Science.gov

Sample records for earwig anisolabis maritima

  1. Provisioning Mass by Females of the Maritime Earwig, Anisolabis maritima, is not Adjusted Based on the Number of Young

    PubMed Central

    Suzuki, Seizi

    2011-01-01

    The amount of parental provisioning is thought to reflect the need of offspring. This hypothesis was tested in the case of provisioning food mass to young with controlled clutch size using the maritime earwig, Anisolabis maritima Bonelli (Dermaptera: Anisolabididae). The female provisioned a constant mass of food to the young irrespective of the number of nymphs and the distance of food carrying. In addition, the survival rate of young did not change with adjusted clutch size. This study showed that A. maritima females appear to provide food mass to their nymphs independent of their number. PMID:22239204

  2. 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

  3. 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

  4. 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

  5. Earwig management tool: an IPM decision aid system for augmentation of European earwig populations (Dermaptera: Forficulidae) in pip fruit orchards.

    PubMed

    Beliën, T; Moerkens, R; Leirs, H; Peusens, G

    2012-01-01

    A key element of integrated pest management (IPM) is the suppression of potential pest outbreaks by beneficial arthropods. The European earwig, Forficula auricularia L., is an important natural enemy of a wide range of insect pests in pip fruit orchards. However, earwig population sizes vary greatly from location to location, illustrating their sensitivity to biotic and abiotic factors, especially human interventions relating to orchard management. In order to help growers sparing and augmenting earwig populations in their pip fruit orchards, we developed a software tool that integrates a sophisticated earwig phenology model with management recommendations. The program is based on a day degree model for earwigs which is fed by temperature data collected by the pcfruit research centre. In addition, a pesticide database with known side effects of a wide range of products on the different life stages of earwigs is integrated in the system. The output gives the current status of the earwig population and management recommendations for activities critical for their survival. Hence, by consultation of this user-friendly software fruit growers can predict the earwig development in the field at any time, and organize the timing of orchard management actions taking into account the presence of (sensitive) life stages of the earwig life cycle. Doing so, negative effects specific orchard management actions, such as badly timed spray applications and soil tillage, can be avoided. PMID:23885434

  6. 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...

  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. 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...

  10. 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

  11. Contact Toxicity and Residual Efficacy of Indoxacarb against the European Earwig (Dermaptera: Forficulidae)

    PubMed Central

    Jones, Susan C.; Bryant, Joshua L.

    2012-01-01

    Indoxacarb (Arilon 20WG) was evaluated against a nuisance pest, the European earwig (Forficula auricularia), and was found to be an effective contact toxicant with residual activity on substrates commonly encountered in urban environments. Within 16 h of being directly sprayed with indoxacarb, ?90% of earwigs from two populations were either ataxic, moribund, or dead, and 100% displayed these symptoms of severe intoxication at 1 d. Brief exposure (5 min or 1 h) to dried residues on either a porous (pine wood) or non-porous (ceramic tile) substrate also was sufficient to cause severe intoxication of earwigs within 1 d. In all bioassays, indoxacarb-treated earwigs showed no signs of recovery during the 21-d observation period. In outdoor urban habitats, intoxicated earwigs would be more vulnerable to desiccation, predation, or pathogens leading to higher mortality than in a laboratory setting. PMID:26466616

  12. Contact Toxicity and Residual Efficacy of Indoxacarb against the European Earwig (Dermaptera: Forficulidae).

    PubMed

    Jones, Susan C; Bryant, Joshua L

    2012-01-01

    Indoxacarb (Arilon 20WG) was evaluated against a nuisance pest, the European earwig (Forficula auricularia), and was found to be an effective contact toxicant with residual activity on substrates commonly encountered in urban environments. Within 16 h of being directly sprayed with indoxacarb, ?90% of earwigs from two populations were either ataxic, moribund, or dead, and 100% displayed these symptoms of severe intoxication at 1 d. Brief exposure (5 min or 1 h) to dried residues on either a porous (pine wood) or non-porous (ceramic tile) substrate also was sufficient to cause severe intoxication of earwigs within 1 d. In all bioassays, indoxacarb-treated earwigs showed no signs of recovery during the 21-d observation period. In outdoor urban habitats, intoxicated earwigs would be more vulnerable to desiccation, predation, or pathogens leading to higher mortality than in a laboratory setting. PMID:26466616

  13. Earwigs ( Labidura riparia) mimic rotting-flesh odor to deceive vertebrate predators

    NASA Astrophysics Data System (ADS)

    Byers, John A.

    2015-08-01

    Many insects repel predators with caustic chemicals, while insects mimicking odors of wastes/dead insects to fool predators have not been documented. We found that the shore earwig, Labidura riparia (Dermaptera: Labiduridae) when bitten by anole lizards, Anolis carolinenesus, spits a rotting-flesh odor that deceives these insectivores into rejecting prey. Once a lizard attacked and rejected an earwig, the lizard did not attack another earwig during several weeks despite consuming other prey, indicating associative learning after one trial. The fetid odor was found in the head-prothorax containing salivary glands of both male and female earwigs and was comprised of ˜100 ng dimethyl disulfide and ˜600 ng dimethyl trisulfide. Nymphs had <5 ng of either compound. Adults also spit odorous sulfides after prolonged attacks by harvester ants, Pogonomyrmex rugosus, who were only deterred by the earwig's forceps. Sulfides released by the earwig are similar to odors of carrion/feces, which may be innately repulsive to some vertebrate predators. The mean initial discharge percentage (IDP) of sulfides from a cohort of earwigs was 62 %; however, IDPs of individuals were highly variable (3-99 %; mean 57 %). The discharge refill time (DRT) to refill 50 % of the earwig's allomone reservoir was estimated at 13 h. A positive relationship in sulfide amounts with body weight was found only in females in 2009, suggesting metabolic cost tradeoffs were revealed when sulfide content was half that in 2010. This is the first report of insects releasing sulfur-containing compounds that may mimic carrion-fecal odors as a deceptive defense against vertebrate predators.

  14. Earwigs (Labidura riparia) mimic rotting-flesh odor to deceive vertebrate predators.

    PubMed

    Byers, John A

    2015-08-01

    Many insects repel predators with caustic chemicals, while insects mimicking odors of wastes/dead insects to fool predators have not been documented. We found that the shore earwig, Labidura riparia (Dermaptera: Labiduridae) when bitten by anole lizards, Anolis carolinenesus, spits a rotting-flesh odor that deceives these insectivores into rejecting prey. Once a lizard attacked and rejected an earwig, the lizard did not attack another earwig during several weeks despite consuming other prey, indicating associative learning after one trial. The fetid odor was found in the head-prothorax containing salivary glands of both male and female earwigs and was comprised of ? 100 ng dimethyl disulfide and ? 600 ng dimethyl trisulfide. Nymphs had <5 ng of either compound. Adults also spit odorous sulfides after prolonged attacks by harvester ants, Pogonomyrmex rugosus, who were only deterred by the earwig's forceps. Sulfides released by the earwig are similar to odors of carrion/feces, which may be innately repulsive to some vertebrate predators. The mean initial discharge percentage (IDP) of sulfides from a cohort of earwigs was 62 %; however, IDPs of individuals were highly variable (3-99 %; mean 57 %). The discharge refill time (DRT) to refill 50 % of the earwig's allomone reservoir was estimated at 13 h. A positive relationship in sulfide amounts with body weight was found only in females in 2009, suggesting metabolic cost tradeoffs were revealed when sulfide content was half that in 2010. This is the first report of insects releasing sulfur-containing compounds that may mimic carrion-fecal odors as a deceptive defense against vertebrate predators. PMID:26071006

  15. European earwig (Forficula auricularia) as a novel host for the entomopathogenic nematode Steinernema carpocapsae.

    PubMed

    Hodson, A K; Friedman, M L; Wu, L N; Lewis, E E

    2011-05-01

    The natural history of many entomopathogenic nematode species remains unknown, despite their wide commercial availability as biological control agents. The ambushing entomopathogenic nematode, Steinernema carpocapsae, and the introduced European earwig, Forficula auricularia, forage on the soil surface. Since they likely encounter one another in nature, we hypothesized that earwigs are susceptible to nematode infection. In the laboratory, the LC(50) for F. auricularia was 226 S. carpocapsae/earwig and the reproductive potential was 123.5 infective juvenile nematodes/mg tissue. This susceptibility depended on host body size with significantly higher mortality rates seen in larger earwigs. In a study of host recognition behavior, S. carpocapsae infective juveniles responded to earwig cuticle as strongly as they did to Galleria mellonella cuticle. We also found that earwigs exposed to S. carpocapsae cleaned and scratched their front, middle and back legs significantly more than controls. Coupled with previous field data, these findings lead us to suggest that F. auricularia may be a potential host for S. carpocapsae. PMID:21356215

  16. Impact of insecticide exposure on the predation activity of the European earwig Forficula auricularia.

    PubMed

    Malagnoux, Laure; Capowiez, Yvan; Rault, Magali

    2015-09-01

    The European earwig Forficula auricularia is an effective predator in apple orchards. It is therefore crucial to study whether insecticides affect this natural pest control agent. Predation activity, i.e., the number of aphids eaten in 24 h, was determined under laboratory conditions after exposure of fourth-instar nymphs and adult earwigs to widely used insecticides (acetamiprid, chlorpyrifos-ethyl, deltamethrin, and spinosad), which were applied at the normal application rates. Inhibition of acetylcholinesterase and carboxylesterase activities were also measured as indicators of pesticide exposure. Predation activity decreased significantly in nymphs exposed to spinosad (62%) and chlorpyrifos-ethyl (98%) compared with controls. A similar response was found for both esterase activities. Spinosad had a stronger effect on AChE (-33%) whereas chlorpyrifos-ethyl affected CbE activity preferentially (-59%). Spinosad (20% of controls), acetamiprid (28%), and chlorpyrifos-ethyl (66%) also significantly decreased the predation behavior of adult male but not female (5 to 40%) earwigs. Adult AChE and CbE activities were also significantly reduced (28 to 67% of controls) in pesticide-exposed earwigs. Our results suggest that earwigs should be included in the environmental risk assessment framework for authorization of newly marketed plant protection products. Their predation behavior appears to be a sensitive and complementary biomarker. PMID:25963069

  17. 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

  18. Tissue distribution, characterization and in vitro inhibition of B-esterases in the earwig Forficula auricularia.

    PubMed

    Malagnoux, Laure; Capowiez, Yvan; Rault, Magali

    2014-10-01

    Earwigs are important natural enemies of numerous pests in pome fruit orchards worldwide. Studying the effects of agricultural practices on these biological control agents is important for understanding its vulnerability in the field. The aim of this study was to characterize the B-esterase activities in the European earwig Forficula auricularia and to evaluate in vitro its sensitivity to organophosphate and carbamate pesticides. Acetylcholinesterase (AChE) activity was mainly measured with 1.5 mM acetylthiocholine as the substrate in the microsomal fraction of earwig heads (70% of total AChE activity). Carboxylesterase (CbE) activities were measured with three substrates [5 mM 4-nitrophenyl acetate (4-NPA), 1mM 4-nitrophenyl valerate (4-NPV), and 2 mM ?-naphtyl acetate (?-NA)] to examine different isoenzymes, which were present mainly in the cytosolic fraction (about 70-88% of total activities) of all earwig tissues. CbE activity was higher than AChE activity, especially with ?-NA, then 4-NPA and lastly 4-NPV. Chlorpyrifos-oxon an organophosphate, and carbaryl a carbamate pesticide, inhibited AChE and CbE activities in a concentration-dependent manner. Earwig CbE activities showed a stronger sensitivity to organophosphate than AChE, with the strongest effect for chlorpyrifos-oxon on male carboxylesterase activities. CbE and AChE showed about the same sensitivity to carbamate pesticides regardless of sex. These results suggest that B-type esterases in the European earwig F.auricularia are suitable biomarkers of pesticide exposure. PMID:25048940

  19. 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

  20. 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

    ...We, the U.S. Fish and Wildlife Service (Service), determine endangered status under the Endangered Species Act of 1973, as amended (Act), for two species of Hawaiian damselflies, the flying earwig Hawaiian damselfly (Megalagrion nesiotes) on the island of Maui and the Pacific Hawaiian damselfly (M. pacificum) on the islands of Hawaii, Maui, and Molokai. This final rule implements the Federal......

  1. The Temperature Dependent Proteomic Analysis of Thermotoga maritima

    PubMed Central

    Wang, Quanhui; Bai, Xue; Chen, Zhen; Zhao, Jingjing; Xu, Ningzhi; Liu, Siqi

    2012-01-01

    Thermotoga maritima (T. maritima) is a typical thermophile, and its proteome response to environmental temperature changes has yet to be explored. This study aims to uncover the temperature-dependent proteins of T. maritima using comparative proteomic approach. T. maritima was cultured under four temperatures, 60°C, 70°C, 80°C and 90°C, and the bacterial proteins were extracted and electrophoresed in two-dimensional mode. After analysis of gel images, a total of 224 spots, either cytoplasm or membrane, were defined as temperature-dependent. Of these spots, 75 unique bacterial proteins were identified using MALDI TOF/TOF MS. As is well known, the chaperone proteins such as heat shock protein 60 and elongation factor Tu, were up-regulated in abundance due to increased temperature. However, several temperature-dependent proteins of T. maritima responded very differently when compared to responses of the thermophile T. tengcongensis. Intriguingly, a number of proteins involved in central carbohydrate metabolism were significantly up-regulated at higher temperature. Their corresponding mRNA levels were elevated accordingly. The increase in abundance of several key enzymes indicates that a number of central carbohydrate metabolism pathways of T. maritima are activated at higher temperatures. PMID:23071576

  2. A "spare" compensates for the risk of destruction of the elongated penis of earwigs (Insecta: Dermaptera)

    NASA Astrophysics Data System (ADS)

    Kamimura, Yoshitaka; Matsuo, Yoh

    2001-11-01

    Male animals in several groups have multiple intromittent organs that outnumber the corresponding female gonopore. In Dermaptera (earwigs), males of the family Anisolabididae have paired, elongated male intromittent organs (virgae), while females have a single sperm-storage organ (spermatheca). Several authors have assumed that one of the paired virgae is non-functional, because it points in the "wrong" direction. We investigated the mating success of handicapped males of Euborellia plebeja in which one of their paired virgae was removed experimentally. These handicapped males succeeded in inseminating a mate. Males with genital damage are found in the field, suggesting that the "spare" functions under natural conditions. Based on phylogenetic information on earwigs, we discuss possible evolutionary scenarios for this genital peculiarity.

  3. 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

  4. When the body hides the ancestry: phylogeny of morphologically modified epizoic earwigs based on molecular evidence.

    PubMed

    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

  5. 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

  6. Abiotic modulation of Spartina maritima photobiology in different latitudinal populations

    NASA Astrophysics Data System (ADS)

    Duarte, B.; Couto, T.; Freitas, J.; Valentim, J.; Silva, H.; Marques, J. C.; Dias, J. M.; Caçador, I.

    2013-09-01

    Spartina maritima has a very wide distribution in the northern hemisphere salt marshes crossing a wide variety of climatic environments. Therefore, it is not strange that some differences arise when observing the photosynthetic mechanisms of different populations inhabiting different latitudes. During this study it could be observed that climate is the most important factor controlling the photosynthetic traits of different populations distributed along a climatic gradient, namely the air temperature, humidity and light environment. Also some sediment physicochemical parameters such as pH and pore water salinity showed important influences driving the photosynthetic mechanisms in S. maritima. Furthermore S. maritima is one of the most abundant halophytes colonizing the Portuguese salt marshes. These facts have greater importance if one considers the large abundance of this halophytic species and how climate change will affect their metabolism and thus the ecosystem services provided by this species to the estuarine system.

  7. 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

  8. 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

  9. Side effects of plant protection products and biological interactions on the European earwig Forficula auricularia L.

    PubMed

    Peusens, G; Moerkens, R; Beliën, T; Gobin, B

    2009-01-01

    Plant protection products are designed to control pests but can have negative side effects on non-target arthropods thus disturbing the important population of natural enemies required for biological control. Although the European earwig, Forficula auricularia L, (Dermaptera: Forficulidae) is not considered to be a key beneficial in pome fruit, it is an important predator of several pests, e.g. woolly apple aphid and pear sucker. The impact of non-selective plant protection products at crucial moments in their (univoltine) life cycle can be of significant relevance compared to insects with numerous generations. Foliar applications in spring when nymphs are migrating into the trees can reduce the number of adults in summer and subsequently affect the population size next year. Multiple and/or combined spraying during summer on adults may have a cumulative effect resulting in less over wintering females which possibly exhibit poor reproductive performance. Previous residual contact bioassays already revealed the harmful side effect of several formulated products on adults. Insects showing sub lethal symptoms recovered partially or died eventually. As spinosad caused significant toxicological effects it was subsequently tested in 3 different dose rates on adults and N4-nymphs. We noticed not only a clear dose-response relationship but N4-nymphs proved to be more susceptible than adults; even a dilution of 1/9-th of the registered dose rate still caused a mortality of 45.5 % after 20 days. Understanding the earwig's population dynamics is essential for efficient practical biocontrol. It proves difficult to increase population levels to sufficient high numbers for optimal pest control. Local biological factors might be limiting. Therefore, we tested two hypotheses that pertain to population limitation: 1. Bird predation during summer, 2. Small mammal nest predation during winter. Enclosure experiments showed no negative bird effect on earwig densities unless large bird flocks inhabited the area. Small mammals did not actively predate the over wintering nests, although other predatory arthropods may be important. PMID:20222599

  10. 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.

  11. 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...

  12. Wigeongrass (Ruppia maritima L.): a literature review

    USGS Publications Warehouse

    Kantrud, H.A.

    1991-01-01

    Wigeongrass (Ruppia maritima L.) is a submersed macrophyte of nearly cosmopolitan distribution and worldwide importance as a waterfowl food. Unfortunately, the plant no longer inhabits vast areas disturbed by human activities. Taxonomic status of the plant is uncertain, especially in North America. In mild climates, in habitats subject to environmental extremes, the plant behaves as an annual (vegetation perishes), or as a perennial in deeper, more stable habitats (some vegetative parts grow year round). Drupelets (seeds) provide a mechanism for wigeongrass to survive periods of drought and excessive water salinity. These sexual propagules can be washed ashore or carried by birds or fish for long distances.Wigeongrass mostly occurs in temporarily to permanently flooded mesohaline-hyperhaline estuarine wetlands, but it also occurs inland in fresh to hypersaline palustrine and lacustrine wetlands. Most populations inhabit warm, relatively unpolluted, and well lit waters 2S conditions. Turbidity frequently limits wigeongrass growth in waters overlying easily suspendible bottom substrates.Wigeongrass often occurs in monotypic stands, yet grows with many other submersed and emergent macrophytes. Dominance in certain wetlands sometimes alternates with dominance by other submersed macrophytes as salinities, seasonal temperature cycles, or other environmental factors change. The shading effect of metaphytic, planktonic, or epiphytic algae often reduces production.Wigeongrass and its detritus provide food and cover for a large invertebrate biota, although direct consumption of the living plants is minimal. Wigeongrass beds in coastal wetlands are heavily used by fish. The plant is recognized worldwide as an important food of migrant and wintering waterfowl, wading birds, and shorebirds. In subtropical climates, wintering waterfowl can quickly consume entire stands.Propagation and management of wigeongrass has occurred for nearly 60 years in the southern and eastern United States. During the seventies and eighties, sophisticated water level and salinity management techniques have been developed to encourage growth of the plant.Future research should concentrate on determining the means to reduce light-limiting turbidity in many wetland types; understanding the ways in which human activities on and near wetlands affect wigeongrass production; and developing reliable and predictable techniques to stimulate wigeongrass production by water level manipulations and other means in different environmental settings. Trophic interactions and the effects of biomanipulation of fish populations in managed wigeongrass habitat--now little understood--also require more study.

  13. Male-male competition and large size mating advantage in European earwigs, Forficula auricularia.

    PubMed

    Forslund

    2000-04-01

    European earwigs are sexually dimorphic in forceps shape and length. Male forceps are thought to be weapons in male contests for access to females, but recent findings suggest that females choose males on the basis of their forceps length. I investigated sexual selection on forceps length and body size and the occurrence of male-male competition. When I controlled for forceps length experimentally and statistically, relatively heavy males had greater copulation success than relatively light males. When I controlled for body size, males with relatively longer forceps had no tendency for greater copulation success than males with shorter forceps. Relatively heavy males more often took over copulations from smaller males than vice versa. Male contests were important for the outcome of mate competition, as males commonly interrupted and took over copulations. My results therefore suggest that intrasexual selection is significant in competition for copulations in male earwigs, and acts on body size. This contrasts with previous findings, which have shown intersexual selection on forceps length to be important. However, both modes of sexual selection may be acting through a two-stage process, where male-male competition first determines which males have access to females, and then through female choice among available males. Morphological measurements supported the conclusion that forceps length and body size are male secondary sexual characters, as these characters had large variance and skewed distributions in males, but were normally distributed in females. Copyright 2000 The Association for the Study of Animal Behaviour. PMID:10792930

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

    PubMed

    Tomkins; Simmons

    1998-08-01

    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 three of four populations of the European earwig, Forficula auricularia, females mated sooner with males with longer forceps although there was no female preference based on forceps asymmetry. We isolated the potentially confounding influences of forceps length and asymmetry by independently manipulating each trait. Manipulations of forceps length confirmed that females preferred males with longer forceps. However, manipulations of asymmetry revealed that although females pay attention to forceps condition, they show no preferences based on asymmetry. No relationships were found between the length and asymmetry of forceps in field populations, and there were no differences in condition between symmetrical and asymmetrical males. Our results are consistent with the notion that female choice has contributed to the sexual dimorphism in earwig forceps. However, they refute the notion that fluctuating asymmetry plays a role in sexual selection. Copyright 1998 The Association for the Study of Animal Behaviour PMID:9787025

  15. 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

  16. Pheromonal basis of aggregation in European earwig,Forficula auricularia L. (Dermaptera: Forficulidae).

    PubMed

    Walker, K A; Jones, T H; Fell, R D

    1993-09-01

    The aggregation behavior of the European earwigForficula auricularia was investigated. Bioassays of frass extracts, cuticular washings, and the defensive exudate have been conducted to locate the source of an aggregation pheromone, and aggregation behavior has been demonstrated with extracts of frass and the washings of male cuticular lipids. Chemical investigations revealed the presence of a unique pattern of typical normal, monomethyl-, and dimethylalkanes, along with a series of fatty acids and the well-known defensive quinones from these insects. It has been concluded from the bioassays of a number of authentic compounds and the lack of a chemically discernible difference between male and female extracts that the aggregation pheromone ofF. auricularia is quite probably a minor component of the male cuticular lipids. PMID:24249377

  17. 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...

  18. Synergistic TRAIL sensitizers from Barleria alluaudii and Diospyros maritima#

    PubMed Central

    Whitson, Emily L.; Sun, Han; Thomas, Cheryl L.; Henrich, Curtis J.; Sayers, Thomas J.; McMahon, James B.; Griesinger, Christian; McKee, Tawnya C.

