysaccharides under normal and stressed conditions. Emphasis is on two model organisms, for which completed genome sequences are available: Pyrococcus furiosus (growth Topt of 98°C), an archaeon, and Thermotoga maritima (growth Topt of 80°C), a bacterium. Both organisms are obligately anaerobic heterotrophs that reduce sulfur facultatively. Whole genome cDNA spotted microarrays were used to follow transcriptional response to a variety of environmental conditions in order to identify genes encoding proteins involved in the acquisition, synthesis, processing and utilization of polypeptides and polysaccharides. This project provided new insights into the physiological aspects of hyperthermophiles as these relate to microbial biochemistry and biological function in high temperature habitats. The capacity of these microorganisms to produce biohydrogen from renewable feedstocks makes them important for future efforts to develop biofuels.

  15. Taxonomic synopsis of invasive and native Spartina (Poaceae, Chloridoideae) in the Pacific Northwest (British Columbia, Washington and Oregon), including the first report of Spartina ×townsendii for British Columbia, Canada

    PubMed Central

    Saarela, Jeffery M.

    2012-01-01

    Abstract Five species of the grass genus Spartina are invading salt marshes along the Pacific coast of North America, of which three have been documented in British Columbia, Canada, in only the last decade. A taxonomic synopsis of the two native (Spartina gracilis, Spartina pectinata) and five introduced Spartina taxa (Spartina anglica, Spartina alterniflora, Spartina densiflora, Spartina patens, Spartina ×townsendii) in the Pacific Northwest is presented to facilitate their identification, including nomenclature, a new taxonomic key, new descriptions for a subset of taxa, and representative specimens. Spartina ×townsendii is newly reported for the flora of British Columbia. The non-coastal species Spartina pectinata is reported from an urban site in British Columbia, the first confirmed report of the taxon for the province. Lectotypes are newly designated for Spartina anglica C.E. Hubb., Spartina maritima subvar. fallax St.-Yves, and Spartina cynosuroides f. major St.-Yves. PMID:22461730

  16. New crystal forms of Diocleinae lectins in the presence of different dimannosides

    PubMed Central

    Moreno, Frederico Bruno Mendes Batista; Bezerra, Gustavo Arruda; de Oliveira, Taianá Maia; de Souza, Emmanuel Prata; da Rocha, Bruno Anderson Matias; Benevides, Raquel Guimarães; Delatorre, Plínio; Cavada, Benildo Sousa; de Azevedo, Walter Filgueira

    2006-01-01

    Studying the interactions between lectins and sugars is important in order to explain the differences observed in the biological activities presented by the highly similar proteins of the Diocleinae subtribe. Here, the crystallization and preliminary X-­ray data of Canavalia gladiata lectin (CGL) and C. maritima lectin (CML) complexed with Man(?1-2)Man(?1)OMe, Man(?1-3)Man(?1)OMe and Man(?1-4)Man(?1)OMe in two crystal forms [the complexes with Man(?1-3)Man(?1)OMe and Man(?1-4)Man(?1)OMe crystallized in space group P32 and those with Man(?1-2)Man(?1)OMe crystallized in space group I222], which differed from those of the native proteins (P21212 for CML and C222 for CGL), are reported. The crystal complexes of ConA-like lectins with Man(?1-4)Man(?1)OMe are reported here for the first time. PMID:17077488

  17. In silico method for modelling metabolism and gene product expression at genome scale

    SciTech Connect

    Lerman, Joshua A.; Hyduke, Daniel R.; Latif, Haythem; Portnoy, Vasiliy A.; Lewis, Nathan E.; Orth, Jeffrey D.; Rutledge, Alexandra C.; Smith, Richard D.; Adkins, Joshua N.; Zengler, Karsten; Palsson, Bernard O.

    2012-07-03

    Transcription and translation use raw materials and energy generated metabolically to create the macromolecular machinery responsible for all cellular functions, including metabolism. A biochemically accurate model of molecular biology and metabolism will facilitate comprehensive and quantitative computations of an organism's molecular constitution as a function of genetic and environmental parameters. Here we formulate a model of metabolism and macromolecular expression. Prototyping it using the simple microorganism Thermotoga maritima, we show our model accurately simulates variations in cellular composition and gene expression. Moreover, through in silico comparative transcriptomics, the model allows the discovery of new regulons and improving the genome and transcription unit annotations. Our method presents a framework for investigating molecular biology and cellular physiology in silico and may allow quantitative interpretation of multi-omics data sets in the context of an integrated biochemical description of an organism.

  18. Cover Cropping Alters the Diet of Arthropods in a Banana Plantation: A Metabarcoding Approach

    PubMed Central

    Mollot, Gregory; Duyck, Pierre-François; Lefeuvre, Pierre; Lescourret, Françoise; Martin, Jean-François; Piry, Sylvain; Canard, Elsa; Tixier, Philippe

    2014-01-01

    Plant diversification using cover crops may promote natural regulation of agricultural pests by supporting alternative prey that enable the increase of arthropod predator densities. However, the changes in the specific composition of predator diet induced by cover cropping are poorly understood. Here, we hypothesized that the cover crop can significantly alter the diet of predators in agroecosystems. The cover crop Brachiaria decumbens is increasingly used in banana plantations to control weeds and improve physical soil properties. In this paper, we used a DNA metabarcoding approach for the molecular analysis of the gut contents of predators (based on mini-COI) to identify 1) the DNA sequences of their prey, 2) the predators of Cosmopolites sordidus (a major pest of banana crops), and 3) the difference in the specific composition of predator diets between a bare soil plot (BSP) and a cover cropped plot (CCP) in a banana plantation. The earwig Euborellia caraibea, the carpenter ant Camponotus sexguttatus, and the fire ant Solenopsis geminata were found to contain C. sordidus DNA at frequencies ranging from 1 to 7%. While the frequencies of predators positive for C. sordidus DNA did not significantly differ between BSP and CCP, the frequency at which E. caraibea was positive for Diptera was 26% in BSP and 80% in CCP; the frequency at which C. sexguttatus was positive for Jalysus spinosus was 14% in BSP and 0% in CCP; and the frequency at which S. geminata was positive for Polytus mellerborgi was 21% in BSP and 3% in CCP. E. caraibea, C. sexguttatus and S. geminata were identified as possible biological agents for the regulation of C. sordidus. The detection of the diet changes of these predators when a cover crop is planted indicates the possible negative effects on pest regulation if predators switch to forage on alternative prey. PMID:24695585

  19. Parental antagonism and parent–offspring co-adaptation interact to shape family life

    PubMed Central

    Meunier, Joël; Kölliker, Mathias

    2012-01-01

    The family is an arena for conflicts between offspring, mothers and fathers that need resolving to promote the evolution of parental care and the maintenance of family life. Co-adaptation is known to contribute to the resolution of parent–offspring conflict over parental care by selecting for combinations of offspring demand and parental supply that match to maximize the fitness of family members. However, multiple paternity and differences in the level of care provided by mothers and fathers can generate antagonistic selection on offspring demand (mediated, for example, by genomic imprinting) and possibly hamper co-adaptation. While parent–offspring co-adaptation and parental antagonism are commonly considered two major processes in the evolution of family life, their co-occurrence and the evolutionary consequences of their joint action are poorly understood. Here, we demonstrate the simultaneous and entangled effects of these two processes on outcomes of family interactions, using a series of breeding experiments in the European earwig, Forficula auricularia, an insect species with uniparental female care. As predicted from parental antagonism, we show that paternally inherited effects expressed in offspring influence both maternal care and maternal investment in future reproduction. However, and as expected from the entangled effects of parental antagonism and co-adaptation, these effects critically depended on postnatal interactions with caring females and maternally inherited effects expressed in offspring. Our results demonstrate that parent–offspring co-adaptation and parental antagonism are entangled key drivers in the evolution of family life that cannot be fully understood in isolation. PMID:22810433

  20. Functional analysis of centipede development supports roles for Wnt genes in posterior development and segment generation.

    PubMed

    Hayden, Luke; Schlosser, Gerhard; Arthur, Wallace

    2015-01-01

    The genes of the Wnt family play important and highly conserved roles in posterior growth and development in a wide range of animal taxa. Wnt genes also operate in arthropod segmentation, and there has been much recent debate regarding the relationship between arthropod and vertebrate segmentation mechanisms. Due to its phylogenetic position, body form, and possession of many (11) Wnt genes, the centipede Strigamia maritima is a useful system with which to examine these issues. This study takes a functional approach based on treatment with lithium chloride, which causes ubiquitous activation of canonical Wnt signalling. This is the first functional developmental study performed in any of the 15,000 species of the arthropod subphylum Myriapoda. The expression of all 11 Wnt genes in Strigamia was analyzed in relation to posterior development. Three of these genes, Wnt11, Wnt5, and WntA, were strongly expressed in the posterior region and, thus, may play important roles in posterior developmental processes. In support of this hypothesis, LiCl treatment of S. maritima embryos was observed to produce posterior developmental defects and perturbations in AbdB and Delta expression. The effects of LiCl differ depending on the developmental stage treated, with more severe effects elicited by treatment during germband formation than by treatment at later stages. These results support a role for Wnt signalling in conferring posterior identity in Strigamia. In addition, data from this study are consistent with the hypothesis of segmentation based on a "clock and wavefront" mechanism operating in this species. PMID:25627713

  1. Experimental observations on sediment resuspension within submerged model canopies under oscillatory flow

    NASA Astrophysics Data System (ADS)

    Ros, Àlex; Colomer, Jordi; Serra, Teresa; Pujol, Dolors; Soler, Marianna; Casamitjana, Xavier

    2014-12-01

    A set of laboratory experiments were conducted to study the effect of submerged aquatic vegetation in sediment resuspension under progressive waves. Three vegetation models (rigid, flexible and real plants of Ruppia maritima), six wave frequencies (in the range F=0.6-1.6 Hz) and four plant densities (Solid Plant Fractions, SPF in the range of 1-10%) were used. The sediment bed properties corresponded to a salt marsh wetland with a bimodal particle size distribution with two particle populations (population 1: particle diameters in the range of 2.5 to 6.0 ?m, and population 2: particle diameters in the range of 6.0 to 100 ?m). Within the canopy, wave velocities were attenuated for all the canopies studied and for all the frequencies analyzed. The change in the TKE (?TKE) compared with the case without plants was studied. For the rigid canopy model, in comparison to the unimpeded experiment, an increase in ?TKE inside the canopy for smaller frequencies (F=0.6-1.2 Hz) was observed together with stem Reynolds numbers Rep above 250. As a result, sediment resuspension for both sediment populations was higher than that of the unimpeded experiment. However, at higher frequencies (F=1.4 and 1.6 Hz) and higher plant densities (SPF=5%, 7.5% and 10%), the ?TKE inside the canopy decreased, coinciding with stem Reynolds number Rep below 250. As a result, sediment resuspension for larger canopy densities and larger frequencies was reduced. For the flexible vegetation model, in comparison with the unimpeded experiment, a reduction in the ?TKE inside the canopy was nearly always found. Resuspended sediment concentrations were found to decrease as flexible canopy densities increased. For the flexible vegetation the stem Reynolds number was Rep<250 and no production of ?TKE was observed. The real case of a canopy of R. maritima behaved similarly to the flexible model canopy.

  2. Hyperthermostable acetyl xylan esterase

    PubMed Central

    Drzewiecki, Katharina; Angelov, Angel; Ballschmiter, Meike; Tiefenbach, Klaus?Jürgen; Sterner, Reinhard; Liebl, Wolfgang

    2010-01-01

    Summary An esterase which is encoded within a Thermotoga maritima chromosomal gene cluster for xylan degradation and utilization was characterized after heterologous expression of the corresponding gene in Escherichia coli and purification of the enzyme. The enzyme, designated AxeA, shares amino acid sequence similarity and its broad substrate specificity with the acetyl xylan esterase from Bacillus pumilus, the cephalosporin C deacetylase from Bacillus subtilis, and other (putative) esterases, allowing its classification as a member of carbohydrate esterase family 7. The recombinant enzyme displayed activity with p?nitrophenyl?acetate as well as with various acetylated sugar substrates such as glucose penta?acetate, acetylated oat spelts xylan and DMSO (dimethyl sulfoxide)?extracted beechwood xylan, and with cephalosporin C. Thermotoga maritimaAxeA represents the most thermostable acetyl xylan esterase known to date. In a 10?min assay at its optimum pH?of 6.5 the enzyme's activity peaked at 90°C. The inactivation half?life of AxeA at a protein concentration of 0.3?µg?µl?1 in the absence of substrate was about 13?h at 98°C and about 67?h at 90°C. Differential scanning calorimetry analysis of the thermal stability of AxeA corroborated its extreme heat resistance. A multi?phasic unfolding behaviour was found, with two apparent exothermic peaks at approximately 100–104°C and 107.5°C. In accordance with the crystal structure, gel filtration analysis at ambient temperature revealed that the enzyme has as a homohexameric oligomerization state, but a dimeric form was also found. PMID:21255309

  3. Stability of endoglucanases from mesophilic fungus and thermophilic bacterium in acidified polyols.

    PubMed

    Chong, Barrie Fong; Harrison, Mark D; O'Hara, Ian M

    2014-01-01

    Recent developments in chemical pretreatments of lignocellulosic biomass using polyols as co-solvents (e.g., glycerol and ethylene glycol) at temperatures less than 100°C may allow the effective use of thermostable and non-thermostable cellulases in situ during the saccharification process. The potential of biomass saccharifying enzymes, endoglucanases (EG) from a thermophilic bacterium (Thermotoga maritima) and a mesophilic fungus (Trichoderma longibrachiatum), to retain their activity in aqueous buffer, acidified glycerol, and acidified ethylene glycol used as co-solvents at pretreatment temperatures at or below 100°C were examined. The results show that despite its origin, T. longibrachiatum EG (Tl-EG) retained 75% of its activity after exposure to 100°C for 5 min in aqueous buffer while T. maritima EG (Tm-EG) retained only 5% activity. However, at 90°C both enzymes retained over 87% of their activity. In acidified (0.1% (w/w) H2SO4) glycerol, Tl-EG retained similar activity (80%) to that obtained in glycerol alone, while Tm-EG retained only 35%. With acidified ethylene glycol under these conditions, both Tl-EG and Tm-EG retained 36% of their activity. The results therefore show that Tl-EG is more stable in both acidified glycerol and ethylene glycol than Tm-EG. A preliminary kinetic study showed that pure glycerol improved the thermal stability of Tl-EG but destabilized Tm-EG, relative to the buffer solution. The half-lives of both Tl-EG and Tm-EG are 4.5 min in acidified glycerol, indicating that the effectiveness of these enzymes under typical pretreatment times of greater than 15 min will be considerably diminished. Attempts have been made to explain the differences in the results obtained between the two enzymes. PMID:24910337

  4. Ligand-induced conformational changes in a thermophilic ribose-binding protein

    SciTech Connect

    Cuneo, Matthew J.; Beese, Lorena S.; Hellinga, Homme W. (Duke)

    2009-05-21

    Members of the periplasmic binding protein (PBP) superfamily are involved in transport and signaling processes in both prokaryotes and eukaryotes. Biological responses are typically mediated by ligand-induced conformational changes in which the binding event is coupled to a hinge-bending motion that brings together two domains in a closed form. In all PBP-mediated biological processes, downstream partners recognize the closed form of the protein. This motion has also been exploited in protein engineering experiments to construct biosensors that transduce ligand binding to a variety of physical signals. Understanding the mechanistic details of PBP conformational changes, both global (hinge bending, twisting, shear movements) and local (rotamer changes, backbone motion), therefore is not only important for understanding their biological function but also for protein engineering experiments. Here we present biochemical characterization and crystal structure determination of the periplasmic ribose-binding protein (RBP) from the hyperthermophile Thermotoga maritima in its ribose-bound and unliganded state. The T. maritima RBP (tmRBP) has 39% sequence identity and is considerably more resistant to thermal denaturation (appTm value is 108 C) than the mesophilic Escherichia coli homolog (ecRBP) (appTm value is 56 C). Polar ligand interactions and ligand-induced global conformational changes are conserved among ecRBP and tmRBP; however local structural rearrangements involving side-chain motions in the ligand-binding site are not conserved. Although the large-scale ligand-induced changes are mediated through similar regions, and are produced by similar backbone movements in tmRBP and ecRBP, the small-scale ligand-induced structural rearrangements differentiate the mesophile and thermophile. This suggests there are mechanistic differences in the manner by which these two proteins bind their ligands and are an example of how two structurally similar proteins utilize different mechanisms to form a ligand-bound state.

  5. The multiple target use of spirodiclofen (Envidor 240 SC) in IPM pomefruit in Belgium.

    PubMed

    De Maeyer, Luk; Geerinck, Rik

    2009-01-01

    Envidor 240 SC, active ingredient spirodiclofen is a broad spectrum acaricide acting via lipid biosynthesis inhibition (LBI) with no cross resistance to currently available acaricides and with additional insecticidal properties. Envidor is positive IPM listed but in frame of resistance management limited to one application per season. In pear growing Envidor constitutes an important tool in pear sucker control in a tandem strategy with abamectine. Being totally selective on predatory bugs Anthocoris nemoralis, Envidor installs a favourable low prey/predator ratio avoiding any damage of further 3rd or 4th Psylla generations. The application of Envidor on the second Psylla generation coincides with the migration of Lepidosaphes ulmi scales and with the spread of rustmites Epitremerus pyri on which season long control is achieved. On apples, Envidor settled as an important tool for scales control especially on the wood but recently its acaricidal use revivals. This is induced by the withdrawal of totylfluanid with its regulating mite control and with the further efficacy decline of registered METI-acaricides. Even with full introduction of Typhlodromus pyri, mites and rustmites may unexpectedly flear up. On Typhlodromus pyri, Envidor is IOBC 2 classified (slightly harmful) but the favourable low prey/predator ratio and within season recovery make it full IPM compatible. On Aculus schlechtendali, apple rustmite with a short generation cyclus, the larval and fecundity effects of Envidor lead to an explicit knock down efficacy. On mixed populations of Panonychus ulmi with longer generation cyclus, Envidor shows a slow initial effect with culminating efficacy after 2-3 weeks and a long lasting efficacy of more than 100 days, avoiding any leaf or consequent fruit damage. High rain fastness and the right positioning at 30-50 % hatching of winter eggs make of Envidor a very consistent correction acaride. The addition of a surfactant is not recommended for mite control. Up to now, no shifting in susceptibility of Envidor on Panonychus ulmi or Tetranychus urticae is found in Belgian orchards. Since Envidor combines both in apples and pears an efficacy on multiple pests occurring simultaneously after flowering, with a good selectivity profile on predators, parasitoïds, syrphids, lacewings and earwigs, it remains a most important tool in modern IPM pomefruit. PMID:20218531

  6. Nectar-carbohydrate production and composition vary in relation to nectary anatomy and location within individual flowers of several species of Brassicaceae.

    PubMed

    Davis, A R; Pylatuik, J D; Paradis, J C; Low, N H

    1998-06-01

    Nectar-carbohydrate production and composition were investigated by high-performance liquid chromatography and enzymology in nine species from five tribes of the Brassicaceae. In six species (Arabidopsis thaliana (L.) Heynh., Brassica napus L., B. rapa L., Lobularia maritima (L.) Desv., Raphanus sativus L., Sinapis arvensis L.) that produced nectar from both lateral nectaries (associated with the short stamens) and median nectaries (outside the long stamens), on average 95% of the total nectar carbohydrate was collected from the lateral ones. Nectar from these glands possessed a higher glucose/fructose ratio (usually 1.0-1.2) than that from the median nectaries (0.2-0.9) within the same flower. Comparatively little sucrose was detected in any nectar samples except from Matthiola bicornus (Sibth. et Sm.) DC., which possessed lateral nectaries only and produced a sucrose-dominant exudate. The anatomy of the nectarial tissue in nectar-secreting flowers of six species, Hesperis matronalis L., L. maritima, M. bicornus, R. sativus, S. arvensis, and Sisymbrium loeselii L., was studied by light and scanning-electron microscopy. Phloem alone supplied the nectaries. However, in accordance with their overall nectar-carbohydrate production, the lateral glands received relatively rich quantities of phloem that penetrated far into the glandular tissue, whereas median glands were supplied with phloem that often barely innervated them. All nectarial tissue possessed modified stomata (with the exception of the median glands of S. loeselii, which did not produce nectar); further evidence was gathered to indicate that these structures do not regulate nectar flow by guard-cell movements. The numbers of modified stomata per gland showed no relation to nectar-carbohydrate production. Taken together, the data on nectar biochemistry and nectary anatomy indicate the existence of two distinct nectary types in those Brassicacean species that possess both lateral and median nectaries, regardless of whether nectarial tissue is united around the entire receptacle or not. It is proposed that the term "nectarium" be used to represent collectively the multiple nectaries that can be found in individual flowers. PMID:9637073

  7. Crystal Structure of a Two-Subunit TrkA Octameric Gating Ring Assembly.

    PubMed

    Deller, Marc C; Johnson, Hope A; Miller, Mitchell D; Spraggon, Glen; Elsliger, Marc-André; Wilson, Ian A; Lesley, Scott A

    2015-01-01

    The TM1088 locus of T. maritima codes for two proteins designated TM1088A and TM1088B, which combine to form the cytosolic portion of a putative Trk K+ transporter. We report the crystal structure of this assembly to a resolution of 3.45 Å. The high resolution crystal structures of the components of the assembly, TM1088A and TM1088B, were also determined independently to 1.50 Å and 1.55 Å, respectively. The TM1088 proteins are structurally homologous to each other and to other K+ transporter proteins, such as TrkA. These proteins form a cytosolic gating ring assembly that controls the flow of K+ ions across the membrane. TM1088 represents the first structure of a two-subunit Trk assembly. Despite the atypical genetics and chain organization of the TM1088 assembly, it shares significant structural homology and an overall quaternary organization with other single-subunit K+ gating ring assemblies. This structure provides the first structural insights into what may be an evolutionary ancestor of more modern single-subunit K+ gating ring assemblies. PMID:25826626

  8. Protein motions during catalysis by dihydrofolate reductases

    PubMed Central

    Allemann, Rudolf K; Evans, Rhiannon M; Tey, Lai-hock; Maglia, Giovanni; Pang, Jiayun; Rodriguez, Robert; Shrimpton, Paul J; Swanwick, Richard S

    2006-01-01

    Dihydrofolate reductase (DHFR) maintains the intracellular pool of tetrahydrofolate through catalysis of hydrogen transfer from reduced nicotinamide adenine dinucleotide to 7,8-dihydrofolate. We report results for pre-steady-state kinetic studies of the temperature dependence of the rates and the hydrogen/deuterium-kinetic isotope effects for the reactions catalysed by the enzymes from the mesophilic Escherichia coli and the hyperthermophilic Thermatoga maritima. We propose an evolutionary pattern in which catalysis progressed from a relatively rigid active site structure in the ancient thermophilic DHFR to a more flexible and kinetically more efficient structure in E. coli that actively promotes hydrogen transfer at physiological pH by modulating the tunnelling distance. The E. coli enzyme appeared relatively robust, in that kinetically severely compromised mutants still actively propagated the reaction. The reduced hydrogen transfer rates of the extensively studied Gly121Val mutant of DHFR from E. coli were most likely due to sterically unfavourable long-range effects from the introduction of the bulky isopropyl group. PMID:16873119

  9. Protein motions during catalysis by dihydrofolate reductases.

    PubMed

    Allemann, Rudolf K; Evans, Rhiannon M; Tey, Lai-hock; Maglia, Giovanni; Pang, Jiayun; Rodriguez, Robert; Shrimpton, Paul J; Swanwick, Richard S

    2006-08-29

    Dihydrofolate reductase (DHFR) maintains the intracellular pool of tetrahydrofolate through catalysis of hydrogen transfer from reduced nicotinamide adenine dinucleotide to 7,8-dihydrofolate. We report results for pre-steady-state kinetic studies of the temperature dependence of the rates and the hydrogen/deuterium-kinetic isotope effects for the reactions catalysed by the enzymes from the mesophilic Escherichia coli and the hyperthermophilic Thermatoga maritima. We propose an evolutionary pattern in which catalysis progressed from a relatively rigid active site structure in the ancient thermophilic DHFR to a more flexible and kinetically more efficient structure in E. coli that actively promotes hydrogen transfer at physiological pH by modulating the tunnelling distance. The E. coli enzyme appeared relatively robust, in that kinetically severely compromised mutants still actively propagated the reaction. The reduced hydrogen transfer rates of the extensively studied Gly121Val mutant of DHFR from E. coli were most likely due to sterically unfavourable long-range effects from the introduction of the bulky isopropyl group. PMID:16873119

  10. Different reaction mechanisms for mesophilic and thermophilic dihydrofolate reductases.

    PubMed

    Loveridge, E Joel; Behiry, Enas M; Swanwick, Richard S; Allemann, Rudolf K

    2009-05-27

    We report here solvent kinetic isotope effects for two dihydrofolate reductases, namely the monomeric, mesophilic enzyme from E. coli (EcDHFR) and the dimeric, thermophilic enzyme from Thermotoga maritima (TmDHFR). Multiple isotope effects reveal mechanistic differences between the two enzymes. EcDHFR follows a stepwise mechanism in which proton transfer precedes hydride transfer, whereas the two steps are concerted in TmDHFR. At elevated pH, EcDHFR also follows a concerted reaction pathway. TmDHFR at pH 7 behaves more like EcDHFR at elevated pH suggesting that the restricted motions of TmDHFR resulting from dimerization preclude it from modulating the pK(a) of its substrate as efficiently as EcDHFR. The reduced reaction rates of TmDHFR therefore appear to be a consequence of its quaternary structure, which is required for increased thermostability but which also prevents active modulation of the reactivity of the active site bound substrate observed in EcDHFR. PMID:19419144

  11. Screening of 18 species for digestate phytodepuration.

    PubMed

    Pavan, Francesca; Breschigliaro, Simone; Borin, Maurizio

    2015-02-01

    This experiment assesses the aptitude of 18 species in treating the digestate liquid fraction (DLF) in a floating wetland treatment system. The pilot system was created in NE Italy in 2010 and consists of a surface-flow system with 180 floating elements (Tech-IA®) vegetated with ten halophytes and eight other wetland species. The species were transplanted in July 2011 in basins filled with different proportions of DLF/water (DLF/w); periodic increasing of the DLF/w ratio was imposed after transplanting, reaching the worst conditions for plants in summer 2012 (highest EC value 7.3 mS cm/L and NH4-N content 225 mg/L). It emerged that only Cynodon dactylon, Typha latifolia, Elytrigia atherica, Halimione portulacoides, Salicornia fruticosa, Artemisia caerulescens, Spartina maritima and Puccinellia palustris were able to survive under the system conditions. Halophytes showed higher dry matter production than other plants. The best root development (up to 40-cm depth) was recorded for Calamagrostis epigejos, Phragmites australis, T. latifolia and Juncus maritimus. The highest nitrogen (10-15 g/m(2)) and phosphorus (1-4 g/m(2)) uptakes were obtained with P. palustris, Iris pseudacorus and Aster tripolium. In conclusion, two halophytes, P. palustris and E. atherica, present the highest potential to be used to treat DLF in floating wetlands. PMID:25005162

  12. Allosteric Inhibitors at the Heterodimer Interface of Imidazole Glycerol Phosphate Synthase

    NASA Astrophysics Data System (ADS)

    Snoeberger, Ning-Shiuan Nicole

    Imidazole glycerol phosphate synthase (IGPS) from Thermotoga maritima is a heterodimeric enzyme composed of the HisH and HisF proteins. It is attractive as a pathological target since it is absent in mammals but found in plant and opportunistic human pathogens. IGPS was experimentally determined to be a V-type allosteric enzyme that is involved in an essential biosynthetic pathway of microorganisms. The enzyme catalyzes the hydrolysis of glutamine to form NH3 in the HisH protein, followed by cyclization of NH3 with N'-[(5'-phosphoribulosyl)imino]-5-aminoimidazole-4-carboxamide-ribonucleotide (PRFAR) in the HisF subunit, forming imidazole glycerol phosphate (IGP) and 5-aminoimidazole-4-carboxamide ribotide (AICAR) that enter the histidine and purine biosynthetic pathways. Allosteric motions induced upon the binding of the effector PRFAR to HisF propagate through the non-covalent HisH/HisF interface and synchronize catalytic activity at the two distant active sites. However, the nature of the allosteric pathway and the feasibility of manipulating signal transduction by using allosteric drug-like molecules remain to be established. Molecular docking studies of commercial drugs at the HisH/HisF interface were used to identify stable candidates with a potential allosteric effect on the reaction mechanism. Molecular dynamic simulations and calculations of NMR chemical shifts were combined to elucidate the allosteric pathway of IGPS.

  13. Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA

    PubMed Central

    Reiter, Nicholas J.; Osterman, Amy; Torres-Larios, Alfredo; Swinger, Kerren K.; Pan, Tao; Mondragón, Alfonso

    2010-01-01

    Ribonuclease (RNase) P is the universal ribozyme responsible for 5?-end tRNA processing. We report the crystal structure of the Thermotoga maritima RNase P holoenzyme in complex with tRNAPhe. The 154 kDa complex consists of a large catalytic RNA (P RNA), a small protein cofactor, and mature tRNA. The structure shows that RNA-RNA recognition occurs through shape complementarity, specific intermolecular contacts, and base pairing interactions. Soaks with a pre-tRNA 5? leader sequence with and without metal help identify the 5? substrate path and potential catalytic metal ions. The protein binds on top of a universally conserved structural module in P RNA and interacts with the leader, but not with mature tRNA. The active site is composed of phosphate backbone moieties, a universally conserved uridine nucleobase, and at least two catalytically important metal ions. The active site structure and conserved RNase P/tRNA contacts suggest a universal mechanism of catalysis by RNase P. PMID:21076397

  14. The bacterial ribonuclease P holoenzyme requires specific, conserved residues for efficient catalysis and substrate positioning.

    PubMed

    Reiter, Nicholas J; Osterman, Amy K; Mondragón, Alfonso

    2012-11-01

    RNase P is an RNA-based enzyme primarily responsible for 5'-end pre-tRNA processing. A structure of the bacterial RNase P holoenzyme in complex with tRNAPhe revealed the structural basis for substrate recognition, identified the active site location, and showed how the protein component increases functionality. The active site includes at least two metal ions, a universal uridine (U52), and P RNA backbone moieties, but it is unclear whether an adjacent, bacterially conserved protein loop (residues 52-57) participates in catalysis. Here, mutagenesis combined with single-turnover reaction kinetics demonstrate that point mutations in this loop have either no or modest effects on catalytic efficiency. Similarly, amino acid changes in the 'RNR' region, which represent the most conserved region of bacterial RNase P proteins, exhibit negligible changes in catalytic efficiency. However, U52 and two bacterially conserved protein residues (F17 and R89) are essential for efficient Thermotoga maritima RNase P activity. The U52 nucleotide binds a metal ion at the active site, whereas F17 and R89 are positioned >20 Å from the cleavage site, probably making contacts with N(-4) and N(-5) nucleotides of the pre-tRNA 5'-leader. This suggests a synergistic coupling between transition state formation and substrate positioning via interactions with the leader. PMID:22904083

  15. Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum.