    2012-01-01

    Barleria alluaudii and Diospyros maritima were both investigated as part of an ongoing search for synergistic TRAIL (tumor necrosis factor-?-related apoptosis-inducing ligand) sensitizers. As a result of this study, two naphthoquinone epoxides, 2,3-epoxy-2,3-dihydrolapachol (1) and 2,3-epoxy-2,3-dihydro-8-hydroxylapachol (2), both not previously isolated from natural sources, and the known 2-methyl anthraquinone (3) were identified from B. alluaudii. Time-dependent density functional theory (TD-DFT) calculations of electronic circular dichroism (ECD) spectra were utilized to establish the absolute configuration of 1 and 2. Additionally, five known naphthoquinone derivatives, maritinone (4), elliptinone (5), plumbagin (6), (+)-cis-isoshinanolone (7), and ethylidene-6,6?-biplumbagin (8) were isolated from D. maritima. Compounds 1, 2, and 4–6 showed varying levels of synergy with TRAIL. Maritinone (4) and elliptinone (5) showed the highest synergistic effect, with more than a three-fold increase in activity observed with TRAIL than with compound alone. PMID:22313254

  19. Maternal care, mother-offspring aggregation and age-dependent coadaptation in the European earwig.

    PubMed

    Gómez, Y; Kölliker, M

    2013-09-01

    Benefits and costs of parental care are expected to change with offspring development and lead to age-dependent coadaptation expressed as phenotypic (behavioural) matches between offspring age and parental reproductive stage. Parents and offspring interact repeatedly over time for the provision of parental care. Their behaviours should be accordingly adjusted to each other dynamically and adaptively, and the phenotypic match between offspring age and parental stage should stabilize the repeated behavioural interactions. In the European earwig (Forficula auricularia), maternal care is beneficial for offspring survival, but not vital, allowing us to investigate the extent to which the stability of mother-offspring aggregation is shaped by age-dependent coadaptation. In this study, we experimentally cross-fostered nymphs of different age classes (younger or older) between females in early or late reproductive stage to disrupt age-dependent coadaptation, thereby generating female-nymph dyads that were phenotypically matched or mismatched. The results revealed a higher stability in aggregation during the first larval instar when care is most intense, a steeper decline in aggregation tendency over developmental time and a reduced developmental rate in matched compared with mismatched families. Furthermore, nymph survival was positively correlated with female-nymph aggregation stability during the early stages when maternal care is most prevalent. These results support the hypothesis that age-related phenotypically plastic coadaptation affects family dynamics and offspring developmental rate. PMID:23937357

  20. Sibling cooperation in earwig families provides insights into the early evolution of social life.

    PubMed

    Falk, Joachim; Wong, Janine W Y; Kölliker, Mathias; Meunier, Joël

    2014-04-01

    The evolutionary transition from solitary to social life is driven by direct and indirect fitness benefits of social interactions. Understanding the conditions promoting the early evolution of social life therefore requires identification of these benefits in nonderived social systems, such as animal families where offspring are mobile and able to disperse and will survive independently. Family life is well known to provide benefits to offspring through parental care, but research on sibling interactions generally focused on fitness costs to offspring due to competitive behaviors. Here we show experimentally that sibling interactions also reflect cooperative behaviors in the form of food sharing in nonderived families of the European earwig, Forficula auricularia. Food ingested by individual offspring was transferred to their siblings through mouth-to-anus contacts and active allo-coprophagy. These transfers occurred in both the presence and the absence of the tending mothers, even though the direct contact with the mothers limited sibling food sharing. Neither food deprivation or relatedness influenced the total amount of transferred food, but relatedness affected frass release and the behavioral mechanisms mediating food sharing. Related offspring obtained food predominately through allo-coprophagy, whereas unrelated offspring obtained food through mouth-to-anus contacts. Overall, this study emphasizes that sibling cooperation may be a key process promoting the early evolution of social life. PMID:24642498

  1. Effect of Oxygen and Redox Potential on Glucose Fermentation in Thermotoga maritima under Controlled Physicochemical Conditions

    PubMed Central

    Lakhal, Raja; Auria, Richard; Davidson, Sylvain; Ollivier, Bernard; Dolla, Alain; Hamdi, Moktar; Combet-Blanc, Yannick

    2010-01-01

    Batch cultures of Thermotoga maritima were performed in a bioreactor equipped with instruments adapted for experiments performed at 80°C to mimic the fluctuating oxidative conditions in the hot ecosystems it inhabits. When grown anaerobically on glucose, T. maritima was shown to significantly decrease the redox potential (Eh) of the culture medium down to about ?480?mV, as long as glucose was available. Addition of oxygen into T. maritima cultures during the stationary growth phase led to a drastic reduction in glucose consumption rate. However, although oxygen was toxic, our experiment unambiguously proved that T. maritima was able to consume it during a 12-hour exposure period. Furthermore, a shift in glucose metabolism towards lactate production was observed under oxidative conditions. PMID:21461371

  2. Efficient harvesting of marine microalgae Nannochloropsis maritima using magnetic nanoparticles.

    PubMed

    Hu, Yi-Ru; Wang, Feng; Wang, Shi-Kai; Liu, Chun-Zhao; Guo, Chen

    2013-06-01

    An efficient magnetic separation technology using Fe(3)O(4) nanoparticles was developed for harvesting marine microalgae Nannochloropsis maritima from culture broth. Recovery capacity of these nanoparticles was affected by microalgal growth phase and reached the peak value when the microalgal growth reached its maximal biomass after 18 days. The recovery efficiency of microalgal cells from the culture medium reached more than 95% at the particle dosage of 120 mg/L within 4 min. Electrostatic attraction at acidic pH and cell aggregation under neutral and alkaline conditions was beneficial for harvesting the algal cells. Higher operation temperature resulted in higher adsorption capacity of these nanoparticles for microalgawl cells. Reuse of the culture medium obtained from magnetic separation gave similar biomass production in comparison with that from centrifugation separation after 5 recycles. Together with these results provide a great potential in high-efficient and economical harvesting of tiny marine microalgae using magnetic separation technology in practice. PMID:23639490

  3. Quinone- and nitroreductase reactions of Thermotoga maritima thioredoxin reductase.

    PubMed

    Valiauga, Benjaminas; Rouhier, Nicolas; Jacquot, Jean-Pierre; Čėnas, Narimantas

    2015-01-01

    The Thermotoga maritima NADH:thioredoxin reductase (TmTR) contains FAD and a catalytic disulfide in the active center, and uses a relatively poorly studied physiological oxidant Grx-1-type glutaredoxin. In order to further assess the redox properties of TmTR, we used series of quinoidal and nitroaromatic oxidants with a wide range of single-electron reduction potentials (E(1)7, -0.49-0.09 V). We found that TmTR catalyzed the mixed single- and two-electron reduction of quinones and nitroaromatic compounds, which was much faster than the reduction of Grx-1. The reactivity of both groups of oxidants increased with an increase in their E(1)7, thus pointing to the absence of their structural specificity. The maximal rates of quinone reduction in the steady-state reactions were lower than the maximal rates of reduction of FAD by NADH, obtained in presteady-state experiments. The mixed-type reaction inhibition by NAD(+) was consistent with its competition for a NADH binding site in the oxidized enzyme form, and also with the reoxidation of the reduced enzyme form. The inhibition data yielded a value of the standard potential for TmTR of -0.31±0.03 V at pH 7.0, which may correspond to the FAD/FADH2 redox couple. Overall, the mechanism of quinone- and nitroreductase reactions of T. maritima TR was similar to the previously described mechanism of Arabidopsis thaliana TR, and points to their prooxidant and possibly cytotoxic role. PMID:26098718

  4. 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.

  5. When it is costly to have a caring mother: food limitation erases the benefits of parental care in earwigs.

    PubMed

    Meunier, Joël; Kölliker, Mathias

    2012-08-23

    The aggregation of parents with offspring is generally associated with different forms of care that improve offspring survival at potential costs to parents. Under poor environments, the limited amount of resources available can increase the level of competition among family members and consequently lead to adaptive changes in parental investment. However, it remains unclear as to what extent such changes modify offspring fitness, particularly when offspring can survive without parents such as in the European earwig, Forficula auricularia. Here, we show that under food restriction, earwig maternal presence decreased offspring survival until adulthood by 43 per cent. This effect was independent of sibling competition and was expressed after separation from the female, indicating lasting detrimental effects. The reduced benefits of maternal presence on offspring survival were not associated with higher investment in future reproduction, suggesting a condition-dependent effect of food restriction on mothers and local mother-offspring competition for food. Overall, these findings demonstrate for the first time a long-term negative effect of maternal presence on offspring survival in a species with maternal care, and highlight the importance of food availability in the early evolution of family life. PMID:22535642

  6. When it is costly to have a caring mother: food limitation erases the benefits of parental care in earwigs

    PubMed Central

    Meunier, Joël; Kölliker, Mathias

    2012-01-01

    The aggregation of parents with offspring is generally associated with different forms of care that improve offspring survival at potential costs to parents. Under poor environments, the limited amount of resources available can increase the level of competition among family members and consequently lead to adaptive changes in parental investment. However, it remains unclear as to what extent such changes modify offspring fitness, particularly when offspring can survive without parents such as in the European earwig, Forficula auricularia. Here, we show that under food restriction, earwig maternal presence decreased offspring survival until adulthood by 43 per cent. This effect was independent of sibling competition and was expressed after separation from the female, indicating lasting detrimental effects. The reduced benefits of maternal presence on offspring survival were not associated with higher investment in future reproduction, suggesting a condition-dependent effect of food restriction on mothers and local mother–offspring competition for food. Overall, these findings demonstrate for the first time a long-term negative effect of maternal presence on offspring survival in a species with maternal care, and highlight the importance of food availability in the early evolution of family life. PMID:22535642

  7. Cytotoxic constituents from the stems of Diospyros maritima.

    PubMed

    Kuo, Y H; Chang, C I; Li, S Y; Chou, C J; Chen, C F; Kuo, Y H; Lee, K H

    1997-08-01

    One novel coumaric acid ester of lupeol, dioslupecin A (1), three naphthoquinones, 8'-hydroxyisodiospyrin (2), isodiospyrin (3), and plumbagin (4), three triterpenes, lupeol, lupenone and taraxerone, and four sterols, beta-sitosterol, stigmasterol, stigmast-4-en-3-one and ergosta-4,6,8(14),22-tetraen-3-one were isolated from the n-hexane extract of the stems of Diospyros maritima Blume. The structural determination of 1 was based on 1D and 2D NMR spectra (including 1H-1H COSY, 1H-13C COSY, and HMBC). All compounds were evaluated for in vitro cytotoxicity in 4 cancer cell lines. Compound 2 showed similar cytotoxicity against hepatoma (HEPA-3B, ED50 = 1.72 micrograms/ml), nasopharynx carcinoma (KB, ED50 = 1.85 micrograms/ml), colon carcinoma (COLO-205, ED50 = 2.24 micrograms/ml) and cervical carcinoma (HELA, ED50 = 1.92 micrograms/ml). Compounds 3 and 4 exhibited strong cytotoxicity against HEPA-3B, KB, COLO-205 and HELA (ED50 = 0.25, 1.81, 0.13 and 0.27 micrograms/ml for 3; ED50 = 0.87, 3.27, 0.56 and 0.35 micrograms/ml for 4, respectively. PMID:9270382

  8. Contribution of Spartina maritima to the reduction of eutrophication in estuarine systems.

    PubMed

    Sousa, Ana I; Lillebø, Ana I; Caçador, Isabel; Pardal, Miguel A

    2008-12-01

    Salt marshes are among the most productive ecosystems in the world, performing important ecosystem functions, particularly nutrient recycling. In this study, a comparison is made between Mondego and Tagus estuaries in relation to the role of Spartina maritima in nitrogen retention capacity and cycling. Two mono-specific S. maritima stands per estuary were studied during 1yr (biomass, nitrogen (N) pools, litter production, decomposition rates). Results showed that the oldest Tagus salt marsh population presented higher annual belowground biomass and N productions, and a slower decomposition rate for litter, contributing to the higher N accumulation in the sediment, whereas S. maritima younger marshes had higher aboveground biomass production. Detritus moved by tides represented a huge amount of aboveground production, probably significant when considering the N balance of these salt marshes. Results reinforce the functions of salt marshes as contributing to a reduction of eutrophication in transitional waters, namely through sedimentation processes. PMID:18684544

  9. POLYMERIZATION PROPERTIES OF THE T. MARITIMA ACTIN, MreB

    PubMed Central

    Bean, Greg J.; Amann, Kurt J.

    2008-01-01

    MreB is a bacterial ortholog of actin that affects cell shape, polarity and chromosome segregation. Although a significant body of work has explored its cellular functions, we know very little about the biochemical behavior of MreB. We have cloned, overexpressed in E. coli, and purified untagged MreB1 from Thermotoga maritima. We have characterized the conditions that regulate its monomer-to-polymer assembly reaction, the critical concentrations of that reaction, the manner in which MreB uses nucleotides, its stability, and the structure of the assembled polymer. MreB requires a bound purine nucleotide for polymerization and rapidly hydrolyzes it following assembly. MreB assembly contains two distinct components, one that does not require divalent cations and one that does, which may comprise the nucleation and elongation phases of assembly, respectively. MreB assembly is strongly favored by increasing temperature or protein concentration but inhibited differentially by high concentrations of monovalent salts. Polymerization rate increases and bulk critical concentration decreases with increasing temperature, but in contrast to previous reports, MreB is capable of polymerizing across a broad range of temperatures. MreB polymers are shorter, stiffer, and scatter more light than eukaryotic actin filaments. Due to rapid ATP hydrolysis and phosphate release, we suggest that most assembled MreB in cells is in the ADP-bound state. Because of only moderate differences between the ATP and ADP critical concentrations, treadmilling may occur, but we do not predict dynamic instability in cells. Because of the relatively low cellular concentration of MreB and the observed structural properties of the polymer, a single MreB assembly may exist in cells. PMID:18095710

  10. 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

  11. Characterization of the Thermotoga maritima Chemotaxis Methylation System that Lacks Methyltransferase CheR:MCP Tethering

    PubMed Central

    Perez, Eduardo; Stock, Ann M.

    2013-01-01

    Summary Sensory adaptation in bacterial chemotaxis is mediated by covalent modifications of specific glutamate and glutamine residues within the cytoplasmic domains of methyl-accepting proteins (MCPs). In Escherichia coli and Salmonella enterica, efficient methylation of MCPs depends on the localization of methyltransferase CheR to MCP clusters through an interaction between the CheR ?-subdomain and a pentapeptide sequence (NWETF or NWESF) at the C terminus of the MCP. In vitro methylation analyses utilizing S. enterica and Thermotoga maritima CheR proteins and MCPs indicate that MCP methylation in T. maritima occurs independently of a pentapeptide-binding motif. Kinetic and binding measurements demonstrate that despite efficient methylation, the interaction between T. maritima CheR and T. maritima MCPs is of relatively low affinity. Comparative protein sequence analyses of CheR ?-subdomains from organisms having MCPs that contain and/or lack pentapeptide-binding motifs identified key similarities and differences in residue conservation, suggesting the existence of two distinct classes of CheR proteins: pentapeptide-dependent and pentapeptide-independent methyltransferases. Analysis of MCP C-terminal ends showed that only ~10% of MCPs contain a putative C-terminal binding motif, the majority of which are restricted to the different proteobacteria classes (?, ?, ?, ?). These findings suggest that tethering of CheR to MCPs is a relatively recent event in evolution and that the pentapeptide-independent methylation system is more common than the well characterized pentapeptide-dependent methylation system. PMID:17163981

  12. Draft Genome Sequence of a Heterotrophic Facultative Anaerobic Thermophilic Bacterium, Ardenticatena maritima Strain 110ST

    PubMed Central

    Yoshida, Takashi; Nakamura, Ryuhei

    2015-01-01

    Ardenticatena maritima strain 110ST is a filamentous bacterium isolated from an iron-rich coastal hydrothermal field, and it is a unique isolate capable of dissimilatory iron or nitrate reduction among the members of the bacterial phylum Chloroflexi. Here, we report the draft genome sequence comprising 3,569,367 bp, containing 3,355 predicted coding sequences (CDSs). PMID:26430053

  13. 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...

  14. GENETIC STRUCTURE AND PATTERNS OF SELECTION IN NATURAL POPULATIONS OF BETA VULGARIS SSP. MARITIMA.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Thirty one accessions, including one sugar beet (Beta vulgaris ssp. vulgaris) 30 wild beet (29 Beta vulgaris ssp. maritima and 1 Beta macrocarpa) were included in this study. 29 Accessions were collected from wild populations along the coast of France (Atlantic and Mediterranean) and have associate...

  15. IMPACTS OF SALINITY AND NUTRIENT STRESS TO RUPPIA MARITIMA AND ZOSTERA MARINA: A MESOCOSM EXPERIMENT

    EPA Science Inventory

    Healthy seagrass beds were once found throughout the shallow areas of Narragansett Bay, R.I. but have disappeared due to infilling, pollution and disease. In Greenwich Bay, a highly developed embayment within Narragansett Bay, Ruppia maritima has colonized an area on the norther...

  16. ASSESSING THE IMPACTS OF SALINITY AND NUTRIENT STRESS TO RUPPIA MARITIMA AND ZOSTERA MARINA

    EPA Science Inventory

    Healthy seagrass beds were once found throughout the shallow areas of Narragansett Bay, R.I. but have disappeared due to infilling, pollution and disease. In Greenwich Bay, a highly developed embayment within Narragansett Bay, Ruppia maritima has colonized an area on the norther...

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

    SciTech Connect

    Tagliabue, M.D.; Thursby, G.B.; Walker, H.A.; 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.

  18. Chemical composition and biological effects of Artemisia maritima and Artemisia nilagirica essential oils from wild plants of western Himalaya.

    PubMed

    Stappen, Iris; Wanner, Jürgen; Tabanca, Nurhayat; Wedge, David E; Ali, Abbas; Khan, Ikhlas A; Kaul, Vijay K; Lal, Brij; Jaitak, Vikas; Gochev, Velizar; Girova, Tania; Stoyanova, Albena; Schmidt, Erich; Jirovetz, Leopold

    2014-08-01

    Artemisia species possess pharmacological properties that are used for medical purposes worldwide. In this paper, the essential oils from the aerial parts of Artemisia nilagirica and Artemisia maritima from the western Indian Himalaya region are described. The main compounds analyzed by simultaneous GC/MS and GC/FID were camphor and 1,8-cineole from A. maritima, and camphor and artemisia ketone from A. nilagirica. Additionally, the oils were evaluated for their antibacterial, antifungal, mosquito biting deterrent, and larvicidal activities. A. nilagirica essential oil demonstrated nonselective antifungal activity against plant pathogens Colletotrichum acutatum, Colletotrichum fragariae, and Colletotrichum gloeosporioides, whereas A. maritima did not show antifungal activity. Both Artemisia spp. exhibited considerable mosquito biting deterrence, whereas only A. nilagirica showed larvicidal activity against Aedes aegypti. Antibacterial effects assessed by an agar dilution assay demonstrated greater activity of A. maritima essential oil against Staphylococcus aureus and Pseudomonas aeruginosa compared to A. nilagirica. PMID:25127023

  19. Negative association between parental care and sibling cooperation in earwigs: a new perspective on the early evolution of family life?

    PubMed

    Kramer, J; Thesing, J; Meunier, J

    2015-07-01

    The evolution of family life requires net fitness benefits for offspring, which are commonly assumed to mainly derive from parental care. However, an additional source of benefits for offspring is often overlooked: cooperative interactions among juvenile siblings. In this study, we examined how sibling cooperation and parental care could jointly contribute to the early evolution of family life. Specifically, we tested whether the level of food transferred among siblings (sibling cooperation) in the European earwig Forficula auricularia (1) depends on the level of maternal food provisioning (parental care) and (2) is translated into offspring survival, as well as female investment into future reproduction. We show that higher levels of sibling food transfer were associated with lower levels of maternal food provisioning, possibly reflecting a compensatory relationship between sibling cooperation and maternal care. Furthermore, the level of sibling food transfer did not influence offspring survival, but was associated with negative effects on the production of the second and terminal clutch by the tending mothers. These findings indicate that sibling cooperation could mitigate the detrimental effects on offspring survival that result from being tended by low-quality mothers. More generally, they are in line with the hypothesis that sibling cooperation is an ancestral behaviour that can be retained to compensate for insufficient levels of parental investment. PMID:25975926

  20. 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

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

    SciTech Connect

    Huntemann, Marcel; Lu, Megan; Nolan, Matt; Lapidus, Alla L.; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, N; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Jeffries, Cynthia; Detter, J. Chris; Brambilla, Evelyne-Marie; Rohde, Manfred; Spring, Stefan; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Mavromatis, K

    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.

  2. 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.

  3. Optimization of expression and properties of the recombinant acetohydroxyacid synthase of Thermotoga maritima

    PubMed Central

    Eram, Mohammad S.; Sarafuddin, Benozir; Gong, Frank; Ma, Kesen

    2015-01-01

    The data provide additional support of the characterization of the biophysical and biochemical properties of the enzyme acetohydroxyacid synthase from the hyperthermophilic bacterium Thermotoga maritima (Eram et al., 2015) [1]. The genes encoding the enzyme subunits have been cloned and expressed in the mesophilic host Escherichia coli. Detailed data include information about the optimization of the expression conditions, biophysical properties of the enzyme and reconstitution of the holoenzyme from individually expressed and purified subunits. PMID:26629492

  4. Comparative Transcriptome Analysis of the Cosmopolitan Marine Fungus Corollospora maritima Under Two Physiological Conditions

    PubMed Central

    Velez, Patricia; Alejandri-Ramírez, Naholi D.; González, María C.; Estrada, Karel J.; Sanchez-Flores, Alejandro; Dinkova, Tzvetanka D.

    2015-01-01

    Marine sandy beaches represent dynamic environments often subject to harsh conditions and climate fluctuations, where natural and anthropogenic inputs of freshwater from fluvial and pluvial sources alter salinity, which has been recognized as a key variable affecting the distribution of aquatic organisms and influencing critical physiological processes. The marine arenicolous fungus Corollospora maritima is a worldwide-distributed saprobe that has been reported to present tolerance to freshwater. Here, we present a transcriptome analysis that will provide the first insight of the genomic content for this fungus and a gene expression comparison between two different salinity conditions. We also identified genes that are candidates for being differentially expressed in response to environmental variations on salinity during the fungal growth. The de novo reconstruction of C. maritima transcriptome Illumina sequencing provided a total of 14,530 transcripts (16 megabases). The comparison between the two growth conditions rendered 103 genes specifically overexpressed in seawater, and 132 genes specifically up-regulated under freshwater. Using fungal isolates collected from different beaches, the specific environmental regulation of particular transcript differential expression was confirmed by RT-qPCR. To our knowledge, this is the first analysis that explores the marine fungus C. maritima molecular responses to overcome freshwater stress, and these data could shed light to understand the fungal adaptation and plasticity mechanisms to the marine habitat. PMID:26116293

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

    PubMed Central

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

    2010-01-01

    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?-deoxy-5?-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. PMID:20124698

  6. 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.

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

    SciTech Connect

    Tagliabue, M.D.; Thursby, G.B.; Walker, H.A.; 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.

  8. Comparative Transcriptome Analysis of the Cosmopolitan Marine Fungus Corollospora maritima Under Two Physiological Conditions.

    PubMed

    Velez, Patricia; Alejandri-Ramírez, Naholi D; González, María C; Estrada, Karel J; Sanchez-Flores, Alejandro; Dinkova, Tzvetanka D

    2015-09-01

    Marine sandy beaches represent dynamic environments often subject to harsh conditions and climate fluctuations, where natural and anthropogenic inputs of freshwater from fluvial and pluvial sources alter salinity, which has been recognized as a key variable affecting the distribution of aquatic organisms and influencing critical physiological processes. The marine arenicolous fungus Corollospora maritima is a worldwide-distributed saprobe that has been reported to present tolerance to freshwater. Here, we present a transcriptome analysis that will provide the first insight of the genomic content for this fungus and a gene expression comparison between two different salinity conditions. We also identified genes that are candidates for being differentially expressed in response to environmental variations on salinity during the fungal growth. The de novo reconstruction of C. maritima transcriptome Illumina sequencing provided a total of 14,530 transcripts (16 megabases). The comparison between the two growth conditions rendered 103 genes specifically overexpressed in seawater, and 132 genes specifically up-regulated under freshwater. Using fungal isolates collected from different beaches, the specific environmental regulation of particular transcript differential expression was confirmed by RT-qPCR. To our knowledge, this is the first analysis that explores the marine fungus C. maritima molecular responses to overcome freshwater stress, and these data could shed light to understand the fungal adaptation and plasticity mechanisms to the marine habitat. PMID:26116293

  9. An epidemiological assessment of Ambrosia maritima on the transmission of schistosomiasis in the Egyptian Nile Delta.

    PubMed

    Barakat, R; Farghaly, A; el-Sawy, M F; Soliman, N K; Duncan, J; Zaki, A; Miller, F D

    1993-09-01

    Ambrosia maritima (Damsissa), a proven molluscicide, was investigated in a seven year epidemiological trial in four villages in the northern Egyptian Nile Delta. Schistosoma mansoni prevalence and other measures of infection were initially high in the four villages before the trial began. Two villages were used to test the impact of A. maritima application both on snail populations and on infection in the village population. Two villages were held as controls and not treated with A. maritima. The entire population of all four villages was included in the study. Prevalence and other measures of infection fell dramatically following treatment with praziquantel 40 mg kg-1 body weight. On annual follow ups, the prevalence of infection and geometric mean egg counts began to increase back to original levels in both test and control villages; age adjusted incidence rates were lower in one test village, but higher in the other when compared to the control villages. Snail populations were destroyed in the treated canals and drains located near the test villages. The lack of a clear epidemiologic impact is discussed. PMID:8256093

  10. 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

  11. Moving closer towards restoration of contaminated estuaries: Bioaugmentation with autochthonous rhizobacteria improves metal rhizoaccumulation in native Spartina maritima.

    PubMed

    Mesa, Jennifer; Rodríguez-Llorente, Ignacio David; Pajuelo, Eloisa; Piedras, José María Barcia; Caviedes, Miguel Angel; Redondo-Gómez, Susana; Mateos-Naranjo, Enrique

    2015-12-30

    Spartina maritima is an ecosystem engineer that has shown to be useful for phytoremediation purposes. A glasshouse experiment using soil from a metal-contaminated estuary was designed to investigate the effect of a native bacterial consortium, isolated from S. maritima rizhosphere and selected owing to their plant growth promoting properties and multiresistance to heavy metals, on plant growth and metal accumulation. Plants of S. maritima were randomly assigned to three soil bioaugmentation treatments (without inoculation, one inoculation and repeated inoculations) for 30 days. Growth parameters and photosynthetic traits, together with total concentrations of several metals were determined in roots and/or leaves. Bacterial inoculation improved root growth, through a beneficial effect on photosynthetic rate (AN) due to its positive impact on functionality of PSII and chlorophyll concentration. Also, favoured intrinsic water use efficiency of S. maritima, through the increment in AN, stomatal conductance and in root-to-shoot ratio. Moreover, this consortium was able to stimulate plant metal uptake specifically in roots, with increases of up to 19% for As, 65% for Cu, 40% for Pb and 29% for Zn. Thus, bioaugmentation of S. maritima with the selected bacterial consortium can be claimed to enhance plant adaptation and metal rhizoaccumulation during marsh restoration programs. PMID:26188869

  12. Structural Insight inot the low Affinity Between Thermotoga maritima CheA and CheB Compared to their Escherichia coli/Salmonella typhimurium Counterparts

    SciTech Connect

    S Park; B Crane

    2011-12-31

    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 {beta}4/{alpha}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.

  13. 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

  14. 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

  15. 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

  16. Effects of Oil-Contaminated Sediments on Submerged Vegetation: An Experimental Assessment of Ruppia maritima.

    PubMed

    Martin, Charles W; Hollis, Lauris O; Turner, R Eugene

    2015-01-01

    Oil spills threaten the productivity of ecosystems through the degradation of coastal flora and the ecosystem services these plants provide. While lab and field investigations have quantified the response of numerous species of emergent vegetation to oil, the effects on submerged vegetation remain uncertain. Here, we discuss the implications of oil exposure for Ruppia maritima, one of the most common species of submerged vegetation found in the region affected by the recent Deepwater Horizon oil spill. We grew R. maritima in a range of manipulated sediment oil concentrations: 0, 0.26, 0.53, and 1.05 mL oil /L tank volume, and tracked changes in growth (wet weight and shoot density/length), reproductive activity (inflorescence and seed production), root characteristics (mass, length, diameter, and area), and uprooting force of plants. While no statistical differences were detected in growth, plants exhibited significant changes to reproductive output, root morphology, and uprooting force. We found significant reductions in inflorescences and fruiting bodies at higher oil concentrations. In addition, the roots growing in the high oil were shorter and wider. Plants in medium and high oil required less force to uproot. A second experiment was performed to separate the effects of root morphology and oiled sediment properties and indicated that there were also changes to sediment cohesion that contributed to a reduction in uprooting forces in medium and high oil. Given the importance of sexual reproduction for these plants, oil contamination may have substantial population-level effects. Moreover, areas containing buried oil may be more susceptible to high energy storm events due to the reduction in uprooting force of foundation species such as R. maritima. PMID:26430971

  17. 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.

  18. Effects of Oil-Contaminated Sediments on Submerged Vegetation: An Experimental Assessment of Ruppia maritima

    PubMed Central

    Martin, Charles W.; Hollis, Lauris O.; Turner, R. Eugene

    2015-01-01

    Oil spills threaten the productivity of ecosystems through the degradation of coastal flora and the ecosystem services these plants provide. While lab and field investigations have quantified the response of numerous species of emergent vegetation to oil, the effects on submerged vegetation remain uncertain. Here, we discuss the implications of oil exposure for Ruppia maritima, one of the most common species of submerged vegetation found in the region affected by the recent Deepwater Horizon oil spill. We grew R. maritima in a range of manipulated sediment oil concentrations: 0, 0.26, 0.53, and 1.05 mL oil /L tank volume, and tracked changes in growth (wet weight and shoot density/length), reproductive activity (inflorescence and seed production), root characteristics (mass, length, diameter, and area), and uprooting force of plants. While no statistical differences were detected in growth, plants exhibited significant changes to reproductive output, root morphology, and uprooting force. We found significant reductions in inflorescences and fruiting bodies at higher oil concentrations. In addition, the roots growing in the high oil were shorter and wider. Plants in medium and high oil required less force to uproot. A second experiment was performed to separate the effects of root morphology and oiled sediment properties and indicated that there were also changes to sediment cohesion that contributed to a reduction in uprooting forces in medium and high oil. Given the importance of sexual reproduction for these plants, oil contamination may have substantial population-level effects. Moreover, areas containing buried oil may be more susceptible to high energy storm events due to the reduction in uprooting force of foundation species such as R. maritima. PMID:26430971

  19. Isolation and analysis of genes for amylolytic enzymes of the hyperthermophilic bacterium Thermotoga maritima.

    PubMed

    Bibel, M; Brettl, C; Gosslar, U; Kriegshäuser, G; Liebl, W

    1998-01-01

    In addition to the previously identified 4-alpha-glucanotransferase gene mgtA and the alpha-amylase gene amyA of Thermotoga maritima strain MSB8 we have now isolated three further genes encoding amylolytic enzymes from a gene library of this ancestral bacterium. The genes code for the extremely thermostable enzymes pullulanase (pulA), maltodextrin phosphorylase (agpA) and alpha-glucosidase (aglA) and have the potential to encode polypeptides with calculated molecular masses of 96.3 kDa, 96.1 kDa and 52.5 kDa, respectively. Comparative amino acid sequence analysis revealed that PulA and AgpA are clearly related to other known enzymes with similar function. AglA, on the other hand, was not related to other alpha-glucosidases but appears to belong to an enzyme family containing alpha-galactosidases and 6-phospho-beta-glucosidases. Enzyme properties are reported which demonstrate the extreme thermostability of these T. maritima enzymes. PMID:9453151

  20. Crystallization and preliminary X-ray diffraction analysis of a lectin from Canavalia maritima seeds

    SciTech Connect

    Almeida Gadelha, Carlos Alberto de; Moreno, Frederico Bruno Mendes Batista; Santi-Gadelha, Tatiane; Cajazeiras, João Batista; Rocha, Bruno Anderson M. da; Rustiguel, Joane Kathelen Rodrigues; Freitas, Beatriz Tupinamba; Canduri, Fernanda; Delatorre, Plínio; Azevedo, Walter Filgueira Jr de; Cavada, Benildo S.

    2005-01-01

    A lectin from C. maritima was crystallized using the vapour-diffusion method and crystals diffracted to 2.1 Å resolution. A molecular-replacement search found a solution with a correlation coefficient of 69.2% and an R factor of 42.5%, refinement is in progress. A lectin from Canavalia maritima seeds (ConM) was purified and submitted to crystallization experiments. The best crystals were obtained using the vapour-diffusion method at a constant temperature of 293 K and grew in 7 d. A complete structural data set was collected to 2.1 Å resolution using a synchrotron-radiation source. The ConM crystal belongs to the orthorhombic space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 67.15, b = 70.90, c = 97.37 Å. A molecular-replacement search found a solution with a correlation coefficient of 69.2% and an R factor of 42.5%. Crystallographic refinement is under way.

  1. The chloroplast genome of the hexaploid Spartina maritima (Poaceae, Chloridoideae): Comparative analyses and molecular dating.

    PubMed

    Rousseau-Gueutin, M; Bellot, S; Martin, G E; Boutte, J; Chelaifa, H; Lima, O; Michon-Coudouel, S; Naquin, D; Salmon, A; Ainouche, K; Ainouche, M

    2015-12-01

    The history of many plant lineages is complicated by reticulate evolution with cases of hybridization often followed by genome duplication (allopolyploidy). In such a context, the inference of phylogenetic relationships and biogeographic scenarios based on molecular data is easier using haploid markers like chloroplast genome sequences. Hybridization and polyploidization occurred recurrently in the genus Spartina (Poaceae, Chloridoideae), as illustrated by the recent formation of the invasive allododecaploid S. anglica during the 19th century in Europe. Until now, only a few plastid markers were available to explore the history of this genus and their low variability limited the resolution of species relationships. We sequenced the complete chloroplast genome (plastome) of S. maritima, the native European parent of S. anglica, and compared it to the plastomes of other Poaceae. Our analysis revealed the presence of fast-evolving regions of potential taxonomic, phylogeographic and phylogenetic utility at various levels within the Poaceae family. Using secondary calibrations, we show that the tetraploid and hexaploid lineages of Spartina diverged 6-10 my ago, and that the two parents of the invasive allopolyploid S. anglica separated 2-4 my ago via long distance dispersal of the ancestor of S. maritima over the Atlantic Ocean. Finally, we discuss the meaning of divergence times between chloroplast genomes in the context of reticulate evolution. PMID:26182838

  2. An auto-inhibited state in the structure of Thermotoga maritima NusG

    PubMed Central

    Drögemüller, Johanna; Stegmann, Christian M.; Mandal, Angshuman; Steiner, Thomas; Burmann, Björn M.; Gottesman, Max E.; Wöhrl, Birgitta M.; Rösch, Paul; Wahl, Markus C.; Schweimer, Kristian

    2013-01-01

    Summary NusG is a conserved regulatory protein interacting with RNA polymerase (RNAP) and other proteins to form multi-component complexes that modulate transcription. The crystal structure of Thermotoga maritima NusG (TmNusG) shows a three-domain architecture, comprising well conserved amino-terminal (NTD) and carboxy-terminal (CTD) domains with an additional, species-specific domain inserted into the NTD. NTD and CTD directly contact each other, occluding a surface of the NTD for binding to RNAP and a surface on the CTD interacting either with transcription termination factor Rho or transcription anti-termination factor NusE. NMR spectroscopy confirmed the intra-molecular NTD-CTD interaction up to the optimal growth temperature of Thermotoga maritima. The domain interaction involves a dynamic equilibrium between open and closed states and contributes significantly to the overall fold stability of the protein. Wild type TmNusG and deletion variants could not replace for endogenous Escherichia coli NusG, suggesting that the NTD-CTD interaction of TmNusG represents an auto-inhibited state. PMID:23415559

  3. Structural and functional characterization of a noncanonical nucleoside triphosphate pyrophosphatase from Thermotoga maritima

    SciTech Connect

    Awwad, Khaldeyah; Desai, Anna; Smith, Clyde; Sommerhalter, Monika

    2013-02-01

    A 2.15 Å resolution crystal structure of TM0159 with bound IMP and enzyme-kinetic data are presented. This noncanonical nucleoside triphosphatase from T. maritima helps to maintain a correct pool of DNA and RNA precursor molecules. The hyperthermophilic bacterium Thermotoga maritima has a noncanonical nucleoside triphosphatase that catalyzes the conversion of inosine triphosphate (ITP), deoxyinosine triphosphate (dITP) and xanthosine triphosphate (XTP) into inosine monophosphate (IMP), deoxyinosine monophosphate (IMP) and xanthosine monophosphate (XMP), respectively. The k{sub cat}/K{sub m} values determined at 323 and 353 K fall between 1.31 × 10{sup 4} and 7.80 × 10{sup 4} M{sup −1} s{sup −1}. ITP and dITP are slightly preferred over XTP. Activity towards canonical nucleoside triphosphates (ATP and GTP) was not detected. The enzyme has an absolute requirement for Mg{sup 2+} as a cofactor and has a preference for alkaline conditions. A protein X-ray structure of the enzyme with bound IMP was obtained at 2.15 Å resolution. The active site houses a well conserved network of residues that are critical for substrate recognition and catalysis. The crystal structure shows a tetramer with two possible dimer interfaces. One of these interfaces strongly resembles the dimer interface that is found in the structures of other noncanonical nucleoside pyrophosphatases from human (human ITPase) and archaea (Mj0226 and PhNTPase)

  4. 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

  5. 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.

  6. 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/...

  7. The hyperthermophilic anaerobe Thermotoga Maritima is able to cope with limited amount of oxygen: insights into its defence strategies.

    PubMed

    Le Fourn, Céline; Fardeau, Marie-Laure; Ollivier, Bernard; Lojou, Elisabeth; Dolla, Alain

    2008-07-01

    Thermotoga maritima, an anaerobic hyperthermophilic bacterium, was found able to grow in the presence of low concentrations of oxygen of up to 0.5% (v/v). Differential proteomics and transcripts analysis by qRT-PCR were used to identify the defence strategies used by T. maritima to protect itself against oxygen. A flavoprotein, homologous to rubredoxin oxygen oxidoreductase was found to be overproduced when cells were cultured in oxidative conditions. The recombinant protein, produced in Escherichia coli, exhibited an oxygen reductase activity, which could account for the observed decrease in oxygen concentration during growth. The gene encoding this oxygen reductase belongs to a multicistronic unit that includes genes encoding proteins involved in exopolysaccharide biosynthesis, which may be related to a biofilm formation induced by the presence of oxygen. Enzymes involved in reactive oxygen species detoxification, iron-sulfur centre synthesis/repair and the cysteine biosynthesis pathway were also overproduced. All these enzymatic systems together contribute to the defence strategy of T. maritima against oxygen. Because of the position of T. maritima in deep branches of the phylogenetic tree, we suggest that these strategies can be considered as ancestral mechanisms first developed by anaerobic microorganisms on the early Earth to protect themselves against primary abiotic or biotic oxygen production. PMID:18397308

  8. Exploring the genome of the salt-marsh Spartina maritima (Poaceae, Chloridoideae) through BAC end sequence analysis.

    PubMed

    Ferreira de Carvalho, J; Chelaifa, H; Boutte, J; Poulain, J; Couloux, A; Wincker, P; Bellec, A; Fourment, J; Bergès, H; Salmon, A; Ainouche, M

    2013-12-01

    Spartina species play an important ecological role on salt marshes. Spartina maritima is an Old-World species distributed along the European and North-African Atlantic coasts. This hexaploid species (2n = 6x = 60, 2C = 3,700 Mb) hybridized with different Spartina species introduced from the American coasts, which resulted in the formation of new invasive hybrids and allopolyploids. Thus, S. maritima raises evolutionary and ecological interests. However, genomic information is dramatically lacking in this genus. In an effort to develop genomic resources, we analysed 40,641 high-quality bacterial artificial chromosome-end sequences (BESs), representing 26.7 Mb of the S. maritima genome. BESs were searched for sequence homology against known databases. A fraction of 16.91% of the BESs represents known repeats including a majority of long terminal repeat (LTR) retrotransposons (13.67%). Non-LTR retrotransposons represent 0.75%, DNA transposons 0.99%, whereas small RNA, simple repeats and low-complexity sequences account for 1.38% of the analysed BESs. In addition, 4,285 simple sequence repeats were detected. Using the coding sequence database of Sorghum bicolor, 6,809 BESs found homology accounting for 17.1% of all BESs. Comparative genomics with related genera reveals that the microsynteny is better conserved with S. bicolor compared to other sequenced Poaceae, where 37.6% of the paired matching BESs are correctly orientated on the chromosomes. We did not observe large macrosyntenic rearrangements using the mapping strategy employed. However, some regions appeared to have experienced rearrangements when comparing Spartina to Sorghum and to Oryza. This work represents the first overview of S. maritima genome regarding the respective coding and repetitive components. The syntenic relationships with other grass genomes examined here help clarifying evolution in Poaceae, S. maritima being a part of the poorly-known Chloridoideae sub-family. PMID:23877482

  9. Crystal Structure of the Flagellar Rotor Protein FliN from Thermotoga maritima†

    PubMed Central

    Brown, Perry N.; Mathews, Michael A. A.; Joss, Lisa A.; Hill, Christopher P.; Blair, David F.

    2005-01-01

    FliN is a component of the bacterial flagellum that is present at levels of more than 100 copies and forms the bulk of the C ring, a drum-shaped structure at the inner end of the basal body. FliN interacts with FliG and FliM to form the rotor-mounted switch complex that controls clockwise-counterclockwise switching of the motor. In addition to its functions in motor rotation and switching, FliN is thought to have a role in the export of proteins that form the exterior structures of the flagellum (the rod, hook, and filament). Here, we describe the crystal structure of most of the FliN protein of Thermotoga maritima. FliN is a tightly intertwined dimer composed mostly of ? sheet. Several well-conserved hydrophobic residues form a nonpolar patch on the surface of the molecule. A mutation in the hydrophobic patch affected both flagellar assembly and switching, showing that this surface feature is important for FliN function. The association state of FliN in solution was studied by analytical ultracentrifugation, which provided clues to the higher-level organization of the protein. T. maritima FliN is primarily a dimer in solution, and T. maritima FliN and FliM together form a stable FliM1-FliN4 complex. Escherichia coli FliN forms a stable tetramer in solution. The arrangement of FliN subunits in the tetramer was modeled by reference to the crystal structure of tetrameric HrcQBC, a related protein that functions in virulence factor secretion in Pseudomonas syringae. The modeled tetramer is elongated, with approximate dimensions of 110 by 40 by 35Å, and it has a large hydrophobic cleft formed from the hydrophobic patches on the dimers. On the basis of the present data and available electron microscopic images, we propose a model for the organization of FliN subunits in the C ring. PMID:15805535

  10. Uptake of selenium by Ruppia maritima from microcosm sediments under controlled redox conditions

    SciTech Connect

    Bailey, F.C.; Dunlap, J.L.; Klaine, S.J.

    1994-12-31

    Redox potential plays a vital role in the speciation, bioavailability, and toxicity of metals and metalloids in sediments. The authors previously reported the development of a unique system which drives and maintains the redox of microcosm sediments with electrical current. The effectiveness of the redox control system has been validated by dosing microcosm sediments with acid volatile sulfide (AVS) and exerting either reducing conditions to maintain AVS or oxidizing conditions to induce a significant loss of AVS. Uptake of selenite, selenite and seleno-methionine from microcosm sediments by the aquatic plant Ruppia maritima was determined under redox conditions appropriate for each selenium species. Selenate uptake was determined for oxidizing and neutral conditions, while selenite and seleno-methionine uptake was determined for neutral and reducing redox potentials.