    PubMed

    Kazanov, Marat D; Li, Xiaoqing; Gelfand, Mikhail S; Osterman, Andrei L; Rodionov, Dmitry A

    2013-01-01

    Large and functionally heterogeneous families of transcription factors have complex evolutionary histories. What shapes specificities toward effectors and DNA sites in paralogous regulators is a fundamental question in biology. Bacteria from the deep-branching lineage Thermotogae possess multiple paralogs of the repressor, open reading frame, kinase (ROK) family regulators that are characterized by carbohydrate-sensing domains shared with sugar kinases. We applied an integrated genomic approach to study functions and specificities of regulators from this family. A comparative analysis of 11 Thermotogae genomes revealed novel mechanisms of transcriptional regulation of the sugar utilization networks, DNA-binding motifs and specific functions. Reconstructed regulons for seven groups of ROK regulators were validated by DNA-binding assays using purified recombinant proteins from the model bacterium Thermotoga maritima. All tested regulators demonstrated specific binding to their predicted cognate DNA sites, and this binding was inhibited by specific effectors, mono- or disaccharides from their respective sugar catabolic pathways. By comparing ligand-binding domains of regulators with structurally characterized kinases from the ROK family, we elucidated signature amino acid residues determining sugar-ligand regulator specificity. Observed correlations between signature residues and the sugar-ligand specificities provide the framework for structure functional classification of the entire ROK family. PMID:23209028

  16. The bacterial ribonuclease P holoenzyme requires specific, conserved residues for efficient catalysis and substrate positioning

    PubMed Central

    Reiter, Nicholas J.; Osterman, Amy K.; Mondragón, Alfonso

    2012-01-01

    RNase P is an RNA-based enzyme primarily responsible for 5?-end pre-tRNA processing. A structure of the bacterial RNase P holoenzyme in complex with tRNAPhe revealed the structural basis for substrate recognition, identified the active site location, and showed how the protein component increases functionality. The active site includes at least two metal ions, a universal uridine (U52), and P RNA backbone moieties, but it is unclear whether an adjacent, bacterially conserved protein loop (residues 52–57) participates in catalysis. Here, mutagenesis combined with single-turnover reaction kinetics demonstrate that point mutations in this loop have either no or modest effects on catalytic efficiency. Similarly, amino acid changes in the ‘RNR’ region, which represent the most conserved region of bacterial RNase P proteins, exhibit negligible changes in catalytic efficiency. However, U52 and two bacterially conserved protein residues (F17 and R89) are essential for efficient Thermotoga maritima RNase P activity. The U52 nucleotide binds a metal ion at the active site, whereas F17 and R89 are positioned >20 Å from the cleavage site, probably making contacts with N?4 and N?5 nucleotides of the pre-tRNA 5?-leader. This suggests a synergistic coupling between transition state formation and substrate positioning via interactions with the leader. PMID:22904083

  17. A role for [Fe4S4] clusters in tRNA recognition--a theoretical study.

    PubMed

    Stiebritz, Martin T

    2014-05-01

    Over the past several years, structural studies have led to the unexpected discovery of iron-sulfur clusters in enzymes that are involved in DNA replication/repair and protein biosynthesis. Although these clusters are generally well-studied cofactors, their significance in the new contexts often remains elusive. One fascinating example is a tryptophanyl-tRNA synthetase from the thermophilic bacterium Thermotoga maritima, TmTrpRS, that has recently been structurally characterized. It represents an unprecedented connection among a primordial iron-sulfur cofactor, RNA and protein biosynthesis. Here, a possible role of the [Fe4S4] cluster in tRNA anticodon-loop recognition is investigated by means of density functional theory and comparison with the structure of a human tryptophanyl-tRNA synthetase/tRNA complex. It turns out that a cluster-coordinating cysteine residue, R224, and polar main chain atoms form a characteristic structural motif for recognizing a putative 5' cytosine or 5' 2-thiocytosine moiety in the anticodon loop of the tRNA molecule. This motif provides not only affinity but also specificity by creating a structural and energetical penalty for the binding of other bases, such as uracil. PMID:24753428

  18. Microfluidic glycosyl hydrolase screening for biomass-to-biofuel conversion.

    PubMed

    Bharadwaj, Rajiv; Chen, Zhiwei; Datta, Supratim; Holmes, Bradley M; Sapra, Rajat; Simmons, Blake A; Adams, Paul D; Singh, Anup K

    2010-11-15

    The hydrolysis of biomass to fermentable sugars using glycosyl hydrolases such as cellulases and hemicellulases is a limiting and costly step in the conversion of biomass to biofuels. Enhancement in hydrolysis efficiency is necessary and requires improvement in both enzymes and processing strategies. Advances in both areas in turn strongly depend on the progress in developing high-throughput assays to rapidly and quantitatively screen a large number of enzymes and processing conditions. For example, the characterization of various cellodextrins and xylooligomers produced during the time course of saccharification is important in the design of suitable reactors, enzyme cocktail compositions, and biomass pretreatment schemes. We have developed a microfluidic-chip-based assay for rapid and precise characterization of glycans and xylans resulting from biomass hydrolysis. The technique enables multiplexed separation of soluble cellodextrins and xylose oligomers in around 1 min (10-fold faster than HPLC). The microfluidic device was used to elucidate the mode of action of Tm_Cel5A, a novel cellulase from hyperthermophile Thermotoga maritima . The results demonstrate that the cellulase is active at 80 °C and effectively hydrolyzes cellodextrins and ionic-liquid-pretreated switchgrass and Avicel to glucose, cellobiose, and cellotriose. The proposed microscale approach is ideal for quantitative large-scale screening of enzyme libraries for biomass hydrolysis, for development of energy feedstocks, and for polysaccharide sequencing. PMID:20964411

  19. The role of food supplements in the treatment of the infertile man.

    PubMed

    Comhaire, Frank H; Mahmoud, Ahmed

    2003-01-01

    Recently, concerns have been raised about the presumptive increased risk of serious undesirable side effects in children born after IVF and intracytoplasmic sperm injection (ICSI). These treatments must, therefore, be reserved as the ultimate option after evidence-based and cause-directed treatment of the male patient with deficient semen has been exhausted. The present authors found that sperm quality and function improved with the intake of complementary food supplementation using a combination of zinc and folic acid, or the antioxidant astaxanthin (Astacarox), or an energy-providing combination containing (actyl)-carnitine (Proxeed). Also, double blind trials showed that the latter two substances increase spontaneous or intrauterine insemination- (IUI-) assisted conception rates. Extracts of Pinus maritima bark (Pycnogenol), which inhibits the cyclo-oxygenase enzyme, reducing prostaglandin production and inflammatory reaction, and extracts of the Peruvian plant Lepidium meyenii were shown to improve sperm morphology and concentration, respectively, in uncontrolled trials. Linseed (flaxseed) oil contains alfa-linolenic acid and lignans. The former corrects the deficient intake of omega-3 essential fatty acids, which is correlated with impaired sperm motility among subfertile men. Lignans are precursors of enterolacton, which inhibits aromatase and reduces the ratio of 16-OH over 2-OH oestrogen metabolites. The resulting reduction in oestrogen load may favourably influence Sertoli cell function. PMID:14656398

  20. A Multiproxy Investigation of Late-Glacial Climate and Vegetation Change at Pine Ridge Pond, Southwest New Brunswick, Canada

    NASA Astrophysics Data System (ADS)

    Levesque, André J.; Cwynar, Les C.; Walker, Ian R.

    1994-11-01

    Pollen, plant macrofossil, chironomid, and lithological analyses of late-glacial sediment from Pine Ridge Pond all indicate that the warming following deglaciation was punctuated on two separate occasions by a return to colder climes; initially by a brief and moderate cold episode (the Killarney Oscillation), followed shortly by the Younger Dryas. The Killarney Oscillation, AMS 14C dated at between 11,290 and 10,960 yr B.P., is characterized by abrupt and simultaneous increases in Betula (birch) pollen and Betula glandulosa (dwarf birch) macrofossils and a decline in tree pollen. The Younger Dryas is distinguished by the reversion of a short-lived closed Picea (spruce) forest to a prolonged forest-tundra stage (ca. 10, 820 to 9500(?) yr B.P.), during which macrofossils of arctic/alpine plants such as Salix herbaces, Cassiope hypnoides, Armeria maritima, and Thalictrum alpinum make their sole late-glacial appearance. Chironomid-inferred summer surface-water temperatures indicate a cooling of approximately 8 and 12°C during the Killarney Oscillation and Younger Dryas, respectively, and coarse-sand analysis indicates increased erosion on the landscape during these same intervals.

  1. Anaerobic High-Throughput Cultivation Method for Isolation of Thermophiles Using Biomass-Derived Substrates

    SciTech Connect

    Hamilton-Brehm, Scott [ORNL; Vishnivetskaya, Tatiana A [ORNL; Allman, Steve L [ORNL; Mielenz, Jonathan R [ORNL; Elkins, James G [ORNL

    2012-01-01

    Flow cytometry (FCM) techniques have been developed for sorting mesophilic organisms, but the difficulty increases if the target microbes are thermophilic anaerobes. We demonstrate a reliable, high-throughput method of screening thermophilic anaerobic organisms using FCM and 96-well plates for growth on biomass-relevant substrates. The method was tested using the cellulolytic thermophiles Clostridium ther- mocellum (Topt = 55 C), Caldicellulosiruptor obsidiansis (Topt = 78 C) and the fermentative hyperthermo- philes, Pyrococcus furiosus (Topt = 100 C) and Thermotoga maritima (Topt = 80 C). Multi-well plates were incubated at various temperatures for approximately 72 120 h and then tested for growth. Positive growth resulting from single cells sorted into individual wells containing an anaerobic medium was verified by OD600. Depending on the growth substrate, up to 80 % of the wells contained viable cultures, which could be transferred to fresh media. This method was used to isolate thermophilic microbes from Rabbit Creek, Yellowstone National Park (YNP), Wyoming. Substrates for enrichment cultures including crystalline cellulose (Avicel), xylan (from Birchwood), pretreated switchgrass and Populus were used to cultivate organisms that may be of interest to lignocellulosic biofuel production.

  2. Carboxyl terminal domain basic amino acids of mycobacterial topoisomerase I bind DNA to promote strand passage

    PubMed Central

    Ahmed, Wareed; Bhat, Anuradha Gopal; Leelaram, Majety Naga; Menon, Shruti; Nagaraja, Valakunja

    2013-01-01

    Bacterial DNA topoisomerase I (topoI) carries out relaxation of negatively supercoiled DNA through a series of orchestrated steps, DNA binding, cleavage, strand passage and religation. The N-terminal domain (NTD) of the type IA topoisomerases harbor DNA cleavage and religation activities, but the carboxyl terminal domain (CTD) is highly diverse. Most of these enzymes contain a varied number of Zn2+ finger motifs in the CTD. The Zn2+ finger motifs were found to be essential in Escherichia coli topoI but dispensable in the Thermotoga maritima enzyme. Although, the CTD of mycobacterial topoI lacks Zn2+ fingers, it is indispensable for the DNA relaxation activity of the enzyme. The divergent CTD harbors three stretches of basic amino acids needed for the strand passage step of the reaction as demonstrated by a new assay. We also show that the basic amino acids constitute an independent DNA-binding site apart from the NTD and assist the simultaneous binding of two molecules of DNA to the enzyme, as required during the catalytic step. Although the NTD binds to DNA in a site-specific fashion to carry out DNA cleavage and religation, the basic residues in CTD bind to non-scissile DNA in a sequence-independent manner to promote the crucial strand passage step during DNA relaxation. The loss of Zn2+ fingers from the mycobacterial topoI could be associated with Zn2+ export and homeostasis. PMID:23771144

  3. A thermostable exo-?-fructosidase immobilised through rational design.

    PubMed

    Martínez, Duniesky; Cutiño-Avila, Bessy; Pérez, Enrique Rosendo; Menéndez, Carmen; Hernández, Lázaro; Del Monte-Martínez, Alberto

    2014-02-15

    Thermotoga maritima exo-?-fructosidase (BfrA) secreted by a recombinant Pichia pastoris strain was optimally immobilised on Glyoxyl-Sepharose CL 4B using the Rational Design of Immobilised Derivatives (RDID) strategy. Covalent attachment of the N-glycosylated BfrA onto the activated support at pH 10 allowed total recovery of the loaded enzyme and its activity. The immobilisation process caused no variation in the catalytic properties of the enzyme and allowed further enhancement of the thermal stability. Complete inversion of cane sugar (2.04 M) in a batch stirred tank reactor at 60 °C was achieved with a productivity of 22.2 g of substrate hydrolysed/gram of biocatalyst/hour. Half-life of the immobilised enzyme of 5 days at 60 °C was determined in a continuously operated fixed-bed column reactor. Our results promote the applicability of the BfrA-immobilised biocatalyst for the complete hydrolysis of concentrated sucrose solutions under industrial conditions, especially at a high reaction temperature. PMID:24128552

  4. Flow synthesis of phenylserine using threonine aldolase immobilized on Eupergit support

    PubMed Central

    Tibhe, Jagdish D; Fu, Hui; Noël, Timothy; Wang, Qi; Meuldijk, Jan

    2013-01-01

    Summary Threonine aldolase (TA) from Thermotoga maritima was immobilized on an Eupergit support by both a direct and an indirect method. The incubation time for the direct immobilization method was optimized for the highest amount of enzyme on the support. By introducing the immobilized TA in a packed-bed microreactor, a flow synthesis of phenylserine was developed, and the effects of temperature and residence time were studied in particular. Calculations of the Damköhler number revealed that no mass transfer limitations are given in the micro-interstices of the packed bed. The yield does not exceed 40% and can be rationalized by the natural equilibrium as well as product inhibition which was experimentally proven. The flow synthesis with the immobilized enzyme was compared with the corresponding transformation conducted with the free enzyme. The product yield was further improved by operating under slug flow conditions which is related to the very short residence time distribution. In all cases 20% diastereomeric excess (de) and 99% enantiomeric excess (ee) were observed. A continuous run of the reactant solution was carried out for 10 hours in order to check enzyme stability at higher temperature. Stable operation was achieved at 20 minute residence time. Finally, the productivity of the reactor was calculated, extrapolated to parallel run units, and compared with data collected previously. PMID:24204429

  5. Palynological analysis of camelid coprolites: seasonality in the use of the site Cerro Casa de Piedra 7 (Santa Cruz, Argentina)

    NASA Astrophysics Data System (ADS)

    Velázquez, Nadia Jimena; Burry, Lidia Susana; Fugassa, Martín Horacio; Civalero, María Teresa; Aschero, Carlos Alberto

    2014-01-01

    Palynological, palaeoparasitological and paleobotanical studies of coprolites found in archaeological sites from Perito Moreno National Park (47°57?S72°05?W) yielded information on diet, palaeoenvironment and health. These studies allowed adding evidence to the reconstruction of life history of the hunter-gatherers that inhabited Patagonia during the Holocene. We examined the season of the year when camelid Lama guanicoe coprolites (5400 ± 64 yr 14C BP to 9640 ± 190 yr 14C BP) were deposited at Cerro Casa de Piedra 7 (site CCP7). The study used palynological evidence and comparison with pollen spectra of modern feces collected during summer, fall, winter and spring of 2010. The dominant types were: pollen of Nothofagus, Empetrum rubrum, Asteraceae subfam. Asteroideae, Nassauvia, Caryophyllaceae and Poaceae; fern spores; remains of Eimeria macusaniensis; and plant remains of Poaceae, Festuca pallescens, Stipa speciosa, Armeria maritima, Gaultheria mucronata and E. rubrum. Pollen spectra of modern and fossil feces were used for multivariate analysis. Coprolites associated to fall and winter modern feces. These results and those obtained from pollen concentration values and the presence of pollen types indicators of seasonality, allowed the determination of summer, fall and winter coprolites. However, caution must be taken with the seasonality results of coprolites dated earlier than 9000 years BP since the environmental conditions differed from now. The site was probably a camelid shelter during the unfavorable seasons.

  6. Flow synthesis of phenylserine using threonine aldolase immobilized on Eupergit support.

    PubMed

    Tibhe, Jagdish D; Fu, Hui; Noël, Timothy; Wang, Qi; Meuldijk, Jan; Hessel, Volker

    2013-01-01

    Threonine aldolase (TA) from Thermotoga maritima was immobilized on an Eupergit support by both a direct and an indirect method. The incubation time for the direct immobilization method was optimized for the highest amount of enzyme on the support. By introducing the immobilized TA in a packed-bed microreactor, a flow synthesis of phenylserine was developed, and the effects of temperature and residence time were studied in particular. Calculations of the Damköhler number revealed that no mass transfer limitations are given in the micro-interstices of the packed bed. The yield does not exceed 40% and can be rationalized by the natural equilibrium as well as product inhibition which was experimentally proven. The flow synthesis with the immobilized enzyme was compared with the corresponding transformation conducted with the free enzyme. The product yield was further improved by operating under slug flow conditions which is related to the very short residence time distribution. In all cases 20% diastereomeric excess (de) and 99% enantiomeric excess (ee) were observed. A continuous run of the reactant solution was carried out for 10 hours in order to check enzyme stability at higher temperature. Stable operation was achieved at 20 minute residence time. Finally, the productivity of the reactor was calculated, extrapolated to parallel run units, and compared with data collected previously. PMID:24204429

  7. Effect of conductive polymers coated anode on the performance of microbial fuel cells (MFCs) and its biodiversity analysis.

    PubMed

    Li, Chao; Zhang, Libin; Ding, Lili; Ren, Hongqiang; Cui, Hao

    2011-06-15

    Conductive polymer, one of the most attractive electrode materials, has been applied to coat anode of MFC to improve its performance recently. In this paper, two conductive polymer materials, polyaniline (PANI) and poly(aniline-co-o-aminophenol) (PAOA) were used to modify carbon felt anode and physical and chemical properties of the modified anodes were studied. The power output and biodiversity of modified anodes, along with unmodified carbon anode were compared in two-chamber MFCs. Results showed that the maximum power density of PANI and PAOA MFC could reach 27.4 mW/m(2) and 23.8 mW/m(2), comparing with unmodified MFC, increased by 35% and 18% separately. Low temperature caused greatly decrease of the maximum voltage by 70% and reduced the sorts of bacteria on anodes in the three MFCs. Anode biofilm analysis showed different bacteria enrichment: a larger mount of bacteria and higher biodiversity were found on the two modified anodes than on the unmodified one. For PANI anode, the two predominant bacteria were phylogenetically closely related to Hippea maritima and an uncultured clone MEC_Bicarb_Ac-008; for PAOA, Clostridiales showed more enrichment. Compare PAOA with PANI, the former introduced phenolic hydroxyl group by copolymerization o-aminophenol with aniline, which led to a different microbial community and the mechanism of group effect was proposed. PMID:21549585

  8. Structures of the N-terminal modules imply large domain motions during catalysis by methionine synthase.

    PubMed

    Evans, John C; Huddler, Donald P; Hilgers, Mark T; Romanchuk, Gail; Matthews, Rowena G; Ludwig, Martha L

    2004-03-16

    B(12)-dependent methionine synthase (MetH) is a large modular enzyme that utilizes the cobalamin cofactor as a methyl donor or acceptor in three separate reactions. Each methyl transfer occurs at a different substrate-binding domain and requires a different arrangement of modules. In the catalytic cycle, the cobalamin-binding domain carries methylcobalamin to the homocysteine (Hcy) domain to form methionine and returns cob(I)alamin to the folate (Fol) domain for remethylation by methyltetrahydrofolate (CH(3)-H(4)folate). Here, we describe crystal structures of a fragment of MetH from Thermotoga maritima comprising the domains that bind Hcy and CH(3)-H(4)folate. These substrate-binding domains are (beta alpha)(8) barrels packed tightly against one another with their barrel axes perpendicular. The properties of the domain interface suggest that the two barrels remain associated during catalysis. The Hcy and CH(3)-H(4)folate substrates are bound at the C termini of their respective barrels in orientations that position them for reaction with cobalamin, but the two active sites are separated by approximately 50 A. To complete the catalytic cycle, the cobalamin-binding domain must travel back and forth between these distant active sites. PMID:14752199

  9. Structures of the N-terminal modules imply large domain motions during catalysis by methionine synthase

    PubMed Central

    Evans, John C.; Huddler, Donald P.; Hilgers, Mark T.; Romanchuk, Gail; Matthews, Rowena G.; Ludwig, Martha L.

    2004-01-01

    B12-dependent methionine synthase (MetH) is a large modular enzyme that utilizes the cobalamin cofactor as a methyl donor or acceptor in three separate reactions. Each methyl transfer occurs at a different substrate-binding domain and requires a different arrangement of modules. In the catalytic cycle, the cobalamin-binding domain carries methylcobalamin to the homocysteine (Hcy) domain to form methionine and returns cob(I)alamin to the folate (Fol) domain for remethylation by methyltetrahydrofolate (CH3-H4folate). Here, we describe crystal structures of a fragment of MetH from Thermotoga maritima comprising the domains that bind Hcy and CH3-H4folate. These substrate-binding domains are (??)8 barrels packed tightly against one another with their barrel axes perpendicular. The properties of the domain interface suggest that the two barrels remain associated during catalysis. The Hcy and CH3-H4folate substrates are bound at the C termini of their respective barrels in orientations that position them for reaction with cobalamin, but the two active sites are separated by ?50 Å. To complete the catalytic cycle, the cobalamin-binding domain must travel back and forth between these distant active sites. PMID:14752199

  10. Structure and characterization of the 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Aeropyrum pernix

    PubMed Central

    Zhou, Lily; Wu, Jing; Janakiraman, Vijayalakshmi; Shumilin, Igor A.; Bauerle, Ronald; Kretsinger, Robert H.

    2011-01-01

    The first enzyme in the shikimic acid biosynthetic pathway, 3-deoxy-D-arabinoheptulosonate 7-phosphate synthase (DAH7PS), varies significantly in size and complexity in the bacteria and plants that express it. The DAH7PS from the archaebacterium Aeropyrum pernix (DAH7PSAp) is among the smallest and least complex of the DAH7PS enzymes, leading to the hypothesis that DAH7PSAp would not be subject to feedback regulation by shikimic acid pathway products. We overexpressed DAH7PSAp in Escherichia coli, purified it, and characterized its enzymatic activity. We then solved its X-ray crystal structure with a divalent manganese ion and phosphoenolpyruvate bound (PDBID: 1VS1). DAH7PSAp is a homodimeric metalloenzyme in solution. Its enzymatic activity increases dramatically above 60°C, with optimum activity at 95°C. Its pH optimum at 60°C is 5.7. DAH7PSAp follows Michaelis-Menten kinetics at 60° C, with a KM for erythrose 4-phosphate of 280 ?M, a KM for phosphoenolpyruvate of 891 ?M, and a kcat of 1.0 s-1. None of the downstream products of the shikimate biosynthetic pathway we tested inhibited the activity of DAH7PSAp. The structure of DAH7PSAp is similar to the structures of DAH7PS from Thermatoga maritima (PDB ID: 3PG8) and Pyrococcus furiosus (PDB ID: 1ZCO), and is consistent with its designation as an unregulated DAH7PS. PMID:22035970

  11. Paleobiology of the Sand Beneath the Valders Diamicton at Valders, Wisconsin

    NASA Astrophysics Data System (ADS)

    Maher, Louis J.; Miller, Norton G.; Baker, Richard G.; Curry, B. Brandon; Mickelson, David M.

    1998-03-01

    Previously undescribed pollen, plant macrofossils, molluscs, and ostracodes were recovered from a 2.5-m-thick glaciolacustrine unit of silty sand and clay at Valders, Wisconsin. The interstadial sediment was deposited about 12,200 14C yr B.P. after retreat of the Green Bay lobe that deposited diamicton of the Horicon Formation, and before advance of the Lake Michigan lobe that deposited the red-brown diamicton of the Valders Member of the Kewaunee Formation. Fluctuations of abundance of Candona subtriangulata, Cytherissa lacustris,and three other species define four ostracode biozones in the lower 1.7 m, suggesting an open lake environment that oscillated in depth and proximity to glacial ice. Pollen is dominated by Piceaand Artemisia,but the low percentages of many other types of long-distance origin suggest that the terrestrial vegetation was open and far from the forest border. The upper part of the sediment, a massive sand deposited in either a shallow pond or a sluggish stream, contains a local concentration of plant macrofossils. The interpretation of a cold open environment is supported by the plant macrofossils of more than 20 species, dominated by those of open mineral soils ( Arenaria rubella, Cerastium alpinumtype, Silene acaulis, Sibbaldia procumbens, Dryas integrifolia, Vaccinium uliginosumvar. alpinum, Armeria maritima,etc.) that in North America occur largely in the tundra and open tundra-forest ecotone of northern Canada. Ice-wedge casts occur in the sand.

  12. Clusters of Branched Aliphatic Side Chains Serve As Cores of Stability in the Native State of the HisF TIM Barrel Protein

    PubMed Central

    Gangadhara, Basavanapura N.; Laine, Jennifer M.; Kathuria, Sagar V.; Massi, Francesca; Matthews, C. Robert

    2013-01-01

    Imidazole-3-glycerol phosphate synthase is a heterodimeric allosteric enzyme that catalyzes consecutive reactions in imidazole biosynthesis through its HisF and HisH subunits. The unusually slow unfolding reaction of the isolated HisF TIM barrel domain from the thermophilic bacteria, Thermotoga maritima, enabled an NMR-based site-specific analysis of the main-chain hydrogen bonds that stabilize its native conformation. Very strong protection against exchange with solvent deuterium in the native state was found in a subset of buried positions in ?-helices and pervasively in the underlying ?-strands associated with a pair of large clusters of isoleucine, leucine and valine (ILV) side chains located in the ?7(??)8(??)1–2 and ?2(??)3–6?7 segments of the (??)8 barrel. The most densely packed region of the large cluster, ?3(??)4–6?7, correlates closely with the core of stability previously observed in computational, protein engineering and NMR dynamics studies, demonstrating a key role for this cluster in determining the thermodynamic and structural properties of the native state of HisF. When considered with the results of previous studies where ILV clusters were found to stabilize the hydrogen-bonded networks in folding intermediates for other TIM barrel proteins, it appears that clusters of branched aliphatic side chains can serve as cores of stability across the entire folding reaction coordinate of one of the most common motifs in biology. PMID:23333740

  13. Structure-guided discovery of new deaminase enzymes.

    PubMed

    Hitchcock, Daniel S; Fan, Hao; Kim, Jungwook; Vetting, Matthew; Hillerich, Brandan; Seidel, Ronald D; Almo, Steven C; Shoichet, Brian K; Sali, Andrej; Raushel, Frank M

    2013-09-18

    A substantial challenge for genomic enzymology is the reliable annotation for proteins of unknown function. Described here is an interrogation of uncharacterized enzymes from the amidohydrolase superfamily using a structure-guided approach that integrates bioinformatics, computational biology, and molecular enzymology. Previously, Tm0936 from Thermotoga maritima was shown to catalyze the deamination of S-adenosylhomocysteine (SAH) to S-inosylhomocysteine (SIH). Homologues of Tm0936 homologues were identified, and substrate profiles were proposed by docking metabolites to modeled enzyme structures. These enzymes were predicted to deaminate analogues of adenosine including SAH, 5'-methylthioadenosine (MTA), adenosine (Ado), and 5'-deoxyadenosine (5'-dAdo). Fifteen of these proteins were purified to homogeneity, and the three-dimensional structures of three proteins were determined by X-ray diffraction methods. Enzyme assays supported the structure-based predictions and identified subgroups of enzymes with the capacity to deaminate various combinations of the adenosine analogues, including the first enzyme (Dvu1825) capable of deaminating 5'-dAdo. One subgroup of proteins, exemplified by Moth1224 from Moorella thermoacetica, deaminates guanine to xanthine, and another subgroup, exemplified by Avi5431 from Agrobacterium vitis S4, deaminates two oxidatively damaged forms of adenine: 2-oxoadenine and 8-oxoadenine. The sequence and structural basis of the observed substrate specificities were proposed, and the substrate profiles for 834 protein sequences were provisionally annotated. The results highlight the power of a multidisciplinary approach for annotating enzymes of unknown function. PMID:23968233

  14. Molecular details of ligand selectivity determinants in a promiscuous ?-glucan periplasmic binding protein

    PubMed Central

    2013-01-01

    Background Members of the periplasmic binding protein (PBP) superfamily utilize a highly conserved inter-domain ligand binding site that adapts to specifically bind a chemically diverse range of ligands. This paradigm of PBP ligand binding specificity was recently altered when the structure of the Thermotoga maritima cellobiose-binding protein (tmCBP) was solved. The tmCBP binding site is bipartite, comprising a canonical solvent-excluded region (subsite one), adjacent to a solvent-filled cavity (subsite two) where specific and semi-specific ligand recognition occur, respectively. Results A molecular level understanding of binding pocket adaptation mechanisms that simultaneously allow both ligand specificity at subsite one and promiscuity at subsite two has potentially important implications in ligand binding and drug design studies. We sought to investigate the determinants of ligand binding selectivity in tmCBP through biophysical characterization of tmCBP in the presence of varying ?-glucan oligosaccharides. Crystal structures show that whilst the amino acids that comprise both the tmCBP subsite one and subsite two binding sites remain fixed in conformation regardless of which ligands are present, the rich hydrogen bonding potential of water molecules may facilitate the ordering and the plasticity of this unique PBP binding site. Conclusions The identification of the roles these water molecules play in ligand recognition suggests potential mechanisms that can be utilized to adapt a single ligand binding site to recognize multiple distinct ligands. PMID:24090243

  15. A peroxiredoxin Q homolog from gentians is involved in both resistance against fungal disease and oxidative stress.

    PubMed

    Kiba, Akinori; Nishihara, Masahiro; Tsukatani, Nobue; Nakatsuka, Takashi; Kato, Yoshiaki; Yamamura, Saburo

    2005-06-01

    An antifungal protein (GtAFP1) showing antimicrobial activity against phytopathogenic fungi was purified from leaves of Gentiana triflora. The deduced amino acid sequence of the cDNA of the corresponding gene, GtAFP1, showed 94, 75, 72 and 63% amino acid identities with peroxiredoxin Q from Populus balsamifera x P. deltoides subsp. trichocarpa, Sedum lineare, Suaeda maritima and Arabidopsis thaliana, respectively. The GtAFP1 gene is suggested to be present in the genome in one to two copies and was expressed in the leaves, roots and stems. Expression of GtAFP1 was induced by treatment with salicylic acid, but not methyl jasmonate. Recombinant GtAFP1 protein showed not only antifungal activity but also thioredoxin-dependent peroxidase activity. Overexpression of GtAFP1 in tobacco plants improved tolerance not only against fungal diseases but also against oxidative stress. These results indicate that GtAFP1 might act as a disease and oxidative stress defensive gene in plants and could be useful for engineering stress-resistant plants. PMID:15840643

  16. Chemical and in vitro assessment of Alaskan coastal vegetation antioxidant capacity.

    PubMed

    Kellogg, Joshua; Lila, Mary Ann

    2013-11-20

    Alaska Native (AN) communities have utilized tidal plants and marine seaweeds as food and medicine for generations, yet the bioactive potential of these resources has not been widely examined. This study screened six species of Alaskan seaweed ( Fucus distichus , Saccharina latissima , Saccharina groenlandica , Alaria marginata , Pyropia fallax , and Ulva lactuca ) and one tidal plant ( Plantago maritima ) for antioxidant activity. Total polyphenolic content (TPC) was determined, and chemical antioxidant capacity was assessed by 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging, ferrous ion chelating, and nitric oxide (NO) inhibition assays. In vitro inhibition of radical oxygen species (ROS) generation and NO synthesis was evaluated in a RAW 264.7 macrophage culture. Greatest TPC (557.2 ?g phloroglucinol equivalents (PGE)/mg extract) was discovered in the ethyl acetate fraction of F. distichus, and highest DDPH scavenging activity was exhibited by F. distichus and S. groenlandica fractions (IC50 = 4.29-5.12 ?g/mL). These results support the potential of Alaskan coastal vegetation, especially the brown algae, as natural sources of antioxidants for preventing oxidative degeneration and maintaining human health. PMID:24147955

  17. Ecological correlates of variable organ sizes and fat loads in the most northerly-wintering shorebirds

    USGS Publications Warehouse

    Ruthrauff, Daniel R.; Dekinga, A.; Gill, R.E., Jr.; Summers, R.W.; Piersma, T.

    2013-01-01

    Shorebirds at northern latitudes during the nonbreeding season typically carry relatively large lipid stores and exhibit an up-regulation of lean tissues associated with digestion and thermogenesis. Intraspecific variation in these tissues across sites primarily reflects differences in environmental conditions. Rock (Calidris ptilocnemis (Coues, 1873)) and Purple (Calidris maritima (Brünnich, 1764)) sandpipers are closely related species having the most northerly nonbreeding distributions among shorebirds, living at latitudes up to 61°N in Cook Inlet, Alaska, and up to 71°N in northern Norway, respectively. Cook Inlet is the coldest known site used by nonbreeding shorebirds, and the region’s mudflats annually experience extensive coverage of foraging sites by sea and shore-fast ice. Accordingly, Rock Sandpipers increase their fat stores to nearly 20% of body mass during winter. In contrast, Purple Sandpipers exploit predictably ice-free rocky intertidal foraging sites and maintain low (<6.5%) fat stores. Rock Sandpipers increase the mass of lean tissues from fall to winter, including contour feathers, stomach, and liver components. They also have greater lean pectoralis and supracoracoideus muscle and liver and kidney tissues compared with Purple Sandpipers in winter. This demonstrates a combined emphasis on digestive processes and thermogenesis, whereas Purple Sandpipers primarily augment organs associated with digestive processes. The high winter fat loads and increased lean tissues of Rock Sandpipers in Cook Inlet reflect the region’s persistent cold and abundant but sporadically unavailable food resources.

  18. The biological soil crusts of the San Nicolas Island: Enigmatic algae from a geographically isolated ecosystem

    USGS Publications Warehouse

    Flechtner, V.R.; Johansen, J.R.; Belnap, J.

    2008-01-01

    Composite soil samples from 7 sites on San Nicolas Island were evaluated quantitatively and qualitatively for the presence of cyanobacteria and eukaryotic microalgae. Combined data demonstrated a rich algal flora with 19 cyanobacterial and 19 eukaryotic microalgal genera being identified, for a total of 56 species. Nine new species were identified and described among the cyanobacteria and the eukaryotic microalgae that were isolated: Leibleinia edaphica, Aphanothece maritima, Chroococcidiopsis edaphica, Cyanosarcina atroveneta, Hassallia californica, Hassallia pseudoramosissima, Microchaete terrestre, Palmellopsis californiens, and Pseudotetracystis compactis. Distinct distributional patterns of algal taxa existed among sites on the island and among soil algal floras of western North America. Some algal taxa appeared to be widely distributed across many desert regions, including Microcoleus vaginatus, Nostoc punctiforme, Nostoc paludosum, and Tolypothrix distorta, Chlorella vulgaris, Diplosphaera cf. chodatii, Myrmecia astigmatica, Myrmecia biatorellae, Hantzschia amphioxys, and Luticola mutica. Some taxa share a distinctly southern distribution with soil algae from southern Arizona, southern California, and Baja California (e.g., Scenedesmus deserticola and Eustigmatos magnus). The data presented herein support the view that the cyanobacterial and microalgal floras of soil crusts possess significant biodiversity, much of it previously undescribed.

  19. Cross-linked polymer nanofibers for hyperthermophilic enzyme immobilization: approaches to improve enzyme performance.

    PubMed

    Tang, Christina; Saquing, Carl D; Morton, Stephen W; Glatz, Brittany N; Kelly, Robert M; Khan, Saad A

    2014-08-13

    We report an enzyme immobilization method effective at elevated temperatures (up to 105 °C) and sufficiently robust for hyperthermophilic enzymes. Using a model hyperthermophilic enzyme, ?-galactosidase from Thermotoga maritima, immobilization within chemically cross-linked poly(vinyl alcohol) (PVA) nanofibers to provide high specific surface area is achieved by (1) electrospinning a blend of a PVA and enzyme and (2) chemically cross-linking the polymer to entrap the enzyme within a water insoluble PVA fiber. The resulting enzyme-loaded nanofibers are water-insoluble at elevated temperatures, and enzyme leaching is not observed, indicating that the cross-linking effectively immobilizes the enzyme within the fibers. Upon immobilization, the enzyme retains its hyperthermophilic nature and shows improved thermal stability indicated by a 5.5-fold increase in apparent half-life at 90 °C, but with a significant decrease in apparent activity. The loss in apparent activity is attributed to enzyme deactivation and mass transfer limitations. Improvements in the apparent activity can be achieved by incorporating a cryoprotectant during immobilization to prevent enzyme deactivation. For example, immobilization in the presence of trehalose improved the apparent activity by 10-fold. Minimizing the mat thickness to reduce interfiber diffusion was a simple and effective method to further improve the performance of the immobilized enzyme. PMID:25058141

  20. Microbiological evidence for Fe(III) reduction on early Earth.

    PubMed

    Vargas, M; Kashefi, K; Blunt-Harris, E L; Lovley, D R

    1998-09-01

    It is generally considered that sulphur reduction was one of the earliest forms of microbial respiration, because the known microorganisms that are most closely related to the last common ancestor of modern life are primarily anaerobic, sulphur-reducing hyperthermophiles. However, geochemical evidence indicates that Fe(III) is more likely than sulphur to have been the first external electron acceptor of global significance in microbial metabolism. Here we show that Archaea and Bacteria that are most closely related to the last common ancestor can reduce Fe(III) to Fe(II) and conserve energy to support growth from this respiration. Surprisingly, even Thermotoga maritima, previously considered to have only a fermentative metabolism, could grow as a respiratory organism when Fe(III) was provided as an electron acceptor. These results provide microbiological evidence that Fe(III) reduction could have been an important process on early Earth and suggest that microorganisms might contribute to Fe(III) reduction in modern hot biospheres. Furthermore, our discovery that hyperthermophiles that had previously been thought to require sulphur for cultivation can instead be grown without the production of toxic and corrosive sulphide, should aid biochemical investigations of these poorly understood organisms. PMID:9738498

  1. Comparison of three ionic liquid-tolerant cellulases by molecular dynamics.

    PubMed

    Jaeger, Vance; Burney, Patrick; Pfaendtner, Jim

    2015-02-17

    We have employed molecular dynamics to investigate the differences in ionic liquid tolerance among three distinct family 5 cellulases from Trichoderma viride, Thermogata maritima, and Pyrococcus horikoshii. Simulations of the three cellulases were conducted at a range of temperatures in various binary mixtures of the ionic liquid 1-ethyl-3-methyl-imidazolium acetate with water. Our analysis demonstrates that the effects of ionic liquids on the enzymes vary in each individual case from local structural disturbances to loss of much of one of the enzyme's secondary structure. Enzymes with more negatively charged surfaces tend to resist destabilization by ionic liquids. Specific and unique structural changes in the enzymes are induced by the presence of ionic liquids. Disruption of the secondary structure, changes in dynamical motion, and local changes in the binding pocket are observed in less tolerant enzymes. Ionic-liquid-induced denaturation of one of the enzymes is indicated over the 500 ns timescale. In contrast, the most tolerant cellulase behaves similarly in water and in ionic-liquid-containing mixtures. Unlike the heuristic approaches that attempt to predict enzyme stability using macroscopic properties, molecular dynamics allows us to predict specific atomic-level structural and dynamical changes in an enzyme's behavior induced by ionic liquids and other mixed solvents. Using these insights, we propose specific experimentally testable hypotheses regarding the origin of activity loss for each of the systems investigated in this study. PMID:25692593

  2. FtsA forms actin-like protofilaments

    PubMed Central

    Szwedziak, Piotr; Wang, Qing; Freund, Stefan MV; Löwe, Jan

    2012-01-01

    FtsA is an early component of the Z-ring, the structure that divides most bacteria, formed by tubulin-like FtsZ. FtsA belongs to the actin family of proteins, showing an unusual subdomain architecture. Here we reconstitute the tethering of FtsZ to the membrane via FtsA's C-terminal amphipathic helix in vitro using Thermotoga maritima proteins. A crystal structure of the FtsA:FtsZ interaction reveals 16 amino acids of the FtsZ tail bound to subdomain 2B of FtsA. The same structure and a second crystal form of FtsA reveal that FtsA forms actin-like protofilaments with a repeat of 48?Å. The identical repeat is observed when FtsA is polymerized using a lipid monolayer surface and FtsAs from three organisms form polymers in cells when overexpressed, as observed by electron cryotomography. Mutants that disrupt polymerization also show an elongated cell division phenotype in a temperature-sensitive FtsA background, demonstrating the importance of filament formation for FtsA's function in the Z-ring. PMID:22473211

  3. Posttranscriptional modification of tRNA in thermophilic archaea (Archaebacteria).

    PubMed Central

    Edmonds, C G; Crain, P F; Gupta, R; Hashizume, T; Hocart, C H; Kowalak, J A; Pomerantz, S C; Stetter, K O; McCloskey, J A

    1991-01-01

    Nucleoside modification has been studied in unfractionated tRNA from 11 thermophilic archaea (archaebacteria), including phylogenetically diverse representatives of thermophilic methanogens and sulfur-metabolizing hyperthermophiles which grow optimally in the temperature range of 56 (Thermoplasma acidophilum) to 105 degrees C (Pyrodictium occultum), and for comparison from the most thermophilic bacterium (eubacterium) known, Thermotoga maritima (80 degrees C). Nine nucleosides are found to be unique to the archaea, six of which are structurally novel in being modified both in the base and by methylation in ribose and occur primarily in tRNA from the extreme thermophiles in the Crenarchaeota of the archaeal phylogenetic tree. 2-Thiothymine occurs in tRNA from Thermococcus sp., and constitutes the only known occurrence of the thymine moiety in archaeal RNA, in contrast to its near-ubiquitous presence in tRNA from bacteria and eukarya. A total of 33 modified nucleosides are rigorously characterized in archaeal tRNA in the present study, demonstrating that the structural range of posttranscriptional modifications in archaeal tRNA is more extensive than previously known. From a phylogenetic standpoint, certain tRNA modifications occur in the archaea which are otherwise unique to either the bacterial or eukaryal domain, although the overall patterns of modification are more typical of eukaryotes than bacteria. PMID:1708763

  4. Phylogenetic Analyses of Meloidogyne Small Subunit rDNA.

    PubMed

    De Ley, Irma Tandingan; De Ley, Paul; Vierstraete, Andy; Karssen, Gerrit; Moens, Maurice; Vanfleteren, Jacques

    2002-12-01

    Phylogenies were inferred from nearly complete small subunit (SSU) 18S rDNA sequences of 12 species of Meloidogyne and 4 outgroup taxa (Globodera pallida, Nacobbus abberans, Subanguina radicicola, and Zygotylenchus guevarai). Alignments were generated manually from a secondary structure model, and computationally using ClustalX and Treealign. Trees were constructed using distance, parsimony, and likelihood algorithms in PAUP* 4.0b4a. Obtained tree topologies were stable across algorithms and alignments, supporting 3 clades: clade I = [M. incognita (M. javanica, M. arenaria)]; clade II = M. duytsi and M. maritima in an unresolved trichotomy with (M. hapla, M. microtyla); and clade III = (M. exigua (M. graminicola, M. chitwoodi)). Monophyly of [(clade I, clade II) clade III] was given maximal bootstrap support (mbs). M. artiellia was always a sister taxon to this joint clade, while M. ichinohei was consistently placed with mbs as a basal taxon within the genus. Affinities with the outgroup taxa remain unclear, although G. pallida and S. radicicola were never placed as closest relatives of Meloidogyne. Our results show that SSU sequence data are useful in addressing deeper phylogeny within Meloidogyne, and that both M. ichinohei and M. artiellia are credible outgroups for phylogenetic analysis of speciations among the major species. PMID:19265950

  5. Crystal Structure of a Two-Subunit TrkA Octameric Gating Ring Assembly

    PubMed Central

    Deller, Marc C.; Johnson, Hope A.; Miller, Mitchell D.; Spraggon, Glen; Elsliger, Marc-André; Wilson, Ian A.; Lesley, Scott A.

    2015-01-01

    The TM1088 locus of T. maritima codes for two proteins designated TM1088A and TM1088B, which combine to form the cytosolic portion of a putative Trk K+ transporter. We report the crystal structure of this assembly to a resolution of 3.45 Å. The high resolution crystal structures of the components of the assembly, TM1088A and TM1088B, were also determined independently to 1.50 Å and 1.55 Å, respectively. The TM1088 proteins are structurally homologous to each other and to other K+ transporter proteins, such as TrkA. These proteins form a cytosolic gating ring assembly that controls the flow of K+ ions across the membrane. TM1088 represents the first structure of a two-subunit Trk assembly. Despite the atypical genetics and chain organization of the TM1088 assembly, it shares significant structural homology and an overall quaternary organization with other single-subunit K+ gating ring assemblies. This structure provides the first structural insights into what may be an evolutionary ancestor of more modern single-subunit K+ gating ring assemblies. PMID:25826626

  6. Effects of Posidonia oceanica beach-cast on germination, growth and nutrient uptake of coastal dune plants.

    PubMed

    Del Vecchio, Silvia; Marbà, Núria; Acosta, Alicia; Vignolo, Clara; Traveset, Anna

    2013-01-01

    Seagrass meadows play an important role in marine ecosystems. A part of seagrass production is also exported to adjacent coastal terrestrial systems, possibly influencing their functioning. In this work we experimentally analyzed the effect of Posidonia oceanica beach-cast on plant germination, growth, and nutrient uptake of two plant species (Cakile maritima and Elymus farctus) that grow on upper beaches and fore dunes along the Mediterranean coasts. We compared plants growing in simple sand (control) with those growing in a substrate enriched with P. oceanica wrack (treatment) in laboratory. P. oceanica wrack doubled the N substrate pool and kept the substrate humid. Plants growing in the treated substrate grew faster, were twice as large as those growing in the control substrate, while tissues were enriched in N and P (Cakile by the 1.3 fold in N and 2.5 fold in P; Elymus by 1.5 fold in N and 2 fold in P). Our results suggest a positive effect of seagrass litter for the enhancing of dune species, highlighting its role for the conservation of coastal dune ecosystems. PMID:23894678

  7. The structure of the TrmE GTP-binding protein and its implications for tRNA modification

    PubMed Central

    Scrima, Andrea; Vetter, Ingrid R; Armengod, M Eugenia; Wittinghofer, Alfred

    2005-01-01

    TrmE is a 50 kDa guanine nucleotide-binding protein conserved between bacteria and man. It is involved in the modification of uridine bases (U34) at the first anticodon (wobble) position of tRNAs decoding two-family box triplets. The precise role of TrmE in the modification reaction is hitherto unknown. Here, we report the X-ray structure of TrmE from Thermotoga maritima. The structure reveals a three-domain protein comprising the N-terminal ?/? domain, the central helical domain and the G domain, responsible for GTP binding and hydrolysis. The N-terminal domain induces dimerization and is homologous to the tetrahydrofolate-binding domain of N,N-dimethylglycine oxidase. Biochemical and structural studies show that TrmE indeed binds formyl-tetrahydrofolate. A cysteine residue, necessary for modification of U34, is located close to the C1-group donor 5-formyl-tetrahydrofolate, suggesting a direct role of TrmE in the modification analogous to DNA modification enzymes. We propose a reaction mechanism whereby TrmE actively participates in the formylation reaction of uridine and regulates the ensuing hydrogenation reaction of a Schiff's base intermediate. PMID:15616586

  8. 'Hot' Macromolecular Crystals

    SciTech Connect

    Koclega, Katarzyna D.; Chruszcz, Maksymilian; Zimmerman, Matthew D.; Bujacz, Grzegorz; Minor, Wladek (UV); (ITB-Poland)

    2010-09-07

    Transcriptional regulator protein TM1030 from the hyperthermophile Thermotoga maritima, as well as its complex with DNA, was crystallized at a wide range of temperatures. Crystallization plates were incubated at 4, 20, 37, and 50 C over 3 weeks. The best crystals of TM1030 in complex with DNA were obtained at 4, 20, and 37 C, while TM1030 alone crystallized almost equally well in all temperatures. The crystals grown at different temperatures were used for X-ray diffraction experiments and their structures were compared. Surprisingly, the models of TM1030 obtained from crystals grown at different temperatures are similar in quality. While there are some examples of structures of proteins grown at elevated temperatures in the PDB, these temperatures appear to be underrepresented. Our studies show that crystals of some proteins may be grown and are stable at broad range of temperatures. We suggest that crystallization experiments at elevated temperatures could be used as a standard part of the crystallization protocol.

  9. Effects of Posidonia Oceanica Beach-Cast on Germination, Growth and Nutrient Uptake of Coastal Dune Plants

    PubMed Central

    Del Vecchio, Silvia; Marbà, Núria; Acosta, Alicia; Vignolo, Clara; Traveset, Anna

    2013-01-01

    Seagrass meadows play an important role in marine ecosystems. A part of seagrass production is also exported to adjacent coastal terrestrial systems, possibly influencing their functioning. In this work we experimentally analyzed the effect of Posidonia oceanica beach-cast on plant germination, growth, and nutrient uptake of two plant species (Cakile maritima and Elymus farctus) that grow on upper beaches and fore dunes along the Mediterranean coasts. We compared plants growing in simple sand (control) with those growing in a substrate enriched with P. oceanica wrack (treatment) in laboratory. P. oceanica wrack doubled the N substrate pool and kept the substrate humid. Plants growing in the treated substrate grew faster, were twice as large as those growing in the control substrate, while tissues were enriched in N and P (Cakile by the 1.3 fold in N and 2.5 fold in P; Elymus by 1.5 fold in N and 2 fold in P). Our results suggest a positive effect of seagrass litter for the enhancing of dune species, highlighting its role for the conservation of coastal dune ecosystems. PMID:23894678

  10. A survey of zinc, copper and cadmium concentrations in salt marsh plants along the Dutch coast.

    PubMed

    Otte, M L; Bestebroer, S J; van der Linden, J M; Rozema, J; Broekman, R A

    1991-01-01

    In autumn 1986, plants and soil were collected from the lower and the higher salt marsh zones of salt marshes along the Dutch coast. The main purpose was to get an overview of Zn, Cu and Cd concentrations in six dominant species of salt marsh plants. The roots and shoots of the plants were analysed for Zn, Cu and Cd. The highest heavy metal concentrations were found in plants collected from salt marshes near harbour areas and/or that are known to receive contaminated fluvial sediment. Dicotyledonous plant species tended to have similar heavy metal concentrations in roots and shoots, whereas in monocotyledonous species the concentrations in the roots were two to three times higher than in the shoots. Differences in accumulation in the roots between elements and between plant species were found. Cd was accumulated more than Zn or Cu. Triglochin maritima shows a low Cd uptake by roots, whereas Spartina anglica and Scirpus maritimus tend to accumulate it. The fraction of soil particles smaller than 63 microm, loss on ignition and Zn, Cu and Cd concentrations were determined in soil samples. The highest Zn, Cu and Cd concentrations in the soil were found at salt marshes in the Western Scheldt area and were nine, five and 20 times higher than background levels, respectively. PMID:15092100

  11. Long-term effects of mercury in a salt marsh: hysteresis in the distribution of vegetation following recovery from contamination.

    PubMed

    Válega, M; Lillebø, A I; Pereira, M E; Duarte, A C; Pardal, M A

    2008-03-01

    During four decades, the Ria de Aveiro was subjected to the loading of mercury from a chlor-alkali industry, resulting in the deposition of several tons of mercury in the sediments. The present study evaluates the impact of this disturbance and the recovery processes, temporally and spatially, by means of examining the richness of the species of salt marsh plants and mercury concentrations in sediments over the last fifty years. The temporal assessment showed that the mercury loading induced a shift in the species composition of the salt marsh from a non-disturbed salt marsh with higher species richness to an alternative state dominated by Phragmites australis. The horizontal assessment, through a mercury gradient, presents the same trend, indicating that P. australis is the species most tolerant to higher mercury concentrations, comparative to Halimione portulacoides, Arthrocnemum fruticosum, Triglochin maritima, Juncus maritimus and Scirpus maritimus. After the reduction of mercury discharges in 1994, the salt marsh shows a slowly return path recovery response. The hysteresis in the response results in the temporal gap between the reduction in mercury concentrations in the sediment and the salt marsh species richness response, comparatively to the existing diversity in the local reference marsh. PMID:18061237

  12. High-resolution screening combined with HPLC-HRMS-SPE-NMR for identification of potential health-promoting constituents in sea aster and searocket--new Nordic food ingredients.

    PubMed

    Wubshet, Sileshi G; Schmidt, Jeppe S; Wiese, Stefanie; Staerk, Dan

    2013-09-11

    Sea aster (Aster tripolium L.) and searocket (Cakile maritima Scop.), potential ingredients in the New Nordic Diet, were analyzed by high-resolution radical scavenging and high-resolution ?-glucosidase inhibition assays. Results from the two bioactivity profiles were used to guide subsequent structural analysis toward constituents with potential health-promoting effects. Structural analysis was performed by high-performance liquid chromatography-high-resolution mass spectrometry-solid-phase extraction and automated tube transfer nuclear magnetic resonance spectroscopy, that is, HPLC-HRMS-SPE-ttNMR. High-resolution mass spectrometry together with detailed analysis of one- and two-dimensional proton detected NMR experiments enabled unambiguous assignment of the targeted analytes. This revealed a series of caffeoyl esters (1, 2, 5), flavonoid glycosides (3, 4, 6, 11-15), flavonoids (7-9), sinapate esters (10, 16, 17), and sinapinic acid (18) associated with radical scavenging and/or ?-glucosidase inhibition. In vitro assays implemented in this study showed that sea aster holds potential as a future functional food ingredient for lowering postprandial blood glucose level for diabetics, but further investigations are needed to prove the effect in vivo. PMID:23962163

  13. Triad pattern algorithm for predicting strong promoter candidates in bacterial genomes

    PubMed Central

    Dekhtyar, Michael; Morin, Amelie; Sakanyan, Vehary

    2008-01-01

    Background Bacterial promoters, which increase the efficiency of gene expression, differ from other promoters by several characteristics. This difference, not yet widely exploited in bioinformatics, looks promising for the development of relevant computational tools to search for strong promoters in bacterial genomes. Results We describe a new triad pattern algorithm that predicts strong promoter candidates in annotated bacterial genomes by matching specific patterns for the group I ?70 factors of Escherichia coli RNA polymerase. It detects promoter-specific motifs by consecutively matching three patterns, consisting of an UP-element, required for interaction with the ? subunit, and then optimally-separated patterns of -35 and -10 boxes, required for interaction with the ?70 subunit of RNA polymerase. Analysis of 43 bacterial genomes revealed that the frequency of candidate sequences depends on the A+T content of the DNA under examination. The accuracy of in silico prediction was experimentally validated for the genome of a hyperthermophilic bacterium, Thermotoga maritima, by applying a cell-free expression assay using the predicted strong promoters. In this organism, the strong promoters govern genes for translation, energy metabolism, transport, cell movement, and other as-yet unidentified functions. Conclusion The triad pattern algorithm developed for predicting strong bacterial promoters is well suited for analyzing bacterial genomes with an A+T content of less than 62%. This computational tool opens new prospects for investigating global gene expression, and individual strong promoters in bacteria of medical and/or economic significance. PMID:18471287

  14. Domain structure of the Acetogenium kivui surface layer revealed by electron crystallography and sequence analysis.

    PubMed Central

    Lupas, A; Engelhardt, H; Peters, J; Santarius, U; Volker, S; Baumeister, W

    1994-01-01

    The three-dimensional structure of the Acetogenium kivui surface layer (S-layer) has been determined to a resolution of 1.7 nm by electron crystallographic techniques. Two independent reconstructions were made from layers negatively stained with uranyl acetate and Na-phosphotungstate. The S-layer has p6 symmetry with a center-to-center spacing of approximately 19 nm. Within the layer, six monomers combine to form a ring-shaped core surrounded by a fenestrated rim and six spokes that point towards the axis of threefold symmetry and provide lateral connectivity to other hexamers in the layer. The structure of the A. kivui S-layer protein is very similar to that of the Bacillus brevis middle wall protein, with which it shares an N-terminal domain of homology. This domain is found in several other extracellular proteins, including the S-layer proteins from Bacillus sphaericus and Thermus thermophilus, Omp alpha from Thermotoga maritima, an alkaline cellulase from Bacillus strain KSM-635, and xylanases from Clostridium thermocellum and Thermoanaerobacter saccharolyticum, and may serve to anchor these proteins to the peptidoglycan. To our knowledge, this is the first example of a domain conserved in several S-layer proteins. Images PMID:8113161

  15. [Impacts of Ochotona pallasi disturbance on alpine grassland community characteristics].

    PubMed

    Zhao, Guo-qin; Li, Guang-yong; Ma, Wen-hu; Zhao, Dian-zhi; Li, Xiao-yan

    2013-08-01

    Plateau pika is the main fossorial mammal in the alpine grassland in Qinghai Lake Watershed of Northwest China. Based on the field investigation data from 18 alpine grassland quadrats in the Watershed, and by using redundancy analysis (RDA) and the surface fitting offered by 'R-Vegan' , the disturbance intensity of plateau pika (Ochotona pallasi) was classified as four levels. In order to explore the impacts of plateau pika disturbance on the alpine grassland ecosystem and its grazing quality, the community characteristics under different disturbance intensities by plateau pika were analyzed, and a conceptual model about the alpine grassland community succession was proposed. The results showed that with the increase of the disturbance intensity, the dominant species changed from Juncus roemerianus to Poa pratensis and Laux maritima. When the disturbance was small, the community had high quantitative values of coverage, aboveground biomass, biodiversity, and species richness, but the proportion of weeds was also high. When the disturbance was large, the quantitative values were the lowest, while the proportion of weeds was the highest. When the disturbance was moderate, the community had relatively high quantitative values, and the proportion of grasses and sedges was the highest. It was concluded that the community' s characteristic values under low plateau pika disturbance intensity were high but the grazing quality was low, while high disturbance intensity resulted in the grassland degradation. Therefore, the disturbance intensity in the threshold could maintain the stability of alpine grassland ecosystem and improve its grazing quality. PMID:24380328

  16. Na+-pyrophosphatase: a novel primary sodium pump.

    PubMed

    Malinen, Anssi M; Belogurov, Georgiy A; Baykov, Alexander A; Lahti, Reijo

    2007-07-31

    Membrane-bound pyrophosphatase (PPase) is commonly believed to couple pyrophosphate (PPi) hydrolysis to H+ transport across the membrane. Here, we demonstrate that two newly isolated bacterial membrane PPases from the mesophile Methanosarcina mazei (Mm-PPase) and the moderate thermophile Moorella thermoacetica and a previously described PPase from the hyperthermophilic bacterium Thermotoga maritima catalyze Na+ rather than H+ transport into Escherichia coli inner membrane vesicles (IMV). When assayed in uncoupled IMV, the three PPases exhibit an absolute requirement for Na+ but display the highest hydrolyzing activity in the presence of both Na+ and K+. Steady-state kinetic analysis of PPi hydrolysis by Mm-PPase revealed two Na+ binding sites. One of these sites can also bind K+, resulting in a 10-fold increase in the affinity of the other site for Na+ and a 2-fold increase in maximal velocity. PPi-driven 22Na+ transport into IMV containing Mm-PPase was unaffected by the protonophore carbonyl cyanide m-chlorophenylhydrazone, inhibited by the Na+ ionophore monensin, and activated by the K+ ionophore valinomycin. The Na+ transport was accompanied by the generation of a positive inside membrane potential as reported by Oxonol VI. These findings define Na+-dependent PPases as electrogenic Na+ pumps. Phylogenetic analysis suggests that ancient gene duplication preceded the split of Na+- and H+-PPases. PMID:17605473

  17. Simultaneous RP-HPLC-DAD separation, and determination of flavonoids and phenolic acids in Plantago L. species.

    PubMed

    Juriši? Grubeši?, Renata; Sre?nik, Goran; Kremer, Dario; Vukovi? Rodríguez, Jadranka; Nikoli?, Toni; Vladimir-Kneževi?, Sanda

    2013-07-01

    A rapid reversed-phase (RP) high-performance liquid chromatography method was developed and applied for simultaneous separation, and determination of flavonoids and phenolic acids in eight Plantago L. taxa (P. altissima L., P. argentea Chaix, P. coronopus L., P. holosteum Scop. ssp. depauperata Pilger, P. holosteum ssp. holosteum, P. holosteum ssp. scopulorum (Degen) Horvati?, P. lagopus L., and P. maritima L.) growing in Croatia. Chromatographic separation was carried out on Zorbax Eclipse XDB-C18 using gradient elution with a H2 O (pH?2.5, adjusted with CF3 COOH) and MeCN mixture at 30°. The contents of analyzed phenolic compounds (% of the dry weight of the leaves, dw) varied among examined species: rutin (max. 0.024%, P. argentea), hyperoside (max. 0.020%, P. lagopus), quercitrin (max. 0.013%, P. holosteum ssp. holosteum), quercetin (max. 0.028%, P. holosteum ssp. scopulorum), chlorogenic acid (max. 0.115%, P. lagopus), and caffeic acid (max. 0.046%, P. coronopus). Isoquercitrin was detected only in P. argentea (0.020%), while isochlorogenic acid content was below limit of quantification in all investigated species. Multivariate analyses (UPGMA and PCA) showed significant differences in contents of investigated polyphenolic compounds between different Plantago taxa. Accordingly, investigated substances might be employed as chemotaxonomic markers in the study of the complex genus Plantago. PMID:23847075

  18. Different status of the gene for ribosomal protein S16 in the chloroplast genome during evolution of the genus Arabidopsis and closely related species.

    PubMed

    Roy, Shradha; Ueda, Minoru; Kadowaki, Koh-ichi; Tsutsumi, Nobuhiro

    2010-01-01

    The ribosomal protein S16 (RPS16), the product of the rps16, is generally encoded in the chloroplast genomes of flowering plants. However, it has been reported that chloroplast-encoded RPS16 in mono- and dicotyledonous plants has been substituted by the product of nuclear-encoded rps16, which was transferred from the mitochondria to the nucleus before the early divergence of angiosperms. Current databases show that the chloroplast-encoded rps16 has become a pseudogene in four species of the Brassicaceae (Aethionema grandiflorum, Arabis hirsuta, Draba nemorosa, and Lobularia maritima). Further analysis of Arabidopsis thaliana and its close relatives has shown that pseudogenization has also occurred via the loss of its splicing capacity (Arabidopsis thaliana and Olimarabidopsis pumila). In contrast, the spliced product of chloroplast-encoded rps16 is observed in close relatives of Arabidopsis thaliana (Arabidopsis arenosa, Arabidopsis lyrata, and Crucihimalaya lasiocarpa). In this study, we identified the different functional status of rps16 in several chloroplast genomes in the genus Arabidopsis and its close relatives. Our results strongly suggest that nuclear- and chloroplast-encoded rps16 genes coexisted for at least 126 million years. We raise the possibility of the widespread pseudogenization of rps16 in the angiosperm chloroplast genomes via the loss of its splicing capacity, even when the rps16 encoded in the chloroplast genome is transcriptionally active. PMID:21317544

  19. Persistent organochlorine levels in six prey species of the gyrfalcon Falco rusticolus in Iceland.

    PubMed

    Olafsdóttir, K; Petersen, A E; Magnúsdóttir, E V; Björnsson, T; Jóhannesson, T

    2001-01-01

    Our previous investigations have revealed very high levels of organochlorines (OCs) in the Icelandic gyrfalcon Falco rusticolus, a resident top predator. We now examine six potential prey species of birds, both resident and migratory, in order to elucidate the most likely route of the OCs to the gyrfalcon. The ptarmigan Lagopus mutus, the most important prey of the gyrfalcon, contained very low levels of OCs. Bioaccumulation of polychlorinated biphenyls (PCBs) and DDTs in mallards Anas platyrhynchos, tufted ducks Aythya fuligula, golden plovers Pluvialis apricaria, purple sandpipers Calidris maritima, and black guillemots Cepphus grylle reflected their position in the foodchain. The differences in OC-levels seem nevertheless too high just to reflect the different food-chain levels of these species in Iceland. The winter grounds of the migratory golden plovers and tufted ducks appear to be more contaminated than the Icelandic terrestrial habitat of ptarmigans or the freshwater habitat as reflected in mallards, both resident species. However, spending the winter on the coast in Iceland, results in high levels of contaminants in purple sandpipers and black guillemots. Our results indicate OC contamination of the marine ecosystem in Iceland while the terrestrial and freshwater ecosystems are little affected. It is postulated that gyrfalcons receive the major part of the observed contamination from prey other than ptarmigan, especially birds associated with the marine ecosystem and also from migratory birds. PMID:11234542

  20. Phylogenetic Analyses of Meloidogyne Small Subunit rDNA

    PubMed Central

    De Ley, Irma Tandingan; De Ley, Paul; Vierstraete, Andy; Karssen, Gerrit; Moens, Maurice; Vanfleteren, Jacques

    2002-01-01

    Phylogenies were inferred from nearly complete small subunit (SSU) 18S rDNA sequences of 12 species of Meloidogyne and 4 outgroup taxa (Globodera pallida, Nacobbus abberans, Subanguina radicicola, and Zygotylenchus guevarai). Alignments were generated manually from a secondary structure model, and computationally using ClustalX and Treealign. Trees were constructed using distance, parsimony, and likelihood algorithms in PAUP* 4.0b4a. Obtained tree topologies were stable across algorithms and alignments, supporting 3 clades: clade I = [M. incognita (M. javanica, M. arenaria)]; clade II = M. duytsi and M. maritima in an unresolved trichotomy with (M. hapla, M. microtyla); and clade III = (M. exigua (M. graminicola, M. chitwoodi)). Monophyly of [(clade I, clade II) clade III] was given maximal bootstrap support (mbs). M. artiellia was always a sister taxon to this joint clade, while M. ichinohei was consistently placed with mbs as a basal taxon within the genus. Affinities with the outgroup taxa remain unclear, although G. pallida and S. radicicola were never placed as closest relatives of Meloidogyne. Our results show that SSU sequence data are useful in addressing deeper phylogeny within Meloidogyne, and that both M. ichinohei and M. artiellia are credible outgroups for phylogenetic analysis of speciations among the major species. PMID:19265950

  1. A rare case of a natural contact zone in Morocco between an autopolyploid and an allopolyploid of Centaurea aspera with sterile tetraploid hybrids.

    PubMed

    Garmendia, A; Ferriol, M; Juarez, J; Zaj?c, A; Ka?u?ny, K; Merle, H

    2015-05-01

    A new contact zone between Centaurea aspera and Centaurea seridis was found in Morocco. Chromosome counts and flow cytometry showed that both taxa were tetraploid (4x = 44). A literature review and morphometric analysis established that C. aspera corresponds to the autopolyploid C. aspera subsp. gentilii and C. seridis corresponds to the allopolyploid C. seridis var. auriculata. This contact area was compared with the homologous contact zones in Spain formed by the diploid C. aspera subsp. stenophylla and the tetraploid C. seridis subsp. maritima. Natural hybrids between parental species were frequent in both areas. In Spain, hybrids were triploid (from reduced gametes A and gamete AB), highly sterile and exerted a 'triploid block'. In Morocco, cytometry showed that hybrids were tetraploid and, therefore, probably fertile, but all the capitula lacked achenes. It is likely that the resulting genome of the new tetraploid hybrid (AAAB), through the fusion of reduced gametes AA (from subsp. gentilii) and AB (from var. auriculata), could explain irregularities in meiosis through formation of aneuploid gametes and, therefore, infertility of the hybrid. Moroccan sterile tetraploid hybrids develop, but have the identical irregularities to Spanish triploids, probably due to the odd number of homologous chromosomes. The new hybrid is first described as C. x subdecurrens nothosubsp. paucispinus. In addition, distribution and ecological traits are analysed. PMID:25363815

  2. A legacy of contrasting spatial genetic structure on either side of the Atlantic–Mediterranean transition zone in a marine protist

    PubMed Central

    Lowe, Chris D.; Martin, Laura E.; Montagnes, David J. S.; Watts, Phillip C.