  11. Structural characterization of the putative ABC–type 2 transporter from Thermotoga maritima MSB8

    PubMed Central

    Filippova, Ekaterina V.; Tkaczuk, Karolina L.; Chruszcz, Maksymilian; Xu, Xiaohui; Savchenko, Alexei; Edwards, Aled; Minor, Wladek

    2014-01-01

    This study describes the structure of the putative ABC-type 2 transporter TM0543 from Thermotoga maritima MSB8 determined at a resolution of 2.3 Å. In comparative sequence-clustering analysis, TM0543 displays similarity to NatAB-like proteins, which are components of the ABC-type Na+ efflux pump permease. However, the overall structure fold of the predicted nucleotide-binding domain reveals that it is different from any known structure of ABC-type efflux transporters solved to date. The structure of the putative TM0543 domain also exhibits different dimer architecture and topology of its presumed ATP binding pocket, which may indicate that it does not bind nucleotide at all. Structural analysis of calcium ion binding sites found at the interface between TM0543 dimer subunits suggests that protein may be involved in ion-transporting activity. A detailed analysis of the protein sequence and structure is presented and discussed. PMID:25306867

  12. Isolation and characterization of 28 microsatellite loci for a Korean endemic, Lespedeza maritima (Fabaceae)1

    PubMed Central

    Jin, Dong-Pil; Cho, Won-Bum; Choi, In-Su; Choi, Byoung-Hee

    2016-01-01

    Premise of the study: We developed microsatellite primers for Lespedeza maritima (Fabaceae), a Korean endemic shrub, and conducted cross-amplifications for closely related species. Methods and Results: We produced 28 polymorphic microsatellite markers through reference mapping of 300-bp paired-end reads obtained from Illumina MiSeq data. For 47 individual plants from two populations, the total alleles numbered two to 13, and observed and expected heterozygosities ranged from 0.067 to 0.867 and from 0.064 to 0.848, respectively. Most of these markers were well amplified in closely related species. Conclusions: In future research, the microsatellite markers described here will help reveal the taxonomic entity of this species. PMID:26819860

  13. Adaptive Evolution of Thermotoga maritima Reveals Plasticity of the ABC Transporter Network

    PubMed Central

    Latif, Haythem; Sahin, Merve; Tarasova, Janna; Tarasova, Yekaterina; Portnoy, Vasiliy A.; Nogales, Juan

    2015-01-01

    Thermotoga maritima is a hyperthermophilic anaerobe that utilizes a vast network of ABC transporters to efficiently metabolize a variety of carbon sources to produce hydrogen. For unknown reasons, this organism does not metabolize glucose as readily as it does glucose di- and polysaccharides. The leading hypothesis implicates the thermolability of glucose at the physiological temperatures at which T. maritima lives. After a 25-day laboratory evolution, phenotypes were observed with growth rates up to 1.4 times higher than and glucose utilization rates exceeding 50% those of the wild type. Genome resequencing revealed mutations in evolved cultures related to glucose-responsive ABC transporters. The native glucose ABC transporter, GluEFK, has more abundant transcripts either as a result of gene duplication-amplification or through mutations to the operator sequence regulating this operon. Conversely, BglEFGKL, a transporter of beta-glucosides, is substantially downregulated due to a nonsense mutation to the solute binding protein or due to a deletion of the upstream promoter. Analysis of the ABC2 uptake porter families for carbohydrate and peptide transport revealed that the solute binding protein, often among the transcripts detected at the highest levels, is predominantly downregulated in the evolved cultures, while the membrane-spanning domain and nucleotide binding components are less varied. Similar trends were observed in evolved strains grown on glycerol, a substrate that is not dependent on ABC transporters. Therefore, improved growth on glucose is achieved through mutations favoring GluEFK expression over BglEFGKL, and in lieu of carbon catabolite repression, the ABC transporter network is modulated to achieve improved growth fitness. PMID:26048924

  14. cDNA cloning of Batis maritima methyl chloride transferase and purification of the enzyme

    PubMed Central

    Ni, Xinhai; Hager, Lowell P.

    1998-01-01

    Methyl chloride transferase catalyzes the synthesis of methyl chloride from S-adenosine-l-methionine and chloride ion. This enzyme has been purified 2,700-fold to homogeneity from Batis maritima, a halophytic plant that grows abundantly in salt marshes. The purification of the enzyme was accomplished by a combination of ammonium sulfate fractionation, column chromatography on Sephadex G100 and adenosine-agarose, and TSK-250 size-exclusion HPLC. The purified enzyme exhibits a single band on SDS/PAGE with a molecular mass of approximately 22.5 kDa. The molecular mass of the purified enzyme was 22,474 Da as determined by matrix-associated laser desorption ionization mass spectrometry. The methylase can function in either a monomeric or oligomeric form. A 32-aa sequence of an internal fragment of the methylase was determined (GLVPGCGGGYDVVAMANPER FMVGLDIXENAL, where X represents unknown residue) by Edman degradation, and a full-length cDNA of the enzyme was obtained by rapid amplification of cDNA ends–PCR amplification of cDNA oligonucleotides. The cDNA gene contains an ORF of 690 bp encoding an enzyme of 230 aa residues having a predicted molecular mass of 25,761 Da. The disparity between the observed and calculated molecular mass suggests that the methylase undergoes posttranslational cleavage, possibly during purification. Sequence homologies suggest that the B. maritima methylase defines a new family of plant methyl transferases. A possible function for this novel methylase in halophytic plants is discussed. PMID:9789006

  15. 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

  16. Adaptive Evolution of Thermotoga maritima Reveals Plasticity of the ABC Transporter Network.

    PubMed

    Latif, Haythem; Sahin, Merve; Tarasova, Janna; Tarasova, Yekaterina; Portnoy, Vasiliy A; Nogales, Juan; Zengler, Karsten

    2015-08-15

    Thermotoga maritima is a hyperthermophilic anaerobe that utilizes a vast network of ABC transporters to efficiently metabolize a variety of carbon sources to produce hydrogen. For unknown reasons, this organism does not metabolize glucose as readily as it does glucose di- and polysaccharides. The leading hypothesis implicates the thermolability of glucose at the physiological temperatures at which T. maritima lives. After a 25-day laboratory evolution, phenotypes were observed with growth rates up to 1.4 times higher than and glucose utilization rates exceeding 50% those of the wild type. Genome resequencing revealed mutations in evolved cultures related to glucose-responsive ABC transporters. The native glucose ABC transporter, GluEFK, has more abundant transcripts either as a result of gene duplication-amplification or through mutations to the operator sequence regulating this operon. Conversely, BglEFGKL, a transporter of beta-glucosides, is substantially downregulated due to a nonsense mutation to the solute binding protein or due to a deletion of the upstream promoter. Analysis of the ABC2 uptake porter families for carbohydrate and peptide transport revealed that the solute binding protein, often among the transcripts detected at the highest levels, is predominantly downregulated in the evolved cultures, while the membrane-spanning domain and nucleotide binding components are less varied. Similar trends were observed in evolved strains grown on glycerol, a substrate that is not dependent on ABC transporters. Therefore, improved growth on glucose is achieved through mutations favoring GluEFK expression over BglEFGKL, and in lieu of carbon catabolite repression, the ABC transporter network is modulated to achieve improved growth fitness. PMID:26048924

  17. Purification and characterization of Thermotoga maritima homoserine transsuccinylase indicates it is a transacetylase.

    PubMed

    Goudarzi, Maryam; Born, Timothy L

    2006-10-01

    The methionine biosynthetic pathway found in bacteria is controlled at the first step, acylation of the gamma-hydroxyl of homoserine. This reaction is catalyzed by one of two unique enzymes, homoserine transacetylase or homoserine transsuccinylase, which have no amino acid sequence similarity. We cloned, expressed, and purified homoserine transsuccinylase from the thermophilic bacterium Thermotoga maritima. Substrate specificity experiments demonstrated that acetyl-coenzyme A (CoA) is the preferred acyl donor and is used at least 30-fold more efficiently than succinyl-CoA. Steady-state kinetic experiments confirm that the enzyme utilizes a ping-pong kinetic mechanism in which the acetate group of acetyl-CoA is initially transferred to an enzyme nucleophile before subsequent transfer to homoserine. The maximal velocity, V/K (acetyl-CoA) and V/K (homoserine), all exhibited bell-shaped pH curves with apparent pKs of 6.0-6.9 and 8.2-8.8. The enzyme was inactivated by iodoacetamide in a pH-dependent manner, with an apparent pK of 6.3, suggesting the presence of an active-site cysteine residue which forms an acetyl-enzyme thioester intermediate during catalytic turnover, similar to observations with other transsuccinylases. In addition, the enzyme is highly stable at elevated temperatures, maintaining full activity at 70 degrees C. Taken together, these data suggest that the T. maritima enzyme functions biochemically as a transacetylase, despite having the sequence of a transsuccinylase. PMID:16708165

  18. 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

    2015-04-01

    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

  19. 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

  20. Endophytic Cultivable Bacteria of the Metal Bioaccumulator Spartina maritima Improve Plant Growth but Not Metal Uptake in Polluted Marshes Soils

    PubMed Central

    Mesa, Jennifer; Mateos-Naranjo, Enrique; Caviedes, Miguel A.; Redondo-Gómez, Susana; Pajuelo, Eloisa; Rodríguez-Llorente, Ignacio D.

    2015-01-01

    Endophytic bacterial population was isolated from Spartina maritima tissues, a heavy metal bioaccumulator cordgrass growing in the estuaries of Tinto, Odiel, and Piedras River (south west Spain), one of the most polluted areas in the world. Strains were identified and ability to tolerate salt and heavy metals along with plant growth promoting and enzymatic properties were analyzed. A high proportion of these bacteria were resistant toward one or several heavy metals and metalloids including As, Cu, and Zn, the most abundant in plant tissues and soil. These strains also exhibited multiple enzymatic properties as amylase, cellulase, chitinase, protease and lipase, as well as plant growth promoting properties, including nitrogen fixation, phosphates solubilization, and production of indole-3-acetic acid (IAA), siderophores and 1-aminocyclopropane-1-carboxylate (ACC) deaminase. The best performing strains (Micrococcus yunnanensis SMJ12, Vibrio sagamiensis SMJ18, and Salinicola peritrichatus SMJ30) were selected and tested as a consortium by inoculating S. maritima wild plantlets in greenhouse conditions along with wild polluted soil. After 30 days, bacterial inoculation improved plant photosynthetic traits and favored intrinsic water use efficiency. However, far from stimulating plant metal uptake, endophytic inoculation lessened metal accumulation in above and belowground tissues. These results suggest that inoculation of S. maritima with indigenous metal-resistant endophytes could mean a useful approach in order to accelerate both adaption and growth of this indigenous cordgrass in polluted estuaries in restorative operations, but may not be suitable for rhizoaccumulation purposes. PMID:26733985

  1. Endophytic Cultivable Bacteria of the Metal Bioaccumulator Spartina maritima Improve Plant Growth but Not Metal Uptake in Polluted Marshes Soils.

    PubMed

    Mesa, Jennifer; Mateos-Naranjo, Enrique; Caviedes, Miguel A; Redondo-Gómez, Susana; Pajuelo, Eloisa; Rodríguez-Llorente, Ignacio D

    2015-01-01

    Endophytic bacterial population was isolated from Spartina maritima tissues, a heavy metal bioaccumulator cordgrass growing in the estuaries of Tinto, Odiel, and Piedras River (south west Spain), one of the most polluted areas in the world. Strains were identified and ability to tolerate salt and heavy metals along with plant growth promoting and enzymatic properties were analyzed. A high proportion of these bacteria were resistant toward one or several heavy metals and metalloids including As, Cu, and Zn, the most abundant in plant tissues and soil. These strains also exhibited multiple enzymatic properties as amylase, cellulase, chitinase, protease and lipase, as well as plant growth promoting properties, including nitrogen fixation, phosphates solubilization, and production of indole-3-acetic acid (IAA), siderophores and 1-aminocyclopropane-1-carboxylate (ACC) deaminase. The best performing strains (Micrococcus yunnanensis SMJ12, Vibrio sagamiensis SMJ18, and Salinicola peritrichatus SMJ30) were selected and tested as a consortium by inoculating S. maritima wild plantlets in greenhouse conditions along with wild polluted soil. After 30 days, bacterial inoculation improved plant photosynthetic traits and favored intrinsic water use efficiency. However, far from stimulating plant metal uptake, endophytic inoculation lessened metal accumulation in above and belowground tissues. These results suggest that inoculation of S. maritima with indigenous metal-resistant endophytes could mean a useful approach in order to accelerate both adaption and growth of this indigenous cordgrass in polluted estuaries in restorative operations, but may not be suitable for rhizoaccumulation purposes. PMID:26733985

  2. The influence of Spartina maritima on carbon retention capacity in salt marshes from warm-temperate estuaries.

    PubMed

    Sousa, Ana I; Lillebø, Ana I; Pardal, Miguel A; Caçador, Isabel

    2010-01-01

    Salt marshes constitute highly productive systems playing an important role on ecosystem functions. The aim of this study is to compare the role of Spartina maritima salt marshes on carbon cycling. Thus, four salt marshes located in two mesotidal estuarine systems (Tagus and Mondego, two salt marshes per estuary) were studied. The S. maritima above- and belowground biomass, carbon production, decomposition rates (through a litterbag experiment) and carbon content in the sediment were estimated for a one year period in both systems and compared. In Corroios (located at the Tagus estuary) S. maritima salt marsh had the highest belowground production (1008 gC m(-2) y(-1)), slower decomposition rate (k=0.0024 d(-1)), and the highest carbon content in sediments (750 gC m(-2) y(-1)); and thus, the highest carbon retention capacity. The other three salt marshes had comparatively higher aboveground productions, higher decomposition rates and lower carbon retention capacity. Therefore, Corroios had the most important carbon cycling characteristics. As a whole, results show that differences in carbon cycling in salt marshes depend mostly on its own characteristics and maturity, rather than the system itself. The intrinsic characteristics of the salt marshes, namely the physicochemical conditions determined by the maturity of the system, are more important factors affecting the role of warm-temperate mesotidal salt marshes as carbon sinks. PMID:20304438

  3. Structure of the endonuclease IV homologue from Thermotoga maritima in the presence of active-site divalent metal ions

    SciTech Connect

    Tomanicek, Stephen J.; Hughes, Ronny C.; Ng, Joseph D.; Coates, Leighton

    2010-10-05

    The most frequent lesion in DNA is at apurinic/apyrimidinic (AP) sites resulting from DNA-base losses. These AP-site lesions can stall DNA replication and lead to genome instability if left unrepaired. The AP endonucleases are an important class of enzymes that are involved in the repair of AP-site intermediates during damage-general DNA base-excision repair pathways. These enzymes hydrolytically cleave the 5{prime}-phosphodiester bond at an AP site to generate a free 3{prime}-hydroxyl group and a 5{prime}-terminal sugar phosphate using their AP nuclease activity. Specifically, Thermotoga maritima endonuclease IV is a member of the second conserved AP endonuclease family that includes Escherichia coli endonuclease IV, which is the archetype of the AP endonuclease superfamily. In order to more fully characterize the AP endonuclease family of enzymes, two X-ray crystal structures of the T. maritima endonuclease IV homologue were determined in the presence of divalent metal ions bound in the active-site region. These structures of the T. maritima endonuclease IV homologue further revealed the use of the TIM-barrel fold and the trinuclear metal binding site as important highly conserved structural elements that are involved in DNA-binding and AP-site repair processes in the AP endonuclease superfamily.

  4. Thermotoga maritima AglA, an extremely thermostable NAD+-, Mn2+-, and thiol-dependent alpha-glucosidase.

    PubMed

    Raasch, C; Streit, W; Schanzer, J; Bibel, M; Gosslar, U; Liebl, W

    2000-08-01

    The gene for the alpha-glucosidase AglA of the hyperthermophilic bacterium Thermotoga maritima MSB8, which was identified by phenotypic screening of a T. maritima gene library, is located within a cluster of genes involved in the hydrolysis of starch and maltodextrins and the uptake of maltooligosaccharides. According to its primary structure as deduced from the nucleotide sequence of the gene, AglA belongs to family 4 of glycosyl hydrolases. The enzyme was recombinantly expressed in Escherichia coli, purified, and characterized. The T. maritima alpha-glucosidase has the unusual property of requiring NAD+ and Mn2+ for activity. Co2+ and Ni2+ also activated AglA, albeit less efficiently than Mn2+. T. maritima AglA represents the first example of a maltodextrin-degrading alpha-glucosidase with NAD+ and Mn2+ requirement. In addition, AglA activity depended on reducing conditions. This third requirement was met by the addition of dithiothreitol (DTT) or beta-mercaptoethanol to the assay. Using gel permeation chromatography, T. maritima AglA behaved as a dimer (two identical 55-kDa subunits), irrespective of metal depletion or metal addition, and irrespective of the presence or absence of NAD+ or DTT. The enzyme hydrolyzes maltose and other small maltooligosaccharides but is inactive against the polymeric substrate starch. AglA is not specific with respect to the configuration at the C-4 position of its substrates because glycosidic derivatives of D-galactose are also hydrolyzed. In the presence of all cofactors, maximum activity was recorded at pH 7.5 and 90 degrees C (4-min assay). AglA is the most thermoactive and the most thermostable member of glycosyl hydrolase family 4. When incubated at 50 degrees C and 70 degrees C, the recombinant enzyme suffered partial inactivation during the first hours of incubation, but thereafter the residual activity did not drop below about 50% and 20% of the initial value, respectively, within a period of 48 h. PMID:10972187

  5. A bacterial genetic screen identifies functional coding sequences of the insect mariner transposable element Famar1 amplified from the genome of the earwig, Forficula auricularia.

    PubMed

    Barry, Elizabeth G; Witherspoon, David J; Lampe, David J

    2004-02-01

    Transposons of the mariner family are widespread in animal genomes and have apparently infected them by horizontal transfer. Most species carry only old defective copies of particular mariner transposons that have diverged greatly from their active horizontally transferred ancestor, while a few contain young, very similar, and active copies. We report here the use of a whole-genome screen in bacteria to isolate somewhat diverged Famar1 copies from the European earwig, Forficula auricularia, that encode functional transposases. Functional and nonfunctional coding sequences of Famar1 and nonfunctional copies of Ammar1 from the European honey bee, Apis mellifera, were sequenced to examine their molecular evolution. No selection for sequence conservation was detected in any clade of a tree derived from these sequences, not even on branches leading to functional copies. This agrees with the current model for mariner transposon evolution that expects neutral evolution within particular hosts, with selection for function occurring only upon horizontal transfer to a new host. Our results further suggest that mariners are not finely tuned genetic entities and that a greater amount of sequence diversification than had previously been appreciated can occur in functional copies in a single host lineage. Finally, this method of isolating active copies can be used to isolate other novel active transposons without resorting to reconstruction of ancestral sequences. PMID:15020471

  6. A bacterial genetic screen identifies functional coding sequences of the insect mariner transposable element Famar1 amplified from the genome of the earwig, Forficula auricularia.

    PubMed Central

    Barry, Elizabeth G; Witherspoon, David J; Lampe, David J

    2004-01-01

    Transposons of the mariner family are widespread in animal genomes and have apparently infected them by horizontal transfer. Most species carry only old defective copies of particular mariner transposons that have diverged greatly from their active horizontally transferred ancestor, while a few contain young, very similar, and active copies. We report here the use of a whole-genome screen in bacteria to isolate somewhat diverged Famar1 copies from the European earwig, Forficula auricularia, that encode functional transposases. Functional and nonfunctional coding sequences of Famar1 and nonfunctional copies of Ammar1 from the European honey bee, Apis mellifera, were sequenced to examine their molecular evolution. No selection for sequence conservation was detected in any clade of a tree derived from these sequences, not even on branches leading to functional copies. This agrees with the current model for mariner transposon evolution that expects neutral evolution within particular hosts, with selection for function occurring only upon horizontal transfer to a new host. Our results further suggest that mariners are not finely tuned genetic entities and that a greater amount of sequence diversification than had previously been appreciated can occur in functional copies in a single host lineage. Finally, this method of isolating active copies can be used to isolate other novel active transposons without resorting to reconstruction of ancestral sequences. PMID:15020471

  7. Urgineaglyceride A: a new monoacylglycerol from the Egyptian Drimia maritima bulbs.

    PubMed

    Mohamed, Gamal A; Ibrahim, Sabrin R M; Shaala, Lamiaa A; Alshali, Khalid Z; Youssef, Diaa T A

    2014-01-01

    One new compound, (2S)-1-O-(Z)-tetracos-6-enoate glycerol (1) named urgineaglyceride A, along with six known compounds, 3,5,7,3',5'-pentahydroxydihydroflavonol (2), stigmasterol (3), (25S)-5β-furostane-3β-22α-26-triol (4), scillaridin A (5), (2S)-(+)-2-hydroxynaringenin-4'-O-β-D-glucopyranoside (6) and quercetin-3'-O-β-D-glucopyranoside (7), were isolated from the EtOAc fraction of Drimia maritima (L.) Stearn bulbs. Their structures were secured based on their IR, UV, 1D and 2D NMR data, in addition to HR-MS data and comparison with the literature data. The isolated compounds were evaluated for their in vitro growth inhibitory activity against A549 non-small cell lung cancer (NSCLC), U373 glioblastoma (GBM) and PC-3 prostate cancer cell lines. Compounds 2 and 3 displayed variable activities against the tested cancer cell lines. Compound 2 was a selective inhibitor of the NSCLC cell line with an IC₅₀ of 2.3 μM, whereas 3 was selective against GBM with IC₅₀ of 0.5 μM and against PC-3 with 2.0 μM. PMID:24938488

  8. XX/XY System of Sex Determination in the Geophilomorph Centipede Strigamia maritima.

    PubMed

    Green, Jack E; Dalíková, Martina; Sahara, Ken; Marec, František; Akam, Michael

    2016-01-01

    We show that the geophilomorph centipede Strigamia maritima possesses an XX/XY system of sex chromosomes, with males being the heterogametic sex. This is, to our knowledge, the first report of sex chromosomes in any geophilomorph centipede. Using the recently assembled Strigamia genome sequence, we identified a set of scaffolds differentially represented in male and female DNA sequence. Using quantitative real-time PCR, we confirmed that three candidate X chromosome-derived scaffolds are present at approximately twice the copy number in females as in males. Furthermore, we confirmed that six candidate Y chromosome-derived scaffolds contain male-specific sequences. Finally, using this molecular information, we designed an X chromosome-specific DNA probe and performed fluorescent in situ hybridization against mitotic and meiotic chromosome spreads to identify the Strigamia XY sex-chromosome pair cytologically. We found that the X and Y chromosomes are recognizably different in size during the early pachytene stage of meiosis, and exhibit incomplete and delayed pairing. PMID:26919730

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

    PubMed

    Green, Jack E; Akam, Michael

    2014-08-15

    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

  10. The centipede Strigamia maritima possesses a large complement of Wnt genes with diverse expression patterns.

    PubMed

    Hayden, Luke; Arthur, Wallace

    2014-05-01

    The genes of the Wnt family play important roles in the development of many animals. In the arthropods, these genes are known to have multiple functions, including roles in posterior development and segmentation. Despite this, secondary loss of Wnt genes is common among the Arthropoda. Unlike many arthropods, Strigamia maritima, a geophilomorph centipede, possesses a large complement of Wnt ligands, with 11 Wnt genes present. In this study, the expression of each of these genes was examined across a range of stages during embryonic development. The expression of Wnt genes in Strigamia displays much variability. Most Wnt genes are expressed in segmental stripes in the trunk; near the proctodeum; and in the head region. However, despite this overall broad similarity, there are many differences between the various Wnt genes in their exact patterns of expression. These data should be considered in the context of different hypotheses regarding the functional relationships between the Wnt genes and the degree of redundancy present in this system. The findings of this study are consistent with one particular model of Wnt activity, the combinatorial model, whereby the combination of Wnt ligands present in a particular region defines its identity. These findings should also be useful in attempts to reconstruct the evolutionary history of Wnt signaling in arthropods. PMID:24754405

  11. XX/XY System of Sex Determination in the Geophilomorph Centipede Strigamia maritima

    PubMed Central

    Green, Jack E.; Dalíková, Martina; Sahara, Ken; Marec, František; Akam, Michael

    2016-01-01

    We show that the geophilomorph centipede Strigamia maritima possesses an XX/XY system of sex chromosomes, with males being the heterogametic sex. This is, to our knowledge, the first report of sex chromosomes in any geophilomorph centipede. Using the recently assembled Strigamia genome sequence, we identified a set of scaffolds differentially represented in male and female DNA sequence. Using quantitative real-time PCR, we confirmed that three candidate X chromosome-derived scaffolds are present at approximately twice the copy number in females as in males. Furthermore, we confirmed that six candidate Y chromosome-derived scaffolds contain male-specific sequences. Finally, using this molecular information, we designed an X chromosome-specific DNA probe and performed fluorescent in situ hybridization against mitotic and meiotic chromosome spreads to identify the Strigamia XY sex-chromosome pair cytologically. We found that the X and Y chromosomes are recognizably different in size during the early pachytene stage of meiosis, and exhibit incomplete and delayed pairing. PMID:26919730

  12. 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

  13. Synthetic symmetrization in the crystallization and structure determination of CelA from Thermotoga maritima

    PubMed Central

    Forse, G Jason; Ram, Nina; Banatao, D Rey; Cascio, Duilio; Sawaya, Michael R; Klock, Heath E; Lesley, Scott A; Yeates, Todd O

    2011-01-01

    Protein crystallization continues to be a major bottleneck in X-ray crystallography. Previous studies suggest that symmetric proteins, such as homodimers, might crystallize more readily than monomeric proteins or asymmetric complexes. Proteins that are naturally monomeric can be made homodimeric artificially. Our approach is to create homodimeric proteins by introducing single cysteines into the protein of interest, which are then oxidized to form a disulfide bond between the two monomers. By introducing the single cysteine at different sequence positions, one can produce a variety of synthetically dimerized versions of a protein, with each construct expected to exhibit its own crystallization behavior. In earlier work, we demonstrated the potential utility of the approach using T4 lysozyme as a model system. Here we report the successful application of the method to Thermotoga maritima CelA, a thermophilic endoglucanase enzyme with low sequence identity to proteins with structures previously reported in the Protein Data Bank. This protein had resisted crystallization in its natural monomeric form, despite a broad survey of crystallization conditions. The synthetic dimerization of the CelA mutant D188C yielded well-diffracting crystals with molecules in a packing arrangement that would not have occurred with native, monomeric CelA. A 2.4 Å crystal structure was determined by single anomalous dispersion using a seleno-methionine derivatized protein. The results support the notion that synthetic symmetrization can be a useful approach for enlarging the search space for crystallizing monomeric proteins or asymmetric complexes. PMID:21082721

  14. 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

  15. Structural and functional characterization of a noncanonical nucleoside triphosphate pyrophosphatase from Thermotoga maritima

    PubMed Central

    Awwad, Khaldeyah; Desai, Anna; Smith, Clyde; Sommerhalter, Monika

    2013-01-01

    The hyperthermophilic bacterium Thermotoga maritima has a noncanonical nucleoside triphosphatase that catalyzes the conversion of inosine triphosphate (ITP), deoxyinosine triphosphate (dITP) and xanthosine triphosphate (XTP) into inosine monophosphate (IMP), deoxyinosine monophosphate (IMP) and xanthosine monophosphate (XMP), respectively. The k cat/K m values determined at 323 and 353?K fall between 1.31 × 104 and 7.80 × 104? M ?1?s?1. ITP and dITP are slightly preferred over XTP. Activity towards canonical nucleoside triphosphates (ATP and GTP) was not detected. The enzyme has an absolute requirement for Mg2+ as a cofactor and has a preference for alkaline conditions. A protein X-ray structure of the enzyme with bound IMP was obtained at 2.15?Å resolution. The active site houses a well conserved network of residues that are critical for substrate recognition and catalysis. The crystal structure shows a tetramer with two possible dimer interfaces. One of these interfaces strongly resembles the dimer interface that is found in the structures of other noncanonical nucleoside pyrophosphatases from human (human ITPase) and archaea (Mj0226 and PhNTPase). PMID:23385455

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

    PubMed

    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

    2012-06-01

    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 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 and paraoxon were determined to 2.4 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 Ser hydroxyl rotation prevents reversal of the reaction and allows access of a water molecule for completion of the reaction. PMID:22411095

  17. Disentangling the causes of heterogeneity in male fecundity in gynodioecious Beta vulgaris ssp. maritima.

    PubMed

    De Cauwer, I; Arnaud, J-F; Klein, E K; Dufay, M

    2012-08-01

    Variation among individuals in reproductive success is advocated as a major process driving evolution of sexual polymorphisms in plants, such as gynodioecy where females and hermaphrodites coexist. In gynodioecious Beta vulgaris ssp. maritima, sex determination involves cytoplasmic male sterility (CMS) genes and nuclear restorers of male fertility. Both restored CMS and non-CMS hermaphrodites co-occur. Genotype-specific differences in male fitness are theoretically expected to explain the maintenance of cytonuclear polymorphism. Using genotypic information on seedlings and flowering plants within two metapopulations, we investigated whether male fecundity was influenced by ecological, phenotypic and genetic factors, while taking into account the shape and scale of pollen dispersal. Along with spatially restricted pollen flow, we showed that male fecundity was affected by flowering synchrony, investment in reproduction, pollen production and cytoplasmic identity of potential fathers. Siring success of non-CMS hermaphrodites was higher than that of restored CMS hermaphrodites. However, the magnitude of the difference in fecundity depended on the likelihood of carrying restorer alleles for non-CMS hermaphrodites. Our results suggest the occurrence of a cost of silent restorers, a condition supported by scarce empirical evidence, but theoretically required to maintain a stable sexual polymorphism in gynodioecious species. PMID:22691102

  18. Crystal structures of Thermotoga maritima reverse gyrase: inferences for the mechanism of positive DNA supercoiling

    PubMed Central

    Rudolph, Markus G.; del Toro Duany, Yoandris; Jungblut, Stefan P.; Ganguly, Agneyo; Klostermeier, Dagmar

    2013-01-01

    Reverse gyrase is an ATP-dependent topoisomerase that is unique to hyperthermophilic archaea and eubacteria. The only reverse gyrase structure determined to date has revealed the arrangement of the N-terminal helicase domain and the C-terminal topoisomerase domain that intimately cooperate to generate the unique function of positive DNA supercoiling. Although the structure has elicited hypotheses as to how supercoiling may be achieved, it lacks structural elements important for supercoiling and the molecular mechanism of positive supercoiling is still not clear. We present five structures of authentic Thermotoga maritima reverse gyrase that reveal a first view of two interacting zinc fingers that are crucial for positive DNA supercoiling. The so-called latch domain, which connects the helicase and the topoisomerase domains is required for their functional cooperation and presents a novel fold. Structural comparison defines mobile regions in parts of the helicase domain, including a helical insert and the latch that are likely important for DNA binding during catalysis. We show that the latch, the helical insert and the zinc fingers contribute to the binding of DNA to reverse gyrase and are uniquely placed within the reverse gyrase structure to bind and guide DNA during strand passage. A possible mechanism for positive supercoiling by reverse gyrases is presented. PMID:23209025

  19. Detection of the strand exchange reaction using DNAzyme and Thermotoga maritima recombinase A.

    PubMed

    Jo, Hunho; Lee, Seonghwan; Min, Kyoungin; Ban, Changill

    2012-02-01

    We have designed multiple detection systems for the DNA strand exchange process. Thermostable Thermotoga maritima recombinase A (TmRecA), a core protein in homologous recombination, and DNAzyme, a catalytic DNA that can cleave a specific DNA sequence, are introduced in this work. In a colorimetric method, gold nanoparticles (AuNPs) modified with complementary DNAs (cDNAs) were assembled by annealing. Aggregated AuNPs were then separated irreversibly by TmRecA and DNAzyme, leading to a distinct color change in the particles from purple to red. For the case of fluorometric detection, fluorescein isothiocyanate (FITC)-labeled DNA as a fluorophore and black hole quencher 1 (BHQ1)-labeled DNA as a quencher were used; successful strand exchange was clearly detected by variations in fluorescence intensity. In addition, alterations in the impedance of a gold electrode with immobilized DNA were employed to monitor the regular exchange of DNA strands. All three methods provided sufficient evidence of efficient strand exchange reactions and have great potential for applications in the monitoring of recombination, discovery of new DNAzymes, detection of DNAzymes, and measurement of other protein activities. PMID:22178915

  20. Crystal structure of a phosphatase with a unique substrate binding domain from Thermotoga maritima.

    PubMed

    Shin, Dong Hae; Roberts, Anne; Jancarik, Jaru; Yokota, Hisao; Kim, Rosalind; Wemmer, David E; Kim, Sung-Hou

    2003-07-01

    We have determined the crystal structure of a phosphatase with a unique substrate binding domain from Thermotoga maritima, TM0651 (gi 4981173), at 2.2 A resolution by selenomethionine single-wavelength anomalous diffraction (SAD) techniques. TM0651 is a member of the haloacid dehalogenase (HAD) superfamily, with sequence homology to trehalose-6-phosphate phosphatase and sucrose-6(F)-phosphate phosphohydrolase. Selenomethionine labeled TM0651 crystallized in space group C2 with three monomers per asymmetric unit. Each monomer has approximate dimensions of 65 x 40 x 35 A(3), and contains two domains: a domain of known hydrolase fold characteristic of the HAD family, and a domain with a new tertiary fold consisting of a six-stranded beta-sheet surrounded by four alpha-helices. There is one disulfide bond between residues Cys35 and Cys265 in each monomer. One magnesium ion and one sulfate ion are bound in the active site. The superposition of active site residues with other HAD family members indicates that TM0651 is very likely a phosphatase that acts through the formation of a phosphoaspartate intermediate, which is supported by both NMR titration data and a biochemical assay. Structural and functional database searches and the presence of many aromatic residues in the interface of the two domains suggest the substrate of TM0651 is a carbohydrate molecule. From the crystal structure and NMR data, the protein likely undergoes a conformational change upon substrate binding. PMID:12824492

  1. 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

  2. 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

  3. 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

  4. Development and cross-species amplification of microsatellite loci for Puccinellia maritima, an important engineer saltmarsh species.

    PubMed

    Rouger, R; Vallejo-Marin, M; Jump, A S

    2014-01-01

    The grass Puccinellia maritima is an important saltmarsh ecosystem engineer exhibiting wide morphological variation, which is partially genetically determined. Nevertheless, nothing is known about its population genetics or how neutral genetic variation is distributed throughout its geographical range. Here, we describe 12 polymorphic microsatellites pooled into two multiplexes for this octoploid species. Assessment of 24 samples from three populations revealed 4 to 29 alleles per locus, with variation in allele presence and abundance between populations. The transferability of these markers is reported based on their cross-amplification in six other Puccinellia species of different ploidy levels. PMID:24841787

  5. Complexed Structures of Formylglycinamide Ribonucleotide Amidotransferase from Thermotoga maritima Describe a Novel ATP Binding Protein Superfamily

    SciTech Connect

    Morar, Mariya; Anand, Ruchi; Hoskins, Aaron A.; Stubbe, JoAnne; Ealick, Steven E.

    2008-09-11

    Formylglycinamide ribonucleotide amidotransferase (FGAR-AT) catalyzes the ATP-dependent synthesis of formylglycinamidine ribonucleotide (FGAM) from formylglycinamide ribonucleotide (FGAR) and glutamine in the fourth step of the purine biosynthetic pathway. FGAR-AT is encoded by the purL gene. Two types of PurL have been detected. The first type, found in eukaryotes and Gram-negative bacteria, consists of a single 140 kDa polypeptide chain and is designated large PurL (lgPurL). The second type, small PurL (smPurL), is found in archaea and Gram-positive bacteria and consists of an 80 kDa polypeptide chain. SmPurL requires two additional gene products, PurQ and PurS, for activity. PurL is a member of a protein superfamily that contains a novel ATP-binding domain. Structures of several members of this superfamily are available in the unliganded form. We determined five different structures of FGAR-AT from Thermotoga maritima in the presence of substrates, a substrate analogue, and a product. These complexes have allowed a detailed description of the novel ATP-binding motif. The availability of a ternary complex enabled mapping of the active site, thus identifying potential residues involved in catalysis. The complexes show a conformational change in the active site compared to the unliganded structure. Surprising discoveries, an ATP molecule in an auxiliary site of the protein and the conformational changes associated with its binding, provoke speculation about the regulatory role of the auxiliary site in formation of the PurLSQ complex as well as the evolutionary relationship of PurLs from different organisms.

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

    SciTech Connect

    Morar, Mariya; Hoskins, Aaron A.; Stubbe, JoAnne; Ealick, Steven E.

    2008-10-02

    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 (FGAM), ADP, P{sub i}, and glutamate. Two forms of PurL have been characterized, large and small. Large PurL, present in most Gram-negative bacteria and eukaryotes, consists of a single polypeptide chain and contains three major domains: the N-terminal domain, the FGAM synthetase domain, and the glutaminase domain, with a putative ammonia channel located between the active sites of the latter two. Small PurL, present in Gram-positive bacteria and archaea, is structurally homologous to the FGAM synthetase domain of large PurL, and forms a complex with two additional gene products, PurQ and PurS. The structure of the PurS dimer is homologous with the N-terminal domain of large PurL, while PurQ, whose structure has not been reported, contains the glutaminase activity. In Bacillus subtilis, the formation of the PurLQS complex is dependent on glutamine and ADP and has been demonstrated by size-exclusion chromatography. In this work, a structure of the PurLQS complex from Thermotoga maritima is described revealing a 2:1:1 stoichiometry of PurS:Q:L, respectively. The conformational changes observed in TmPurL upon complex formation elucidate the mechanism of metabolite-mediated recruitment of PurQ and PurS. The flexibility of the PurS dimer is proposed to play a role in the activation of the complex and the formation of the ammonia channel. A potential path for the ammonia channel is identified.

  7. 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

  8. Characterization of Thermotoga maritima glycerol dehydrogenase for the enzymatic production of dihydroxyacetone.

    PubMed

    Beauchamp, Justin; Gross, Phillip G; Vieille, Claire

    2014-08-01

    NAD-dependent Thermotoga maritima glycerol dehydrogenase (TmGlyDH) converts glycerol into dihydroxyacetone (DHA), a valuable synthetic precursor and sunless tanning agent. In this work, recombinant TmGlyDH was characterized to determine if it can be used to catalyze DHA production. The pH optima for glycerol oxidation and DHA reduction at 50 °C were 7.9 and 6.0, respectively. Under the conditions tested, TmGlyDH had a linear Arrhenius plot up to 80 °C. TmGlyDH was more thermostable than other glycerol dehydrogenases, remaining over 50 % active after 7 h at 50 °C. TmGlyDH was active on racemic 1,2-propanediol and produced (R)-1,2-propanediol from hydroxyacetone with an enantiomeric excess above 99 %, suggesting that TmGlyDH can also be used for chiral synthesis. (R)-1,2-propanediol production from hydroxyacetone was demonstrated for the first time in a one-enzyme cycling reaction using glycerol as the second substrate. Negative cooperativity was observed with glycerol and DHA, but not with the cofactor. Apparent kinetic parameters for glycerol, DHA, and NAD(H) were determined over a broad pH range. TmGlyDH showed little activity with N(6)-carboxymethyl-NAD(+) (N(6)-CM-NAD), an NAD(+) analog modified for easy immobilization to amino groups, but the double mutation V44A/K157G increased catalytic efficiency with N(6)-CM-NAD(+) ten-fold. Finally, we showed for the first time that a GlyDH is active with immobilized N(6)-CM-NAD(+), suggesting that N(6)-CM-NAD(+) can be immobilized on an electrode to allow TmGlyDH activity in a system that reoxidizes the cofactor electrocatalytically. PMID:24664447

  9. Anti-hyperalgesic and Anti-inflammatory Activity of Alternanthera Maritima Extract and 2?-O-?-L-rhamnopyranosylvitexin in Mice.

    PubMed

    de Santana Aquino, Diana Figuereido; Piccinelli, Ana Claudia; Soares, Fabíola Lacerda Pires; Arena, Arielle Cristina; Salvador, Marcos José; Kassuya, Candida Aparecida Leite

    2015-12-01

    Alternanthera maritima are used in Brazilian popular medicine for the treatment of inflammatory and infectious diseases. Species of Alternanthera have demonstrated biological activities in previous scientific studies. The aim of this study was to determine whether the ethanol extract of the aerial parts of A. maritima (EEAM) and the isolated compound 2?-O-?-L-rhamnopyranosyl-vitexin inhibit mechanical hyperalgesia and parameters of inflammation in mice. The oral administration of EEAM significantly inhibited carrageenan (Cg)-induced paw edema and reduced leukocyte migration into the pleural cavity. 2?-O-?-L-rhamnopyranosylvitexin significantly inhibited paw edema and reduced both leukocyte migration and the leakage of protein into the pleural cavity. Both EEAM and 2?-O-?-L-rhamnopyranosylvitexin significantly prevented the Cg-induced hyperalgesia. Local administration of 2?-O-?-L-rhamnopyranosylvitexin significantly prevented the Cg- and tumor necrosis factor (TNF)-induced hyperalgesia. In conclusion, this study demonstrated that EEAM is an anti-inflammatory and anti-hyperalgesic agent, and the results suggested that 2?-O-?-L-rhamnopyranosylvitexin is responsible for the effects of EEAM and the mechanism involves the TNF pathway. PMID:26045342

  10. Molecular and biochemical characterization of the thermoactive family 1 pectate lyase from the hyperthermophilic bacterium Thermotoga maritima.

    PubMed Central

    Kluskens, Leon D; van Alebeek, Gert-Jan W M; Voragen, Alphons G J; de Vos, Willem M; van der Oost, John

    2003-01-01

    The ability of the hyperthermophilic bacterium Thermotoga maritima to grow on pectin as a sole carbon source coincides with the secretion of a pectate lyase A (PelA) in the extracellular medium. The pel A gene of T. maritima was functionally expressed in Escherichia coli as the first heterologously produced thermophilic pectinase, and purified to homogeneity. Gel filtration indicated that the native form of PelA is tetrameric. Highest activity (422 units/mg, with a K(m) of 0.06 mM) was demonstrated on polygalacturonic acid (PGA), whereas pectins with an increasing degree of methylation were degraded at a decreasing rate. In the tradition of pectate lyases, PelA demonstrated full dependency on Ca(2+) for stability and activity. The enzyme is highly thermoactive and thermostable, operating optimally at 90 degrees C and pH 9.0, with a half-life for thermal inactivation of almost 2 h at 95 degrees C, and an apparent melting temperature of 102.5 degrees C. Detailed characterization of the product formation with PGA indicated that PelA has a unique eliminative exo-cleavage pattern liberating unsaturated trigalacturonate as the major product, in contrast with unsaturated digalacturonate for other exopectate lyases known. The unique exo-acting mode of action was supported by progression profiles of PelA on oligogalacturonides (degree of polymerization, 3-8) and the examination of the bond cleavage frequencies. PMID:12443532

  11. Anthelmintic activity of Artemisia vestita Wall ex DC. and Artemisia maritima L. against Haemonchus contortus from sheep.

    PubMed

    Irum, Shamaila; Ahmed, Haroon; Mukhtar, Muhammad; Mushtaq, Muhammad; Mirza, Bushra; Donskow-?ysoniewska, Katarzyna; Qayyum, Mazhar; Simsek, Sami

    2015-09-15

    Current study was designed to evaluate in vivo and in vitro anthelmintic activity of Artemisia vestita Wall ex DC. and Artemisia maritima L. against Haemonchus contortus in comparison with ivermectin to investigate the effect of plant extracts on survival of infective L3 and adults under in vitro condition. Plant extracts were given to H. contortus infected sheep orally and it was infected with L3 stage of H. contortus at dose of 5000 larvae/sheep. Total of 25-30 larvae were incubated with plant extracts in PBS alone and ivermectin at different concentration used as positive control. It was recorded that there is a significant decrease in fecal egg count (FEC) after post-treatment period for both plants. The highest fecal egg count reduction for A. vestita was 87.2% at 100mg/kg while for A. maritima it was 84.5% on day 28 post-treatment. Investigated extracts indicated significant activity against larvae and adult worms. PMID:26194429

  12. Molecular and biochemical characterization of bifunctional pyruvate decarboxylases and pyruvate ferredoxin oxidoreductases from Thermotoga maritima and Thermotoga hypogea.

    PubMed

    Eram, Mohammad S; Wong, Alton; Oduaran, Erica; Ma, Kesen

    2015-12-01

    Hyperthermophilic bacteria Thermotoga maritima and Thermotoga hypogea produce ethanol as a metabolic end product, which is resulted from acetaldehyde reduction catalysed by an alcohol dehydrogenase (ADH). However, the enzyme that is involved in the production of acetaldehyde from pyruvate is not well characterized. An oxygen sensitive and coenzyme A-dependent pyruvate decarboxylase (PDC) activity was found to be present in cell free extracts of T. maritima and T. hypogea. Both enzymes were purified and found to have pyruvate ferredoxin oxidoreductase (POR) activity, indicating their bifunctionality. Both PDC and POR activities from each of the purified enzymes were characterized in regards to their optimal assay conditions including pH dependency, oxygen sensitivity, thermal stability, temperature dependency and kinetic parameters. The close relatedness of the PORs that was shown by sequence analysis could be an indication of the presence of such bifunctionality in other hyperthermophilic bacteria. This is the first report of a bifunctional PDC/POR enzyme in hyperthermophilic bacteria. The PDC and the previously reported ADHs are most likely the key enzymes catalysing the production of ethanol from pyruvate in bacterial hyperthermophiles. PMID:26032540

  13. Crystallization and preliminary crystallographic analysis of an esterase with a novel domain from the hyperthermophile Thermotoga maritima

    SciTech Connect

    Sun, Lei; Levisson, Mark; Hendriks, Sjon; Akveld, Twan; Kengen, Servé W. M.; Dijkstra, Bauke W.; Oost, John van der

    2007-09-01

    A thermostable esterase (EstA) from Thermotoga maritima was cloned and purified. Crystals of EstA and its selenomethionine derivative were grown and diffract to beyond 2.6 Å resolution at 100 K using synchrotron radiation. A predicted esterase (EstA) with an unusual new domain from the hyperthermophilic bacterium Thermotoga maritima has been cloned and overexpressed in Escherichia coli. The purified protein was crystallized by the hanging-drop vapour-diffusion technique in the presence of lithium sulfate and polyethylene glycol 8000. Selenomethionine-substituted EstA crystals were obtained under the same conditions and three different-wavelength data sets were collected to 2.6 Å resolution. The crystal belongs to space group H32, with unit-cell parameters a = b = 130.2, c = 306.2 Å. There are two molecules in the asymmetric unit, with a V{sub M} of 2.9 Å{sup 3} Da{sup ?1} and 58% solvent content.