    2012-01-01

    The mechanisms that underpin the varied spatial genetic structures exhibited by free-living marine microorganisms remain controversial, with most studies emphasizing a high dispersal capability that should redistribute genetic diversity in contrast to most macroorganisms whose populations often retain a genetic signature of demographic response to historic climate fluctuations. We quantified the European phylogeographic structure of the marine flagellate Oxyrrhis marina and found a marked difference in spatial genetic structure, population demography, and genetic diversity between the northwest Atlantic and Mediterranean Sea that reflects the persistent separation of these regions as well as context-dependent population responses to contrasting environments. We found similar geographic variation in the level of genetic diversity in the sister species Oxyrrhis maritima. Because the capacity for wide dispersal is not always realized, historic genetic footprints of range expansion and contraction persist in contemporary populations of marine microbes, as they do in larger species. Indeed, the well-described genetic effects of climatic variation on macroorganisms provide clear, testable hypotheses about the processes that drive genetic divergence in marine microbes and thus about the response to future environmental change. PMID:23213247

  3. Nomenclatural changes, new country records and range extensions of Baridinae (Coleoptera, Curculionidae) from China.

    PubMed

    Prena, Jens; Yang, Jiani; Ren, Li; Wang, Zhiliang; Liu, Ning; Zhang, Runzhi

    2014-01-01

    Thirteen relatively frequently collected species of baridine weevils from mainland China were mapped to improve our understanding of biogeographic patterns and distributional ranges of Baridinae in the Palaearctic and Oriental regions. This simple case study showed that taxonomists tend to underestimate the spatial scope required in regional investigations and descriptive works often resulting in widespread species being described numerous times. Several apparently uncommon species with uncertain relationships, known previously only from moderately high latitudes in the Palaearctic region, showed Oriental affinities. In each region, species may occur over many thousands of kilometers not only in East-West but also in North-South directions. New synonyms are Mimophilus Faust (=Baridiomorphus Voss), Acythopeus inflatirostris Voss (=Acythopeus proximus Voss), Baris albisquama Zaslavskij (=Baris ljaodunensis Zaslavskij), Mimophilus tragicus Faust (=Baridiomorphus conicollis Voss), Moreobaris deplanata (Roelofs) (=Acythopeus patruelis Voss), Baris pilosa Roelofs (=Baris blennus Marshall, =Baris piliventris Zaslavskij, =Baris pygidialis Voss, =Baris suvorovi Reitter), Baris artemisiae (Panzer) (=Baris corvina Voss), Pellobaris melancholica (Roelofs) (=Paracythopeus collaris Voss), Pteridobaris maritima (Roelofs) (=Baris quinquecarinata Zaslavskij) and Ulobaris kuchenbeisseri Hartmann (=Baris pseudospitzyi Zaslavskij, =Baris ussuriensis ussuriensis Zaslavskij, =Baris ussuriensis chinganensis Zaslavskij). New combinations are Athesapeuta gracilis (Voss) (from Eumycterus Schönherr), Athesapeuta inornata (Voss) (from Baris Germar) and Nespilobaris inflatirostris (Voss) (from Acythopeus Pascoe). Baridius vestitus Perris (not Boheman) and Baris pygidialis Hustache (not Voss) are newly recognized primary homonyms. A lectotype is designated for Moreobaris deplanata. Twenty-four species are recorded newly from China.  PMID:25082044

  4. Impacts of the 1998 and 2010 mass coral bleaching events on the Western Gulf of Thailand

    NASA Astrophysics Data System (ADS)

    Sutthacheep, Makamas; Yucharoen, Mathinee; Klinthong, Wanlaya; Pengsakun, Sittiporn; Sangmanee, Kanwara; Yeemin, Thamasak

    2013-11-01

    A long-term study of coral reef ecology in the Gulf of Thailand provides a good opportunity to examine the temporal variation on the impact of mass coral bleaching at those reef sites. We compared the bleaching and mortality of corals between the mass bleaching events in 1998 and 2010 at a coral community in the Western Gulf of Thailand. The aim was to identify the coral species which were most likely to suffer from (and to be able to tolerate) changes in seawater temperature. Significant differences in the susceptibility of the coral taxa to bleaching events between the years 1998 and 2010 and among coral species were documented. Bleaching was significantly different between the most dominant corals. Diploastrea heliopora was the most resistant coral to bleaching in both years. Some coral species showed more resistance to bleaching in 2010. The coral mortality following the mass bleaching events in 1998 and 2010 varied significantly between the years and the coral taxa. Mortality of some dominant coral taxa was also lower in 2010. Seven coral species, i.e. Astreopora myriophthalma, Pachyseris rugosa, Turbinaria mesenterina, Goniastrea pectinata, Favia pallida, F. maritima, Favites halicora, Platygyra daedalea and Galaxea fascicularis, were tolerant to the coral bleaching events. An ecosystem-based approach to managing coral reefs in the Gulf of Thailand is needed to identify appropriate marine protected area networks and to strengthen marine and coastal resource policies in order to build coral reef resilience.

  5. Abiotic methyl bromide formation from vegetation, and its strong dependence on temperature.

    PubMed

    Wishkerman, Asher; Gebhardt, Sarah; McRoberts, Colin W; Hamilton, John T G; Williams, Jonathan; Keppler, Frank

    2008-09-15

    Methyl bromide (CH3Br) is the most abundant brominated organic compound in the atmosphere. It is known to originate from natural and anthropogenic sources, although many uncertainties remain regarding strengths of both sources and sinks and the processes leading to its formation. In this study a potential new CH3Br source from vegetation has been examined, analogous to the recently discovered abiotic formation of methyl chloride from plant pectin. Several plant samples with known bromine content, including ash (Fraxinus excelsior), saltwort (Batis maritima), tomato reference material (NIST-1573a), hay reference material (IAEA V-10), and also bromine enriched pectin, were incubated in the temperature range of 25-50 degrees C and analyzed for CH3Br emission using gas chromatography/mass spectrometry. All plant samples inspected showed an exponential increase in CH3Br emission as a function of temperature increase, i.e., emissions were observed to approximately double with every 5 degrees C rise in temperature. Next to temperature, it was found that emissions of CH3Br were also dependent on the bromine content of the plants. The highest CH3Br release rates were found for the saltwort which contained the highest bromine concentration. Arrhenius plots confirmed that the observed emissions were from an abiotic origin. The contribution of abiotic CH3Br formation from vegetation to the global budget will vary geographically as a result of regional differences in both temperature and bromide content of terrestrial plants. PMID:18853797

  6. Fluorescence in insects

    NASA Astrophysics Data System (ADS)

    Welch, Victoria L.; Van Hooijdonk, Eloise; Intrater, Nurit; Vigneron, Jean-Pol

    2012-10-01

    Fluorescent molecules are much in demand for biosensors, solar cells, LEDs and VCSEL diodes, therefore, considerable efforts have been expended in designing and tailoring fluorescence to specific technical applications. However, naturally occurring fluorescence of diverse types has been reported from a wide array of living organisms: most famously, the jellyfish Aequorea victoria, but also in over 100 species of coral and in the cuticle of scorpions, where it is the rule, rather than the exception. Despite the plethora of known insect species, comparatively few quantitative studies have been made of insect fluorescence. Because of the potential applications of natural fluorescence, studies in this field have relevance to both physics and biology. Therefore, in this paper, we review the literature on insect fluorescence, before documenting its occurrence in the longhorn beetles Sternotomis virescens, Sternotomis variabilis var. semi rufescens, Anoplophora elegans and Stellognatha maculata, the tiger beetles Cicindela maritima and Cicindela germanica and the weevil Pachyrrhynchus gemmatus purpureus. Optical features of insect fluorescence, including emitted wavelength, molecular ageing and naturally occurring combinations of fluorescence with bioluminescence and colour-producing structures are discussed.

  7. Effects of two plant extracts on larval leafminer Liriomyza trifolii (Diptera: Agromyzidae) in tomatoes.

    PubMed

    Civelek, H S; Weintraub, P G

    2004-10-01

    Aqueous extracts from two plants, Urginea maritima L. (Liliaceae) and Euphorbia myrsinites L. (Euphorbiaceae), were tested for their insecticidal activity against the leafminer Liriomyza trifolii (Burgess) on infested tomato, Lycopersicon esculentum Mill., plants in the laboratory and field. Two grams of plant material was extracted with 100 ml of water and then diluted 1:100, 1:50, and 1:25 with distilled water. Diluted plant extract was either applied to the infested tomato leaves or by soil drench and was compared with foliar application of cyromazine. All dilutions of both plant extracts caused significant control of the leafminer larvae and maintained populations below those of the nontreated control plants in all trials. Only at the most concentrated dilutions (1:25) were the plant extracts statistically similar to the cyromazine treatment. Furthermore, greenhouse yields from all of the foliar treatments were statistically similar to the cyromazine treatment and significantly better than the nontreated control. Four species of leafminer parasitoids were found in the greenhouse; however, the percentage of parasitism was significantly less in all treated replicates than in the nontreated control replicates. Aqueous extracts from these two plant extracts exhibited both translaminar and systemic activity and are potential candidates as new organic insecticides. PMID:15568346

  8. A role for [Fe4S4] clusters in tRNA recognition—a theoretical study

    PubMed Central

    Stiebritz, Martin T.

    2014-01-01

    Over the past several years, structural studies have led to the unexpected discovery of iron–sulfur clusters in enzymes that are involved in DNA replication/repair and protein biosynthesis. Although these clusters are generally well-studied cofactors, their significance in the new contexts often remains elusive. One fascinating example is a tryptophanyl-tRNA synthetase from the thermophilic bacterium Thermotoga maritima, TmTrpRS, that has recently been structurally characterized. It represents an unprecedented connection among a primordial iron–sulfur cofactor, RNA and protein biosynthesis. Here, a possible role of the [Fe4S4] cluster in tRNA anticodon-loop recognition is investigated by means of density functional theory and comparison with the structure of a human tryptophanyl-tRNA synthetase/tRNA complex. It turns out that a cluster-coordinating cysteine residue, R224, and polar main chain atoms form a characteristic structural motif for recognizing a putative 5? cytosine or 5? 2-thiocytosine moiety in the anticodon loop of the tRNA molecule. This motif provides not only affinity but also specificity by creating a structural and energetical penalty for the binding of other bases, such as uracil. PMID:24753428

  9. Assembly and mechanism of a group II ECF transporter.

    PubMed

    Karpowich, Nathan K; Wang, Da-Neng

    2013-02-12

    Energy-coupling factor (ECF) transporters are a recently discovered family of primary active transporters for micronutrients and vitamins, such as biotin, thiamine, and riboflavin. Found exclusively in archaea and bacteria, including the human pathogens Listeria, Streptococcus, and Staphylococcus, ECF transporters may be the only means of vitamin acquisition in these organisms. The subunit composition of ECF transporters is similar to that of ATP binding cassette (ABC) importers, whereby both systems share two homologous ATPase subunits (A and A'), a high affinity substrate-binding subunit (S), and a transmembrane coupling subunit (T). However, the S subunit of ECF transporters is an integral membrane protein, and the transmembrane coupling subunits do not share an obvious sequence homology between the two transporter families. Moreover, the subunit stoichiometry of ECF transporters is controversial, and the detailed molecular interactions between subunits and the conformational changes during substrate translocation are unknown. We have characterized the ECF transporters from Thermotoga maritima and Streptococcus thermophilus. Our data suggests a subunit stoichiometry of 2S:2T:1A:1A' and that S subunits for different substrates can be incorporated into the same transporter complex simultaneously. In the first crystal structure of the A-A' heterodimer, each subunit contains a novel motif called the Q-helix that plays a key role in subunit coupling with the T subunits. Taken together, these findings suggest a mechanism for coupling ATP binding and hydrolysis to transmembrane transport by ECF transporters. PMID:23359690

  10. Thermus thermophilus L4 ribosomal protein: purification and sensitivity alteration against erythromycin of E. coli cells harboring a single amino acid mutant of TthL4 within its extended loop.

    PubMed

    Leontiadou, F; Tsagkalia, A; Choli-Papadopoulou, T

    2007-09-01

    Protein L4 from the thermophilic bacterium Thermus thermophilus (TthL4) was heterologously overproduced in Escherichia coli cells and purified under native conditions by using ion exchange chromatography. Although it's known strong binding to RNA (23S rRNA as well as mRNA) the yield of the purified protein was 6 mg per 10 g of cells and it is similar to that referred for Thermotoga maritima L4 ribosomal protein. In addition, E. coli cells harboring the wild type Thermus thermophilus L4 (wtTthL4) ribosomal protein as well as its mutant having changed the highly conserved glutamic acid 56 by alanine (TthL4-Ala 56) were incorporated into E. coli ribosomes after transformation of the host cells with the recombined vector. The cells having incorporated the mutant TthL4-Ala56 are more sensitive against erythromycin related to that containing the wtTthL4 protein.The resistance to the drug indicates that the mutated amino acid Glu56 is probably critical for the local ribosomal conformation and that its mutation induces conformational disturbances that are "transferred" to the entrance of the major exit tunnel, the place where the drug does bind. PMID:17048124

  11. Evidence for gene flow via seed dispersal from crop to wild relatives in Beta vulgaris (Chenopodiaceae): consequences for the release of genetically modified crop species with weedy lineages.

    PubMed

    Arnaud, J-F; Viard, F; Delescluse, M; Cuguen, J

    2003-08-01

    Gene flow and introgression from cultivated to wild plant populations have important evolutionary and ecological consequences and require detailed investigations for risk assessments of transgene escape into natural ecosystems. Sugar beets (Beta vulgaris ssp. vulgaris) are of particular concern because: (i) they are cross-compatible with their wild relatives (the sea beet, B. vulgaris ssp. maritima); (ii) crop-to-wild gene flow is likely to occur via weedy lineages resulting from hybridization events and locally infesting fields. Using a chloroplastic marker and a set of nuclear microsatellite loci, the occurrence of crop-to-wild gene flow was investigated in the French sugar beet production area within a 'contact-zone' in between coastal wild populations and sugar beet fields. The results did not reveal large pollen dispersal from weed to wild beets. However, several pieces of evidence clearly show an escape of weedy lineages from fields via seed flow. Since most studies involving the assessment of transgene escape from crops to wild outcrossing relatives generally focused only on pollen dispersal, this last result was unexpected: it points out the key role of a long-lived seed bank and highlights support for transgene escape via man-mediated long-distance dispersal events. PMID:12908976

  12. Use of digital multispectral videography to assess seagrass distribution in San Quinti??n Bay, Baja California, Mexico [Uso de videografi??a multiespectral digital para evaluar la distributio??n del pasto marino en Bahi??a San Quinti??n, Baja California, Me??xico

    USGS Publications Warehouse

    Ward, D.H.; Tibbitts, T.L.; Morton, A.; Carrera-Gonzalez, E.; Kempka, R.

    2004-01-01

    Apparent threats to the spatial distribution of seagrass in San Quinti??n Bay prompted us to make a detailed assessment of habitats in the bay. Six coastal habitats and three seagrass subclasses were delineated using airborne digital multispectral videography (DMSV), Eelgrass, Zostera marina, was the predominant seagrass and covered 40% (1949 ha) of the areal extent of the bay in 1999. Eelgrass grew over a wide range of tidal depths from about -3.0 in mean lower low water (MLLW) to about 1.0 m MLLW, but greatest spatial extent occurred in intertidal areas -0.6 m to 1.0 m MLLW. Exposed-continuous (i.e., high density) eelgrass was the most abundant habitat in the bay. Widgeongrass, Ruppia maritima, was the only other seagrass present and covered 3% (136 ha) of the areal extent of the entire bay. Widgeongrass grew in single species stands in the upper intertidal (??? 0.4 MLLW) and intermixed with eelgrass at lower tidal depths. Overall accuracy of the six habitat classes and three subclasses in the DMSV map was relatively high at 84%. Our detailed map of San Quintin Bay can be used in future change detection analyses to monitor the health of seagrasses in the bay.

  13. Structure and mechanism of an intramembrane liponucleotide synthetase central for phospholipid biosynthesis

    PubMed Central

    Liu, Xiuying; Yin, Yan; Wu, Jinjun; Liu, Zhenfeng

    2014-01-01

    Phospholipids are elemental building-block molecules for biological membranes. Biosynthesis of phosphatidylinositol, phosphatidylglycerol and phosphatidylserine requires a central liponucleotide intermediate named cytidine-diphosphate diacylglycerol (CDP-DAG). The CDP-DAG synthetase (Cds) is an integral membrane enzyme catalysing the formation of CDP-DAG, an essential step for phosphoinositide recycling during signal transduction. Here we report the structure of the Cds from Thermotoga maritima (TmCdsA) at 3.4?Å resolution. TmCdsA forms a homodimer and each monomer contains nine transmembrane helices arranged into a novel fold with three domains. An unusual funnel-shaped cavity penetrates half way into the membrane, allowing the enzyme to simultaneously accept hydrophilic substrate (cytidine 5?-triphosphate (CTP)/deoxy-CTP) from cytoplasm and hydrophobic substrate (phosphatidic acid) from membrane. Located at the bottom of the cavity, a Mg2+-K+ hetero-di-metal centre coordinated by an Asp-Asp dyad serves as the cofactor of TmCdsA. The results suggest a two-metal-ion catalytic mechanism for the Cds-mediated synthesis of CDP-DAG at the membrane–cytoplasm interface. PMID:24968740

  14. The Root-Knot Nematode Producing Galls on Spartina alterniflora Belongs to the Genus Meloidogyne: Rejection of Hypsoperine and Spartonema spp.

    PubMed Central

    Plantard, Olivier; Valette, Sylvie; Gross, Michael F.

    2007-01-01

    Root-knot nematodes are a major group of plant-parasitic nematodes, but their sister group within the Tylenchida remains to be identified. To find the sister group and for any investigation of the evolutionary biology of the genus Meloidogyne, it would be useful to identify the most basal species within Meloidogyninae. Meloidogyne spartinae, a root-knot nematode parasitic on cordgrass (Spartina spp.), constitutes a potentially interesting early diverging (or at least highly divergent) root-knot nematode because it was originally described in a different genus, Hypsoperine (and later Spartonema), due to its unique anatomy and biology (although it was later put in synonymy by some, but not all, taxonomists). We have sequenced the whole 18S rDNA of this species and compared it to other sequences of this region that are available in GenBank for numerous Meloidogyne species. Phylogenetic analysis unambiguously locates the branch corresponding to M. spartinae as a lately diverging species, more closely related to M. maritima, M. duytsi or the M. ardenensis-hapla group. Thus, the distinction of a separate genus (Hypsoperine or Spartonema) for this species is not justified. PMID:19259481

  15. [Pseudo-(venocuran-)lupus--a minor episode in the history of medicine].

    PubMed

    Wälli, F; Grob, P J; Müller-Schoop, J

    1981-09-19

    Pseudolupus is a syndrome characterized by recurrent fever arthralgia, myalgia, involvement of lung and heart, high sedimentation rate, leukocytosis and lymphopenia. The diagnosis is established by the presence of circulating antimitochondrial antibodies. In 1975 it was found that the disease was due to prolonged treatment with Venocuran, a drug against venous disorders composed of phenopyrazone (pyrazolone derivative), horse-chestnut extract, and Miroton (glycosides extracted from white squill [Urginea maritima], convallaria, oleander and adonis). The drug was then withdrawn. No new cases have come to our attention since then. 15 patients with severe pseudolupus known to us in 1975 have now been followed up. In 6 of the patients all symptoms disappeared within weeks or a few months after withdrawal of the drug. However, the other 9 patients had at least 1 and often 2--3 relapses in the following months to years. In some patients, symptoms remained as long as 4--5 years. Antimitochondrial antibodies persisted in 4 patients for more than 3 years and in 1 patient are still detectable now. The pathomechanism of pseudolupus has not been elucidated. PMID:7280640

  16. The structural and biochemical characterization of human RNase H2 complex reveals the molecular basis for substrate recognition and Aicardi-Goutières syndrome defects.

    PubMed

    Figiel, Ma?gorzata; Chon, Hyongi; Cerritelli, Susana M; Cybulska, Magdalena; Crouch, Robert J; Nowotny, Marcin

    2011-03-25

    RNase H2 cleaves RNA sequences that are part of RNA/DNA hybrids or that are incorporated into DNA, thus, preventing genomic instability and the accumulation of aberrant nucleic acid, which in humans induces Aicardi-Goutières syndrome, a severe autoimmune disorder. The 3.1 ? crystal structure of human RNase H2 presented here allowed us to map the positions of all 29 mutations found in Aicardi-Goutières syndrome patients, several of which were not visible in the previously reported mouse RNase H2. We propose the possible effects of these mutations on the protein stability and function. Bacterial and eukaryotic RNases H2 differ in composition and substrate specificity. Bacterial RNases H2 are monomeric proteins and homologs of the eukaryotic RNases H2 catalytic subunit, which in addition possesses two accessory proteins. The eukaryotic RNase H2 heterotrimeric complex recognizes RNA/DNA hybrids and (5')RNA-DNA(3')/DNA junction hybrids as substrates with similar efficiency, whereas bacterial RNases H2 are highly specialized in the recognition of the (5')RNA-DNA(3') junction and very poorly cleave RNA/DNA hybrids in the presence of Mg(2+) ions. Using the crystal structure of the Thermotoga maritima RNase H2-substrate complex, we modeled the human RNase H2-substrate complex and verified the model by mutational analysis. Our model indicates that the difference in substrate preference stems from the different position of the crucial tyrosine residue involved in substrate binding and recognition. PMID:21177858

  17. A study of antioxidant activity, enzymatic inhibition and in vitro toxicity of selected traditional sudanese plants with anti-diabetic potential

    PubMed Central

    2014-01-01

    Background Diabetes mellitus is a chronic metabolic disease with life-threatening complications. Despite the enormous progress in conventional medicine and pharmaceutical industry, herbal-based medicines are still a common practice for the treatment of diabetes. This study evaluated ethanolic and aqueous extracts of selected Sudanese plants that are traditionally used to treat diabetes. Methods Extraction was carried out according to method described by Sukhdev et. al. and the extracts were tested for their glycogen phosphorylase inhibition, Brine shrimp lethality and antioxidant activity using (DPPH) radical scavenging activity and iron chelating activity. Extracts prepared from the leaves of Ambrosia maritima, fruits of Foeniculum vulgare and Ammi visnaga, exudates of Acacia Senegal, and seeds of Sesamum indicum and Nigella sativa. Results Nigella sativa ethanolic extract showed no toxicity on Brine shrimp Lethality Test, while its aqueous extract was toxic. All other extracts were highly toxic and ethanolic extracts of Foeniculum vulgare exhibited the highest toxicity. All plant extracts with exception of Acacia senegal revealed significant antioxidant activity in DPPH free radical scavenging assay. Conclusions These results highly agree with the ethnobotanical uses of these plants as antidiabetic. This study endorses further studies on plants investigated, to determine their potential for type 2 diabetes management. Moreover isolation and identification of active compounds are highly recommended. PMID:24885334

  18. Crystal structure of a 4-thiouridine synthetase–RNA complex reveals specificity of tRNA U8 modification

    PubMed Central

    Neumann, Piotr; Naumann, Peter-Thomas; Erwin, Whitney M.; Lauhon, Charles T.; Ficner, Ralf

    2014-01-01

    In prokaryotes and archaea transfer ribonucleic acid (tRNA) stability as well as cellular UV protection relies on the post-transcriptional modification of uracil at position 8 (U8) of tRNAs by the 4-thiouridine synthetase ThiI. Here, we report three crystal structures of ThiI from Thermotoga maritima in complex with a truncated tRNA. The RNA is mainly bound by the N-terminal ferredoxin-like domain (NFLD) and the THUMP domain of one subunit within the ThiI homo-dimer thereby positioning the U8 close to the catalytic center in the pyrophosphatase domain of the other subunit. The recognition of the 3’-CCA end by the THUMP domain yields a molecular ruler defining the specificity for U8 thiolation. This first structure of a THUMP/NFLD-RNA complex might serve as paradigm for the RNA recognition by THUMP domains of other proteins. The ternary ThiI–RNA–ATP complex shows no significant structural changes due to adenosine triphosphate (ATP) binding, but two different states of active site loops are observed independent of the nucleotide loading state. Thereby conformational changes of the active site are coupled with conformational changes of the bound RNA. The ThiI–RNA complex structures indicate that full-length tRNA has to adopt a non-canonical conformation upon binding to ThiI. PMID:24705700

  19. The impact of sika deer grazing on the vegetation and infauna of Arne saltmarsh.

    PubMed

    Hannaford, Justine; Pinn, Eunice H; Diaz, Anita

    2006-01-01

    Arne saltmarsh, an RSPB reserve, is situated in Poole Harbour on the English south coast. In recent years, there has been concern about possible changes in the suitability of the site for Redshank (Trigna totanus) due to sika deer (Cervus nippon) grazing. In order to assess these changes, 50 plots were established in three different locations: 20 in grazed areas, 20 in ungrazed areas and 10 fenced enclosures. Deer grazing was found to significantly affect structural and species diversity of the saltmarsh vegetation. Spartina anglica dominated in ungrazed areas whilst Salicornia ramosissima and, to a lesser extent, Puccinellia maritima dominated in grazed sites. In grazed areas the vegetation cover was significantly lower, as was vegetation height and volume. In addition, significant changes were observed in the root biomass, which was lower in grazed areas. Infaunal diversity was generally low throughout the survey area. However, significant variations were observed. Invertebrates abundance was more abundant in grazed plots than in ungrazed plots, and least abundant in fenced plots. The study indicated that in its current condition, localised areas of Arne saltmarsh do not provide adequate habitat requirements for Tringa totanus. PMID:16246379

  20. Analysis of 13 asteroid lightcurves obtained at the Palmer Divide Observatory

    NASA Astrophysics Data System (ADS)

    Warner, Brian D.

    2006-06-01

    The lightcurves for the following asteroids were obtained and then analyzed to find the synodic period and amplitude. 321 Florentina: 2.8711±0.0003h, 0.37±0.02m; 787 Moskva: 6.056±0.001h, 0.61±0.02m; 839 Valborg: 10.366±0.005h, 0.14±0.02m; 912 Maritima: 48.43±0.05h, >0.12±0.02m; 1176 Lucidor: 4.0791±0.0006h, 0.06±0.02m; 1862 Apollo: 3.0680±0.0002h, 0.30-1.20±0.02m; 2266 Tchaikovsky: 4.883±0.003h, 0.04±0.01m; 2951 Perepadin: 4.7808±0.0001h, 0.60±0.02m; 5108 Lubeck: 8.769±0.003, 0.43±0.02m; (17864) 1998 KK38: 6.56±0.01h, 0.17±0.02m; (18582) 1997 XK9: 114±10h, 0.94±0.02m; (20231) 1997 YK: 48.2±0.1h, >0.22±0.02m. Asteroid 868 Lova was also observed but its long period is only constrained as >24h.

  1. The crystal structure of apo-FtsH reveals domain movements necessary for substrate unfolding and translocation

    PubMed Central

    Bieniossek, Christoph; Niederhauser, Barbara; Baumann, Ulrich M.

    2009-01-01

    The hexameric membrane-spanning ATP-dependent metalloprotease FtsH is universally conserved in eubacteria, mitochondria, and chloroplasts, where it fulfills key functions in quality control and signaling. As a member of the self-compartmentalizing ATPases associated with various cellular activities (AAA+ proteases), FtsH converts the chemical energy stored in ATP via conformational rearrangements into a mechanical force that is used for substrate unfolding and translocation into the proteolytic chamber. The crystal structure of the ADP state of Thermotoga maritima FtsH showed a hexameric assembly consisting of a 6-fold symmetric protease disk and a 2-fold symmetric AAA ring. The 2.6 ? resolution structure of the cytosolic region of apo-FtsH presented here reveals a new arrangement where the ATPase ring shows perfect 6-fold symmetry with the crucial pore residues lining an open circular entrance. Triggered by this conformational change, a substrate-binding edge beta strand appears within the proteolytic domain. Comparison of the apo- and ADP-bound structure visualizes an inward movement of the aromatic pore residues and generates a model of substrate translocation by AAA+ proteases. Furthermore, we demonstrate that mutation of a conserved glycine in the linker region inactivates FtsH. PMID:19955424

  2. Anaerobic high-throughput cultivation method for isolation of thermophiles using biomass-derived substrates.

    PubMed

    Hamilton-Brehm, Scott D; Vishnivetskaya, Tatiana A; Allman, Steve L; Mielenz, Jonathan R; Elkins, James G

    2012-01-01

    Flow cytometry (FCM) techniques have been developed for sorting mesophilic organisms, but the difficulty increases if the target microbes are thermophilic anaerobes. We demonstrate a reliable, high-throughput method of screening thermophilic anaerobic organisms using FCM and 96-well plates for growth on biomass-relevant substrates. The method was tested using the cellulolytic thermophiles Clostridium thermocellum (T(opt) = 55 °C), Caldicellulosiruptor obsidiansis (T(opt) = 78 °C) and the fermentative hyperthermophiles, Pyrococcus furiosus (T(opt) = 100 °C) and Thermotoga maritima (T(opt) = 80 °C). Multi-well plates were incubated at various temperatures for approximately 72-120 h and then tested for growth. Positive growth resulting from single cells sorted into individual wells containing an anaerobic medium was verified by OD(600). Depending on the growth substrate, up to 80 % of the wells contained viable cultures, which could be transferred to fresh media. This method was used to isolate thermophilic microbes from Rabbit Creek, Yellowstone National Park (YNP), Wyoming. Substrates for enrichment cultures including crystalline cellulose (Avicel), xylan (from Birchwood), pretreated switchgrass and Populus were used to cultivate organisms that may be of interest to lignocellulosic biofuel production. PMID:22843398

  3. Structural Insight into the Rotational Switching Mechanism of the Bacterial Flagellar Motor

    PubMed Central

    Kinoshita, Miki; Nakamura, Shuichi; Morimoto, Yusuke V.; Namba, Keiichi

    2011-01-01

    The bacterial flagellar motor can rotate either clockwise (CW) or counterclockwise (CCW). Three flagellar proteins, FliG, FliM, and FliN, are required for rapid switching between the CW and CCW directions. Switching is achieved by a conformational change in FliG induced by the binding of a chemotaxis signaling protein, phospho-CheY, to FliM and FliN. FliG consists of three domains, FliGN, FliGM, and FliGC, and forms a ring on the cytoplasmic face of the MS ring of the flagellar basal body. Crystal structures have been reported for the FliGMC domains of Thermotoga maritima, which consist of the FliGM and FliGC domains and a helix E that connects these two domains, and full-length FliG of Aquifex aeolicus. However, the basis for the switching mechanism is based only on previously obtained genetic data and is hence rather indirect. We characterized a CW-biased mutant (fliG(?PAA)) of Salmonella enterica by direct observation of rotation of a single motor at high temporal and spatial resolution. We also determined the crystal structure of the FliGMC domains of an equivalent deletion mutant variant of T. maritima (fliG(?PEV)). The FliG(?PAA) motor produced torque at wild-type levels under a wide range of external load conditions. The wild-type motors rotated exclusively in the CCW direction under our experimental conditions, whereas the mutant motors rotated only in the CW direction. This result suggests that wild-type FliG is more stable in the CCW state than in the CW state, whereas FliG(?PAA) is more stable in the CW state than in the CCW state. The structure of the TM-FliGMC(?PEV) revealed that extremely CW-biased rotation was caused by a conformational change in helix E. Although the arrangement of FliGC relative to FliGM in a single molecule was different among the three crystals, a conserved FliGM-FliGC unit was observed in all three of them. We suggest that the conserved FliGM-FliGC unit is the basic functional element in the rotor ring and that the PAA deletion induces a conformational change in a hinge-loop between FliGM and helix E to achieve the CW state of the FliG ring. We also propose a novel model for the arrangement of FliG subunits within the motor. The model is in agreement with the previous mutational and cross-linking experiments and explains the cooperative switching mechanism of the flagellar motor. PMID:21572987

  4. Characterization and Regulation of Sulfur Reductase Activity in Thermotoga neapolitana

    PubMed Central

    Childers, Susan E.; Noll, Kenneth M.