  14. Redox-Active Profile Characterization of Remirea maritima Extracts and Its Cytotoxic Effect in Mouse Fibroblasts (L929) and Melanoma (B16F10) Cells.

    PubMed

    Dória, Grace Anne A; Santos, Anderson R; Bittencourt, Leonardo S; Bortolin, Rafael C; Menezes, Paula P; Vasconcelos, Bruno S; Souza, Rebeca O; Fonseca, Maria José V; Santos, Alan Diego C; Saravanan, Shanmugam; Silva, Francilene A; Gelain, Daniel P; Moreira, José Cláudio F; Prata, Ana Paula N; Quintans-Júnior, Lucindo J; Araújo, Adriano A S

    2015-01-01

    Remirea maritima is a tropical plant with a reticulated root system belonging to the family Cyperaceae, also known to have biologically active secondary metabolites. However, very few data on R. maritima's biological actions are available and there are no reports regarding the redox-active profile of this plant. In this study, we examined the total phenolic content of Remirea maritima hydroalcoholic (RMHA) extracts, redox properties against different reactive species generated in vitro and their cytotoxic effect against fibroblasts (L929) and melanoma (B16F10) cells. Total reactive antioxidant potential index (TRAP) and total antioxidant reactivity (TAR) results revealed that RMHA at all concentrations tested showed significant antioxidant capacity. RMHA was also effective against hydroxyl radical formation, reduction of Fe3+ to Fe2+ and in scavenging nitric oxide (NO) radicals. In vitro, the level of lipid peroxidation was reduced by RMHA extract and the data showed significant oxidative damage protection. The RMHA cytotoxicity was evaluated by a neutral red assay in fibroblast (L929) and melanome (B16F10) cells. The obtained results showed that the RMHA (40 and 80 µg/mL, respectively) reduced 70% of the viable cells. In conclusion, this study represents the first report regarding the antioxidant and anti-proliferative potential of R. maritima against B16F10 melanoma cells. PMID:26121396

  15. Draft Genome Sequence of Ardenticatena maritima 110S, a Thermophilic Nitrate- and Iron-Reducing Member of the Chloroflexi Class Ardenticatenia

    PubMed Central

    Ward, Lewis M.; Pace, Laura A.; Fischer, Woodward W.

    2015-01-01

    We report here the draft genome sequence of Ardenticatena maritima 110S, the first sequenced member of class Ardenticatenia of the phylum Chloroflexi. This thermophilic organism is capable of a range of physiologies, including aerobic respiration and iron reduction. It also encodes a complete denitrification pathway with a novel nitric oxide reductase. PMID:26586887

  16. Thermotoga maritima IscU. Structural characterization and dynamics of a new class of metallochaperone.

    PubMed

    Bertini, Ivano; Cowan, J A; Del Bianco, Cristina; Luchinat, Claudio; Mansy, Sheref S

    2003-08-22

    Members of the IscU family of proteins are among the most conserved of all protein groups, extending across all three kingdoms of life. IscU serves as a scaffold for the assembly of intermediate iron-sulfur cluster centers and further mediates delivery to apo protein targets. Several proteins that mediate delivery of single metal ions to apo targets (termed metallochaperones) have recently been characterized structurally. Each displays a ferredoxin-like betaalphabetabetaalphabeta motif as a structural core. Assembly and delivery of a polynuclear iron-sulfur cluster is, however, a more complex pathway and presumably would demand a distinctive protein mediator. Here, we demonstrate Thermotoga maritima IscU (Tm IscU) to display unique structural and motional characteristics that distinguish it from other members of this class of proteins. In particular, IscU adopts a mobile, physiologically relevant, molten globule-like state that is vastly different from the previously identified ferredoxin-like fold that has thus far been characterized for other metallochaperones. The secondary structural content of Tm IscU is consistent with previous circular dichroism measurements on apo and holo protein, consisting of six alpha-helices and three beta-strands, the latter forming an anti-parallel beta-sheet. Extensive dynamics studies are consistent with a protein that has reasonably well defined secondary structural elements, but with a tertiary structure that is fluxional among widely different conformational arrangements. Analogous conformational flexibility does not exist in other structurally characterized metallochaperones; however, such a dynamic molecule may account for the lack of long-range NOEs, and allow both for the flexibility that is necessary for the multiple roles of Fe-S cluster assembly, and recognition and delivery of that cluster to a target protein. Additionally, the fluxionality of IscU is unique in that the protein appears to be more compact (based on 1H/2H exchange, R1, R2, and NOE data) but yet more fluid (lack of long-range NOEs) than typical molten globule proteins. PMID:12909018

  17. The effect of macrofauna, meiofauna and microfauna on the degradation of Spartina maritima detritus from a salt marsh area

    NASA Astrophysics Data System (ADS)

    Lillebø, Ana Isabel; Flindt, Mogens R.; Pardal, Miguel Ângelo; Marques, João Carlos

    1999-07-01

    Decomposition of salt marsh plants results from physical, chemical and biological processes including abiotic and biotic fragmentation, microbial decay and chemical transformation. According to literature data, only a few species have the ability to feed directly on living plant material, so fungi and bacteria seem to be the principal competitors for the organic substrates. Nevertheless, by consuming bacteria, protists and fungi associated to the detritus, macrofauna and meiofauna recycle the incorporated nutrients. Moreover, this nutrient regeneration may be seen as an effective factor in maintaining and stimulating bacterial production. In fact, it is well known that many detritus feeding species have very low assimilation efficiencies. The objective of the present study was to compare the nutrient mass balance of carbon; nitrogen and phosphorus in Spartina maritima covered areas and bare bottom sediment, with and without contribution of macrofauna, meiofauna and microbial populations. Nutrients mass balance was studied taking into account the initial and final nutrient concentrations in the sediment, water and plant material. Faunal activity was measured as a function of remineralised carbon, nitrogen and phosphorus. The experimental set-up included sixteen sub-experiments, which varied with respect to type of fauna, plant biomass and oxic status. Each sub-experiment was performed in small glass containers (3 L) containing about 900 g wwt sediment and 2.5 L estuarine water. Plant material, cut from intact plants, sediment cores and estuarine water were brought from the southern arm of the Mondego estuary (Portugal). The results showed that although the bacterial activity was responsible for the Spartina maritima degradation, the presence of meiofauna and macrofauna significantly enhanced the process. Moreover, the presence of Spartina maritima positively affected the mineralisation of the sediment carbon and nitrogen, especially when the three faunal components were present, and denitrification rates were highest in the presence of the macrofauna and meiofauna. The present study suggests that macrofauna and meiofauna have an important role on the ecosystem nutrient flux and that fauna might function as a sink for excess nutrients, that otherwise could be exported to the coastal waters.

  18. Purification, crystallization, crystallographic analysis and phasing of the CRISPR-associated protein Csm2 from Thermotoga maritima.

    PubMed

    Gallo, Gloria; Augusto, Gilles; Rangel, Giulliana; Zelanis, André; Mori, Marcelo A; Barbosa Campos, Cláudia; Würtele, Martin

    2015-10-01

    The clusters of regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated proteins (Cas) system consists of an intriguing machinery of proteins that confer bacteria and archaea with immunity against phages and plasmids via an RNA-guided interference mechanism. Here, the cloning, recombinant expression in Escherichia coli BL21 (DE3), purification, crystallization and preliminary X-ray diffraction analysis of Csm2 from Thermotoga maritima are reported. Csm2 is thought to be a component of an important protein complex of the type IIIA CRISPR-Cas system, which is involved in the CRISPR-Cas RNA-guided interference pathway. The structure of Csm2 was solved via cadmium single-wavelength anomalous diffraction (Cd-SAD) phasing. Owing to its involvement in the CRISPR-Cas system, the crystal structure of this protein could be of importance in elucidating the mechanism of type IIIA CRISPR-Cas systems in bacteria and archaea. PMID:26457510

  19. X-ray crystal structure of CutA from thermotoga maritima at 1.4 {Angstrom} resolution.

    SciTech Connect

    Savchenko, A.; Skarina, T.; Evdokimova, E.; Watson, J. D.; Laskowski, R.; Arrowsmith, C. H.; Edwards, A. M.; Joachimiak, A.; Zhang, R.; Univ. Health Network; Univ. of Toronto; Birkbeck Coll.

    2004-01-01

    The structure of the CutA protein from Thermotoga maritima (tmCutA) was determined at 1.4 {angstrom} resolution using the Se-Met multiwavelength anomalous diffraction (MAD) technique. This protein (TIGR annotation - TM1056, DNA bases 1,069,580--1,069,885) is conserved in numerous bacteria, archaea and eucarya, including plants and mammals (COG1324). The CutA Escherichia coli homolog - CutAl (35% ID) is involved in divalent cation homeostasis, while the mammalian homolog - mCutA (40% ID) was found to be associated with cell surface acetylcholinesterase. However, the biological function of the CutA proteins is yet to be determined.

  20. Permeability and reactivity of Thermotoga maritima in latex bimodal blend coatings at 80 degrees C: a model high temperature biocatalytic coating.

    PubMed

    Lyngberg, Olav K; Solheid, Chris; Charaniya, Salim; Ma, Yue; Thiagarajan, Venkata; Scriven, L E; Flickinger, Michael C

    2005-06-01

    Thermostable polymers cast as thin, porous coatings or membranes may be useful for concentrating and stabilizing hyperthermophilic microorganisms as biocatalysts. Hydrogel matrices can be unstable above 65 degrees C. Therefore a 55-microm thick, two layer (cell coat + polymer top coat) bimodal, adhesive latex coating of partially coalesced polystyrene particles was investigated at 80 degrees C using Thermotoga maritima as a model hyperthermophile. Coating permeability (pore structure) was critical for maintaining T. maritima viability. The permeability of bimodal coatings generated from 0.8 v/v of a suspension of non-film-forming 800 nm polystyrene particles with high glass transition temperature (T(g) = 94 degrees C, 26.9% total solids) blended with 0.2 v/v of a suspension of film-forming 158 nm polyacrylate/styrene particles (T(g) approximately -5 degrees C, 40.9% total solids) with 0.3 g sucrose/g latex was measured in a KNO3 diffusion cell. Diffusivity ratio remained above 0.04 (D(eff)/D) when incubated at 80 degrees C in artificial seawater (ASW) for 5 days. KNO3 permeability was corroborated by cryogenic-SEM images of the pore structure. In contrast, the permeability of a mono-dispersed acrylate/vinyl acetate latex Rovace SF091 (T(g) approximately 10 degrees C) rapidly decreased and became impermeable after 2 days incubation in ASW at 80 degrees C. Thermotoga maritima were entrapped in these coatings at a cell density of 49 g cell wet weight/liter of coating volume, 25-fold higher than the density in liquid culture. Viable T. maritima were released from single-layer coatings at 80 degrees C but accurate measurement of the percentage of viable entrapped cells by plate counting was not successful. Metabolic activity could be measured in bilayer coatings by utilization of glucose and maltose, which was identical for latex-entrapped and suspended cells. Starch was hydrolyzed for 200 h by latex-entrapped cells due to the slow diffusion of starch through the polymer top coat compared to only 24 h by suspended T. maritima. The observed reactivity and stability of these coatings was surprising since cryo-SEM images suggested that the smaller low T(g) polyacrylate/styrene particles preferentially bound to the T. maritima toga-sheath during coat formation. This model system may be useful for concentrating, entrapment and stabilization of metabolically active hyperthermophiles at 80 degrees C. PMID:15778817

  1. 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

  2. The Elucidation of the Structure of Thermotoga maritima Peptidoglycan Reveals Two Novel Types of Cross-link*

    PubMed Central

    Boniface, Audrey; Parquet, Claudine; Arthur, Michel; Mengin-Lecreulx, Dominique; Blanot, Didier

    2009-01-01

    Thermotoga maritima is a Gram-negative, hyperthermophilic bacterium whose peptidoglycan contains comparable amounts of l- and d-lysine. We have determined the fine structure of this cell-wall polymer. The muropeptides resulting from the digestion of peptidoglycan by mutanolysin were separated by high-performance liquid chromatography and identified by amino acid analysis after acid hydrolysis, dinitrophenylation, enzymatic determination of the configuration of the chiral amino acids, and mass spectrometry. The high-performance liquid chromatography profile contained four main peaks, two monomers, and two dimers, plus a few minor peaks corresponding to anhydro forms. The first monomer was the d-lysine-containing disaccharide-tripeptide in which the d-Glu-d-Lys bond had the unusual ??? arrangement (GlcNAc-MurNAc-l-Ala-?-d-Glu-?-d-Lys). The second monomer was the conventional disaccharide-tetrapeptide (GlcNAc-MurNAc-l-Ala-?-d-Glu-l-Lys-d-Ala). The first dimer contained a disaccharide-l-Ala as the acyl donor cross-linked to the ?-amine of d-Lys in a tripeptide acceptor stem with the sequence of the first monomer. In the second dimer, donor and acceptor stems with the sequences of the second and first monomers, respectively, were connected by a d-Ala4-?-d-Lys3 cross-link. The cross-linking index was 10 with an average chain length of 30 disaccharide units. The structure of the peptidoglycan of T. maritima revealed for the first time the key role of d-Lys in peptidoglycan synthesis, both as a surrogate of l-Lys or meso-diaminopimelic acid at the third position of peptide stems and in the formation of novel cross-links of the l-Ala1(???)d-Lys3 and d-Ala4(???)d-Lys3 types. PMID:19542229

  3. Overproduction, purification, crystallization and preliminary X-ray analysis of the peroxiredoxin domain of a larger natural hybrid protein from Thermotoga maritima

    SciTech Connect

    Barbey, Carole; Rouhier, Nicolas; Haouz, Ahmed; Navaza, Alda; Jacquot, Jean-Pierre

    2008-01-01

    Crystals of the peroxiredoxin domain of a larger natural hybrid protein from T. maritima were obtained which diffracted to 2.9 Å resolution on a synchrotron source. Thermotoga maritima contains a natural hybrid protein constituted of two moieties: a peroxiredoxin domain at the N-terminus and a nitroreductase domain at the C-terminus. The peroxiredoxin (Prx) domain has been overproduced and purified from Escherichia coli cells. The recombinant Prx domain, which is homologous to bacterial Prx BCP and plant Prx Q, folds properly into a stable protein that possesses biological activity. The recombinant protein was crystallized and synchrotron data were collected to 2.9 Å resolution. The crystals belonged to the tetragonal space group I422, with unit-cell parameters a = b = 176.67, c = 141.20 Å.

  4. 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

  5. Haplotype Detection from Next-Generation Sequencing in High-Ploidy-Level Species: 45S rDNA Gene Copies in the Hexaploid Spartina maritima

    PubMed Central

    Boutte, Julien; Aliaga, Benoît; Lima, Oscar; Ferreira de Carvalho, Julie; Ainouche, Abdelkader; Macas, Jiri; Rousseau-Gueutin, Mathieu; Coriton, Olivier; Ainouche, Malika; Salmon, Armel

    2015-01-01

    Gene and whole-genome duplications are widespread in plant nuclear genomes, resulting in sequence heterogeneity. Identification of duplicated genes may be particularly challenging in highly redundant genomes, especially when there are no diploid parents as a reference. Here, we developed a pipeline to detect the different copies in the ribosomal RNA gene family in the hexaploid grass Spartina maritima from next-generation sequencing (Roche-454) reads. The heterogeneity of the different domains of the highly repeated 45S unit was explored by identifying single nucleotide polymorphisms (SNPs) and assembling reads based on shared polymorphisms. SNPs were validated using comparisons with Illumina sequence data sets and by cloning and Sanger (re)sequencing. Using this approach, 29 validated polymorphisms and 11 validated haplotypes were reported (out of 34 and 20, respectively, that were initially predicted by our program). The rDNA domains of S. maritima have similar lengths as those found in other Poaceae, apart from the 5′-ETS, which is approximately two-times longer in S. maritima. Sequence homogeneity was encountered in coding regions and both internal transcribed spacers (ITS), whereas high intragenomic variability was detected in the intergenic spacer (IGS) and the external transcribed spacer (ETS). Molecular cytogenetic analysis by fluorescent in situ hybridization (FISH) revealed the presence of one pair of 45S rDNA signals on the chromosomes of S. maritima instead of three expected pairs for a hexaploid genome, indicating loss of duplicated homeologous loci through the diploidization process. The procedure developed here may be used at any ploidy level and using different sequencing technologies. PMID:26530424

  6. 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

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

    2014-05-01

    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

  7. Haplotype Detection from Next-Generation Sequencing in High-Ploidy-Level Species: 45S rDNA Gene Copies in the Hexaploid Spartina maritima.

    PubMed

    Boutte, Julien; Aliaga, Benoît; Lima, Oscar; Ferreira de Carvalho, Julie; Ainouche, Abdelkader; Macas, Jiri; Rousseau-Gueutin, Mathieu; Coriton, Olivier; Ainouche, Malika; Salmon, Armel

    2015-01-01

    Gene and whole-genome duplications are widespread in plant nuclear genomes, resulting in sequence heterogeneity. Identification of duplicated genes may be particularly challenging in highly redundant genomes, especially when there are no diploid parents as a reference. Here, we developed a pipeline to detect the different copies in the ribosomal RNA gene family in the hexaploid grass Spartina maritima from next-generation sequencing (Roche-454) reads. The heterogeneity of the different domains of the highly repeated 45S unit was explored by identifying single nucleotide polymorphisms (SNPs) and assembling reads based on shared polymorphisms. SNPs were validated using comparisons with Illumina sequence data sets and by cloning and Sanger (re)sequencing. Using this approach, 29 validated polymorphisms and 11 validated haplotypes were reported (out of 34 and 20, respectively, that were initially predicted by our program). The rDNA domains of S. maritima have similar lengths as those found in other Poaceae, apart from the 5'-ETS, which is approximately two-times longer in S. maritima. Sequence homogeneity was encountered in coding regions and both internal transcribed spacers (ITS), whereas high intragenomic variability was detected in the intergenic spacer (IGS) and the external transcribed spacer (ETS). Molecular cytogenetic analysis by fluorescent in situ hybridization (FISH) revealed the presence of one pair of 45S rDNA signals on the chromosomes of S. maritima instead of three expected pairs for a hexaploid genome, indicating loss of duplicated homeologous loci through the diploidization process. The procedure developed here may be used at any ploidy level and using different sequencing technologies. PMID:26530424

  8. Diversity and Ecological Characterization of Sporulating Higher Filamentous Marine Fungi Associated with Spartina maritima (Curtis) Fernald in Two Portuguese Salt Marshes.

    PubMed

    Calado, Maria da Luz; Carvalho, Luís; Pang, Ka-Lai; Barata, Margarida

    2015-10-01

    Fungal communities associated with early stages of decomposition of Spartina maritima (Curtis) Fernald were assessed in two geographically distinct salt marshes in Portugal by direct observation of fungal sporulating structures. Twenty-three fungal taxa were identified from 390 plant samples, 11 of which were common to both study sites. Natantispora retorquens, Byssothecium obiones, Phaeosphaeria spartinicola, Phoma sp. 1 and Stagonospora sp. were the most frequent fungal taxa in the studied communities. The fungal species Anthostomella spissitecta, Camarosporium roumeguerii, Coniothyrium obiones, Decorospora gaudefroyi, Halosarpheia trullifera, Leptosphaeria marina and Stagonospora haliclysta were recorded for the first time on S. maritima plants; with the exception of C. roumeguerii and L. marina, all of these species were also new records for Portugal. The differences between species composition of the communities associated with S. maritima were attributed to differences in abiotic conditions of the salt marshes. Although the fungal taxa were distributed differently along the host plants, common species to both fungal communities were found on the same relative position, e.g. B. obiones, Lulworthia sp. and N. retorquens occurred on the basal plant portions, Buergenerula spartinae, Dictyosporium pelagicum and Phoma sp. 1 on the middle plant portions and P. spartinicola and Stagonospora sp. on the top plant portions. The distinct vertical distribution patterns reflected species-specific salinity requirements and flooding tolerance, but specially substrate preferences. The most frequent fungi in both communities also exhibited wider distribution ranges and produced a higher number of fruiting structures, suggesting a more active key role in the decay process of S. maritima. PMID:25851444

  9. Oxygen uptake rates in the hyperthermophilic anaerobe Thermotoga maritima grown in a bioreactor under controlled oxygen exposure: clues to its defence strategy against oxidative stress.

    PubMed

    Lakhal, Raja; Auria, Richard; Davidson, Sylvain; Ollivier, Bernard; Durand, Marie-Claire; Dolla, Alain; Hamdi, Moktar; Combet-Blanc, Yannick

    2011-06-01

    A 2.3-L bioreactor was specially adapted to grow hyperthermophilic microorganisms under controlled conditions of temperature, pH, redox potential and dissolved O(2). Using this bioreactor regulated at 80°C and pH 7.0, we demonstrated that Thermotoga maritima recovered its growth despite being exposed to oxygen for a short time (30 min with a maximum concentration of 23 ?M of dissolved oxygen). Under these conditions, we demonstrated that O(2) uptake rate, estimated at 73.6 ?moles O(2) min(-1) g proteins(-1) for dissolved oxygen, was optimal and constant, when dissolved oxygen was present in a range of 22-5 ?M. Transcription analyses revealed that during short oxygen exposure, T. maritima expressed genes coding for enzymes to deal with O(2) and reactive oxygen species (ROS) such as peroxides. Thus, genes encoding ROS-scavenging systems, alkyl hydroperoxide reductase (ahp), thioredoxin-dependent thiol peroxidase (bcp 2) and to a lesser extent neelaredoxin (nlr) and rubrerythrin (rbr), were found to be upregulated during oxygen exposure. The oxygen reductase FprA, homologous to the rubredoxin-oxygen oxidoreductase (ROO) found in Desulfovibrio species, is proposed as a primary consumer of O(2) in T. maritima. Moreover, the expression of frpA was shown to depend on the redox (Eh) level of the culture medium. PMID:21400100

  10. Transcriptomic profiling of the salt stress response in excised leaves of the halophyte Beta vulgaris ssp. maritima.

    PubMed

    Skorupa, Monika; Gołębiewski, Marcin; Domagalski, Krzysztof; Kurnik, Katarzyna; Abu Nahia, Karim; Złoch, Michał; Tretyn, Andrzej; Tyburski, Jarosław

    2016-02-01

    Beta vulgaris ssp. maritima is a halophytic relative of cultivated beets. In the present work a transcriptome response to acute salt stress imposed to excised leaves of sea beet was investigated. Salt treatments consisted of adding NaCl directly to the transpiration stream by immersing the petioles of excised leaves into the salt solutions. Sequencing libraries were generated from leaves subjected to either moderate or strong salt stress. Control libraries were constructed from untreated leaves. Sequencing was performed using the Illumina MiSeq platform. We obtained 32970 unigenes by assembling the pooled reads from all the libraries with Trinity software. Screening the nr database returned 18 362 sequences with functional annotation. Using the reference transcriptome we identified 1 246 genes that were differentially expressed after 48h of NaCl stress. Genes related to several cellular functions such as membrane transport, osmoprotection, molecular chaperoning, redox metabolism or protein synthesis were differentially expressed in response to salt stress. The response of sea beet leaves to salt treatments was marked out by transcriptomic up-regulation of genes related to photosynthetic carbon fixation, ribosome biogenesis, cell wall-building and cell wall expansion. Furthermore, several novel and undescribed transcripts were responsive to salinity in leaves of sea beet. PMID:26795151

  11. The Structural Basis of Alpha-Glucan Recognition by a Family 41 Carbohydrate-Binding Module from Therotoga Maritima

    SciTech Connect

    van Bueren,A.; Boraston, A.

    2006-01-01

    Starch recognition by carbohydrate-binding modules (CBMs) is important for the activity of starch-degrading enzymes. The N-terminal family 41 CBM, TmCBM41 (from pullulanase PulA secreted by Thermotoga maritima) was shown to have {alpha}-glucan binding activity with specificity for {alpha}-1, 4-glucans but was able to tolerate the {alpha}-1, 6-linkages found roughly every three or four glucose units in pullulan. Using X-ray crystallography, the structures were solved for TmCBM41 in an uncomplexed form and in complex with maltotetraose and 63-{alpha}-d-glucosyl-maltotriose (GM3). Ligand binding was facilitated by stacking interactions between the {alpha}-faces of the glucose residues and two tryptophan side-chains in the two main subsites of the carbohydrate-binding site. Overall, this mode of starch binding is quite well conserved by other starch-binding modules. The structure in complex with GM3 revealed a third binding subsite with the flexibility to accommodate an {alpha}-1, 4- or an {alpha}-1, 6-linked glucose.

  12. Histone acetylation influences the transcriptional activation of POX in Beta vulgaris L. and Beta maritima L. under salt stress.

    PubMed

    Yolcu, Seher; Ozdemir, Filiz; Güler, Aybüke; Bor, Melike

    2016-03-01

    Acetylation of histone proteins is a type of chromatin modification which facilitates the activation of genes. Recent studies brought up the importance of this reversible and rapid process for the regulation of gene expression especially in plant defense against a variety of environmental stresses. Deciphering the exact mechanisms of chromatin modifications under abiotic stress conditions is important for improving crop plants' performance and yield. In a previous study we compared the salt stress responses of Beta vulgaris (sugar beet) and Beta maritima (wild beet). In accordance with those results we suggested that chromatin remodeling can be an active process in the regulation of genes related to salt stress tolerance of these plants. Therefore we performed ChIP assay in control and salt stressed (250 and 500 mM NaCl) plants and compared the enrichment of acetylation in the associated chromatin sites. We found that the transcriptional activation of one peroxidase (POX) encoding gene was associated with the elevated levels of acetylation in H3K9 and H3K27 sites. The acetylation patterns were remarkably different between two species in which the highest acetylation levels were found at H3K9 and H3K27 in wild beet and sugar beet respectively. PMID:26773543

  13. 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

  14. 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

  15. Effects of fine-scale genetic structure on male mating success in gynodioecious Beta vulgaris ssp. maritima.

    PubMed

    DE Cauwer, Isabelle; Dufay, Mathilde; Cuguen, Joël; Arnaud, Jean-François

    2010-04-01

    Plant mating systems are known to influence population genetic structure because pollen and seed dispersal are often spatially restricted. However, the reciprocal outcomes of population structure on the dynamics of polymorphic mating systems have received little attention. In gynodioecious sea beet (Beta vulgaris ssp. maritima), three sexual types co-occur: females carrying a cytoplasmic male sterility (CMS) gene, hermaphrodites carrying a non-CMS cytoplasm and restored hermaphrodites that carry CMS genes and nuclear restorer alleles. This study investigated the effects of fine-scale genetic structure on male reproductive success of the two hermaphroditic forms. Our study population was strongly structured and characterized by contrasting local sex-ratios. Pollen flow was constrained over short distances and depended on local plant density. Interestingly, restored hermaphrodites sired significantly more seedlings than non-CMS hermaphrodites, despite the previous observation that the former produce pollen of lower quality than the latter. This result was explained by the higher frequency of females in the local vicinity of restored (CMS) hermaphrodites as compared to non-CMS hermaphrodites. Population structure thus strongly influences individual fitness and may locally counteract the expected effects of selection, suggesting that understanding fine scale population processes is central to predicting the evolution of gender polymorphism in angiosperms. PMID:20345690

  16. 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.

  17. The Crystal Structure of Thermotoga maritima Class III Ribonucleotide Reductase Lacks a Radical Cysteine Pre-Positioned in the Active Site.

    PubMed

    Aurelius, Oskar; Johansson, Renzo; Bågenholm, Viktoria; Lundin, Daniel; Tholander, Fredrik; Balhuizen, Alexander; Beck, Tobias; Sahlin, Margareta; Sjöberg, Britt-Marie; Mulliez, Etienne; Logan, Derek T

    2015-01-01

    Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides to deoxyribonucleotides, the building blocks for DNA synthesis, and are found in all but a few organisms. RNRs use radical chemistry to catalyze the reduction reaction. Despite RNR having evolved several mechanisms for generation of different kinds of essential radicals across a large evolutionary time frame, this initial radical is normally always channelled to a strictly conserved cysteine residue directly adjacent to the substrate for initiation of substrate reduction, and this cysteine has been found in the structures of all RNRs solved to date. We present the crystal structure of an anaerobic RNR from the extreme thermophile Thermotoga maritima (tmNrdD), alone and in several complexes, including with the allosteric effector dATP and its cognate substrate CTP. In the crystal structure of the enzyme as purified, tmNrdD lacks a cysteine for radical transfer to the substrate pre-positioned in the active site. Nevertheless activity assays using anaerobic cell extracts from T. maritima demonstrate that the class III RNR is enzymatically active. Other genetic and microbiological evidence is summarized indicating that the enzyme is important for T. maritima. Mutation of either of two cysteine residues in a disordered loop far from the active site results in inactive enzyme. We discuss the possible mechanisms for radical initiation of substrate reduction given the collected evidence from the crystal structure, our activity assays and other published work. Taken together, the results suggest either that initiation of substrate reduction may involve unprecedented conformational changes in the enzyme to bring one of these cysteine residues to the expected position, or that alternative routes for initiation of the RNR reduction reaction may exist. Finally, we present a phylogenetic analysis showing that the structure of tmNrdD is representative of a new RNR subclass IIIh, present in all Thermotoga species plus a wider group of bacteria from the distantly related phyla Firmicutes, Bacteroidetes and Proteobacteria. PMID:26147435

  18. Phenotypic Changes in Transgenic Tobacco Plants Overexpressing Vacuole-Targeted Thermotoga maritima BglB Related to Elevated Levels of Liberated Hormones

    PubMed Central

    Nguyen, Quynh Anh; Lee, Dae-Seok; Jung, Jakyun; Bae, Hyeun-Jong

    2015-01-01

    The hyperthermostable β-glucosidase BglB of Thermotoga maritima was modified by adding a short C-terminal tetrapeptide (AFVY, which transports phaseolin to the vacuole, to its C-terminal sequence). The modified β-glucosidase BglB was transformed into tobacco (Nicotiana tabacum L.) plants. We observed a range of significant phenotypic changes in the transgenic plants compared to the wild-type (WT) plants. The transgenic plants had faster stem growth, earlier flowering, enhanced root systems development, an increased biomass biosynthesis rate, and higher salt stress tolerance in young plants compared to WT. In addition, programed cell death was enhanced in mature plants. Furthermore, the C-terminal AFVY tetrapeptide efficiently sorted T. maritima BglB into the vacuole, which was maintained in an active form and could perform its glycoside hydrolysis function on hormone conjugates, leading to elevated hormone [abscisic acid (ABA), indole 3-acetic acid (IAA), and cytokinin] levels that likely contributed to the phenotypic changes in the transgenic plants. The elevation of cytokinin led to upregulation of the transcription factor WUSCHELL, a homeodomain factor that regulates the development, division, and reproduction of stem cells in the shoot apical meristems. Elevation of IAA led to enhanced root development, and the elevation of ABA contributed to enhanced tolerance to salt stress and programed cell death. These results suggest that overexpressing vacuole-targeted T. maritima BglB may have several advantages for molecular farming technology to improve multiple targets, including enhanced production of the β-glucosidase BglB, increased biomass, and shortened developmental stages, that could play pivotal roles in bioenergy and biofuel production. PMID:26618153

  19. The Crystal Structure of Thermotoga maritima Class III Ribonucleotide Reductase Lacks a Radical Cysteine Pre-Positioned in the Active Site

    PubMed Central

    Aurelius, Oskar; Johansson, Renzo; Bågenholm, Viktoria; Lundin, Daniel; Tholander, Fredrik; Balhuizen, Alexander; Beck, Tobias; Sahlin, Margareta; Sjöberg, Britt-Marie; Mulliez, Etienne; Logan, Derek T.

    2015-01-01

    Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides to deoxyribonucleotides, the building blocks for DNA synthesis, and are found in all but a few organisms. RNRs use radical chemistry to catalyze the reduction reaction. Despite RNR having evolved several mechanisms for generation of different kinds of essential radicals across a large evolutionary time frame, this initial radical is normally always channelled to a strictly conserved cysteine residue directly adjacent to the substrate for initiation of substrate reduction, and this cysteine has been found in the structures of all RNRs solved to date. We present the crystal structure of an anaerobic RNR from the extreme thermophile Thermotoga maritima (tmNrdD), alone and in several complexes, including with the allosteric effector dATP and its cognate substrate CTP. In the crystal structure of the enzyme as purified, tmNrdD lacks a cysteine for radical transfer to the substrate pre-positioned in the active site. Nevertheless activity assays using anaerobic cell extracts from T. maritima demonstrate that the class III RNR is enzymatically active. Other genetic and microbiological evidence is summarized indicating that the enzyme is important for T. maritima. Mutation of either of two cysteine residues in a disordered loop far from the active site results in inactive enzyme. We discuss the possible mechanisms for radical initiation of substrate reduction given the collected evidence from the crystal structure, our activity assays and other published work. Taken together, the results suggest either that initiation of substrate reduction may involve unprecedented conformational changes in the enzyme to bring one of these cysteine residues to the expected position, or that alternative routes for initiation of the RNR reduction reaction may exist. Finally, we present a phylogenetic analysis showing that the structure of tmNrdD is representative of a new RNR subclass IIIh, present in all Thermotoga species plus a wider group of bacteria from the distantly related phyla Firmicutes, Bacteroidetes and Proteobacteria. PMID:26147435

  20. Phenotypic Changes in Transgenic Tobacco Plants Overexpressing Vacuole-Targeted Thermotoga maritima BglB Related to Elevated Levels of Liberated Hormones.

    PubMed

    Nguyen, Quynh Anh; Lee, Dae-Seok; Jung, Jakyun; Bae, Hyeun-Jong

    2015-01-01

    The hyperthermostable ?-glucosidase BglB of Thermotoga maritima was modified by adding a short C-terminal tetrapeptide (AFVY, which transports phaseolin to the vacuole, to its C-terminal sequence). The modified ?-glucosidase BglB was transformed into tobacco (Nicotiana tabacum L.) plants. We observed a range of significant phenotypic changes in the transgenic plants compared to the wild-type (WT) plants. The transgenic plants had faster stem growth, earlier flowering, enhanced root systems development, an increased biomass biosynthesis rate, and higher salt stress tolerance in young plants compared to WT. In addition, programed cell death was enhanced in mature plants. Furthermore, the C-terminal AFVY tetrapeptide efficiently sorted T. maritima BglB into the vacuole, which was maintained in an active form and could perform its glycoside hydrolysis function on hormone conjugates, leading to elevated hormone [abscisic acid (ABA), indole 3-acetic acid (IAA), and cytokinin] levels that likely contributed to the phenotypic changes in the transgenic plants. The elevation of cytokinin led to upregulation of the transcription factor WUSCHELL, a homeodomain factor that regulates the development, division, and reproduction of stem cells in the shoot apical meristems. Elevation of IAA led to enhanced root development, and the elevation of ABA contributed to enhanced tolerance to salt stress and programed cell death. These results suggest that overexpressing vacuole-targeted T. maritima BglB may have several advantages for molecular farming technology to improve multiple targets, including enhanced production of the ?-glucosidase BglB, increased biomass, and shortened developmental stages, that could play pivotal roles in bioenergy and biofuel production. PMID:26618153

  1. Growth of the dune wintergreen ( Pyrola rotundifolia ssp. maritima) at Braunton Burrows in relation to weather factors

    NASA Astrophysics Data System (ADS)

    Hunt, R.; Hope-Simpson, J. F.; Snape, J. B.

    1985-12-01

    The dune wintergreen ( Pyrola rotundifolia ssp. maritima) is an evergreen perennial herb which has spread extensively in recent decades to, and on, various British dune systems including Braunton Burrows, N. Devon. Its multiplication is partly vegetative, by rhizomes bearing leaf rosettes. This study primarily concerns the relation between: (i) the growth of one particular invasive colony on Braunton Burrows, as shown by the numbers of living rosettes counted at midsummer from 1964 74 inclusive; and (ii) concurrent meteorological records made nearby. Monthly weather means were calculated on various quarterly bases. After de-trending the Pyrola data statistically, correlations were sought between the growth in numbers achieved in each year and the local air temperature (three bases), rainfall and duration of bright sunshine. While the annual increase in net numbers appears to have been unaffected by sunshine hours, this increase does seem to have been much diminished by cold nights, particularly in early spring and, though less strongly so, by low rainfall in the latter part of the preceding summer. Taking account of the performance of Pyrola in other habitats on the Burrows, it is suggested that the rainfall correlation may reflect the influence of atmospheric humidity rather than water supply to the roots. Local meteorological records over a 51-year period show combined temperature and rainfall conditions consistently favourable to Pyrola growth throughout a 5-year run to a degree which might be expected to occur in only three such runs out of every hundred. The favourable period (1957 61) occurred between the inferred first occurrence of Pyrola on the Burrows and its observed rapid spread.

  2. Site-Directed Mutagenesis of a Hyperthermophilic Endoglucanase Cel12B from Thermotoga maritima Based on Rational Design

    PubMed Central

    Zhang, Jinfeng; Shi, Hao; Xu, Linyu; Zhu, Xiaoyan; Li, Xiangqian

    2015-01-01

    To meet the demand for the application of high activity and thermostable cellulases in the production of new-generation bioethanol from nongrain-cellulose sources, a hyperthermostable β-1,4-endoglucase Cel12B from Thermotoga maritima was selected for further modification by gene site-directed mutagenesis method in the present study, based on homology modeling and rational design. As a result, two recombinant enzymes showed significant improvement in enzyme activity by 77% and 87%, respectively, higher than the parental enzyme TmCel12B. Furthermore, the two mutants could retain 80% and 90.5% of their initial activity after incubation at 80°C for 8 h, while only 45% for 5 h to TmCel12B. The Km and Vmax of the two recombinant enzymes were 1.97±0.05 mM, 4.23±0.15 μmol·mg-1·min-1 of TmCel12B-E225H-K207G-D37V, and 2.97±0.12 mM, 3.15±0.21 μmol·mg-1·min-1 of TmCel12B-E225H-K207G, respectively, when using CMC-Na as the substrate. The roles of the mutation sites were also analyzed and evaluated in terms of electron density, hydrophobicity of the modeled protein structures. The recombinant enzymes may be used in the hydrolysis of cellulose at higher temperature in the future. It was concluded that the gene mutagenesis approach of a certain active residues may effectively improve the performance of cellulases for the industrial applications and contribute to the study the thermostable mechanism of thermophilic enzymes. PMID:26218520

  3. The structural basis of substrate promiscuity in UDP-hexose 4-epimerase from the hyperthermophilic Eubacterium Thermotoga maritima.

    PubMed

    Shin, Sun-Mi; Choi, Jin Myung; di Luccio, Eric; Lee, Yong-Jik; Lee, Sang-Jae; Lee, Sang Jun; Lee, Sung Haeng; Lee, Dong-Woo

    2015-11-01

    UDP-galactose 4-epimerase (GalE) catalyzes the interconversion of UDP-glucose (UDP-Glc) and UDP-galactose (UDP-Gal), which is a pivotal step in the Leloir pathway for d-galactose metabolism. Although GalE is widely distributed in prokaryotes and eukaryotes, little information is available regarding hyperthermophilic GalE. We overexpressed the TM0509 gene, encoding a putative GalE from Thermotoga maritima (TMGalE), in Escherichia coli and characterized the encoded protein. To further investigate the molecular basis of this enzyme's catalytic function, we determined the crystal structures of TMGalE and TMGalE bound to UDP-Glc at resolutions of 1.9 Å and 2.0 Å, respectively. The enzyme was determined to be a homodimer with a molecular mass of 70 kDa. The enzyme could reversibly catalyze the epimerization of UDP-GalNAc/UDP-GlcNAc as well as UDP-Gal/UDP-Glc at elevated temperatures, with an apparent optimal temperature and pH of 80 °C and 7.0, respectively. Our data showed that TM0509 is a UDP-galactosugar 4-epimerase involved in d-galactose metabolism; consequently, this study provides the first detailed characterization of a hyperthermophilic GalE. Moreover, the promiscuous substrate specificity of TMGalE, which is more similar to human GalE than E. coli GalE, supports the notion that TMGalE might exhibit the earliest form of sugar-epimerizing enzymes in the evolution of galactose metabolism. PMID:26344854

  4. 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

  5. Constitutive high-level expression of a codon-optimized ?-fructosidase gene from the hyperthermophile Thermotoga maritima in Pichia pastoris.

    PubMed

    Menéndez, Carmen; Martínez, Duniesky; Trujillo, Luis E; Mazola, Yuliet; González, Ernesto; Pérez, Enrique R; Hernández, Lázaro

    2013-02-01

    Enzymes for use in the sugar industry are preferred to be thermotolerant. In this study, a synthetic codon-optimized gene encoding a highly thermostable ?-fructosidase (BfrA, EC 3.2.1.26) from the bacterium Thermotoga maritima was expressed in the yeast Pichia pastoris. The gradual increase of the transgene dosage from one to four copies under the control of the constitutive glyceraldehyde 3-phosphate dehydrogenase promoter had an additive effect on BfrA yield without causing cell toxicity. Maximal values of cell biomass (115 g/l, dry weight) and overall invertase activity (241 U/ml) were reached at 72 h in fed-batch fermentations using cane sugar as the main carbon source for growth. Secretion driven by the Saccharomyces cerevisiae ?-factor signal peptide resulted in periplasmic retention (44 %) and extracellular release (56 %) of BfrA. The presence of N-linked oligosaccharides did not influence the optimal activity, thermal stability, kinetic properties, substrate specificity, and exo-type action mode of the yeast-secreted BfrA in comparison to the native unglycosylated enzyme. Complete inversion of cane sugar at initial concentration of 60 % (w/v) was achieved by periplasmic BfrA in undisrupted cells reacting at pH 5.5 and 70 °C, with average productivity of 4.4 g of substrate hydrolyzed per grams of biomass (wet weight) per hour. The high yield of fully active glycosylated BfrA here attained by recombinant P. pastoris in a low-cost fermentation process appears to be attractive for the large-scale production of this thermostable enzyme useful for the manufacture of inverted sugar syrup. PMID:22821437

  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.

    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. The interaction of ammonia and xenon with the imidazole glycerol phosphate synthase from Thermotoga maritima as detected by NMR spectroscopy

    PubMed Central

    Liebold, Christoph; List, Felix; Kalbitzer, Hans Robert; Sterner, Reinhard; Brunner, Eike

    2010-01-01

    The imidazole glycerol phosphate (ImGP) synthase from the hyperthermophilic bacterium Thermotoga maritima is a 1:1 complex of the glutaminase subunit HisH and the cyclase subunit HisF. It has been proposed that ammonia generated by HisH is transported through a channel to the active site of HisF, which generates intermediates of histidine (ImGP) and de novo biosynthesis of 5-aminoimidazole-4-carboxamideribotide. Solution NMR spectroscopy of ammonium chloride-titrated samples was used to study the interaction of NH3 with amino acids inside this channel. Although numerous residues showed 15N chemical shift changes, most of these changes were caused by nonspecific ionic strength effects. However, several interactions appeared to be specific. Remarkably, the amino acid residue Thr 78—which is located in the central channel—shows a large chemical shift change upon titration with ammonium chloride. This result and the reduced catalytic activity of the Thr78Met mutant indicate a special role of this residue in ammonia channeling. To detect and further characterize internal cavities in HisF, which might for example contribute to ammonia channeling, the interaction of HisF with the noble gas xenon was analyzed by solution NMR spectroscopy using 1H-15N HSQC experiments. The results indicate that HisF contains three distinct internal cavities, which could be identified by xenon-induced chemical shift changes of the neighboring amino acid residues. Two of these cavities are located at the active site at opposite ends of the substrate N?-[(5?-phosphoribulosyl)formimino]-5-aminoimidazole-4-carboxamide-ribonucleotide (PRFAR) binding groove. The third cavity is located in the interior of the central ?-barrel of HisF and overlaps with the putative ammonia transport channel. PMID:20665694

  8. Crystallization and preliminary X-ray crystallographic characterization of TrmFO, a folate-dependent tRNA methyltransferase from Thermotoga maritima

    SciTech Connect

    Cicmil, Nenad

    2008-03-01

    T. maritima TrmFO was overexpressed, purified and crystallized. A diffraction data set was collected to a resolution of 2.6 Å. TrmFO, previously classified as GID, is a methyltransferase that catalyzes the formation of 5-methyluridine or ribothymidine (T) at position 54 in tRNA in some Gram-positive bacteria. To date, TrmFO is the only characterized tRNA methyltransferase that does not use S-adenosylmethionine as the methyl-group donor. Instead, the donor of the methyl group is N{sup 5},N{sup 10}-methylenetetrahydrofolate. The crystallization and preliminary X-ray crystallographic studies of TrmFO are reported here. The recombinant protein, cloned from Thermotoga maritima genomic DNA, was overproduced in Esherichia coli and crystallized in 25%(v/v) PEG 4000, 100 mM NaCl and sodium citrate buffer pH 5.0 at 291 K using the hanging-drop vapor-diffusion method. The plate-shaped crystals diffracted to 2.6 Å and belong to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 79.94, b = 92.46, c = 127.20 Å.

  9. Crystallization and preliminary crystallographic studies of PotA, a membrane-associated ATPase of the spermidine-preferential uptake system in Thermotoga maritima.