    1994-01-01

    The growth of the hyperthermophilic, anaerobic bacterium Thermotoga neapolitana is stimulated by elemental sulfur by an unknown mechanism. We detected hydrogen-dependent sulfur reductase (sulfhydrogenase) and polysulfide dehydrogenase activities in cell extracts of this organism, demonstrating that it has at least two pathways for sulfidogenesis. Hydrogen-dependent sulfur reductase and hydrogenase activities are catalyzed by the purified hydrogenase of Thermotoga maritima, and this enzyme was called the sulfhydrogenase (K. Ma, R. N. Schicho, R. M. Kelly, and M. W. W. Adams, Proc. Natl. Acad. Sci. USA 90:5341-5344, 1993). Cells grown without elemental sulfur or cystine had 1.3 to 3.3 times higher sulfhydrogenase activities than those grown with either of these sources of sulfane sulfur. Hydrogenase activity was 2 to 5 times higher. Polysulfide dehydrogenase was up to 48-fold more active in cell extracts than the sulfhydrogenase. The activity of polysulfide dehydrogenase was approximately twofold higher when cells were grown in the presence of elemental sulfur. Its activity was oxygen labile in crude extracts, and it appears to be a cytoplasmic enzyme. Polysulfide was preferred over elemental sulfur as an electron acceptor (Km = 0.15 mM) and was more active with NADH (Km = 0.03 mM) than NADPH (Km = 0.41 mM). Growth in the presence of elemental sulfur appeared to slightly increase the activity of polysulfide dehydrogenase and slightly decrease both activities of sulfhydrogenase (hydrogenase and polysulfide reductase), while growth without elemental sulfur had the opposite effects. The greater activity of polysulfide dehydrogenase and its apparent regulation indicate that it is the more physiologically important means of polysulfide reduction. PMID:16349338

  5. Contribution to the knowledge of the veterinary science and of the ethnobotany in Calabria region (Southern Italy)

    PubMed Central

    Passalacqua, Nicodemo G; De Fine, Giuseppe; Guarrera, Paolo Maria

    2006-01-01

    Background A series of preliminary research projects on plants used in Calabria (Southern Italy) in veterinary science and in other ethno-botanical fields (minor nourishment, domestic and handicraft sector) was carried out in the last twenty years. From the ethno-botanical point of view, Calabria is one of the most interesting region, since in the ancient times it was subject to the dominant cultures of several people (Greeks, Romans, Byzantines, Arabs, Normans etc.). Until some decades ago the road network was poorly developed and villages were isolated, so that the culture of the "subsistence" and some archaic customs were kept. Methods Data were collected by means of "open" interviews to farmers, shepherds and housewives in the last twenty years. More than 100 informants were interviewed, mostly over 50 years old. Plants were identified by local informants through gathering in the area or through examination of the fresh plants collected by the researchers. The collected data were compared with pharmacobotanical papers mainly of southern Italy and with other studies, in order to highlight novelties or concordances of uses. Results The use of 62 taxa distributed into 34 families are described. Among these, 8 are or were employed in veterinary science, 8 as anti-parasitic agents, 19 in minor nourishment, 5 as seasoning, 38 for other uses. Some toxic species for cattle are also mentioned. Conclusion Among the major findings: the use of Helleborus bocconei for bronchitis of bovines and of Scrophularia canina for lameness in veterinary science; Nerium oleander and Urginea maritima as anti-parasitic agents; Epilobium angustifolium, Centaurea napifolia L. and C. sphaerocephala L. in minor nourishment. PMID:17156472

  6. Ocean Acidification and the Loss of Phenolic Substances in Marine Plants

    PubMed Central

    Arnold, Thomas; Mealey, Christopher; Leahey, Hannah; Miller, A. Whitman; Hall-Spencer, Jason M.; Milazzo, Marco; Maers, Kelly

    2012-01-01

    Rising atmospheric CO2 often triggers the production of plant phenolics, including many that serve as herbivore deterrents, digestion reducers, antimicrobials, or ultraviolet sunscreens. Such responses are predicted by popular models of plant defense, especially resource availability models which link carbon availability to phenolic biosynthesis. CO2 availability is also increasing in the oceans, where anthropogenic emissions cause ocean acidification, decreasing seawater pH and shifting the carbonate system towards further CO2 enrichment. Such conditions tend to increase seagrass productivity but may also increase rates of grazing on these marine plants. Here we show that high CO2 / low pH conditions of OA decrease, rather than increase, concentrations of phenolic protective substances in seagrasses and eurysaline marine plants. We observed a loss of simple and polymeric phenolics in the seagrass Cymodocea nodosa near a volcanic CO2 vent on the Island of Vulcano, Italy, where pH values decreased from 8.1 to 7.3 and pCO2 concentrations increased ten-fold. We observed similar responses in two estuarine species, Ruppia maritima and Potamogeton perfoliatus, in in situ Free-Ocean-Carbon-Enrichment experiments conducted in tributaries of the Chesapeake Bay, USA. These responses are strikingly different than those exhibited by terrestrial plants. The loss of phenolic substances may explain the higher-than-usual rates of grazing observed near undersea CO2 vents and suggests that ocean acidification may alter coastal carbon fluxes by affecting rates of decomposition, grazing, and disease. Our observations temper recent predictions that seagrasses would necessarily be “winners” in a high CO2 world. PMID:22558120

  7. Ancestral Patterning of Tergite Formation in a Centipede Suggests Derived Mode of Trunk Segmentation in Trilobites

    PubMed Central

    Ortega-Hernández, Javier; Brena, Carlo

    2012-01-01

    Trilobites have a rich and abundant fossil record, but little is known about the intrinsic mechanisms that orchestrate their body organization. To date, there is disagreement regarding the correspondence, or lack thereof, of the segmental units that constitute the trilobite trunk and their associated exoskeletal elements. The phylogenetic position of trilobites within total-group Euarthropoda, however, allows inferences about the underlying organization in these extinct taxa to be made, as some of the fundamental genetic processes for constructing the trunk segments are remarkably conserved among living arthropods. One example is the expression of the segment polarity gene engrailed, which at embryonic and early postembryonic stages is expressed in extant panarthropods (i.e. tardigrades, onychophorans, euarthropods) as transverse stripes that define the posteriormost region of each trunk segment. Due to its conservative morphology and allegedly primitive trunk tagmosis, we have utilized the centipede Strigamia maritima to study the correspondence between the expression of engrailed during late embryonic to postembryonic stages, and the development of the dorsal exoskeletal plates (i.e. tergites). The results corroborate the close correlation between the formation of the tergite borders and the dorsal expression of engrailed, and suggest that this association represents a symplesiomorphy within Euarthropoda. This correspondence between the genetic and phenetic levels enables making accurate inferences about the dorsoventral expression domains of engrailed in the trunk of exceptionally preserved trilobites and their close relatives, and is suggestive of the widespread occurrence of a distinct type of genetic segmental mismatch in these extinct arthropods. The metameric organization of the digestive tract in trilobites provides further support to this new interpretation. The wider evolutionary implications of these findings suggest the presence of a derived morphogenetic patterning mechanism responsible for the reiterated occurrence of different types of trunk dorsoventral segmental mismatch in several phylogenetically distant, extinct and extant, arthropod groups. PMID:23285116

  8. Evidence for preferential depths of metal retention in roots of salt marsh plants.

    PubMed

    Caetano, Miguel; Vale, Carlos; Cesário, Rute; Fonseca, Nuno

    2008-02-15

    Depth variation (2-cm resolution) of Fe, Mn, Zn, Cr, Ni, Cu, As and Cd concentrations were determined in belowground biomass of Spartina maritima and Sarcocornia fruticosa and in sediments between roots from two marshes in Tagus (Rosário) and Guadiana (Castro Marim) estuaries in Portugal with different anthropogenic pressures. Levels of metals were also determined in aboveground plant parts. Metal concentrations in belowground material were 2-4 orders of magnitude greater than levels in aboveground plant parts providing evidence of weak upward translocation. Although both studied species showed poor extraction of Cr and Ni from sediments, S. fruticosa exhibited a large capability to remove Zn, Cu, As and Cd from contaminated sediments and stabilised them in belowground biomass. Accumulated metals showed a sub-surface concentration maximum or increase to basal roots. To evaluate whether these preferential layers of accumulation resulted from availability in sediments or controlled by plant activity, Enrichment Factors (EF=[Me](root)/[Metal](sediment)) were calculated for each sediment layer. Maximum values in Rosário plant species (Zn=9.3, Cu=18, As=20, Cd=46) exceeded those obtained in Castro Marim (Zn=1.3, Cu=4.3, As=6.1, Cd=18). Moreover, EFs varied with the depth indicating the presence of preferential layers of metal accumulation in roots of both plants, but depth zonation was not the same as in the sediments. These results suggested that levels in belowground biomass either integrated in time changes that occurred in solid sediments and pore water, or metal uptake by roots was not proportional to levels in sediments. The same sequence of metals transferred from sediment to belowground biomass for the two plants was obtained for the two marshes (Cd > As > Cu, Zn), although metals differed from mining ore to industrial/urban sources. PMID:18036637

  9. The genome of the recently domesticated crop plant sugar beet (Beta vulgaris).

    PubMed

    Dohm, Juliane C; Minoche, André E; Holtgräwe, Daniela; Capella-Gutiérrez, Salvador; Zakrzewski, Falk; Tafer, Hakim; Rupp, Oliver; Sörensen, Thomas Rosleff; Stracke, Ralf; Reinhardt, Richard; Goesmann, Alexander; Kraft, Thomas; Schulz, Britta; Stadler, Peter F; Schmidt, Thomas; Gabaldón, Toni; Lehrach, Hans; Weisshaar, Bernd; Himmelbauer, Heinz

    2014-01-23

    Sugar beet (Beta vulgaris ssp. vulgaris) is an important crop of temperate climates which provides nearly 30% of the world's annual sugar production and is a source for bioethanol and animal feed. The species belongs to the order of Caryophylalles, is diploid with 2n = 18 chromosomes, has an estimated genome size of 714-758 megabases and shares an ancient genome triplication with other eudicot plants. Leafy beets have been cultivated since Roman times, but sugar beet is one of the most recently domesticated crops. It arose in the late eighteenth century when lines accumulating sugar in the storage root were selected from crosses made with chard and fodder beet. Here we present a reference genome sequence for sugar beet as the first non-rosid, non-asterid eudicot genome, advancing comparative genomics and phylogenetic reconstructions. The genome sequence comprises 567 megabases, of which 85% could be assigned to chromosomes. The assembly covers a large proportion of the repetitive sequence content that was estimated to be 63%. We predicted 27,421 protein-coding genes supported by transcript data and annotated them on the basis of sequence homology. Phylogenetic analyses provided evidence for the separation of Caryophyllales before the split of asterids and rosids, and revealed lineage-specific gene family expansions and losses. We sequenced spinach (Spinacia oleracea), another Caryophyllales species, and validated features that separate this clade from rosids and asterids. Intraspecific genomic variation was analysed based on the genome sequences of sea beet (Beta vulgaris ssp. maritima; progenitor of all beet crops) and four additional sugar beet accessions. We identified seven million variant positions in the reference genome, and also large regions of low variability, indicating artificial selection. The sugar beet genome sequence enables the identification of genes affecting agronomically relevant traits, supports molecular breeding and maximizes the plant's potential in energy biotechnology. PMID:24352233

  10. Developing genetically engineered encapsulin protein cage nanoparticles as a targeted delivery nanoplatform.

    PubMed

    Moon, Hyojin; Lee, Jisu; Min, Junseon; Kang, Sebyung

    2014-10-13

    Protein cage nanoparticles are excellent candidates for use as multifunctional delivery nanoplatforms because they are built from biomaterials and have a well-defined structure. A novel protein cage nanoparticle, encapsulin, isolated from thermophilic bacteria Thermotoga maritima, is prepared and developed as a versatile template for targeted delivery nanoplatforms through both chemical and genetic engineering. It is pivotal for multifunctional delivery nanoplatforms to have functional plasticity and versatility to acquire targeting ligands, diagnostic probes, and drugs simultaneously. Encapsulin is genetically engineered to have unusual heat stability and to acquire multiple functionalities in a precisely controlled manner. Hepatocellular carcinoma (HCC) cell binding peptide (SP94-peptide, SFSIIHTPILPL) is chosen as a targeting ligand and displayed on the surface of engineered encapsulin (Encap_loophis42C123) through either chemical conjugation or genetic insertion. The effective and selective targeted delivery of SP94-peptide displaying encapsulin (SP94-Encap_loophis42C123) to HepG2 cells is confirmed by fluorescent microscopy imaging. Aldoxorubicin (AlDox), an anticancer prodrug, is chemically loaded to SP94-Encap_loophis42C123 via thiol-maleimide Michael-type addition, and the efficacy of the delivered drugs is evaluated with a cell viability assay. SP94-Encap_loophis42C123-AlDox shows comparable killing efficacy with that of free drugs without the platform's own cytotoxicity. Functional plasticity and versatility of the engineered encapsulin allow us to introduce targeting ligands, diagnostic probes, and therapeutic reagents simultaneously, providing opportunities to develop multifunctional delivery nanoplatforms. PMID:25180761

  11. Structural Diversity Within the Mononuclear and Binuclear Active Sites of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase

    SciTech Connect

    Hall,R.; Brown, S.; Fedorov, A.; Fedorov, E.; Xu, C.; Babbitt, P.; Almo, S.; Raushel, F.

    2007-01-01

    NagA catalyzes the hydrolysis of N-acetyl-D-glucosamine-6-phosphate to D-glucosamine-6-phosphate and acetate. X-ray crystal structures of NagA from Escherichia coli were determined to establish the number and ligation scheme for the binding of zinc to the active site and to elucidate the molecular interactions between the protein and substrate. The three-dimensional structures of the apo-NagA, Zn-NagA, and the D273N mutant enzyme in the presence of a tight-binding N-methylhydroxyphosphinyl-D-glucosamine-6-phosphate inhibitor were determined. The structure of the Zn-NagA confirms that this enzyme binds a single divalent cation at the beta-position in the active site via ligation to Glu-131, His-195, and His-216. A water molecule completes the ligation shell, which is also in position to be hydrogen bonded to Asp-273. In the structure of NagA bound to the tight binding inhibitor that mimics the tetrahedral intermediate, the methyl phosphonate moiety has displaced the hydrolytic water molecule and is directly coordinated to the zinc within the active site. The side chain of Asp-273 is positioned to activate the hydrolytic water molecule via general base catalysis and to deliver this proton to the amino group upon cleavage of the amide bond of the substrate. His-143 is positioned to help polarize the carbonyl group of the substrate in conjunction with Lewis acid catalysis by the bound zinc. The inhibitor is bound in the {alpha}-configuration at the anomeric carbon through a hydrogen bonding interaction of the hydroxyl group at C-1 with the side chain of His-251. The phosphate group of the inhibitor attached to the hydroxyl at C-6 is ion paired with Arg-227 from the adjacent subunit. NagA from Thermotoga maritima was shown to require a single divalent cation for full catalytic activity.

  12. Tyrosine Latching of a Regulatory Gate Affords Allosteric Control of Aromatic Amino Acid Biosynthesis*

    PubMed Central

    Cross, Penelope J.; Dobson, Renwick C. J.; Patchett, Mark L.; Parker, Emily J.

    2011-01-01

    The first step of the shikimate pathway for aromatic amino acid biosynthesis is catalyzed by 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS). Thermotoga maritima DAH7PS (TmaDAH7PS) is tetrameric, with monomer units comprised of a core catalytic (?/?)8 barrel and an N-terminal domain. This enzyme is inhibited strongly by tyrosine and to a lesser extent by the presence of phenylalanine. A truncated mutant of TmaDAH7PS lacking the N-terminal domain was catalytically more active and completely insensitive to tyrosine and phenylalanine, consistent with a role for this domain in allosteric inhibition. The structure of this protein was determined to 2.0 ?. In contrast to the wild-type enzyme, this enzyme is dimeric. Wild-type TmaDAH7PS was co-crystallized with tyrosine, and the structure of this complex was determined to a resolution of 2.35 ?. Tyrosine was found to bind at the interface between two regulatory N-terminal domains, formed from diagonally located monomers of the tetramer, revealing a major reorganization of the regulatory domain with respect to the barrel relative to unliganded enzyme. This significant conformational rearrangement observed in the crystal structures was also clearly evident from small angle X-ray scattering measurements recorded in the presence and absence of tyrosine. The closed conformation adopted by the protein on tyrosine binding impedes substrate entry into the neighboring barrel, revealing an unusual tyrosine-controlled gating mechanism for allosteric control of this enzyme. PMID:21282100

  13. Mobile dunes and eroding salt marshes

    NASA Astrophysics Data System (ADS)

    Neuhaus, R.

    1994-06-01

    The paper deals with general outlines of salt marsh and dune vegetation in the Ellenbogen and Listland area on Sylt (Schleswig-Holstein, FRG). The composition of current salt marsh vegetation is considered to be mainly the result of a long-lasting process of tidal inundation, grazing, and a permanent influence of groundwater seepage from the surrounding dunes. The lower salt marsh communities have shown constancy for 67 years, due to the effect of heavy grazing. The mid-upper salt marsh communities demonstrated a succession from a Puccinellia maritima-dominated community of the lower marsh to a Juncus gerardii-dominated community of the mid-upper salt marsh, which may be due to the transport of sand — over a short time — on the surface of the marsh. The area covered by plant communities of annuals below Mean High Water (MHW) seemed to diminish. Salt marsh soils, especially of the mid-upper marsh, indicate sandy layers resulting from sand drift of the dunes. Dry and wet successional series of the dunes in the Listland/Ellenbogen area both show grassy stages shifting to dwarf shrubs as final stages. White primary dunes can only be found on the accreting shoreline of the Ellenbogen, which is also grazed by sheep; vegetation cover therefore remains dominated by grasses, mosses and lichens. Three mobile dunes (as the most prominent features of this landscape) have been left unaffected by seeding and planting by local authorities. Grazing is considered to be an inadequate tool in nature conservation as long as natural processes are to prevail in the landscape as major determinants.

  14. Assessment of spatial variation in carbon utilization by benthic and pelagic invertebrates in a temperate South African estuary using stable isotope signatures

    NASA Astrophysics Data System (ADS)

    Richoux, Nicole B.; Froneman, P. William

    2007-02-01

    Stable isotope analyses ( ?13C and ?15N) were used to evaluate the spatial variations in carbon flow from primary producers to consumers at two sites in the temperate and permanently open Kariega Estuary on the southeastern coast of South Africa during October 2005 and February 2006. One site was located opposite a salt marsh while the second was upstream of the marsh. Except for significantly enriched ?13C values of Zostera capensis and surface sediments near the salt marsh, the ?13C and ?15N signatures of the producers were similar between sites. The invertebrates were clustered into groups roughly corresponding to the predominant feeding modes. The suspension feeders showed ?13C values closest to the seston, whereas the deposit feeders, detritivores and scavengers/predators had more enriched ?13C values reflecting primary carbon sources that were likely a combination of seston, Spartina maritima and Z. capensis at the upstream site, with an increased influence of benthic algae and Z. capensis at the salt marsh site. The ?15N signatures of the consumers showed a stepwise continuum rather than distinct levels of fractionation, indicating highly complex trophic linkages and significant dietary overlap among the species. Consumers exhibited significantly enriched ?13C values at the salt marsh site, an effect that was attributed to enriched Z. capensis detritus in this region in addition to increased phytoplankton biomass in their diets compared with invertebrates living upstream. The data reinforce the concept that between-site variations in the stable isotope ratios of consumers can result not only from dietary shifts, but also from alterations in the isotope ratios of primary producers.

  15. Isotopic variation of fishes in freshwater and estuarine zones of a large subtropical coastal lagoon

    NASA Astrophysics Data System (ADS)

    Garcia, A. M.; Hoeinghaus, D. J.; Vieira, J. P.; Winemiller, K. O.

    2007-07-01

    We used stable C and N isotope ratios of tissues from 29 fish species from a large subtropical lagoon in southern Brazil to examine spatial variability in isotopic composition and vertical trophic structure across freshwater and estuarine habitats. Nitrogen isotope ratios indicated a smooth gradation in trophic positions among species, with most fishes occupying the secondary and tertiary consumer level. Fish assemblages showed a significant shift in their carbon isotopic signatures between freshwater and estuarine sites. Depleted carbon signatures (from -24.7‰ to -17.8‰) were found in freshwater, whereas more enriched signatures (from -19.1‰ to -12.3‰) were obtained within the estuarine zone downstream. Based on our survey of the C 3 and C 4 plants and isotopic values for phytoplankton and benthic microalgae reported for ecosystems elsewhere, we hypothesized that the observed ?13C differences in the fish assemblage between freshwater and estuarine sites is due to a shift from assimilating organic matter ultimately derived from C 3 freshwater marsh vegetation and phytoplankton at the freshwater site ( ?13C ranging from -25‰ to -19‰), to C 4 salt-marsh (e.g. Spartina) and widgeon grass ( Ruppia maritima), benthic microalgae and marine phytoplankton at the estuarine sites (from -18‰ to -12‰). Our results suggested that fish assemblages are generally supported by autochthonous primary production. Freshwater fishes that likely were displaced downstream into the estuary during periods of high freshwater discharge had depleted ?13C values that were characteristic of the upper lagoon. These results suggest that spatial foodweb subsidies can occur within the lagoon.

  16. Oxidase Activity of a Flavin-Dependent Thymidylate Synthase

    PubMed Central

    Wang, Zhen; Chernyshev, Anatoly; Koehn, Eric M.; Manuel, Antonio; Lesley, Scott A.; Kohen, Amnon

    2009-01-01

    Summary Flavin-dependent thymidylate synthases (FDTSs) catalyze the production of 2?-deoxythymidine-5?-monophosphate (dTMP) from 2?-deoxyuridine-5?-monophosphate (dUMP) and N5, N10-methylene-5,6,7,8-tetrahydrofolate (CH2H4folate). In contrast to human and other classical thymidylate synthases, the activity of FDTS depends on a flavin adenine dinucleotide (FAD) coenzyme, and its catalytic mechanism is very different. Several human pathogens rely on this recently discovered enzyme, making it an attractive target for novel antibiotics. Like many other flavoenzymes, FDTS can function as an oxidase, which catalyzes the reduction of oxygen (O2) to hydrogen peroxide (H2O2) using reduced nicotinamide adenine dinucleotide 2?-phosphate (NADPH) or other reducing agents. In the present study we exploit the oxidase activity of FDTS from Thermatoga maritima to probe the binding and release features of the substrates and products during its synthase activity. The results from both steady state and single turnover experiments suggest a sequential kinetic mechanism of substrate binding during FDTS oxidase activity. CH2H4folate competitively inhibits the oxidase activity, which indicates that CH2H4folate and O2 compete for the same reduced and dUMP-activated enzymatic complex (FDTS-FADH2-NADP+-dUMP). These studies imply that the binding of CH2H4folate precedes NADP+ release during FDTS synthase activity. The inhibition constant of CH2H4folate towards the oxidase activity was determined to be rather small (2 ?M), which indicates a tight binding of CH2H4folate to the FDTS-FADH2-NADP+-dUMP complex. PMID:19459936

  17. Insights into the nitric oxide reductase mechanism of flavodiiron proteins from a flavin-free enzyme

    PubMed Central

    Hayashi, Takahiro; Caranto, Jonathan D.; Wampler, David A.; Kurtz, Donald M.; Moënne-Loccoz, Pierre

    2010-01-01

    Flavodiiron proteins (FDPs) catalyze reductive scavenging of dioxygen and nitric oxide in air sensitive microorganisms. FDPs contain a distinctive non-heme diiron/flavin mononucleotide (FMN) active site. Alternative mechanisms for the nitric oxide reductase (NOR) activity have been proposed consisting of either protonation of a diiron-bridging hyponitrite or “super-reduction” of a diferrous-dinitrosyl by the proximal FMNH2 in the rate-determining step. In order to test these alternative mechanisms, we examined a deflavinated FDP (deflavo-FDP) from Thermotoga maritima. The deflavo-FDP retains an intact diiron site but does not show multi-turnover NOR or O2 reductase (O2R) activity. Reactions of the reduced (diferrous) deflavo-FDP with nitric oxide were examined by UV-vis absorption, EPR, resonance Raman, and FTIR spectroscopies. Anaerobic addition of nitric oxide up to 1 NO:diferrous deflavo-FDP results in formation of a diiron-mononitrosyl complex characterized by a broad S = 1/2 EPR signal arising from antiferromagnetic coupling of an S = 3/2 {FeNO}7 with an S = 2 Fe(II). Further addition of NO results in two reaction pathways, one of which produces N2O and the diferric site and the other of which produces a stable diiron-dinitrosyl complex. Both NO-treated and as-isolated deflavo-FDPs regain full NOR and O2R activities upon simple addition of FMN. The production of N2O upon addition of NO to the mononitrosyl deflavo-FDP supports the hyponitrite mechanism, but the concomitant formation of a stable diiron-dinitrosyl complex in the deflavo-FDP is consistent with a super-reduction pathway in the flavinated enzyme. We conclude that a diiron-mononitrosyl complex is an intermediate in the NOR catalytic cycle of FDPs. PMID:20669924

  18. A New Root-Knot Nematode Parasitizing Sea Rocket from Spanish Mediterranean Coastal Dunes: Meloidogyne dunensis n. sp. (Nematoda: Meloidogynidae)

    PubMed Central

    Palomares Rius, J. E.; Vovlas, N.; Troccoli, A.; Liébanas, G.; Landa, B. B.; Castillo, P.

    2007-01-01

    High infection rates of European sea rocket feeder roots by an unknown root-knot nematode were found in a coastal dune soil at Cullera (Valencia) in central eastern Spain. Morphometry, esterase and malate dehydrogenase electrophoretic phenotypes and phylogenetic trees demonstrated that this nematode species differs clearly from other previously described root-knot nematodes. Studies of host-parasite relationships showed a typical susceptible reaction in naturally infected European sea rocket plants and in artificially inoculated tomato (cv. Roma) and chickpea (cv. UC 27) plants. The species is herein described and illustrated and named as Meloidogyne dunensis n. sp. The new root-knot nematode can be distinguished from other Meloidogyne spp. by: (i) perineal pattern rounded-oval, formed of numerous fine dorsal and ventral cuticle striae and ridges, lateral fields clearly visible; (ii) female excretory pore at the level of stylet knobs, EP/ST ratio 1.6; (iii) second-stage juveniles with hemizonid located 1 to 2 annuli anteriorly to excretory pore and long, narrow, tapering tail; and (iv) males with lateral fields composed of four incisures anteriorly and posteriorly, while six distinct incisures are observed for large part at mid-body. Phylogenetic trees derived from distance and maximum parsimony analyses based on 18S, ITS1–5.8S-ITS2 and D2-D3 of 28S rDNA showed that M. dunensis n. sp. can be differentiated from all described root-knot nematode species, and it is clearly separated from other species with resemblance in morphology, such as M. duytsi, M. maritima, M. mayaguensis and M. minor. PMID:19259488

  19. Ultrafast real-time visualization of active site flexibility of flavoenzyme thymidylate synthase ThyX

    PubMed Central

    Laptenok, Sergey P.; Bouzhir-Sima, Latifa; Lambry, Jean-Christophe; Myllykallio, Hannu; Liebl, Ursula; Vos, Marten H.

    2013-01-01

    In many bacteria the flavoenzyme thymidylate synthase ThyX produces the DNA nucleotide deoxythymidine monophosphate from dUMP, using methylenetetrahydrofolate as carbon donor and NADPH as hydride donor. Because all three substrates bind in close proximity to the catalytic flavin adenine dinucleotide group, substantial flexibility of the ThyX active site has been hypothesized. Using femtosecond time-resolved fluorescence spectroscopy, we have studied the conformational heterogeneity and the conformational interconversion dynamics in real time in ThyX from the hyperthermophilic bacterium Thermotoga maritima. The dynamics of electron transfer to excited flavin adenine dinucleotide from a neighboring tyrosine residue are used as a sensitive probe of the functional dynamics of the active site. The fluorescence decay spanned a full three orders of magnitude, demonstrating a very wide range of conformations. In particular, at physiological temperatures, multiple angstrom cofactor-residue displacements occur on the picoseconds timescale. These experimental findings are supported by molecular dynamics simulations. Binding of the dUMP substrate abolishes this flexibility and stabilizes the active site in a configuration where dUMP closely interacts with the flavin cofactor and very efficiently quenches fluorescence itself. Our results indicate a dynamic selected-fit mechanism where binding of the first substrate dUMP at high temperature stabilizes the enzyme in a configuration favorable for interaction with the second substrate NADPH, and more generally have important implications for the role of active site flexibility in enzymes interacting with multiple poly-atom substrates and products. Moreover, our data provide the basis for exploring the effect of inhibitor molecules on the active site dynamics of ThyX and other multisubstrate flavoenzymes. PMID:23671075

  20. Starch biosynthetic genes and enzymes are expressed and active in the absence of starch accumulation in sugar beet tap-root

    PubMed Central

    2014-01-01

    Background Starch is the predominant storage compound in underground plant tissues like roots and tubers. An exception is sugar beet tap-root (Beta vulgaris ssp altissima) which exclusively stores sucrose. The underlying mechanism behind this divergent storage accumulation in sugar beet is currently not fully known. From the general presence of starch in roots and tubers it could be speculated that the lack in sugar beet tap-roots would originate from deficiency in pathways leading to starch. Therefore with emphasis on starch accumulation, we studied tap-roots of sugar beet using parsnip (Pastinaca sativa) as a comparator. Results Metabolic and structural analyses of sugar beet tap-root confirmed sucrose as the exclusive storage component. No starch granules could be detected in tap-roots of sugar beet or the wild ancestor sea beet (Beta vulgaris ssp. maritima). Analyses of parsnip showed that the main storage component was starch but tap-root tissue was also found to contain significant levels of sugars. Surprisingly, activities of four main starch biosynthetic enzymes, phosphoglucomutase, ADP-glucose pyrophosphorylase, starch synthase and starch branching enzyme, were similar in sugar beet and parsnip tap-roots. Transcriptional analysis confirmed expression of corresponding genes. Additionally, expression of genes involved in starch accumulation such as for plastidial hexose transportation and starch tuning functions could be determined in tap-roots of both plant species. Conclusion Considering underground storage organs, sugar beet tap-root upholds a unique property in exclusively storing sucrose. Lack of starch also in the ancestor sea beet indicates an evolved trait of biological importance. Our findings in this study show that gene expression and enzymatic activity of main starch biosynthetic functions are present in sugar beet tap-root during storage accumulation. In view of this, the complete lack of starch in sugar beet tap-roots is enigmatic. PMID:24758347

  1. Rapid identification of cyst (Heterodera spp., Globodera spp.) and root-knot (Meloidogyne spp.) nematodes on the basis of ITS2 sequence variation detected by PCR-single-strand conformational polymorphism (PCR-SSCP) in cultures and field samples.

    PubMed

    Clapp, J P; van der Stoel, C D; van der Putten, W H

    2000-09-01

    Cyst and root-knot nematodes show high levels of gross morphological similarity. This presents difficulties for the study of their ecology in natural ecosystems. In this study, cyst and root-knot nematode species, as well as some ectoparasitic nematode species, were identified using the second internal transcribed spacer (ITS2) sequence variation detected by polymerase chain reaction-single-strand conformational polymorphism (PCR-SSCP). The ITS2 region was sufficiently variable within the taxa investigated to allow species to be separated on the basis of minor sequence variation. The PCR primers used in this study were effective for 12 species with three genera within the Heteroderinae (Globodera pallida, G. rostochiensis, Heterodera arenaria/avenae, H. ciceri, H. daverti, H. hordecalis, H. mani, H. schachtii, H. trifolii, Meloidogyne ardenensis, M. duytsi and M. maritima). However, pathotypes of Globodera pallida and G. rostochiensis could not be distinguished. The method was tested at two coastal dune locations in The Netherlands (one in the lime-poor dunes of the north and one in calcareous dunes of the south) to determine the population structure of cyst nematodes. At each site, cyst nematodes were associated with three plant species: two plant species on the foredune (Elymus farctus and Ammophila arenaria) and one plant species occurring further inland (Calamagrostis epigejos). Two species of cyst nematodes, H. arenaria and H. hordecalis, were found. H. arenaria associated with vigorous A. arenaria and H. hordecalis in association with degenerating A. arenaria and C. epigejos. The field survey demonstrated that in coastal dunes abiotic factors may be the important affecting the distribution of cyst nematodes. PMID:10972762

  2. Photorespiration and Carbon Limitation Determine Productivity in Temperate Seagrasses

    PubMed Central

    Buapet, Pimchanok; Rasmusson, Lina M.; Gullström, Martin; Björk, Mats

    2013-01-01

    The gross primary productivity of two seagrasses, Zostera marina and Ruppia maritima, and one green macroalga, Ulva intestinalis, was assessed in laboratory and field experiments to determine whether the photorespiratory pathway operates at a substantial level in these macrophytes and to what extent it is enhanced by naturally occurring shifts in dissolved inorganic carbon (DIC) and O2 in dense vegetation. To achieve these conditions in laboratory experiments, seawater was incubated with U. intestinalis in light to obtain a range of higher pH and O2 levels and lower DIC levels. Gross photosynthetic O2 evolution was then measured in this pretreated seawater (pH, 7.8–9.8; high to low DIC:O2 ratio) at both natural and low O2 concentrations (adjusted by N2 bubbling). The presence of photorespiration was indicated by a lower gross O2 evolution rate under natural O2 conditions than when O2 was reduced. In all three macrophytes, gross photosynthetic rates were negatively affected by higher pH and lower DIC. However, while both seagrasses exhibited significant photorespiratory activity at increasing pH values, the macroalga U. intestinalis exhibited no such activity. Rates of seagrass photosynthesis were then assessed in seawater collected from the natural habitats (i.e., shallow bays characterized by high macrophyte cover and by low DIC and high pH during daytime) and compared with open baymouth water conditions (where seawater DIC is in equilibrium with air, normal DIC, and pH). The gross photosynthetic rates of both seagrasses were significantly higher when incubated in the baymouth water, indicating that these grasses can be significantly carbon limited in shallow bays. Photorespiration was also detected in both seagrasses under shallow bay water conditions. Our findings indicate that natural carbon limitations caused by high community photosynthesis can enhance photorespiration and cause a significant decline in seagrass primary production in shallow waters. PMID:24376754

  3. Improved recombinant cellulase expression in chloroplast of tobacco through promoter engineering and 5' amplification promoting sequence.

    PubMed

    Jung, Sera; Lee, Dae-Seok; Kim, Yeon-Ok; Joshi, Chandrashekhar P; Bae, Hyeun-Jong

    2013-11-01

    Economical production of bioethanol from lignocellulosic biomass still faces many technical limitations. Cost-effective production of fermentable sugars is still not practical for large-scale production of bioethanol due to high costs of lignocellulolytic enzymes. Therefore, plant molecular farming, where plants are used as bioreactors, was developed for the mass production of cell wall degrading enzymes that will help reduce costs. Subcellular targeting is also potentially more suitable for the accumulation of recombinant cellulases. Herein, we generated transgenic tobacco plants (Nicotiana tabacum cv. SR1) that accumulated Thermotoga maritima BglB cellulase, which was driven by the alfalfa RbcsK-1A promoter and contained a small subunit of the rubisco complex transit peptide. The generated transformants possessed high specific BglB activity and did not show any abnormal phenotypes. Furthermore, we genetically engineered the RbcsK-1A promoter (MRbcsK-1A) and fused the amplification promoting sequence (aps) to MRbcsK-1A promoter to obtain high expression of BglB in transgenic plants. AMRsB plant lines with aps-MRbcsK-1A promoter showed the highest specific activity of BglB, and the accumulated BglB protein represented up to 9.3 % of total soluble protein. When BglB was expressed in Arabidopsis and tobacco plants, the maximal production capacity of recombinant BglB was 0.59 and 1.42 mg/g wet weight, respectively. These results suggests that suitable recombinant expression of cellulases in subcellular compartments such as chloroplasts will contribute to the cost-effective production of enzymes, and will serve as the solid foundation for the future commercialization of bioethanol production via plant molecular farming. PMID:23771581

  4. Vegetation change on a northeast tidal marsh: Interaction of sea-level rise and marsh accretion

    SciTech Connect

    Warren, R.S.; Niering, W.A. (Connecticut College, New London (United States))

    1993-01-01

    Increasing rates of relative sea-level rise (RSL) have been linked to coastal wetland losses along the Gulf of Mexico and elsewhere. Rapidly rising RSL may be affecting New England tidal marshes. Studies of the Wequetequock-Pawcatuck tidal marshes over four decades have documented dramatic changes in vegetation apparently related primarily to differential rates of marsh accretion and sea-level rise though sediment supply and anthropogenic modifications of the system may also be involved. When initially studied in 1947-1948 the high marsh supported a Juncus gerardi-Spartina patens belting pattern typical of many New England salt marshes. On most of the marsh complex the former Juncus belt has now been replaced by forbs, primarily Triglochin maritima, while the former S. patens high marsh is now a complex of vegetation types-stunted Spartina alterniflora, Distichlis spicata, forbs, and relic stands of S. patens. The mean surface elevation of areas where the vegetation has changed is significantly lower than that of areas still supporting the earlier pattern (4.6 vs. 13.9 cm above mean tide level). The differences in surface elevation reflect differences in accretion of marsh peat. Stable areas have been accreting at the rate of local sea-level rise, 2.0-2.5 mm/yr at least since 1938; changed areas have accreted at about one half that rate. Lower surface elevations result in greater frequency and duration of tidal flooding, and thus in increased peat saturation, salinity, and sulfide concentrations, and in decreased redox potential, as directly measured over the growing season at both changed and stable sites. These edaphic changes may have combined to favor establishment of a wetter, more open vegetation type. Similar changes have been observed on other Long Island Sound marshes and may be a model for the potential effects of sea-level rise on New England tidal salt marshes. 39 refs., 4 figs., 1 tab.

  5. Aquatic Insects of New York Salt Marsh Associated with Mosquito Larval Habitat and their Potential Utility as Bioindicators

    PubMed Central

    Rochlin, Ilia; Dempsey, Mary E.; Iwanejko, Tom; Ninivaggi, Dominick V.

    2011-01-01

    The aquatic insect fauna of salt marshes is poorly characterized, with the possible exception of biting Diptera. Aquatic insects play a vital role in salt marsh ecology, and have great potential importance as biological indicators for assessing marsh health. In addition, they may be impacted by measures to control mosquitoes such as changes to the marsh habitat, altered hydrology, or the application of pesticides. Given these concerns, the goals of this study were to conduct the first taxonomic survey of salt marsh aquatic insects on Long Island, New York, USA and to evaluate their utility for non-target pesticide impacts and environmental biomonitoring. A total of 18 species from 11 families and five orders were collected repeatedly during the five month study period. Diptera was the most diverse order with nine species from four families, followed by Coleoptera with four species from two families, Heteroptera with three species from three families, then Odonata and the hexapod Collembola with one species each. Water boatmen, Trichocorixa verticalis Fieber (Heteroptera: Corixidae) and a shore fly, Ephydra subopaca Loew (Diptera: Ephydridae), were the two most commonly encountered species. An additional six species; Anurida maritima Guérin-Méneville (Collembola: Neanuridae), Mesovelia mulsanti White (Heteroptera: Mesovelidae), Enochrus hamiltoni Horn (Coleoptera: Hydrophilidae), Tropisternus quadristriatus Horn (Coleoptera: Hydrophilidae), Dasyhelea pseudocincta Waugh and Wirth (Diptera: Ceratopogonidae), and Brachydeutera argentata Walker (Diptera: Ephydridae), were found regularly. Together with the less common Erythrodiplax berenice Drury (Odonata: Libellulidae), these nine species were identified as the most suitable candidates for pesticide and environmental impact monitoring due to abundance, position in the food chain, and extended seasonal occurrence. This study represents a first step towards developing an insectbased index of biological integrity for salt marsh health assessment. PMID:22957707

  6. Laboratory Directed Research & Development program. Annual report to the Department of Energy

    SciTech Connect

    Ogeka, G.J.; Romano, A.J.

    1995-12-01

    This report briefly discusses the following projects coordinated at Brookhaven National Laboratory: investigation of the utility of max-entropy methods for the analysis of powder diffraction data; analysis of structures and interactions of nucleic acids and proteins by small angle x-ray diffraction; relaxographic MRI and functional MRI; very low temperature infra-red laser absorption as a potential analytical tool; state-resolved measurements of H{sub 2} photodesorption: development of laser probes of H{sub 2} for in-situ accelerator measurements; Siberian snake prototype development for RHIC; synthesis and characterization of novel microporous solids; ozone depletion, chemistry and physics of stratospheric aerosols; understanding the molecular basis for the synthesis of plant fatty acids possessing unusual double bond positions; structure determination of outer surface proteins of the Lyme disease spirochete; low mass, low-cost multi-wire proportional chambers for muon systems of collider experiments; theory of self-organized criticality; development of the PCR-SSCP technique for the detection, at the single cell level, of specific genetic changes; feasibility of SPECT in imaging of F-18 FDG accumulation in tumors; visible free electron laser oscillator experiment; study of possible 2 + 2 TeV muon-muon collider; ultraviolet FEL R & D; precision machining using hard x-rays; new directions in in-vivo enzyme mapping: catechol-O-methyltransferase; proposal to develop a high rate muon polarimeter; development of intense, tunable 20-femtosecond laser systems; use of extreme thermophilic bacterium thermatoga maritima as a source of ribosomal components and translation factors for structural studies; and biochemical and structural studies of Chaperon proteins from thermophilic bacteria and other experiments.

  7. Structure of the invertebrate fauna in salt marshes of the Wadden Sea coast of Schleswig-Holstein influenced by sheep-grazing

    NASA Astrophysics Data System (ADS)

    Meyer, H.; Fock, H.; Haase, A.; Reinke, H. D.; Tulowitzki, I.

    1995-03-01

    Results of investigations on the influence of five different sheep grazing intensities on the invertebrate fauna of two mainland salt marsh sites of the German Wadden Sea coast are presented for the years 1990 and 1991. The investigation of the invertebrate fauna has been carried out since 1989 in the Puccinellia maritima zone, and the Festuca-Puccinellia as well as the Festuca-Armeria zones, with trapping transects arranged along an inundation gradient. Apart from specific biotic effects, grazing causes changes in environmental characteristics. Effects on microclimate comprise higher ranges of variance in soil-surface temperature on grazed sites. Decreasing food resources caused by grazing bring disadvantages to herbivores, the major part of the invertebrate fauna, due to merotope destruction (e. g. inflorescences of Aster tripolium) and the decline of host plant stands (e. g. A. tripolium, Plantago ssp.). Flower visitors and pollen feeding species that depend on A. tripolium have become extinct. Increasing food resources, caused by grazing, lead to higher population densities of a few specialized grass-feeding and surface-grazing invertebrates (e. g. Mayetiola ssp., Psammotettix putoni, Bledius tricornis). Soil characteristics in the lower salt marsh have not been altered significantly by grazing; hence, the direct effect of grazing and trampling leads to a decrease in population density of many species such as Assiminea grayana, Orchestia gammarellus and collembolans. The biomass and abundance of detritivores and many herbivores increased from 1990 to 1991 on the totally grazed fields, whereas predators diminished in numbers at the same time. A descriptive model is presented, involving grazing, winter temperature, and precipitation as basic factors.

  8. A selection that reports on protein-protein interactions within a thermophilic bacterium.

    PubMed

    Nguyen, Peter Q; Silberg, Jonathan J

    2010-07-01

    Many proteins can be split into fragments that exhibit enhanced function upon fusion to interacting proteins. While this strategy has been widely used to create protein-fragment complementation assays (PCAs) for discovering protein-protein interactions within mesophilic organisms, similar assays have not yet been developed for studying natural and engineered protein complexes at the temperatures where thermophilic microbes grow. We describe the development of a selection for protein-protein interactions within Thermus thermophilus that is based upon growth complementation by fragments of Thermotoga neapolitana adenylate kinase (AK(Tn)). Complementation studies with an engineered thermophile (PQN1) that is not viable above 75 degrees C because its adk gene has been replaced by a Geobacillus stearothermophilus ortholog revealed that growth could be restored at 78 degrees C by a vector that coexpresses polypeptides corresponding to residues 1-79 and 80-220 of AK(Tn). In contrast, PQN1 growth was not complemented by AK(Tn) fragments harboring a C156A mutation within the zinc-binding tetracysteine motif unless these fragments were fused to Thermotoga maritima chemotaxis proteins that heterodimerize (CheA and CheY) or homodimerize (CheX). This enhanced complementation is interpreted as arising from chemotaxis protein-protein interactions, since AK(Tn)-C156A fragments having only one polypeptide fused to a chemotaxis protein did not complement PQN1 to the same extent. This selection increases the maximum temperature where a PCA can be used to engineer thermostable protein complexes and to map protein-protein interactions. PMID:20418388

  9. Complete sucrose hydrolysis by heat-killed recombinant Pichia pastoris cells entrapped in calcium alginate

    PubMed Central

    2014-01-01

    Background An ideal immobilized biocatalyst for the industrial-scale production of invert sugar should stably operate at elevated temperatures (60-70°C) and high sucrose concentrations (above 60%, w/v). Commercial invertase from the yeast Saccharomyces cerevisiae is thermolabile and suffers from substrate inhibition. Thermotoga maritima ?-fructosidase (BfrA) is the most thermoactive and thermostable sucrose-hydrolysing enzyme so far identified and allows complete inversion of the substrate in highly concentrated solutions. Results In this study, heat-killed Pichia pastoris cells bearing N-glycosylated BfrA in the periplasmic space were entrapped in calcium alginate beads. The immobilized recombinant yeast showed maximal sucrose hydrolysis at pH 5–7 and 90°C. BfrA was 65% active at 60°C and had no activity loss after incubation without the substrate at this temperature for 15 h. Complete inversion of cane sugar (2.04 M) at 60°C was achieved in batchwise and continuous operation with respective productivities of 4.37 and 0.88 gram of substrate hydrolysed per gram of dry beads per hour. The half-life values of the biocatalyst were 14 and 20 days when operated at 60°C in the stirred tank and the fixed-bed column, respectively. The reaction with non-viable cells prevented the occurrence of sucrose fermentation and the formation of by-products. Six-month storage of the biocatalyst in 1.46 M sucrose (pH 5.5) at 4°C caused no reduction of the invertase activity. Conclusions The features of the novel thermostable biocatalyst developed in this study are more attractive than those of immobilized S. cerevisiae cells for application in the enzymatic manufacture of inverted sugar syrup in batch and fixed-bed reactors. PMID:24943124

  10. On the distribution and evaluation of Na, Mg and Cl in leaves of selected halophytes

    NASA Astrophysics Data System (ADS)

    Pongrac, Paula; Vogel-Mikuš, Katarina; Regvar, Marjana; Kaligari?, Mitja; Vavpeti?, Primož; Kelemen, Mitja; Grlj, Nataša; Shelef, Oren; Golan-Goldhirsh, Avi; Rachmilevitch, Shimon; Pelicon, Primož

    2013-07-01

    Diverse physiological, biochemical and morphological adaptations enable plants to survive in extreme saline environments where osmotic and ionic stresses limit growth and development. Halophytes are salt-tolerant plants that can withstand extraordinarily high levels of Na and Cl in their leaves. The tissue and cellular distribution patterns of salt ions can be linked to the underlying mechanisms of salt tolerance. Application of fast, reliable, multi-elemental and quantitative techniques such as micro-proton-induced X-ray emission (micro-PIXE) will significantly contribute to and accelerate studies of plant salt tolerance, especially as micro-PIXE also provides spatially resolved quantitative data for light elements, such as Na and Mg. The spatial concentration distributions of Na, Mg, Cl, K, P and S in leaves of four halophytes (Bassia indica, Atriplex prostrata, Spartina maritima and Limonium angustifolium) were determined using micro-PIXE, to study the salt-tolerance strategies of the selected halophytes. Different distribution patterns of the studied elements were seen in the leaves; however, in all four of these plant species, Na was excluded from photosynthetically active chlorophyl tissues. With the exception of L. angustifolium, Cl, P and S contents (representing chloride, phosphate and sulphate ionic forms, respectively) did not ensure charge balance in the leaves, which suggests other anionic compounds, such as nitrate and organic anions, have crucial roles in maintaining electroneutrality in these halophytes. By increasing soil salinisation worldwide, the possibility to reliably complement spatial distributions of Na, Mg, Cl, K, P and S with plant structural morphology will contribute significantly to our understanding of plant tolerance mechanisms at the tissue and cell levels. In addition, these kinds of studies are of particular value for designing crop plants with high salt tolerance and for the development of phytoremediation technologies.

  11. Primary production dynamics in a pristine groundwater influenced coastal lagoon of the Yucatan Peninsula

    NASA Astrophysics Data System (ADS)

    Medina-Gómez, Israel; Herrera-Silveira, Jorge A.

    2006-06-01

    Dzilam lagoon is a shallow (0.6 m mean depth) ecosystem with 9.4 km 2 surface area, located in the north coast of the Yucatan Peninsula, and connected to the Gulf of Mexico through a permanent inlet. Freshwater input is possible through numerous sinkholes distributed throughout the lagoon, which also represent a continuous source of nitrate and silicate. The low anthropogenic influence has maintained a pristine condition in Dzilam lagoon, manifested in a spatial heterogeneity of water quality and primary production strongly related to the environmental fluctuations. To determine the annual variability of primary production and identify the factors controlling it, 12 monthly samplings were undertaken at six stations, from September 1998 to August 1999. Thus, physical-chemical parameters, inorganic nutrients concentrations, chlorophyll- a, phytoplankton production and seagrass biomass were measured. The water residence time in Dzilam lagoon is higher during dry season due to the significant evaporation rate, and shorter in rainy season because of increase in precipitation and volume of groundwater discharge. The multivariate analysis results suggest that the salinity gradient, changes in aquatic vegetation biomass, and the remineralized nutrients in sediments constitute key processes depicting the water quality and net primary production in Dzilam lagoon. Furthermore, the biogeochemical benthic processes, combined with a longer stay of phytoplankton cells within the lagoon, enhanced primary production in the water column during dry season, as opposite as rainy period, when the inferior water residence time yielded lower production values. The seagrasses ( Halodule wrightii and Ruppia maritima) showed the highest biomass (110.5 g dw/m 2/d) in dry season, while the lowest recordings were observed during cold fronts, with a salient belowground contribution (rhizomes and roots). Seagrasses and phytoplankton participation to the total primary production in Dzilam lagoon were seasonally alternated, yielding a high primary productivity along the annual cycle. Despite of this complementary arrangement, the submerged aquatic vegetation displayed an overall higher contribution during the year (65%) relate to phytoplankton.

  12. Structural Basis for Substrate Binding and the Catalytic Mechanism of Type III Pantothenate Kinase

    SciTech Connect

    Yang, Kun; Strauss, Erick; Huerta, Carlos; Zhang, Hong (Stellenbosch); (UTSMC)

    2008-07-15

    Pantothenate kinase (PanK) catalyzes the first step of the universal five-step coenzyme A (CoA) biosynthetic pathway. The recently characterized type III PanK (PanK-III, encoded by the coaX gene) is distinct in sequence, structure and enzymatic properties from both the long-known bacterial type I PanK (PanK-I, exemplified by the Escherichia coli CoaA protein) and the predominantly eukaryotic type II PanK (PanK-II). PanK-III enzymes have an unusually high K{sub m} for ATP, are resistant to feedback inhibition by CoA, and are unable to utilize the N-alkylpantothenamide family of pantothenate analogues as alternative substrates, thus making type III PanK ineffective in generating CoA analogues as antimetabolites in vivo. Previously, we reported the crystal structure of the PanK-III from Thermotoga maritima and identified it as a member of the 'acetate and sugar kinase/heat shock protein 70/actin' (ASKHA) superfamily. Here we report the crystal structures of the same PanK-III in complex with one of its substrates (pantothenate), its product (phosphopantothenate) as well as a ternary complex structure of PanK-III with pantothenate and ADP. These results are combined with isothermal titration calorimetry experiments to present a detailed structural and thermodynamic characterization of the interactions between PanK-III and its substrates ATP and pantothenate. Comparison of substrate binding and catalytic sites of PanK-III with that of eukaryotic PanK-II revealed drastic differences in the binding modes for both ATP and pantothenate substrates, and suggests that these differences may be exploited in the development of new inhibitors specifically targeting PanK-III.

  13. Structure, diversity and evolution of myriapod hemocyanins.

    PubMed

    Pick, Christian; Scherbaum, Samantha; Hegedüs, Elöd; Meyer, Andreas; Saur, Michael; Neumann, Ruben; Markl, Jürgen; Burmester, Thorsten

    2014-04-01

    Oxygen transport in the hemolymph of many arthropods is mediated by hemocyanins, large copper-containing proteins that are well-studied in Chelicerata and Crustacea, but had long been considered unnecessary in the subphylum of Myriapoda. Only recently has it become evident that hemocyanins are present in Scutigeromorpha (Chilopoda) and Spirostreptida (Diplopoda). Here we present evidence for a more widespread occurrence of hemocyanin in the myriapods. By means of RT-PCR, western blotting and database searches, hemocyanins were identified in the symphylans Hanseniella audax and Symphylella vulgaris, the chilopod Scolopendra subspinipes dehaani and the diplopod Polydesmus angustus. No hemocyanins were found in the diplopods Polyxenus lagurus, Cylindroiulus punctatus, Glomeris marginata, Glomeris pustulata and Arthrosphaera brandtii, or the chilopods Lithobius forficatus, Geophilus flavus and Strigamia maritima. This suggests multiple independent losses in myriapod taxa. Two independent hemocyanin subunits were found that were already present in the myriapod stem line. We specifically investigated the structure of the hemocyanin of P. angustus, which consists of three distinct subunits that occur in an approximately equimolar ratio. As deduced by 3D electron microscopy, the quaternary structure is a 3 × 6-mer that resembles the half structure of the 6 × 6-mer hemocyanin from Scutigera coleoptrata. It was analyzed more closely by homology modeling of 1 × 6-mers and their rigid-body fitting to the electron density map of the 3 × 6-mer. In addition, we obtained the cDNA sequence of a putative myriapod phenoloxidase. Phenoloxidases are related to the arthropod hemocyanins, but diverged before radiation of the arthropod subphyla. PMID:24520955

  14. Insertion of Endocellulase Catalytic Domains into Thermostable Consensus Ankyrin Scaffolds: Effects on Stability and Cellulolytic Activity

    PubMed Central

    Cunha, Eva S.; Hatem, Christine L.

    2013-01-01

    Degradation of cellulose for biofuels production holds promise in solving important environmental and economic problems. However, the low activities (and thus high enzyme-to-substrate ratios needed) of hydrolytic cellulase enzymes, which convert cellulose into simple sugars, remain a major barrier. As a potential strategy to stabilize cellulases and enhance their activities, we have embedded cellulases of extremophiles into hyperstable ?-helical consensus ankyrin domain scaffolds. We found the catalytic domains CelA (CA, GH8; Clostridium thermocellum) and Cel12A (C12A, GH12; Thermotoga maritima) to be stable in the context of the ankyrin scaffold and to be active against both soluble and insoluble substrates. The ankyrin repeats in each fusion are folded, although it appears that for the C12A catalytic domain (CD; where the N and C termini are distant in the crystal structure), the two flanking ankyrin domains are independent, whereas for CA (where termini are close), the flanking ankyrin domains stabilize each other. Although the activity of CA is unchanged in the context of the ankyrin scaffold, the activity of C12A is increased between 2- and 6-fold (for regenerated amorphous cellulose and carboxymethyl cellulose substrates) at high temperatures. For C12A, activity increases with the number of flanking ankyrin repeats. These results showed ankyrin arrays to be a promising scaffold for constructing designer cellulosomes, preserving or enhancing enzymatic activity and retaining thermostability. This modular architecture will make it possible to arrange multiple cellulase domains at a precise spacing within a single polypeptide, allowing us to search for spacings that may optimize reactivity toward the repetitive cellulose lattice. PMID:23974146

  15. Aquatic insects of New York salt marsh associated with mosquito larval habitat and their potential utility as bioindicators.

    PubMed

    Rochlin, Ilia; Dempsey, Mary E; Iwanejko, Tom; Ninivaggi, Dominick V

    2011-01-01

    The aquatic insect fauna of salt marshes is poorly characterized, with the possible exception of biting Diptera. Aquatic insects play a vital role in salt marsh ecology, and have great potential importance as biological indicators for assessing marsh health. In addition, they may be impacted by measures to control mosquitoes such as changes to the marsh habitat, altered hydrology, or the application of pesticides. Given these concerns, the goals of this study were to conduct the first taxonomic survey of salt marsh aquatic insects on Long Island, New York, USA and to evaluate their utility for non-target pesticide impacts and environmental biomonitoring. A total of 18 species from 11 families and five orders were collected repeatedly during the five month study period. Diptera was the most diverse order with nine species from four families, followed by Coleoptera with four species from two families, Heteroptera with three species from three families, then Odonata and the hexapod Collembola with one species each. Water boatmen, Trichocorixa verticalis Fieber (Heteroptera: Corixidae) and a shore fly, Ephydra subopaca Loew (Diptera: Ephydridae), were the two most commonly encountered species. An additional six species; Anurida maritima Guérin-Méneville (Collembola: Neanuridae), Mesovelia mulsanti White (Heteroptera: Mesovelidae), Enochrus hamiltoni Horn (Coleoptera: Hydrophilidae), Tropisternus quadristriatus Horn (Coleoptera: Hydrophilidae), Dasyhelea pseudocincta Waugh and Wirth (Diptera: Ceratopogonidae), and Brachydeutera argentata Walker (Diptera: Ephydridae), were found regularly. Together with the less common Erythrodiplax berenice Drury (Odonata: Libellulidae), these nine species were identified as the most suitable candidates for pesticide and environmental impact monitoring due to abundance, position in the food chain, and extended seasonal occurrence. This study represents a first step towards developing an insect-based index of biological integrity for salt marsh health assessment. PMID:22957707

  16. Seed dormancy distribution: explanatory ecological factors

    PubMed Central

    Wagmann, Kristen; Hautekèete, Nina-Coralie; Piquot, Yves; Meunier, Cécile; Schmitt, S. Eric; Van Dijk, Henk

    2012-01-01

    Background and Aims Knowledge of those traits that vary with latitude should be helpful in predicting how they may evolve locally under climate change. In the sea beet Beta vulgaris ssp. maritima, seed dormancy largely controls the timing of germination, is highly heritable and varies geographically; it is therefore thought to be selected by climate. The aim here was to characterize the variation in seed dormancy among sea beet populations across the French distribution area, as well as the ecological factors in situ that are correlated with and that could therefore select for seed dormancy. The relative importance of genetic inheritance vs. non-genetic variation is also evaluated. Methods The proportions of dormant seeds from 85 natural populations encompassing different climates over the whole French distribution area were measured under controlled conditions. Germination phenology was observed in a common garden experiment. Dormancy variation of seeds collected in situ was compared with that of seeds collected on plants grown in the greenhouse. Key Results The proportions of dormant seeds in the greenhouse were highly variable, covering almost the entire range from 0 to 1, and followed a geographical pattern from lower dormancy at high latitudes to high dormancy at low latitudes. The distribution of dormancy was positively correlated with yearly temperatures, especially summer temperatures. Minimum temperatures in winter did not significantly explain the trait variation. The genetic component of the total variation was significant and is probably completed by an important adjustment to the local conditions brought about by maternal adaptive phenotypic plasticity. Conclusions Dormancy in sea beet could be interpreted as a way to limit summer germination and spread germination over the first autumn and spring or following autumns. This highly heritable trait has the potential to evolve in the relatively near future because of climate change. PMID:22952378

  17. Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications.

    PubMed Central

    Brown, J R; Doolittle, W F

    1995-01-01

    Universal trees based on sequences of single gene homologs cannot be rooted. Iwabe et al. [Iwabe, N., Kuma, K.-I., Hasegawa, M., Osawa, S. & Miyata, T. (1989) Proc. Natl. Acad. Sci. USA 86, 9355-9359] circumvented this problem by using ancient gene duplications that predated the last common ancestor of all living things. Their separate, reciprocally rooted gene trees for elongation factors and ATPase subunits showed Bacteria (eubacteria) as branching first from the universal tree with Archaea (archaebacteria) and Eucarya (eukaryotes) as sister groups. Given its topical importance to evolutionary biology and concerns about the appropriateness of the ATPase data set, an evaluation of the universal tree root using other ancient gene duplications is essential. In this study, we derive a rooting for the universal tree using aminoacyl-tRNA synthetase genes, an extensive multigene family whose divergence likely preceded that of prokaryotes and eukaryotes. An approximately 1600-bp conserved region was sequenced from the isoleucyl-tRNA synthetases of several species representing deep evolutionary branches of eukaryotes (Nosema locustae), Bacteria (Aquifex pyrophilus and Thermotoga maritima) and Archaea (Pyrococcus furiosus and Sulfolobus acidocaldarius). In addition, a new valyl-tRNA synthetase was characterized from the protist Trichomonas vaginalis. Different phylogenetic methods were used to generate trees of isoleucyl-tRNA synthetases rooted by valyl- and leucyl-tRNA synthetases. All isoleucyl-tRNA synthetase trees showed Archaea and Eucarya as sister groups, providing strong confirmation for the universal tree rooting reported by Iwabe et al. As well, there was strong support for the monophyly (sensu Hennig) of Archaea. The valyl-tRNA synthetase gene from Tr. vaginalis clustered with other eukaryotic ValRS genes, which may have been transferred from the mitochondrial genome to the nuclear genome, suggesting that this amitochondrial trichomonad once harbored an endosymbiotic bacterium. Images Fig. 1 PMID:7708661

  18. Handling Temperature Bursts Reaching 464°C: Different Microbial Strategies in the Sisters Peak Hydrothermal Chimney

    PubMed Central

    Kurtz, Stefan; LaRoche, Julie

    2014-01-01

    The active venting Sisters Peak (SP) chimney on the Mid-Atlantic Ridge holds the current temperature record for the hottest ever measured hydrothermal fluids (400°C, accompanied by sudden temperature bursts reaching 464°C). Given the unprecedented temperature regime, we investigated the biome of this chimney with a focus on special microbial adaptations for thermal tolerance. The SP metagenome reveals considerable differences in the taxonomic composition from those of other hydrothermal vent and subsurface samples; these could be better explained by temperature than by other available abiotic parameters. The most common species to which SP genes were assigned were thermophilic Aciduliprofundum sp. strain MAR08-339 (11.8%), Hippea maritima (3.8%), Caldisericum exile (1.5%), and Caminibacter mediatlanticus (1.4%) as well as to the mesophilic Niastella koreensis (2.8%). A statistical analysis of associations between taxonomic and functional gene assignments revealed specific overrepresented functional categories: for Aciduliprofundum, protein biosynthesis, nucleotide metabolism, and energy metabolism genes; for Hippea and Caminibacter, cell motility and/or DNA replication and repair system genes; and for Niastella, cell wall and membrane biogenesis genes. Cultured representatives of these organisms inhabit different thermal niches; i.e., Aciduliprofundum has an optimal growth temperature of 70°C, Hippea and Caminibacter have optimal growth temperatures around 55°C, and Niastella grows between 10 and 37°C. Therefore, we posit that the different enrichment profiles of functional categories reflect distinct microbial strategies to deal with the different impacts of the local sudden temperature bursts in disparate regions of the chimney. PMID:24837379

  19. Ingestion, enzymatic digestion and absorption of particles derived from different vegetal sources by the cockle Cerastoderma edule

    NASA Astrophysics Data System (ADS)

    Arambalza, U.; Urrutia, M. B.; Navarro, E.; Ibarrola, I.

    2010-10-01

    Ingestion, enzymatic digestion and absorption of particulate detrital matter derived from six different vegetal sources by the common cockle Cerastoderma edule was analyzed in a series of seasonal experiments performed in March, May and October 2005. Two green macroalgae: Ulva lactuca and Enteromorpha sp; two vascular plants: Spartina maritima and Juncus maritimus, the red macroalgae Gracilaria gracilis; and the microalgae Isochrysis galbana were used in experiments. Detrital matter was elaborated by freeze-drying, grinding and sieving (< 63 ?m) vegetal tissues. Mono-specific detrital diets of similar organic content (? 60-70%) were elaborated by mixing detritus with ashed silt. We measured i) the biochemical composition of different detritus, ii) physiological components of the absorptive balance (i.e. clearance, ingestion, rejection and absorption rate and absorption efficiency), iii) the capability of the digestive gland to hydrolyze carbohydrates from different detritus (digestibility), as well as iv) glandular cellulase and xylanase activities. Detritus type, season and the interaction detritus-season exerted significant effects upon all the physiological components of absorptive balance. Effects were light at the pre-absorptive level, however, huge variations associated to absorption efficiency promoted large significant differences in absorption rates (AR) of different kind of detritus: irrespective of season, highest values corresponded to cockles fed the green macroalgae ( Ulva and Enteromorpha) and lowest to those fed the vascular plant Juncus maritimus. Recorded significant differences in enzymatic digestibility among detritus were found to explain ? 40% of differences recorded in AR, and the following regression could be fitted: AR = 0.232 (± 0.032) * Digestibility + 0,072 (± 0.015); r 2 = 0.415; F = 51.036; p < 0.001. Digestibility of Ulva and Enteromorpha was found to be significantly correlated with cellulase activity in the digestive gland, whereas digestibility of Juncus, Spartina and Gracilaria was correlated with xylanase activity. Obtained correlations are discussed in the frame of contrasting conclusions in the literature regarding the importance of detritus as a food source for bivalves.

  20. Two Alternative Pathways for the Synthesis of the Rare Compatible Solute Mannosylglucosylglycerate in Petrotoga mobilis?

    PubMed Central

    Fernandes, Chantal; Mendes, Vitor; Costa, Joana; Empadinhas, Nuno; Jorge, Carla; Lamosa, Pedro; Santos, Helena; da Costa, Milton S.

    2010-01-01

    The compatible solute mannosylglucosylglycerate (MGG), recently identified in Petrotoga miotherma, also accumulates in Petrotoga mobilis in response to hyperosmotic conditions and supraoptimal growth temperatures. Two functionally connected genes encoding a glucosyl-3-phosphoglycerate synthase (GpgS) and an unknown glycosyltransferase (gene Pmob_1143), which we functionally characterized as a mannosylglucosyl-3-phosphoglycerate synthase and designated MggA, were identified in the genome of Ptg. mobilis. This enzyme used the product of GpgS, glucosyl-3-phosphoglycerate (GPG), as well as GDP-mannose to produce mannosylglucosyl-3-phosphoglycerate (MGPG), the phosphorylated precursor of MGG. The MGPG dephosphorylation was determined in cell extracts, and the native enzyme was partially purified and characterized. Surprisingly, a gene encoding a putative glucosylglycerate synthase (Ggs) was also identified in the genome of Ptg. mobilis, and an active Ggs capable of producing glucosylglycerate (GG) from ADP-glucose and d-glycerate was detected in cell extracts and the recombinant enzyme was characterized, as well. Since GG has never been identified in this organism nor was it a substrate for the MggA, we anticipated the existence of a nonphosphorylating pathway for MGG synthesis. We putatively identified the corresponding gene, whose product had some sequence homology with MggA, but it was not possible to recombinantly express a functional enzyme from Ptg. mobilis, which we named mannosylglucosylglycerate synthase (MggS). In turn, a homologous gene from Thermotoga maritima was successfully expressed, and the synthesis of MGG was confirmed from GDP-mannose and GG. Based on the measurements of the relevant enzyme activities in cell extracts and on the functional characterization of the key enzymes, we propose two alternative pathways for the synthesis of the rare compatible solute MGG in Ptg. mobilis. PMID:20061481

  1. Depositional History of a Saline Blue Hole on Eleuthera Island, Bahamas: Implications for Sea Level History and Climate Change

    NASA Astrophysics Data System (ADS)

    Brady, K.; Bernard, M.; Bender, S.; Roy, Z.; Boush, L. E.; Myrbo, A.; Brown, E. T.; Buynevich, I. V.; Berman, M.; Gnivecki, P.

    2013-12-01

    Physical, chemical and biological properties of Duck Pond Blue Hole (DPBH), located on the southern portion of Eleuthera Island, Bahamas, were examined to analyze its depositional history and the record of climate and anthropogenic changes on the island. DPBH is a small (.001 km2), circular inland blue hole with average salinity ranging from 20-28 ppt and a maximum depth of ~8 m. Sediment cores were recovered using standard piston coring techniques along a transect consisting of three sites yielding cores of varying lengths--170, 155 and 151 cm, respectively. Radiocarbon dating, x-ray fluorescence (XRF), grain size analysis, loss on ignition (LOI), smear slide and mollusk processing and identification were performed on the cores. The sediment recovered is dominated by brown, tan and white carbonate sand with varying amounts of organic matter. Sedimentation rates vary between 0.1-0.5 mm/year. Mollusks are found throughout the cores but gastropods dominate in the upper portions, which date from 2000 years BP to present day. Bivalves are abundant in intervals dating between 5000 and 2500 years BP. The most common bivalve species were Polymesoda maritima, Anomalocardis auberiana and Ervilia concentrica. The most common gastropods were Cerithidea costata and Cerithium lutosum. Drill holes made by predaceous gastropods occur on some of the gastropods, but on most of the bivalves. Drilling frequency is highest between 5000 and 2500 years BP even though gastropods are rarely preserved in that interval. Through smear slide analysis, diatoms, forams and ostracodes were also found to occur throughout the core record. Peaks in Fe and Sr from XRF scans at 0.5 cm intervals may represent records of high atmospheric dust concentrations and sea level fluctuations, respectively. Plotting mollusk bed depths versus calibrated age reveals a sea level rise over the last 6000 years that includes a rapid rise and subsequent fall at ~2500 year BP.

  2. Breeding productivity of Smith Island black ducks

    USGS Publications Warehouse

    Haramis, G.M.; Jorde, D.G.; Olsen, G.H.; Stotts, D.B.; Harrison, M.K.

    2002-01-01

    We investigated the breeding performance of American black ducks (Anas rubripes) on Smith Island, Chesapeake Bay, to improve our understanding of island black duck breeding ecology and to make management recommendations to enhance productivity. During 1995-96, we implanted 56 female black ducks with 20-g radio transmitters and tracked 35 of the individuals through the breeding season to locate nests, determine nest fate, and identify brood habitat. We also increased preseason banding efforts and compared capture characteristics over 12 years with those from the Deal Island Wildlife Management Area, a banding site on the mainland of Tangier Sound. A low rate of nesting (37%), lack of renesting, and poor hatching success (31%) indicated that island salt marsh habitats present a harsh environment for breeding black ducks. Black ducks located 11 of 13 nests (85%) in black needlerush (Juncus roemerianus) marsh where they were vulnerable to flooding from extreme tides and to egg predators. No nests were found on forested tree hammocks, a feature that distinguishes Smith Island from nearby South Marsh and Bloodsworth Islands. Nest predators included red foxes (Vulpes vulpes), herring gulls (Larus argentams), fish crows (Corvus ossifragus), and, potentially, Norway rats (Rattus norvegicus). Unlike mainland red foxes, foxes radio tracked on Smith Island were found to be capable swimmers and effective low marsh predators. We found shoreline meadows of widgeon grass (Ruppia maritima) to be important foraging sites for black ducks and suspected that the virtual absence of fresh water in this high salinity environment (1217+ ppt) to incur some cost in terms of growth and survival of ducklings. Preseason bandings revealed a high proportion of banded adults and a strong positive correlation in age ratios with the Deal Island banding site. This latter finding strongly suggests a negative universal effect of storm tides on nest success for Tangier Sound black ducks. Management to reduce nest predators, especially gulls and foxes, likely will have the greatest immediate benefit for island breeding black ducks.

  3. Metagenomic cellulases highly tolerant towards the presence of ionic liquids--linking thermostability and halotolerance.

    PubMed

    Ilmberger, Nele; Meske, Diana; Juergensen, Julia; Schulte, Michael; Barthen, Peter; Rabausch, Ulrich; Angelov, Angel; Mientus, Markus; Liebl, Wolfgang; Schmitz, Ruth A; Streit, Wolfgang R

    2012-07-01

    Cellulose is an important renewable resource for the production of bioethanol and other valuable compounds. Several ionic liquids (ILs) have been described to dissolve water-insoluble cellulose and/or wood. Therefore, ILs would provide a suitable reaction medium for the enzymatic hydrolysis of cellulose if cellulases were active and stable in the presence of high IL concentrations. For the discovery of novel bacterial enzymes with elevated stability in ILs, metagenomic libraries from three different hydrolytic communities (i.e. an enrichment culture inoculated with an extract of the shipworm Teredo navalis, a biogas plant sample and elephant faeces) were constructed and screened. Altogether, 14 cellulolytic clones were identified and subsequently assayed in the presence of six different ILs. The most promising enzymes, CelA2, CelA3 (both derived from the biogas plant) and CelA84 (derived from elephant faeces), showed high activities (up to 6.4 U/mg) in the presence of 30% (v/v) ILs. As these enzymes were moderately thermophilic and halotolerant, they retained 40% to 80% relative activity after 34 days in 4 M NaCl, and they were benchmarked with two thermostable enzymes, CelA from Thermotoga maritima and Cel5K from a metagenome library derived from Avachinsky crater in Kamchatka. These enzymes also exhibited high activity (up to 11.1 U/mg) in aqueous IL solutions (30% (v/v)). Some of the enzymes furthermore exhibited remarkable stability in 60% (v/v) IL. After 4 days, CelA3 and Cel5K retained up to 79% and 100% of their activity, respectively. Altogether, the obtained data suggest that IL tolerance appears to correlate with thermophilicity and halotolerance. PMID:22143172

  4. Structural Insights Into Amino Acid Binding and Gene Control by a Lysine Riboswitch

    SciTech Connect

    Serganov, A.; Huang, L; Patel, D

    2008-01-01

    In bacteria, the intracellular concentration of several amino acids is controlled by riboswitches1, 2, 3, 4. One of the important regulatory circuits involves lysine-specific riboswitches, which direct the biosynthesis and transport of lysine and precursors common for lysine and other amino acids. To understand the molecular basis of amino acid recognition by riboswitches, here we present the crystal structure of the 174-nucleotide sensing domain of the Thermotoga maritima lysine riboswitch in the lysine-bound (1.9 A) and free (3.1 A) states. The riboswitch features an unusual and intricate architecture, involving three-helical and two-helical bundles connected by a compact five-helical junction and stabilized by various long-range tertiary interactions. Lysine interacts with the junctional core of the riboswitch and is specifically recognized through shape-complementarity within the elongated binding pocket and through several direct and K+-mediated hydrogen bonds to its charged ends. Our structural and biochemical studies indicate preformation of the riboswitch scaffold and identify conformational changes associated with the formation of a stable lysine-bound state, which prevents alternative folding of the riboswitch and facilitates formation of downstream regulatory elements. We have also determined several structures of the riboswitch bound to different lysine analogues5, including antibiotics, in an effort to understand the ligand-binding capabilities of the lysine riboswitch and understand the nature of antibiotic resistance. Our results provide insights into a mechanism of lysine-riboswitch-dependent gene control at the molecular level, thereby contributing to continuing efforts at exploration of the pharmaceutical and biotechnological potential of riboswitches.

  5. Microfluidic mixing for non-equilibrium single-molecule optical spectroscopy

    NASA Astrophysics Data System (ADS)

    Pfeil, Shawn H.

    We describe a series of experiments made possible by the combination of single-molecule fluorescence spectroscopy and microfluidic mixing. To perform these measurements, a microfluidic sample handling system was developed and characterized. This system allows observation at times as early as 2.4 ms after a reaction is triggered, which is an more than an order of magnitude earlier than previous microfabricated devices. Dilutions as high as 1:19 (v/v) are achieved, allowing measurements of molecular refolding in native conditions. The interconversion of subpopulations, masked by averaging in ensemble measurements, is observed. This technology also facilitates ultra-sensitive chemiluminescence measurements, using only microliters of sample. Microfluidics are designed and fabricated to extend single-molecule measurements to samples out of equilibrium. The system is optimized for sensitive optical detection and experimental convenience. Channels are replica-molded in poly-dimethyl-siloxane (PDMS) elastomer and sealed to coverglass. The resulting devices are compatible with a broad range of chemicals, and exhibit low background fluorescence. The combination of continuous flow, which decouples reaction progress from measurement duration, with low background enables single molecules to be probed at well defined times after a reaction is triggered. Fluid delivery and pressure connections are made using an interface optimized for rapid assembly, rapid sample exchange, and modular device replacement, while providing access for high numerical aperture optics. The kinetics of Csp, the cold shock protein from Thermotoga maritima, are studied with the mixer. An order of magnitude decrease in deadtime puts a new upper limit of 4.6 ms on the time required for collapse after mixing. This result is in agreement with indirect measurements of chain reconfiguration time, which suggest collapse happens on the timescale of 10--100 ns. Measurements of the kinetics of a DNA sequence that binds cocaine put a lower bound on its folding rate of 100 s-1. Single-Molecule measurements at equilibrium, in conjunction with ensemble measurements, demonstrate that this system can be described thermodynamically with a two-state model. In addition, standard free energy changes for folding, in the presence and absence of 1 mM cocaine, are obtained. Ensemble chemiluminescence experiments demonstrate the broad applicability of themixing system. The luciferase-luciferin system from Photinus pyralis, the North American firefly, is studied. Kinetically resolved chemiluminescence measurements are performed using only 50 femtomoles of target, and microliters of sample. This compares favorably to stopped-flow, which requires milliliters of sample and picomoles of target.

  6. Brazil The Duck Lagoon

    NASA Technical Reports Server (NTRS)

    2002-01-01

    This Multi-angle Imaging SpectroRadiometer (MISR) image of Brazil covers an area of about 298 kilometers x 358 kilometers, and was captured by the instrument's vertical-viewing (nadir) camera on December 27, 2001. The 'Lagoa dos Patos', in the Brazilian state of Rio Grande do Sul, translates to 'the Duck Lagoon'. It was named by 16th century Jesuit settlers, who asked the King of Spain to grant them title to the lagoon so that they could breed ducks. The King consented, but revoked his edict when he discovered that the 'duck-pond' (measuring about 14,000 square kilometers) was one of the largest lagoonal systems in the world. Note the sediment plume emanating from the southern end of the lagoon. Sailors in the 16th century imagined this outlet to be the mouth of a large river. Early Portuguese explorers mistook the entrance to the lagoon for the mouth of a great river and called it the Rio Grande. A series of wave-like points and curls form 'cusps' on the inner shores of the lagoon. The lagoon's characteristics change with short-term tide-induced cyclic perturbations, and with longer term large scale meteorological conditions. The distinctive wavelike 'cusps' along the inner shores result from the circulation, erosion and accumulation of sediments driven by wind and tidal action. The El Nino Southern Oscillation (ENSO) circulation affects precipitation amount and continental runoff, thereby changing the contents of the lagoon waters. High rainfall and increased freshwater discharge during El Nino events correspond with elevated dissolved nutrient concentrations and increased phytoplankton growth. La Nina years are dry and the associated low rainfall reduces the freshwater recharge to the lagoon, causing an increase in salinity. Occasional blooms of toxic cyanobacteria (Microcystis aeruginosa), have been registered in the lagoon when nutrient concentrations are elevated. A number of reeds and grasses are important to the lagoon estuary, including widgeon grass (Ruppia maritima) which reaches peak production during summer. Sea turtles (Chelonia mydas) can be found in the lagoon during spring and summer. Although the lowland tapir (Tapirus terrestris) is found in some parts of Rio Grande do Sul, the Baird's tapir (Tapirus bairdii), is not distributed within the image area (it is restricted to Central America). MISR was built and is managed by NASA's Jet Propulsion Laboratory, Pasadena, CA, for NASA's Office of Earth Science, Washington, DC. The Terra satellite is managed by NASA's Goddard Space Flight Center, Greenbelt, MD. JPL is a division of the California Institute of Technology. Image credit: NASA/GSFC/LaRC/JPL, MISR Team.

  7. Elongation Factor-Tu (EF-Tu) proteins structural stability and bioinformatics in ancestral gene reconstruction

    NASA Astrophysics Data System (ADS)

    Dehipawala, Sunil; Nguyen, A.; Tremberger, G.; Cheung, E.; Schneider, P.; Lieberman, D.; Holden, T.; Cheung, T.

    2013-09-01

    A paleo-experimental evolution report on elongation factor EF-Tu structural stability results has provided an opportunity to rewind the tape of life using the ancestral protein sequence reconstruction modeling approach; consistent with the book of life dogma in current biology and being an important component in the astrobiology community. Fractal dimension via the Higuchi fractal method and Shannon entropy of the DNA sequence classification could be used in a diagram that serves as a simple summary. Results from biomedical gene research provide examples on the diagram methodology. Comparisons between biomedical genes such as EEF2 (elongation factor 2 human, mouse, etc), WDR85 in epigenetics, HAR1 in human specificity, DLG1 in cognitive skill, and HLA-C in mosquito bite immunology with EF Tu DNA sequences have accounted for the reported circular dichroism thermo-stability data systematically; the results also infer a relatively less volatility geologic time period from 2 to 3 Gyr from adaptation viewpoint. Comparison to Thermotoga maritima MSB8 and Psychrobacter shows that Thermus thermophilus HB8 EF-Tu calibration sequence could be an outlier, consistent with free energy calculation by NUPACK. Diagram methodology allows computer simulation studies and HAR1 shows about 0.5% probability from chimp to human in terms of diagram location, and SNP simulation results such as amoebic meningoencephalitis NAF1 suggest correlation. Extensions to the studies of the translation and transcription elongation factor sequences in Megavirus Chiliensis, Megavirus Lba and Pandoravirus show that the studied Pandoravirus sequence could be an outlier with the highest fractal dimension and lowest entropy, as compared to chicken as a deviant in the DNMT3A DNA methylation gene sequences from zebrafish to human and to the less than one percent probability in computer simulation using the HAR1 0.5% probability as reference. The diagram methodology would be useful in ancestral gene reconstruction studies in astrobiology and also be applicable to the study of point mutation in conformational thermostabilization research with Synchrotron based X-ray data for drug applications such as Parkinson's disease.

  8. The tryptophan synthase ?-subunit paralogs TrpB1 and TrpB2 in Thermococcus kodakarensis are both involved in tryptophan biosynthesis and indole salvage.

    PubMed

    Hiyama, Takayoshi; Sato, Takaaki; Imanaka, Tadayuki; Atomi, Haruyuki

    2014-07-01

    The last two steps of l-tryptophan (Trp) biosynthesis are catalyzed by Trp synthase, a heterotetramer composed of TrpA and TrpB. TrpB catalyzes the condensation of indole, synthesized by TrpA, and serine to Trp. In the hyperthermophilic archaeon Thermococcus kodakarensis, trpA and trpB (trpB1) are located adjacently in the trpCDEGFB1A operon. Interestingly, several organisms possess a second trpB gene (trpB2) encoding TrpB2, located outside of the trp operon in T. kodakarensis. Until now, the physiological function of trpB2 has not been examined genetically. In the present study, we report the biochemical and physiological analyses of TrpB2 from T. kodakarensis. Kinetic analysis indicated that TrpB2 catalyzed the TrpB reaction but did not interact with TrpA as in the case of TrpB1. When growth phenotypes were examined for gene disruption strains, the double-deletion mutant (?trpB1?trpB2) displayed Trp auxotrophy, whereas individual single mutants (?trpB1 and ?trpB2 strains) did not. It has been proposed previously that, in Thermotoga maritima, TrpB2 provides an alternate route to generate Trp from serine and free indole (indole salvage). To accurately examine the capacity of TrpB1 and TrpB2 in Trp synthesis via indole salvage, we constructed ?trpEB1 and ?trpEB2 strains using strain KUW1 (?pyrF?trpE) as a host, eliminating the route for endogenous indole synthesis. Indole complemented the Trp auxotrophies of ?trpEB1 (?pyrF?trpE?trpB1) and ?trpEB2 (?pyrF?trpE?trpB2) to similar levels. The results indicate that TrpB1 and TrpB2 both contribute to Trp biosynthesis in T. kodakarensis and can utilize free indole, and that indole salvage does not necessarily rely on TrpB2 to a greater extent. PMID:24835339

  9. Post-translational Modification of Ribosomal Proteins

    PubMed Central

    Arragain, Simon; Garcia-Serres, Ricardo; Blondin, Geneviève; Douki, Thierry; Clemancey, Martin; Latour, Jean-Marc; Forouhar, Farhad; Neely, Helen; Montelione, Gaetano T.; Hunt, John F.; Mulliez, Etienne; Fontecave, Marc; Atta, Mohamed

    2010-01-01

    Post-translational modifications of ribosomal proteins are important for the accuracy of the decoding machinery. A recent in vivo study has shown that the rimO gene is involved in generation of the 3-methylthio derivative of residue Asp-89 in ribosomal protein S12 (Anton, B. P., Saleh, L., Benner, J. S., Raleigh, E. A., Kasif, S., and Roberts, R. J. (2008) Proc. Natl. Acad. Sci. U. S. A. 105, 1826–1831). This reaction is formally identical to that catalyzed by MiaB on the C2 of adenosine 37 near the anticodon of several tRNAs. We present spectroscopic evidence that Thermotoga maritima RimO, like MiaB, contains two [4Fe-4S] centers, one presumably bound to three invariant cysteines in the central radical S-adenosylmethionine (AdoMet) domain and the other to three invariant cysteines in the N-terminal UPF0004 domain. We demonstrate that holo-RimO can specifically methylthiolate the aspartate residue of a 20-mer peptide derived from S12, yielding a mixture of mono- and bismethylthio derivatives. Finally, we present the 2.0 ? crystal structure of the central radical AdoMet and the C-terminal TRAM (tRNA methyltransferase 2 and MiaB) domains in apo-RimO. Although the core of the open triose-phosphate isomerase (TIM) barrel of the radical AdoMet domain was conserved, RimO showed differences in domain organization compared with other radical AdoMet enzymes. The unusually acidic TRAM domain, likely to bind the basic S12 protein, is located at the distal edge of the radical AdoMet domain. The basic S12 protein substrate is likely to bind RimO through interactions with both the TRAM domain and the concave surface of the incomplete TIM barrel. These biophysical results provide a foundation for understanding the mechanism of methylthioation by radical AdoMet enzymes in the MiaB/RimO family. PMID:20007320

  10. Selenium removal and mass balance in a constructed flow-through wetland system.

    PubMed

    Gao, S; Tanji, K K; Lin, Z Q; Terry, N; Peters, D W

    2003-01-01

    A field study on the removal of Se from agricultural subsurface drainage was conducted from May 1997 to February 2001 in the Tulare Lake Drainage District (TLDD) of San Joaquin Valley, California. A flow-through wetland system was constructed consisting of ten 15- x 76-m unlined cells that were continuously flooded and planted with either a monotype or combination of plants, including sturdy bulrush [Schoenoplectus robustus (Pursh) M.T. Strong], baltic rush (Juncus balticus Willd.), smooth cordgrass (Spartina alterniflora Loisel.), rabbitsfoot grass [Polypogon monspeliensis (L.) Desf.], salt-grass lDistichlis spicata (L.) Greene], cattail (Typha latifolia L.), tule [Schoenoplectus acutus (Muhl. ex Bigelow) A. Löve & D. Löve], and widgeon grass (Ruppia maritima L.). One cell had no vegetation planted. The objectives of this research were to evaluate Se removal efficiency of each wetland cell and to carry out a mass balance on Se. The inflow drainage water to the cells had average annual Se concentrations of 19 to 22 microg L(-1) dominated by selenate [Se(VI), 95%]. Average weekly water residence time varied from about 3 to 15 d for Cells 1 through 7 (target 7 d), 19 to 33 d for Cells 8 and 9 (target 21 d), and 13 to 18 d for Cell 10 (target 14 d). Average weekly Se concentration ratios of outflow to inflow ranged from 0.45 to 0.79 and mass ratio (concentration x water volume) from 0.24 to 0.52 for year 2000, that is, 21 to 55% reduction in Se concentration and 48 to 76% Se removal in mass by the wetland, respectively. The nonvegetated cell showed the least Se removal both in concentration and in mass. The global mass balance showed that on the average about 59% of the total inflow Se was retained within the cells and Se outputs were outflow (35%), seepage (4%), and volatilization (2%). Independent measurements of the Se retained in the cells totaled 53% of the total Se inflow: 33% in the surface (0-20 cm) sediment, 18% in the organic detrital layer above the sediment, 2% in the fallen litter, < 1% in the standing plants, and < 1% in the surface water. Thus, about 6% of the total Se inflow was unaccounted for in the internal compartments. PMID:12931913

  11. Neutron Reflectometry and QCM-D Study of the Interaction of Cellulase Enzymes with Films of Amorphous Cellulose

    SciTech Connect

    Halbert, Candice E [ORNL; Ankner, John Francis [ORNL; Kent, Michael S [Sandia National Laboratories (SNL); Jaclyn, Murton K [Sandia National Laboratories (SNL); Browning, Jim [ORNL; Cheng, Gang [Joint Bioenergy Institute; Liu, Zelin [Virginia Polytechnic Institute and State University (Virginia Tech); Majewski, Jaroslaw [Los Alamos National Laboratory (LANL); Supratim, Datta [Joint Bioenergy Institute; Michael, Jablin [Los Alamos National Laboratory (LANL); Bulent, Akgun [NIST Center for Neutron Research (NCRN), Gaithersburg, MD; Alan, Esker [Virginia Polytechnic Institute and State University (Virginia Tech); Simmons, Blake [Sandia National Laboratories (SNL)

    2011-01-01

    Improving the efficiency of enzymatic hydrolysis of cellulose is one of the key technological hurdles to reduce the cost of producing ethanol and other transportation fuels from lignocellulosic material. A better understanding of how soluble enzymes interact with insoluble cellulose will aid in the design of more efficient enzyme systems. We report a study involving neutron reflectometry (NR) and quartz crystal microbalance with dissipation (QCM-D) of the interaction of a commercial fungal enzyme extract (T. viride), two purified endoglucanses from thermophilic bacteria (Cel9A from A. acidocaldarius and Cel5A from T. maritima), and a mesophilic fungal endoglucanase (Cel45A from H. insolens) with amorphous cellulose films. The use of amorphous cellulose is motivated by the promise of ionic liquid pretreatment as a second generation technology that disrupts the native crystalline structure of cellulose. NR reveals the profile of water through the film at nm resolution, while QCM-D provides changes in mass and film stiffness. At 20 oC and 0.3 mg/ml, the T. viride cocktail rapidly digested the entire film, beginning from the surface followed by activity throughout the bulk of the film. For similar conditions, Cel9A and Cel5A were active for only a short period of time and only at the surface of the film, with Cel9A releasing 40 from the ~ 700 film and Cel5A resulting in only a slight roughening/swelling effect at the surface. Subsequent elevation of the temperature to the Topt in each case resulted in a very limited increase in activity, corresponding to the loss of an additional 60 from the film for Cel9A and 20 from the film for Cel5A, and very weak penetration into and digestion within the bulk of the film, before the activity again ceased. The results for Cel9A and Cel5A contrast sharply with results for Cel45A where very rapid and extensive penetration and digestion within the bulk of the film was observed at 20 C. We speculate that the large differences are due to the use of the thermophilic enzymes far below their optimal temperatures and also the presence of a cellulose binding module (CBM) on Cel45A while the thermophilic enzymes lack a CBM.

  12. Where on Earth...? MISR Mystery Image Quiz #6

    NASA Technical Reports Server (NTRS)

    2002-01-01

    Here's another chance to play geographical detective! This Multi-angle Imaging SpectroRadiometer (MISR) image covers an area of about 298 kilometers x 358 kilometers, and was captured by the instrument's vertical-viewing (nadir) camera on December 27, 2001. Use any reference materials you like and answer the following five questions: The large lagoon in the image is named for a particular type of bird. Name the bird. Note the sediment plume emanating from the southern end of the lagoon. Sailors in the 16th century imagined this outlet to be the mouth of a large river. What did they call the river? A series of wave-like points and curls form 'cusps' on the inner shores of the lagoon. Which ONE of the following is most responsible for the formation of these cusps? Violent storm impacts on erosion and accretion Wind and tide-driven sediment transport and circulation Tectonic folding associated with nearby mountain ridges Bathymetric effects of dredging operations True or false: Changes in regional precipitation associated with large scale atmospheric circulation patterns have no effect on the salinity of the lagoon's water. Which one of these is NOT distributed within the area covered by this image? Ruppia maritima Chelonia mydas Tapirus bairdii Microcystis aeruginosa E-mail your answers, name (initials are acceptable if you prefer), and your hometown by Tuesday, February 19, 2002 to suggestions@mail-misr.jpl.nasa.gov. Answers will be published on the MISR web site in conjunction with the next weekly image release. The names and home towns of respondents who answer all questions correctly by the deadline will also be published in the order responses were received. The first 3 people on this list who are not affiliated with NASA, JPL, or MISR and who did not win a prize in the last quiz will be sent a print of the image. A new 'Where on Earth...?' mystery appears as the MISR 'image of the week' approximately once per month. A new image of the week is released every Wednesday at noon Pacific time on the MISR home page http://www-misr.jpl.nasa.gov. The image also appears on the Atmospheric Sciences Data Center home page, http://eosweb.larc.nasa.gov, though usually with a several-hour delay. Image courtesy NASA/GSFC/LaRC/JPL, MISR Team.

  13. Structural analysis of chloroplast DNA in Prunus (Rosaceae): evolution, genetic diversity and unequal mutations.

    PubMed

    Katayama, H; Uematsu, C

    2005-11-01

    In order to understand the evolutionary aspects of the chloroplast DNA (cpDNA) structures in Rosaceous plants, a physical map of peach (Prunus persica cv. Hakuhou) cpDNA was constructed. Fourteen lambda phage clones which covered the entire sequence of the peach cpDNA were digested by restriction enzymes (SalI, XhoI, BamHI, SacI, and PstI) used singly or in combination. The molecular size of peach cpDNA was estimated to be about 152 kb. The gene order and contents were revealed to be equivalent to those of standard type of angiosperms by the localization of 31 genes on the physical map. Eighteen accessions from 14 Prunus species (P. persica, P. mira, P. davidiana, P. cerasis, P. cerasifera, P. domestica, P. insititia, P. spinosa, P. salicina, P. maritima, P. armeniaca, P. mume, P. tomentosa, P. zippeliana, and P. salicifolia) and one interspecific hybrid were used for the structural analysis of cpDNAs. Seventeen mutations (16 recognition site changes and one length mutation) were found in the cpDNA of these 18 accessions by RFLP analysis allowing a classification into 11 genome types. Although the base substitution rate in the recognition site (100p = 0.72) of cpDNA in Prunus was similar to that of other plants, i.e., Triticum-Aegilops, Brassica, and Pisum, it differed from Pyrus (100p = 0.15) in Rosaceae. Seven mutations including one length mutation were densely located within a region of about 9.1 kb which includes psbA and atpA in the left border of a large single-copy region of Prunus cpDNAs. The length mutation was detected only in P. persica and consisted of a 277 bp deletion which occurred in a spacer region between the trnS and trnG genes within the 9.1 kb region. Additional fragment length mutations (insertion/deletion), which were not detected by RFLP analysis, were revealed by PCR and sequence analyses in P. zippeliana and P. salicifolia. All of these length mutations occurred within the 9.1 kb region between psbA and atpA. This region could be an intra-molecular recombinational hotspot in Prunus species. PMID:16142464

  14. Modular system for assessment of glycosyl hydrolase secretion in Geobacillus thermoglucosidasius.

    PubMed

    Bartosiak-Jentys, Jeremy; Hussein, Ali H; Lewis, Claire J; Leak, David J

    2013-07-01

    The facultatively anaerobic, thermophilic bacterium Geobacillus thermoglucosidasius is being developed as an industrial micro-organism for cellulosic bioethanol production. Process improvement would be gained by enhanced secretion of glycosyl hydrolases. Here we report the construction of a modular system for combining promoters, signal peptide encoding regions and glycosyl hydrolase genes to facilitate selection of the optimal combination in G. thermoglucosidasius. Initially, a minimal three-part E. coli-Geobacillus sp. shuttle vector pUCG3.8 was constructed using Gibson isothermal DNA assembly. The three PCR amplicons contained the pMB1 E. coli origin of replication and multiple cloning site (MCS) of pUC18, the Geobacillus sp. origin of replication pBST1 and the thermostable kanamycin nucleotidyltransferase gene (knt), respectively. G. thermoglucosidasius could be transformed with pUCG3.8 at an increased efficiency [2.8×10(5) c.f.u. (µg DNA)(-1)] compared to a previously reported shuttle vector, pUCG18. A modular cassette for the inducible expression and secretion of proteins in G. thermoglucosidasius, designed to allow the simple interchange of parts, was demonstrated using the endoglucanase Cel5A from Thermotoga maritima as a secretion target. Expression of cel5A was placed under the control of a cellobiose-inducible promoter (P?glu) together with a signal peptide encoding sequence from a G. thermoglucosidasius C56-YS93 endo-?-1,4-xylanase. The interchange of parts was demonstrated by exchanging the cel5A gene with the 3' region of a gene with homology to celA from Caldicellulosiruptor saccharolyticus and substituting P?glu for the synthetic, constitutive promoter PUp2n38, which increased Cel5A activity five-fold. Cel5A and CelA activities were detected in culture supernatants indicating successful expression and secretion. N-terminal protein sequencing of Cel5A carrying a C-terminal FLAG epitope confirmed processing of the signal peptide sequence. PMID:23704786

  15. A survey of green plant tRNA 3'-end processing enzyme tRNase Zs, homologs of the candidate prostate cancer susceptibility protein ELAC2

    PubMed Central

    2011-01-01

    Background tRNase Z removes the 3'-trailer sequences from precursor tRNAs, which is an essential step preceding the addition of the CCA sequence. tRNase Z exists in the short (tRNase ZS) and long (tRNase ZL) forms. Based on the sequence characteristics, they can be divided into two major types: bacterial-type tRNase ZS and eukaryotic-type tRNase ZL, and one minor type, Thermotoga maritima (TM)-type tRNase ZS. The number of tRNase Zs is highly variable, with the largest number being identified experimentally in the flowering plant Arabidopsis thaliana. It is unknown whether multiple tRNase Zs found in A. thaliana is common to the plant kingdom. Also unknown is the extent of sequence and structural conservation among tRNase Zs from the plant kingdom. Results We report the identification and analysis of candidate tRNase Zs in 27 fully sequenced genomes of green plants, the great majority of which are flowering plants. It appears that green plants contain multiple distinct tRNase Zs predicted to reside in different subcellular compartments. Furthermore, while the bacterial-type tRNase ZSs are present only in basal land plants and green algae, the TM-type tRNase ZSs are widespread in green plants. The protein sequences of the TM-type tRNase ZSs identified in green plants are similar to those of the bacterial-type tRNase ZSs but have distinct features, including the TM-type flexible arm, the variant catalytic HEAT and HST motifs, and a lack of the PxKxRN motif involved in CCA anti-determination (inhibition of tRNase Z activity by CCA), which prevents tRNase Z cleavage of mature tRNAs. Examination of flowering plant chloroplast tRNA genes reveals that many of these genes encode partial CCA sequences. Based on our results and previous studies, we predict that the plant TM-type tRNase ZSs may not recognize the CCA sequence as an anti-determinant. Conclusions Our findings substantially expand the current repertoire of the TM-type tRNase ZSs and hint at the possibility that these proteins may have been selected for their ability to process chloroplast pre-tRNAs with whole or partial CCA sequences. Our results also support the coevolution of tRNase Zs and tRNA 3'-trailer sequences in plants. PMID:21781332

  16. Characterization of RimO, a New Member of the Methylthiotransferase Subclass of the Radical SAM Superfamily†

    PubMed Central

    Lee, Kyung-Hoon; Saleh, Lana; Anton, Brian P.; Madinger, Catherine L.; Benner, Jack S.; Iwig, David F.; Roberts, Richard J.; Krebs, Carsten; Booker, Squire J.

    2009-01-01

    RimO, encoded by the yliG gene in Escherichia coli, has been recently identified in vivo as the enzyme responsible for the attachment of a methylthio group on the ?-carbon of Asp88 of the small ribosomal protein S12 [Anton, B. P., Saleh, L., Benner, J. S., Raleigh, E. A., Kasif, S., and Roberts, R. J. (2008) Proc. Natl. Acad. Sci. USA, 105, 1826–1831]. To date, it is the only enzyme known to catalyze methylthiolation of a protein substrate; the four other naturally occurring methylthio modifications have been observed on tRNA. All members of the methylthiotransferase (MTTase) family, to which RimO belongs, have been shown to contain the canonical CxxxCxxC motif in their primary structures that is typical of the radical S-adenosylmethionine (SAM) family of proteins. MiaB, the only characterized MTTase, and the enzyme experimentally shown to be responsible for methylthiolation of N6-isopentenyladenosine of tRNA in E. coli and Thermotoga maritima, has been demonstrated to harbor two distinct [4Fe–4S] clusters. Herein, we report in vitro biochemical, and spectroscopic characterization of RimO. We show by analytical and spectroscopic methods that RimO, heterologously overproduced in E. coli in the presence of iron–sulfur cluster biosynthesis proteins from Azotobacter vinelandii, contains one [4Fe–4S]2+ cluster. Reconstitution of this form of RimO (RimOrcn) with 57Fe and sodium sulfide results in a protein that contains two [4Fe–4S]2+ clusters, similar to MiaB. We also show by mass spectrometry that RimOrcn catalyzes the attachment of a methylthio group to a peptide substrate analog that mimics the loop structure bearing aspartyl 88 of the S12 ribosomal protein from E. coli. Kinetic analysis of this reaction shows that the activity of RimOrcn in the presence of the substrate analog does not support a complete turnover. We discuss the possible requirement for an assembled ribosome for fully active RimO in vitro. Our findings are consistent with those of other enzymes that catalyze sulfur insertion, such as biotin synthase, lipoyl synthase, and MiaB. PMID:19736993

  17. Cloning, Sequencing, and Characterization of a Heat- and Alkali-Stable Type I Pullulanase from Anaerobranca gottschalkii

    PubMed Central

    Bertoldo, Costanzo; Armbrecht, Martin; Becker, Fiona; Schäfer, Thomas; Antranikian, Garabed; Liebl, Wolfgang

    2004-01-01

    The gene encoding a type I pullulanase was identified from the genome sequence of the anaerobic thermoalkaliphilic bacterium Anaerobranca gottschalkii. In addition, the homologous gene was isolated from a gene library of Anaerobranca horikoshii and sequenced. The proteins encoded by these two genes showed 39% amino acid sequence identity to the pullulanases from the thermophilic anaerobic bacteria Fervidobacterium pennivorans and Thermotoga maritima. The pullulanase gene from A. gottschalkii (encoding 865 amino acids with a predicted molecular mass of 98 kDa) was cloned and expressed in Escherichia coli strain BL21(DE3) so that the protein did not have the signal peptide. Accordingly, the molecular mass of the purified recombinant pullulanase (rPulAg) was 96 kDa. Pullulan hydrolysis activity was optimal at pH 8.0 and 70°C, and under these physicochemical conditions the half-life of rPulAg was 22 h. By using an alternative expression strategy in E. coli Tuner(DE3)(pLysS), the pullulanase gene from A. gottschalkii, including its signal peptide-encoding sequence, was cloned. In this case, the purified recombinant enzyme was a truncated 70-kDa form (rPulAg?). The N-terminal sequence of purified rPulAg? was found 252 amino acids downstream from the start site, presumably indicating that there was alternative translation initiation or N-terminal protease cleavage by E. coli. Interestingly, most of the physicochemical properties of rPulAg? were identical to those of rPulAg. Both enzymes degraded pullulan via an endo-type mechanism, yielding maltotriose as the final product, and hydrolytic activity was also detected with amylopectin, starch, ?-limited dextrins, and glycogen but not with amylose. This substrate specificity is typical of type I pullulanases. rPulAg was inhibited by cyclodextrins, whereas addition of mono- or bivalent cations did not have a stimulating effect. In addition, rPulAg? was stable in the presence of 0.5% sodium dodecyl sulfate, 20% Tween, and 50% Triton X-100. The pullulanase from A. gottschalkii is the first thermoalkalistable type I pullulanase that has been described. PMID:15184138

  18. [Cardiac glycosides: From ancient history through Withering's foxglove to endogeneous cardiac glycosides].

    PubMed

    Norn, Svend; Kruse, Poul R

    2004-01-01

    For centuries, drugs that increase the power of contraction of the failing heart have been used for the treatment of congestive heart failure (dropsy). The cardiac effect is due to the content of cardiac glycosides. Squill or sea onion, Urginea (Scilla) maritima, a seashore plant, was known by the ancient Romans and Syrians and possibly also by the ancient Egyptians. Squills were used erratically, but some prescriptions indicate that they may have been used for the treatment of oedematous states. The toxic effect of strophanthus species was known from poisoned arrows used by the natives in Africa. Digitalis, derived form the foxglove plant, Digitalis purpurea, is mentioned in writings as early as 1250; a Welsh family, known as the Physicians of Myddvai, collected different herbs and digitalis was included in their prescriptions. However, the druge was used erratically until the 18th century, when William Withering, an English physician and botanist, published a monograph describing the clinical effects of an extract of the foxglove plant. Later, in 1785, the indication and the toxicity of digitalis were reported in his book, "An account of the Foxglove and some of its medical uses with practical remarks on dropsy, and other diseases". In Denmark, the leaves of Digitalis purpurea or Digitalis lanata were tested for cardiac glycoside activity. The standardized digitalis powder was used in tinctures, infusions, and tablets. The preparations were included in successive editions of the Danish pharmacopoeia, some of the tinctures already in 1828, i.e. before the standardization of the drug. Isolation of cardiac glycosides from digitalis, strophanthus and squill and determination of their chemical structures initiated biochemical and pharmacological studies. The scientific advances led to an understanding of cardiac muscle contractility and the Na,K pump as the cellular receptor for the inotropic action of digitalis. Examination of putative endogenous ligands to the receptor revealed some endogenous cardiac glycosides of similar or identical structures as those found in digitalis, strophanthus and squill. Increased concentrations of these glycosides are found in patients with heart failure. Further investigations are needed to determine whether the secretion of glycosides might be a physiologic response to a diminished cardiac output. PMID:15685783

  19. [Plague in Zaire].

    PubMed

    Janssens, P G; Pattyn, S R

    1994-01-01

    Two endemic foci of plague have been discovered in Zaïre, the first in the Ituri in 1928, the other in North-Kivu in 1938. They are situated in the region of the great East-African Rift and are adjacent to the Ugandan focus, identified in 1877. A strict surveillance of these endemic foci makes it possible to state that, between 1928 and 1959, 632 cases of plague have been diagnosed in the Ituri, or 20 a year, and 190 in the N-Kivu, or 8 a year. Since then several flare ups have been notified. This situation is very remote from the "black death" concept. Yersinia pestis presents, besides its bipolar staining, many other characteristics such as the indispensable presence of iron to produce virulence, or the fermentation of glycerine and reduction of nitrates as parameters for the identification of 3 biovars, corresponding with a specific geographic distribution: antiqua, medievalis, orientalis or maritima. The antigenic structure has been discussed and also the role of plasmids. Plague is a disease of rats, a variegated gathering of rodents with different degrees of tolerance and sensitiveness to Y.pestis, living in a frail equilibrium. The multimammate houserat was in the Ituri the principal agent until the black rat Rattus rattus invaded the region and a new balance came into being. The frequent changes in taxonomy of Mastomys caused uncertainties. The transmission is due to fleas subject to a blocking of their ventriculum by Y.pestis. Fleas play an active part in the process. Man is only a casual intruder. The pathogenicity is related to its invasiveness and its intracellular localization in macrophages and other R.E. cells, in which Y.pestis can survive. The bubo is characteristic of the disease. In Zaïre a septicaemic tendency has been observed, with a possible involvement of the C.N.S. and of the lungs. The latter may produce among the surrounding relatives primary pneumonic plague. The clinical diagnosis ought to be confirmed by bacteriologic investigation of the puncture fluid of the bubo, the blood, and when necessary the C.S.F. or the sputum by culture and/or animal inoculation. The treatment became very efficient since the availability of sulfamides and later antibiotics: aminoglycosides, chloramphenicol, tetracyclines. A timely administration ensures practically recovery. As soon as Y.pestis was identified vaccination was put into practice and in the first place by killed germs (Haffkine's lymph) to day with formalized F1, for mass vaccination live attenuated strains were used: Tjiwidej (Otten), E.V. (Girard), K120 (Grasset).(ABSTRACT TRUNCATED AT 400 WORDS) PMID:7801703

  20. Response of biotic communities to salinity changes in a Mediterranean hypersaline stream

    PubMed Central

    Velasco, Josefa; Millán, Andrés; Hernández, Juan; Gutiérrez, Cayetano; Abellán, Pedro; Sánchez, David; Ruiz, Mar

    2006-01-01

    Background This study investigates the relationship between salinity and biotic communities (primary producers and macroinvertebrates) in Rambla Salada, a Mediterranean hypersaline stream in SE Spain. Since the 1980's, the mean salinity of the stream has fallen from about 100 g L-1 to 35.5 g L-1, due to intensive irrigated agriculture in the watershed. Furthermore, large dilutions occur occasionally when the water irrigation channel suffers cracks. Results Along the salinity gradient studied (3.5 – 76.4 g L-1) Cladophora glomerata and Ruppia maritima biomass decreased with increasing salinity, while the biomass of epipelic algae increased. Diptera and Coleoptera species dominated the community both in disturbed as in re-established conditions. Most macroinvertebrates species found in Rambla Salada stream are euryhaline species with a broad range of salinity tolerance. Eight of them were recorded in natural hypersaline conditions (~100 g L-1) prior to important change in land use of the watershed: Ephydra flavipes, Stratyomis longicornis, Nebrioporus ceresyi, N. baeticus, Berosus hispanicus, Enochrus falcarius, Ochthebius cuprescens and Sigara selecta. However, other species recorded in the past, such as Ochthebius glaber, O. notabilis and Enochrus politus, were restricted to a hypersaline source or absent from Rambla Salada. The dilution of salinity to 3.5 – 6.8 gL-1 allowed the colonization of species with low salininty tolerance, such as Melanopsis praemorsa, Anax sp., Simulidae, Ceratopogonidae and Tanypodinae. The abundance of Ephydra flavipes and Ochthebius corrugatus showed a positive significant response to salinity, while Anax sp., Simulidae, S. selecta, N. ceresyi, N. baeticus, and B. hispanicus showed significant negative correlations. The number of total macroinvertebrate taxa, Diptera and Coleoptera species, number of families, Margalef's index and Shannon's diversity index decreased with increasing salinity. However, the rest of community parameters, such as the abundance of individuals, evenness and Simpson's index, showed no significant response to changes in salinity. Classification and ordination analysis revealed major differences in macroinvertebrate community structure between hypersaline conditions (76.4 g L-1) and the rest of the communities observed at the lower salinity levels, and revealed that below ~75 g L-1, dissimilarities in the communities were greater between the two habitats studied (runs and pools) than between salinity levels. Conclusion Salinity was the first factor determining community composition and structure in Rambla Salada stream followed by the type of habitat. PMID:17014701

  1. Vibrational Analysis of Mononitrosyl Complexes in Hemerythrin and Flavodiiron Proteins: Relevance to Detoxifying NO Reductase

    PubMed Central

    Hayashi, Takahiro; Caranto, Jonathan D.; Matsumura, Hirotoshi; Kurtz, Donald M.; Moënne-Loccoz, Pierre

    2012-01-01

    Flavodiiron proteins (FDPs) play important roles in the microbial nitrosative stress response in low-oxygen environments by reductively scavenging nitric oxide (NO). Recently, we showed that FMN-free diferrous FDP from Thermotoga maritima exposed to 1 equiv NO forms a stable diiron-mononitrosyl complex (deflavo-FDP(NO)) that can react further with NO to form N2O [Hayashi, T.; Caranto, J. D.; Wampler, D. A.; Kurtz, D. M., Jr.; Moënne-Loccoz, P. Biochemistry 2010, 49, 7040–7049]. Here we report resonance Raman and low-temperature photolysis FTIR data that better define the structure of this diiron-mononitrosyl complex. We first validate this approach using the stable diiron-mononitrosyl complex of hemerythrin, Hr(NO), for which we observe a ?(NO) at 1658 cm?1, the lowest ?(NO) ever reported for a nonheme {FeNO}7 species. Both deflavo-FDP(NO) and the mononitrosyl adduct of the flavinated FPD (FDP(NO)) show ?(NO) at 1681 cm?1, which is also unusually low. These results indicate that, in Hr(NO) and FDP(NO), the coordinated NO is exceptionally electron rich, more closely approaching the Fe(III)(NO?) resonance structure. In the case of Hr(NO), this polarization may be promoted by steric enforcement of an unusually small FeNO angle, while in FDP(NO), the Fe(III)(NO?) structure may be due to a semi-bridging electrostatic interaction with the second Fe(II) ion. In Hr(NO), accessibility and steric constraints prevent further reaction of the diiron-mononitrosyl complex with NO, whereas in FDP(NO) the increased nucleophilicity of the nitrosyl group may promote attack by a second NO to produce N2O. This latter scenario is supported by theoretical modeling [Blomberg, L. M.; Blomberg, M. R.; Siegbahn, P. E. J. Biol. Inorg. Chem. 2007, 12, 79–89]. Published vibrational data on bioengineered models of denitrifying heme-nonheme NO reductases[Hayashi, T.; Miner, K. D.; Yeung, N.; Lin, Y.-W.; Lu, Y.; Moënne-Loccoz, P. Biochemistry 2011, 50, 5939–5947] support a similar mode of activation of a heme {FeNO}7 species by the nearby nonheme Fe(II). PMID:22449095

  2. CHIRP survey of the submerged harbors of King Herod's Caesarea, offshore Israel - looking for evidence of ancient disasters

    NASA Astrophysics Data System (ADS)

    Austin, J. A.; Goodman-Tchernov, B.

    2012-12-01

    Caesarea Maritima, located on the Israel coast south of Haifa, is an ancient city/harbor site built ~2,000 years ago that continues to produce important insights into both the maritime livelihoods of antiquity and natural/anthropogenic influences on coastal structures/processes. The grandiose, three-basin harbor complex was built by Herod the Great. Today, the inner harbor basin is terrestrial, while the majority of the intermediate/outer harbors lies 1-7 m beneath the sea surface. Explanations for the harbor's destruction have included earthquakes, liquefaction, deterioration from erosion, storm undercutting and tsunami damage. Recently, evidence for tsunami events has been discovered offshore during excavation and coring expeditions, specifically trench exposures and pneumatic hammer cores. Stratigraphic horizons containing tsunamite signatures suggest the occurrence of at least three tsunamis in the past ~3,500 yrs. One may correspond with the catastrophic eruption of Santorini ~1500 BC; another appears to have done significant damage to Caesarea ~115 AD, and a third occurred within the period 5th-7th centuries AD. Extant combined bathymetric/magnetic surveys offshore also show unusual, anomalous features. Excavations in 2003 suggest that these features may be part of an ancient designated anchoring station, and support the existence of underlying man-made terrestrial structures from an earlier period when sea-level was lower. The primary goal of the current survey was to correlate recognized/potential tsunamigenic sediment layers throughout the proximal shelf offshore Caesarea, using extremely high-resolution geophysical images. Such surficial sub-bottom profiling will allow archaeologists to proceed with investigations of recognized anthropogenically-influenced submerged coastal features. The field survey was conducted in August 2011. Seismic data were collected using UTIG's portable Knudsen 320BP CHIRP (2.5-5.5 kHz) profiler, affixed to a metal pole mounted on the starboard flank of a ~8 m-long catamaran. Data acquisition was generally conducted from dawn to mid-day, when wind/wave conditions were most favorable. A dense (5-10 m average profile spacing) grid of profiles, both along-strike (spanning the entire harbor complex) and across-strike (from intermediate harbor to ~10-15 m of water), was acquired. Total track length is ~126 line-km. In certain places, multiple sub-bottom horizons can be traced and mapped; sub-seafloor penetrations up to ~ 4-5 m were occasionally achieved, particularly in deeper water. However, sub-bottom penetration is spatially variable in sand-prone sediments. Correlation difficulties relate both to uneven acoustic penetration and to the presence offshore of "kurkar" ridges, calcareous sandstone ridges paralleling the modern shoreline that represent now-submerged Pleistocene dune complexes. These ancient dunes can produce physical barriers that both alter the depositional regime as well as complicate the acoustic mapping task. Mapped horizons within the survey area will be shown, along with preliminary correlations to the stratigraphy described from previously cored sediments (e.g., interpreted "tsunamites").

  3. The applicability of OSL as a sedimentological proxy: new avenues to distinguish extreme events

    NASA Astrophysics Data System (ADS)

    Lopez, G. I.

    2012-12-01

    Signature underwater tsunami deposits have been relatively recently found in the upper Mediterranean shelf offshore Israel. They have been attributed as a potential cause for the demise of the ancient Roman city of Caesarea Maritima and its artificial Herodian harbour of Sebastos. Present annual large winter storm activity (2010-2011; waves heights up to 14 m) has severely impacted the area, showing increased coastal erosion and rigorous movement of nearshore sands, complicating the stratigraphical histories of the near offshore record. Recent sedimentological and geoarchaeological studies conducted in and around the harbour have been aimed to investigate extreme event characterization by different means, using Optically Stimulated Luminescence (OSL). A comparative study of modern and palaeo-storm sediments was launched in order to obtain physical correlation between offshore sediments, enabling further comparison with historical tsunami deposits, as well as modern and ancient sands emplaced during normal marine conditions. A suite of previously collected and identified sediment samples was selected from the same area where the modern storm analogues were collected. The palaeo-samples came from long-vertical hydraulic percussion cores (14-30 m depths) and small horizontal tubes pushed into excavated underwater sediment walls (2-12 m depths). The uniqueness of OSL relays on its capacity to date the last time a mineral grain was effectively exposed to sunlight, just prior to its burial. It is intrinsically related to final depositional process, which should reflect the completeness of the OSL signal resetting (zeroing process), evidenced by the normality and modality of the Equivalent Dose (DE) distribution. In Optical Dating, DE over-dispersion values have been used as a measure of inhomogeneitiy in the natural palaeo-dose of sediments. Such heterogeneity can be due to an array of causes, including insufficient zeroing during transport and deposition, or turbation processes after burial. Environments where sediments are well exposed to daylight at deposition (e.g. aeolian and some coastal) do not show extreme over-dispersion values but rather well clustered DE's as noted by probability-distribution plots. The degrees of variance and skewness of Gaussian or relative-probability distributions are intrinsically related to the scatter factor. Hence, the latter could be used to differentiate between depositional mechanisms and/or environmental settings. In this study, the single-aliquot regenerative-dose (SAR) protocol was used to measure the OSL signals from single grains of quartz from tsunami, storm and normal marine conditions deposits. Over-dispersion analyses were conducted on all samples. Preliminary results suggest the possibility of differentiating between all three types of deposits based on pre-established over-dispersion values and representative single-dose population distributions. Further comparative OSL experiments are currently being carried out on other known tsunamigenic analogues to further evaluate OSL signal behaviours and constrain the findings (2011 Tohoku Tsunami; 1979 night Petatlán Tsunami). Rather than a dating tool, OSL was used to identify signal patterns exclusive to known depositional conditions, in hope of applying it as sedimentological proxy in event stratigraphy and palaeoseismic tsunami research.

  4. Remediation of heavy metal contaminated sites in the Venice lagoon and conterminous areas (Northern Italy)

    NASA Astrophysics Data System (ADS)

    Bini, Claudio; Wahsha, Mohammad; Fontana, Silvia; Maleci, Laura

    2013-04-01

    The lagoon of Venice and the conterminous land are affected by heavy contamination of anthropogenic origin, and for this reason the whole area has been classified as site of national interest, and must be restored. Heavy metals (As, Cd, Cr, Cu, Hg, Mn, Pb, Sb, Se, Zn) and organic compounds (IPA, PCB, Dioxine) have been identified as the main contaminants at various sites, owing to agriculture and industrial wastes discharged on soils and convoyed to the lagoon. Five case studies of soil remediation are here reported. S. Giuliano is a former palustrine area reclaimed since the 60's with various human transported materials (HTM). In this area, hot spots overpassing the reference limits for residential and green areas have been recorded for Cd, Cu, Pb, Zn and IPA. Campalto is a site bordering the Venice lagoon and subjected to oscillating water level, that enhances metal mobility; diffuse contamination by heavy metals, particularly Pb, has been recorded at this site, utilized since 30 years for military and sport (skate) activities. Marghera is dramatically famous for its numerous factories and for oil refineries that affected the lagoon sediments since the 50's. Sediments proved heavily contaminated by As (up to 137 mgkg-1), Cd (57 mgkg-1), Hg (30mgkg-1), Ni, Pb (700 mgkg-1), Zn (5818 mgkg-1). Murano is a small island where many glass factories (the most famous all over the world) are running since XIII century. Glass is stained with several metals and, moreover, some substances are used to regulate fusion temperature, purity, etc., and therefore the surrounding environment is heavily contaminated by these substances. Mean concentrations of As (429 mgkg-1), Cd (1452 mgkg-1), Pb (749 mgkg-1), Zn (1624 mgkg-1), Se (341 mgkg-1), Sb (74 mgkg-1) widely overpass the reference values for both residential and industrial areas in national guidelines. Molo Serbatoi is a former oil container currently under restoration in the port of Venice. Soil contamination by As, Hg, Zn and IPA was recorded, while groundwater proved to be contaminated by As, Cd, Cr, Hg, Pb, Cu, Se, Ni, Mn, Sb, Fe. Restoration of the studied sites has been carried out by phytoremediation with native or exotic vegetation (Fragmites australis, Juncus lacustris,Puccinellia palustris, Limonium serotinum, Salicornia glauca, Spartina maritima, Pteris vittata) or cultivated plants (Heliantus annuus, Zea mais, Brassica napus, Brassica juncea). Results are somewhat contradictory. At S. Giuliano, the exotic fern (Pteris vittata), consistently with data from current literature, showed high ability to accumulate As, particularly in aerial parts. At Campalto, native vegetation proved ineffective for phytoextraction, but suitable for phytostabilization, owing to a root barrier effect. In the lagoon sediments from Marghera, Spartina proved more effective than Fragmites to uptake metals, while cultivated plants could not survive to high heavy metal concentrations. At Murano, Pteris vittata proved highly effective to accumulate As, but also resistant to elevated concentrations of co-existing metals (Cd, Pb, Se, Zn), with clear signals of growth sufference and a drastic reduction of sorption capacity only in the presence of very high Cd concentration. At Molo Serbatoi, phytoremediation could not be applied in absence of a chelating agent (e.g. EDTA), which could enhance metal mobilization: therefore, soil has been stored, selected and finally (the most contaminated part) delivered to a landfill, while groundwater will be remediated by bioremediation techniques.

  5. Threatened and Endangered Species Survey for Patrick Air Force Base, Florida

    NASA Technical Reports Server (NTRS)

    Oddy, Donna M.; Stolen, Eric D.; Schmalzer, Paul A.; Larson, Vickie L.; Hall, Patrice; Hensley, Melissa A.

    1997-01-01

    A review of previous environmental work conducted at Patrick Air Force Base (PAFB) indicated that several threatened, endangered, or species of special concern occurred or had the potential to occur there. This study was implemented to collect more information on protected species at PAFB. A map of landcover types was prepared for PAFB using aerial photography, groundtruthing, and a geographic information system (GIS). Herbaceous vegetation was the most common vegetation type. The second most abundant vegetation type was disturbed shrubs/exotics. The beach and associated dune vegetation comprised 3.2% of the land area, but was the most extensive natural community within PAFB. A few isolated mangrove communities exist along the Banana River. Seventy-seven species of vascular plants occurred on the dunes, including four species listed by state agencies: spider lily (Hymenocallis latifolia), prickly pear cactus (Opuntia stricta), beach star (Remirea maritima), and inkberry (Scaevola plumien). Surveys of other habitats revealed eighty-four species of vascular plants including two state-listed species: spider lily and prickly pear cactus. Many of these areas are dominated by invasive, exotic species, particularly Brazilian pepper (Schinus terebinthifolius) and Australian pine (Casuarina equisetifolia), and native species of open or disturbed sites such as camphorweed (Heterotheca subaxillaris) and beardgrass (Andropogon spp.). Due to the isolation of PAFB from other natural areas, most exotic plant populations on the base are not an immediate threat to intact native plant communities. Dune habitat was surveyed for the southeastem beach mouse (Peromyscus polionotus niveiventris) by quarterly trapping along eight 100 m transects. No beach mice were found. The limited extent of dune habitat, its fragmented condition, and the isolation of PAFB from extant populations of the beach mouse probably accounts for its absence. Surveys of birds on PAFB found an avifauna characteristic of species that occur in the Indian River Lagoon system. Twenty-five species of waterbirds were observed during quarterly surveys on PAFB, including five species listed as species of special concern by the state of Florida: Snowy Egret (Egretta thula), Little Blue Heron (Egretta caerulea), Tricolored Heron (Egretta tricolo4, White Ibis (Eudocimus albus), and Brown Pelican (Pelecanus occidentalis). The Golf Course was used extensively by almost all species of waterbirds on PAFB. Twenty-two species of shorebirds were observed on PAFB. Although no listed species were observed, the potential exists for several protected species of shorebirds to use the beach at PAFB during some parts of the year. The Airfield runways and associated grass areas were important sites at PAFB for loafing and feeding for some shorebirds. Surveys of rooftop nesting by Least Terns (Stema antillarum) on PAFB found a large colony on a rooftop in the PAFB Industrial Area. This colony produced some independent young. Two rooftop Least Tern colonies reported from previous years were inactive during 1996. A small number of Black Skimmers (Rhynchops nigee attempted to nest at the Least Ten colony but were unsuccessful. Surveys for the gopher tortoise (Gopherus polyphemus) revealed burrows and tortoises only at the Waste Study Site; five burrows and three tortoises were observed. No Florida scrub lizards (Sceloporus woodi), eastern indigo snakes (Drymarchon corais couperl), or diamondback terrapins (Malademys terrapin terrapin) were observed. American alligators (Alligator mississippiensis) were observed on the Golf Course and using ditches, ponds, and areas along the Banana River. The amount of dune habitat could be expanded by not mowing areas adjacent to the dunes to allow dune species to colonize and expand. Planting dune species as part of the beach renourishment project will also increase this habitat. Exotic plants dominate several areas on the base and are used by threatened, endangered, and species of special concern. However, the use of native vegetation in landscaping projects thro

  6. Solution NMR structure of ribosome-binding factor A (RbfA), a cold-shock adaptation protein from Escherichia coli.

    PubMed

    Huang, Yuanpeng Janet; Swapna, G V T; Rajan, P K; Ke, Haiping; Xia, Bing; Shukla, Kamal; Inouye, Masayori; Montelione, Gaetano T

    2003-03-21

    Ribosome-binding factor A (RbfA) from Escherichia coli is a cold-shock adaptation protein. It is essential for efficient processing of 16S rRNA and is suspected to interact with the 5'-terminal helix (helix I) of 16S rRNA. RbfA is a member of a large family of small proteins found in most bacterial organisms, making it an important target for structural proteomics. Here, we describe the three-dimensional structure of RbfADelta25, a 108 residue construct with 25 residues removed from the carboxyl terminus of full-length RbfA, determined in solution at pH 5.0 by heteronuclear NMR methods. The structure determination was carried out using largely automated methods for determining resonance assignments, interpreting nuclear Overhauser effect (NOE) spectroscopy (NOESY) spectra, and structure generation. RbfADelta25 has an alpha+beta fold containing three helices and three beta-strands, alpha1-beta1-beta2-alpha2-alpha3-beta3. The structure has type-II KH-domain fold topology, related to conserved KH sequence family proteins whose betaalphaalphabeta subunits are characterized by a helix-turn-helix motif with sequence signature GxxG at the turn. In RbfA, this betaalphaalphabeta subunit is characterized by a helix-kink-helix motif in which the GxxG sequence is replaced by a conserved AxG sequence, including a strongly conserved Ala residue at position 75 forming an interhelical kink. The electrostatic field distribution about RbfADelta25 is bipolar; one side of the molecule is strongly negative and the opposite face has a strong positive electrostatic field. A "dynamic hot spot" of RbfADelta25 has been identified in the vicinity of a beta-bulge at strongly conserved residue Ser39 by 15N R(1), R(2) relaxation rate and heteronuclear 15N-1H NOE measurements. Analyses of these distributions of electrostatic field and internal dynamics, together with evolutionary implications of fold and sequence conservation, suggest that RbfA is indeed a nucleic acid-binding protein, and identify a potential RNA-binding site in or around the conserved polypeptide segment Ser76-Asp100 corresponding to the alpha3-loop-beta3 helix-loop-strand structure. While the structure of RbfADelta25 is most similar to that of the KH domain of the E.coli Era GTPase, its electrostatic field distribution is most similar to the KH1 domain of the NusA protein from Thermotoga maritima, another cold-shock associated RNA-binding protein. Both RbfA and NusA are regulated in the same E.coli operon. Structural and functional similarities between RbfA, NusA, and other bacterial type II KH domains suggest previously unsuspected evolutionary relationships between these cold-shock associated proteins. PMID:12628255

  7. Structure of the ternary complex formed by a chemotaxis receptor signaling domain, the CheA histidine kinase and the coupling protein CheW as determined by pulsed dipolar ESR spectroscopy†

    PubMed Central

    Bhatnagar, Jaya; Borbat, Peter P.; Pollard, Abiola M.; Bilwes, Alexandrine M.; Freed, Jack H.; Crane, Brian R.

    2010-01-01

    The signaling apparatus that controls bacterial chemotaxis is composed of a core complex containing chemoreceptors, the histidine auto-kinase CheA, and the coupling protein CheW. Site-specific spin labeling and pulsed-dipolar ESR spectroscopy (PDS) have been applied to investigate the structure of a soluble ternary complex formed by T. maritima CheA (TmCheA), CheW, and receptor signaling domains. Thirty-five symmetric spin-labels sites (SLSs) were engineered into the five domains of the CheA dimer and CheW to provide distance restraints within the CheA:CheW complex in the absence and presence of a soluble receptor that inhibits kinase activity (Tm14). Additional PDS restraints between spin-labeled CheA, CheW and an engineered single-chain receptor labeled at six different sites allows docking of the receptor structure relative to the CheA:CheW complex. Disulfide cross-linking between selectively incorporated Cys residues finds two pairs of positions that provide further constraints within the ternary complex: one involving Tm14 and CheW, and another involving Tm14 and CheA. The derived structure of the ternary complex indicates a primary site of interaction between CheW and Tm14 that agrees well with previous biochemical and genetic data on transmembrane chemoreceptors. The PDS distance distributions are most consistent with only one CheW directly engaging one dimeric Tm14. The CheA dimerization domain (P3) aligns roughly antiparallel to the receptor conserved signaling tip, but does not interact strongly with it. The angle of the receptor axis with respect to P3 and the CheW-binding P5 domains is bound by two limits differing by ~20°. In one limit, Tm14 aligns roughly along P3 and may interact to some extent with the hinge region near the P3 hairpin loop. In the other limit, Tm14 tilts to interact with the P5 domain of the opposite subunit in an interface that mimics that observed with the P5 homolog CheW. The time-domain ESR data can be simulated from the model only if orientational variability is introduced for the P5, and especially P3 domains. The Tm14 tip also binds beside one of the CheA kinase domains (P4); however, in both bound and unbound states, P4 samples a broad range of distributions that are only minimally affected by Tm14 binding. The CheA P1 domains that contain the substrate histidine are also broadly distributed in space under all conditions. In the context of the hexagonal lattice formed by trimeric transmembrane chemoreceptors, the PDS structure is best accommodated with the P3 domain in the center of a honeycomb edge. PMID:20355710

  8. High tides and rising seas: Potential effects on estuarine waterbirds

    USGS Publications Warehouse

    Erwin, R.M.; Sanders, G.M.; Prosser, D.J.; Cahoon, D.R.

    2006-01-01

    Coastal waterbirds are vulnerable to water-level changes especially under predictions of accelerating sea-level rise and increased storm frequency in the next century. Tidal and wind-driven fluctuations in water levels affecting marshes, their invertebrate communities, and their dependent waterbirds are manifested in daily, monthly, seasonal, annual, and supra-annual (e.g., decadal or 18.6-yr) periodicities. Superimposed on these cyclic patterns is a long-term (50-80 yr) increase in relative sea-level rise that varies from about 2-4 + mm/yr along the Atlantic coastline. At five study sites selected on marsh islands from Cape Cod, Massachusetts to coastal Virginia, we monitored marsh elevation changes and flooding, tide variations over time, and waterbird use. We found from long-term marsh core data that marsh elevations at three of five sites may not be sufficient to maintain pace with current sea-level rise. Results of the short-term (3-4 yr) measures using surface elevation tables suggest a more dramatic difference, with marsh elevation change at four of five sites falling below relative sea-level rise. In addition, we have found a significant increase (in three of four cases) in the rate of surface marsh flooding in New Jersey and Virginia over the past 70-80 yr during May-July when waterbirds are nesting on or near the marsh surface. Short-term, immediate effects of flooding will jeopardize annual fecundity of many species of concern to federal and state agencies, most notably American Black Duck (Anas rubripes), Nelson's Sharp-tailed Sparrow (Ammodramus nelsoni), Saltmarsh Sharp-tailed Sparrow (A. caudacutus), Seaside Sparrow (A. maritima), Coastal Plain Swamp Sparrow (Melospiza georgiana nigrescens), Black Rail (Laterallus jamaicensis), Forster's Tern (Sterna forsteri). Gull-billed Tern (S. nilotica), Black Skimmer (Rynchops niger), and American Oystercatcher (Haemotopus palliatus). Forster's Terns are probably most at risk given the large proportion of their breeding range in the mid-Atlantic and their saltmarsh specialization. At a scale of 1-2 decades, vegetation changes (saltmeadow cordgrass [Spartina patens] and salt grass [Distichlis spicata] converting to smooth cordgrass [Spartina alterniflora]), interior pond expansion and erosion of marshes will reduce nesting habitat for many of these species, but may enhance feeding habitat of migrant shorebirds and/or migrant or wintering waterfowl. At scales of 50-100 yr, reversion of marsh island complexes to open water may enhance populations of open-bay waterfowl, e.g., Bufflehead (Bucephala albeola) and Canvasback (Aythya valisneria), but reduce nesting habitats dramatically for the above named marsh-nesting species, may reduce estuarine productivity by loss of the detrital food web and nursery habitat for fish and invertebrates, and cause redistribution of waterfowl, shorebirds, and other species. Such scenarios are more likely to occur in the mid- and north Atlantic regions since these estuaries are lower in sediment delivery on average than those in the Southeast. A simple hypothetical example from New Jersey is presented where waterbirds are forced to shift from submerged natural marshes to nearby impoundments, resulting in roughly a 10-fold increase in density. Whether prey fauna are sufficiently abundant to support this level of increase remains an open question, but extreme densities in confined habitats would exacerbate competition, increase disease risk, and possibly increase predation.

  9. High tides and rising seas: potential effects on estuarine waterbirds

    USGS Publications Warehouse

    Erwin, R.M.; Sanders, G.M.; Prosser, D.J.; Cahoon, D.R.

    2006-01-01

    Coastal waterbirds are vulnerable to water-level changes especially under predictions of accelerating sea-level rise and increased storm frequency in the next century. Tidal and wind-driven fluctuations in water levels affecting marshes, their invertebrate communities, and their dependent waterbirds are manifested in daily, monthly, seasonal, annual, and supra-annual (e.g., decadal or 18.6-yr) periodicities. Superimposed on these cyclic patterns is a long-term (50?80 yr) increase in relative sea-level rise that varies from about 2?4 + mm/yr along the Atlantic coastline. At five study sites selected on marsh islands from Cape Cod, Massachusetts to coastal Virginia, we monitored marsh elevation changes and flooding, tide variations over time, and waterbird use. We found from longterm marsh core data that marsh elevations at three of five sites may not be sufficient to maintain pace with current sea-level rise. Results of the short-term (3?4 yr) measures using surface elevation tables suggest a more dramatic difference, with marsh elevation change at four of five sites falling below relative sea-level rise. In addition, we have found a significant increase (in three of four cases) in the rate of surface marsh flooding in New Jersey and Virginia over the past 70?80 yr during May?July when waterbirds are nesting on or near the marsh surface. Short-term, immediate effects of flooding will jeopardize annual fecundity of many species of concern to federal and state agencies, most notably American Black Duck (Anas rubripes), Nelson?s Sharp-tailed Sparrow (Ammodramus nelsoni), Saltmarsh Sharp-tailed Sparrow (A. caudacutus), Seaside Sparrow (A. maritima), Coastal Plain Swamp Sparrow (Melospiza georgiana nigrescens), Black Rail (Laterallus jamaicensis), Forster?s Tern (Sterna forsteri), Gull-billed Tern (S. nilotica), Black Skimmer (Rynchops niger), and American Oystercatcher (Haemotopus palliatus). Forster?s Terns are probably most at risk given the large proportion of their breeding range in the mid-Atlantic and their saltmarsh specialization. At a scale of 1?2 decades, vegetation changes (saltmeadow cordgrass [Spartina patens] and salt grass [Distichlis spicata] converting to smooth cordgrass [Spartina alternifl ora]), interior pond expansion and erosion of marshes will reduce nesting habitat for many of these species, but may enhance feeding habitat of migrant shorebirds and/or migrant or wintering waterfowl. At scales of 50?100 yr, reversion of marsh island complexes to open water may enhance populations of open-bay waterfowl, e.g., Bufflehead (Bucephala albeola) and Canvasback (Aythya valisneria), but reduce nesting habitats dramatically for the above named marsh-nesting species, may reduce estuarine productivity by loss of the detrital food web and nursery habitat for fish and invertebrates, and cause redistribution of waterfowl, shorebirds, and other species. Such scenarios are more likely to occur in the mid- and north Atlantic regions since these estuaries are lower in sediment delivery on average than those in the Southeast. A simple hypothetical example from New Jersey is presented where waterbirds are forced to shift from submerged natural marshes to nearby impoundments, resulting in roughly a 10-fold increase in density. Whether prey fauna are sufficiently abundant to support this level of increase remains an open question, but extreme densities in confined habitats would exacerbate competition, increase disease risk, and possibly increase predation.