    PubMed

    Sugiyama, Shigeru; Kashiwagi, Keiko; Kakinouchi, Keisuke; Tomitori, Hideyuki; Kanai, Ken; Murata, Michio; Adachi, Hiroaki; Matsumura, Hiroyoshi; Takano, Kazufumi; Murakami, Satoshi; Inoue, Tsuyoshi; Mori, Yusuke; Igarashi, Kazuei

    2014-06-01

    A membrane-associated ATPase, PotA, is a component of the spermidine-preferential uptake system in prokaryotes that plays an important role in normal cell growth by regulating the cellular polyamine concentration. No three-dimensional structures of membrane-associated ATPases in polyamine-uptake systems have been determined to date. Here, the crystallization and preliminary X-ray diffraction analysis of PotA from Thermotoga maritima are reported. Diffraction data were collected and processed to 2.7 Å resolution from both native and selenomethionine-labelled crystals. Preliminary crystallographic analysis revealed that the crystals belonged to the hexagonal space group P3₁12 (or P3₂12), with unit-cell parameters a=b=88.9, c=221.2 Å, α=90, β=90, γ=120°, indicating that a dimer was present in the asymmetric unit. PMID:24915082

  10. Purification, crystallization and preliminary X-ray diffraction analysis of the putative ABC transporter ATP-binding protein from Thermotoga maritima.

    PubMed

    Ethayathulla, Abdul S; Bessho, Yoshitaka; Shinkai, Akeo; Padmanabhan, Balasundaram; Singh, Tej P; Kaur, Punit; Yokoyama, Shigeyuki

    2008-06-01

    Adenosine triphosphate (ATP) binding cassette transporters (ABC transporters) are ATP hydrolysis-dependent transmembrane transporters. Here, the overproduction, purification and crystallization of the putative ABC transporter ATP-binding protein TM0222 from Thermotoga maritima are reported. The protein was crystallized in the hexagonal space group P6(4)22, with unit-cell parameters a = b = 148.49, c = 106.96 A, gamma = 120.0 degrees . Assuming the presence of two molecules in the asymmetric unit, the calculated V(M) is 2.84 A(3) Da(-1), which corresponds to a solvent content of 56.6%. A three-wavelength MAD data set was collected to 2.3 A resolution from SeMet-substituted TM0222 crystals. Data sets were collected on the BL38B1 beamline at SPring-8, Japan. PMID:18540059

  11. 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.

  12. Iron-sulfur cluster biosynthesis: biochemical characterization of the conformational dynamics of Thermotoga maritima IscU and the relevance for cellular cluster assembly.

    PubMed

    Mansy, Sheref S; Wu, Shu-pao; Cowan, J A

    2004-03-12

    Important for the understanding of the functional properties of the iron-sulfur scaffold IscU is knowledge of the structure and dynamics of this protein class. Structural characterization of Thermotoga maritima IscU by CD (Mansy, S. S., Wu, G., Surerus, K. K., and Cowan, J. A. (2002) J. Biol. Chem. 277, 21397-21404) and high resolution NMR (Bertini, I., Cowan, J. A., Del Bianco, C., Luchinat, C., and Mansy, S. S. (2003) J. Mol. Biol. 331, 907-924) yielded data indicating a high degree of secondary structure. However, the latter also revealed IscU to exist in a dynamic equilibrium between two or more distinct conformations, possibly existing in a molten globule state. Herein, we further characterize the molten globule characteristics of T. maritima IscU by near-ultraviolet circular dichroism, 1-anilino-8-naphthalenesulfonic acid binding, free energy of unfolding, hydrodynamic radius measurements, and limited tryptic digestion. The data suggest unusual dynamic behavior that is not fully consistent with typical protein states such as fully folded, fully unfolded, or molten globule. For instance, the existence of a stable tertiary fold is supported by near-UV CD spectra and hydrodynamic radius measurements, whereas other data are less clearly interpretable and may be viewed as consistent with either a molten globule or fully folded state. However, all of the data are consistent with our previous hypothesis of a protein sampling multiple discrete tertiary conformations in which these structural transitions occur on a "slow" time scale. To describe such proteins, we introduce the term multiple discrete conformers. PMID:14688265

  13. 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

  14. 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

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

    PubMed

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

    2013-02-01

    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

  16. 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.

    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.

  17. Isolation, identification and expression analysis of salt-induced genes in Suaeda maritima, a natural halophyte, using PCR-based suppression subtractive hybridization

    PubMed Central

    Sahu, Binod B; Shaw, Birendra P

    2009-01-01

    Background Despite wealth of information generated on salt tolerance mechanism, its basics still remain elusive. Thus, there is a need of continued effort to understand the salt tolerance mechanism using suitable biotechnological techniques and test plants (species) to enable development of salt tolerant cultivars of interest. Therefore, the present study was undertaken to generate information on salt stress responsive genes in a natural halophyte, Suaeda maritima, using PCR-based suppression subtractive hybridization (PCR-SSH) technique. Results Forward and reverse SSH cDNA libraries were constructed after exposing the young plants to 425 mM NaCl for 24 h. From the forward SSH cDNA library, 429 high quality ESTs were obtained. BLASTX search and TIGR assembler programme revealed overexpression of 167 unigenes comprising 89 singletons and 78 contigs with ESTs redundancy of 81.8%. Among the unigenes, 32.5% were found to be of special interest, indicating novel function of these genes with regard to salt tolerance. Literature search for the known unigenes revealed that only 17 of them were salt-inducible. A comparative analysis of the existing SSH cDNA libraries for NaCl stress in plants showed that only a few overexpressing unigenes were common in them. Moreover, the present study also showed increased expression of phosphoethanolamine N-methyltransferase gene, indicating the possible accumulation of a much studied osmoticum, glycinebetaine, in halophyte under salt stress. Functional categorization of the proteins as per the Munich database in general revealed that salt tolerance could be largely determined by the proteins involved in transcription, signal transduction, protein activity regulation and cell differentiation and organogenesis. Conclusion The study provided a clear indication of possible vital role of glycinebetaine in the salt tolerance process in S. maritima. However, the salt-induced expression of a large number of genes involved in a wide range of cellular functions was indicative of highly complex nature of the process as such. Most of the salt inducible genes, nonetheless, appeared to be species-specific. In light of the observations made, it is reasonable to emphasize that a comparative analysis of ESTs from SSH cDNA libraries generated systematically for a few halophytes with varying salt exposure time may clearly identify the key salt tolerance determinant genes to a minimum number, highly desirable for any genetic manipulation adventure. PMID:19497134

  18. 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

  19. Production of xylobiose from the autohydrolysis explosion liquor of corncob using Thermotoga maritima xylanase B (XynB) immobilized on nickel-chelated Eupergit C.

    PubMed

    Tan, S S; Li, D Y; Jiang, Z Q; Zhu, Y P; Shi, B; Li, L T

    2008-01-01

    In this study, a thermostable recombinant xylanase B (XynB) from Thermotoga maritima MSB8 was immobilized on nickel-chelated Eupergit C 250L. This immobilized XynB was then used to hydrolyze the autohydrolysis explosion liquor of corncob (AELC) in a packed-bed enzyme reactor for continuous production of xylooligosaccharides, especially xylobiose. When tested in batch hydrolysis of AELC, the immobilized XynB still retained its relative activity of 92.5% after 10 cycles of hydrolysis at 90 degrees C. The immobilized XynB retained 83.6% of its initial hydrolysis activity even after 168 h of hydrolysis reaction at 90 degrees C and demonstrated a half-life time of 577.6 h (24 days) for continuous hydrolysis. HPLC showed that xylobiose (49.8%) and xylose (22.6%) were the main hydrolysis products yielded during continuous hydrolysis. Xylobiose was adsorbed on an activated charcoal column and eluted with a linear gradient of 15% (v/v) ethanol to yield xylobiose with 84.7% of recovery. Also, the purity of xylobiose was up to 97.2% as determined by HPLC. Therefore, the immobilized XynB was suitable for the efficient production of xylobiose from AELC. This is the first report on the immobilization of xylanase for xylobiose production. PMID:17258452

  20. Structural analysis of Canavalia maritima and Canavalia gladiata lectins complexed with different dimannosides: new insights into the understanding of the structure-biological activity relationship in legume lectins.

    PubMed

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

    2007-11-01

    Plant lectins, especially those purified from species of the Leguminosae family, represent the best studied group of carbohydrate-binding proteins. The legume lectins from Diocleinae subtribe are highly similar proteins that present significant differences in the potency/efficacy of their biological activities. The structural studies of the interactions between lectins and sugars may clarify the origin of the distinct biological activities observed in this high similar class of proteins. In this way, this work presents a crystallographic study of the ConM and CGL (agglutinins from Canavalia maritima and Canavalia gladiata, respectively) in the following complexes: ConM/CGL:Man(alpha1-2)Man(alpha1-O)Me, ConM/CGL:Man(alpha1-3)Man(alpha1-O)Me and ConM/CGL:Man(alpha1-4)Man(alpha1-O)Me, which crystallized in different conditions and space group from the native proteins. The structures were solved by molecular replacement, presenting satisfactory values for R(factor) and R(free). Comparisons between ConM, CGL and ConA (Canavalia ensiformis lectin) binding mode with the dimannosides in subject, presented different interactions patterns, which may account for a structural explanation of the distincts biological properties observed in the lectins of Diocleinae subtribe. PMID:17881248

  1. The three-dimensional structure of invertase (beta-fructosidase) from Thermotoga maritima reveals a bimodular arrangement and an evolutionary relationship between retaining and inverting glycosidases.

    PubMed

    Alberto, François; Bignon, Christophe; Sulzenbacher, Gerlind; Henrissat, Bernard; Czjzek, Mirjam

    2004-04-30

    Thermotoga maritima invertase (beta-fructosidase) hydrolyzes sucrose to release fructose and glucose, which are major carbon and energy sources for both prokaryotes and eukaryotes. The name "invertase" was given to this enzyme over a century ago, because the 1:1 mixture of glucose and fructose that it produces was named "invert sugar." Despite its name, the enzyme operates with a mechanism leading to the retention of the anomeric configuration at the site of cleavage. The enzyme belongs to family GH32 of the sequence-based classification of glycosidases. The crystal structure, determined at 2-A resolution, reveals two modules, namely a five-bladed beta-propeller with structural similarity to the beta-propeller structures of glycosidase from families GH43 and GH68 connected to a beta-sandwich module. Three carboxylates at the bottom of a deep, negatively charged funnel-shaped depression of the beta-propeller are essential for catalysis and function as nucleophile, general acid, and transition state stabilizer, respectively. The catalytic machinery of invertase is perfectly superimposable to that of the enzymes of families GH43 and GH68. The variation in the position of the furanose ring at the site of cleavage explains the different mechanisms evident in families GH32 and GH68 (retaining) and GH43 (inverting) furanosidases. PMID:14973124

  2. Structural and thermodynamic studies on a salt-bridge triad in the NADP-binding domain of glutamate dehydrogenase from Thermotoga maritima: cooperativity and electrostatic contribution to stability.

    PubMed

    Lebbink, Joyce H G; Consalvi, Valerio; Chiaraluce, Roberta; Berndt, Kurt D; Ladenstein, Rudolf

    2002-12-31

    Cooperative interactions within ion-pair networks of hyperthermostable proteins are thought to be a major determinant for extreme protein stability. While the favorable thermodynamic contributions of optimized electrostatics in general as well as those of pairwise interactions have been documented, cooperativity between pairwise interactions has not yet been studied thermodynamically in proteins from hyperthermophiles. In this study we use the isolated cofactor binding domain of glutamate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima to analyze pairwise and cooperative interactions within the salt-bridge triad Arg190-Glu231-Lys193. The X-ray structure of the domain was solved at 1.43 A and reveals the salt-bridge network with surrounding solvent molecules in detail. All three participating charges in the network were mutated to alanine in all combinations. The X-ray structure of the variant lacking all three charges reveals that the removal of the side chains has no effect on the overall conformation of the protein. Using solvent denaturation and thermodynamic cycles, the interaction energies between each pair of residues in the network were determined in the presence and in the absence of the third residue. Both the Arg190-Glu231 ion pair and the Lys193-Glu231 salt bridge in the absence of the third residue, contribute favorably to the free energy for unfolding of the domain in urea. Using guanidinium chloride as denaturant reveals a strong cooperativity between the two ion-pair interactions, the presence of the second ion pair converts the first interaction from destabilizing into stabilizing by as much as 1.09 kcal/mol. The different energetics of the salt-bridge triad in urea and GdmCl are discussed with reference to the observed anion binding in the crystal structure at high ionic strength and their possible role in a highly charged, high-temperature environment such as the cytoplasm of hyperthermophiles. PMID:12501181

  3. 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.

  4. 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.

  5. A loose domain swapping organization confers a remarkable stability to the dimeric structure of the arginine binding protein from Thermotoga maritima.

    PubMed

    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

  6. Post-translational modification of ribosomal proteins: structural and functional characterization of RimO from Thermotoga maritima, a radical S-adenosylmethionine methylthiotransferase.

    PubMed

    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

    2010-02-19

    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 A 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

  7. Exploring Phylogeographic Congruence in a Continental Island System

    PubMed Central

    Goldberg, Julia; Trewick, Steven A.

    2011-01-01

    A prediction in phylogeographic studies is that patterns of lineage diversity and timing will be similar within the same landscape under the assumption that these lineages have responded to past environmental changes in comparable ways. Eight invertebrate taxa from four different orders were included in this study of mainland New Zealand and Chatham Islands lineages to explore outcomes of island colonization. These comprised two orthopteran genera, one an endemic forest-dwelling genus of cave weta (Rhaphidophoridae, Talitropsis) and the other a grasshopper (Acrididae, Phaulacridum) that inhabits open grassland; four genera of Coleoptera including carabid beetles (Mecodema), stag beetles (Geodorcus), weevils (Hadramphus) and clickbeetles (Amychus); the widespread earwig genus Anisolabis (Dermaptera) that is common on beaches in New Zealand and the Chatham Islands, and an endemic and widespread cockroach genus Celatoblatta (Blattodea). Mitochondrial DNA data were used to reconstruct phylogeographic hypotheses to compare among these taxa. Strikingly, despite a maximum age of the Chathams of ?4 million years there is no concordance among these taxa, in the extent of genetic divergence and partitioning between Chatham and Mainland populations. Some Chatham lineages are represented by insular endemics and others by haplotypes shared with mainland populations. These diverse patterns suggest that combinations of intrinsic (taxon ecology) and extrinsic (extinction and dispersal) factors can result in apparently very different biogeographic outcomes. PMID:26467734

  8. Directional substitution and evolution of nucleotide content in the cytochrome oxidase II gene in earwigs (dermapteran insects).

    PubMed

    Wirth, T; Le Guellec, R; Veuille, M

    1999-12-01

    The cytochrome oxidase subunit II (COII) gene was sequenced for six dermapteran species. The nucleotide composition of this gene is biased in most animals. While the CG content of other insect orders is low (mean, 27.6%; range, 19.5%-33.1%), species from the Forficula genus showed unusually high values (mean, 42.4%; range, 37.3%-44.1%), mostly due to high CG frequencies at third codon positions: the mean CG content at these positions was around 45% (range, 43.9%-46.9%) for Forficula, compared with only 13.3% for other insects. This effect was so strong that in one species, Forficula lesnei, there was no significant difference between the frequencies of the four bases. During evolution, this loss of bias has involved a significant increase in the synonymous substitution rate and an increase of transitions over transversions compared with other insects. A strong directionality of substitutions has favored T-->C and A-->G changes. This phenomenon was also observed between two conspecific populations of Forficula auricularia. A species from a closely related genus, Anechura bipunctata, was intermediate between Forficula and other insects for these parameters, while two remotely related dermapteran species, Labidura riparia and Euborellia moesta, were similar to other insects. These results suggest that the evolution of Forficula DNA content has been both rapid and recent. PMID:10605107

  9. An analysis of segmentation dynamics throughout embryogenesis in the centipede Strigamia maritima

    PubMed Central

    2013-01-01

    Background Most segmented animals add segments sequentially as the animal grows. In vertebrates, segment patterning depends on oscillations of gene expression coordinated as travelling waves in the posterior, unsegmented mesoderm. Recently, waves of segmentation gene expression have been clearly documented in insects. However, it remains unclear whether cyclic gene activity is widespread across arthropods, and possibly ancestral among segmented animals. Previous studies have suggested that a segmentation oscillator may exist in Strigamia, an arthropod only distantly related to insects, but further evidence is needed to document this. Results Using the genes even skipped and Delta as representative of genes involved in segment patterning in insects and in vertebrates, respectively, we have carried out a detailed analysis of the spatio-temporal dynamics of gene expression throughout the process of segment patterning in Strigamia. We show that a segmentation clock is involved in segment formation: most segments are generated by cycles of dynamic gene activity that generate a pattern of double segment periodicity, which is only later resolved to the definitive single segment pattern. However, not all segments are generated by this process. The most posterior segments are added individually from a localized sub-terminal area of the embryo, without prior pair-rule patterning. Conclusions Our data suggest that dynamic patterning of gene expression may be widespread among the arthropods, but that a single network of segmentation genes can generate either oscillatory behavior at pair-rule periodicity or direct single segment patterning, at different stages of embryogenesis. PMID:24289308

  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. Necromenic life style of Histiostoma polypori (Acari: Histiostomatidae).

    PubMed

    Wirth, S

    2009-12-01

    Histiostoma polypori (Histiostomatidae, Astigmata) is associated with the earwig Forficula auricularia, which has an interesting brood behavior: the adult earwig female cares for her eggs and stays with the N2 and N3 nymphs in the nest. Deutonymphs of H. polypori only leave the female earwig to develop on dead earwig N2 and N3 nymphs. The newly molted deutonymphs attach to live earwig N3 nymphs. The earwig's cleaning behavior displaces the deutonymphs to the exuvial suture, around the area between cephalon and prothorax. From there, deutonymphs switch from one earwig stage to the following, always occupying that region. Histiostoma polypori obviously has a necromenic life style, that is, it ascends a carrier organism and develops on the carrier's cadavers. Necromeny within the Histiostomatidae presumably derived at least twice convergently from phoretic transport. PMID:19697142

  12. Cytotoxicity of the Sesquiterpene Lactones Neoambrosin and Damsin from Ambrosia maritima Against Multidrug-Resistant Cancer Cells

    PubMed Central

    Saeed, Mohamed; Jacob, Stefan; Sandjo, Louis P.; Sugimoto, Yoshikazu; Khalid, Hassan E.; Opatz, Till; Thines, Eckhard; Efferth, Thomas

    2015-01-01

    Multidrug resistance is a prevailing phenomenon leading to chemotherapy treatment failure in cancer patients. In the current study two known cytotoxic pseudoguaianolide sesquiterpene lactones; neoambrosin (1) and damsin (2) that circumvent MDR were identified. The two cytotoxic compounds were isolated using column chromatography, characterized using 1D and 2D NMR, MS, and compared with literature values. The isolated compounds were investigated for their cytotoxic potential using resazurin assays and thereafter confirmed with immunoblotting and in silico studies. MDR cells overexpressing ABC transporters (P-glycoprotein, BCRP, ABCB5) did not confer cross-resistance toward (1) and (2), indicating that these compounds are not appropriate substrates for any of the three ABC transporters analyzed. Resistance mechanisms investigated also included; the loss of the functions of the TP53 and the mutated EGFR. The HCT116 p53-/- cells were sensitive to 1 but resistant to 2. It was interesting to note that resistant cells transfected with oncogenic ΔEGFR exhibited hypersensitivity CS toward (1) and (2) (degrees of resistances were 0.18 and 0.15 for (1) and (2), respectively). Immunoblotting and in silico analyses revealed that 1 and 2 silenced c-Src kinase activity. It was hypothesized that inhibition of c-Src kinase activity may explain CS in EGFR-transfected cells. In conclusion, the significant cytotoxicity of 1 and 2 against different drug-resistant tumor cell lines indicate that they may be promising candidates to treat refractory tumors. PMID:26617519

  13. Molecular analysis of hyperthermophilic endoglucanase Cel12B from Thermotoga maritima and the properties of its functional residues

    PubMed Central

    2014-01-01

    Background Although many hyperthermophilic endoglucanases have been reported from archaea and bacteria, a complete survey and classification of all sequences in these species from disparate evolutionary groups, and the relationship between their molecular structures and functions are lacking. The completion of several high-quality gene or genome sequencing projects provided us with the unique opportunity to make a complete assessment and thorough comparative analysis of the hyperthermophilic endoglucanases encoded in archaea and bacteria. Results Structure alignment of the 19 hyperthermophilic endoglucanases from archaea and bacteria which grow above 80°C revealed that Gly30, Pro63, Pro83, Trp115, Glu131, Met133, Trp135, Trp175, Gly227 and Glu229 are conserved amino acid residues. In addition, the average percentage composition of residues cysteine and histidine of 19 endoglucanases is only 0.28 and 0.74 while it is high in thermophilic or mesophilic one. It can be inferred from the nodes that there is a close relationship among the 19 protein from hyperthermophilic bacteria and archaea based on phylogenetic analysis. Among these conserved amino acid residues, as far as Cel12B concerned, two Glu residues might be the catalytic nucleophile and proton donor, Gly30, Pro63, Pro83 and Gly227 residues might be necessary to the thermostability of protein, and Trp115, Met133, Trp135, Trp175 residues is related to the binding of substrate. Site-directed mutagenesis results reveal that Pro63 and Pro83 contribute to the thermostability of Cel12B and Met133 is confirmed to have role in enhancing the binding of substrate. Conclusions The conserved acids have been shown great importance to maintain the structure, thermostability, as well as the similarity of the enzymatic properties of those proteins. We have made clear the function of these conserved amino acid residues in Cel12B protein, which is helpful in analyzing other undetailed molecular structure and transforming them with site directed mutagenesis, as well as providing the theoretical basis for degrading cellulose from woody and herbaceous plants. PMID:24529187

  14. Local and global influences on population declines of coastal waders: Purple Sandpiper Calidris maritima numbers in the Moray Firth, Scotland

    NASA Astrophysics Data System (ADS)

    Summers, Ron W.; Foster, Simon; Swann, Bob; Etheridge, Brian

    2012-05-01

    Declines in numbers by several wader species in Britain have been linked to climate change, but the mechanism for the declines has rarely been explored. Britain lies at the northern end of the East Atlantic Flyway, and supports 1.3 million out of the Flyway's 8.5 million coastal waders (Charadrii) in winter and the Purple Sandpiper is one of the species whose numbers have declined. Here, we examine the dynamics of the decline as observed in the Moray Firth, northeast Scotland, investigating whether the decline was due to poorer apparent survival (return rate) or poorer recruitment of young birds. The maximum number in the Moray Firth declined from 860 in 1987/88 to 236 in 2006/07, with some increase during winters 2007/08 and 2008/09. At the three main high-tide roosts (Balintore, Lossiemouth and Buckie) the maximum combined number declined from 574 to 90. Changes in survival and recruitment (percentage of first-year birds) were examined at these roosts from captured samples, which were ringed and recaptured. There were no significant changes between winters in survival rates, nor were there differences between the survival rates of age groups (first-year and adult) or bill size groups, which represented birds of different sex and breeding origin. Annual survival estimates for the three roosts ranged from 72 to 77%. The percentage of first-year birds varied among roosts and years; the lowest values were during the late 1980s/early 1990s and early 2000s. A free-running population model incorporating varying percentages of first-year birds and constant mortality for each roost provided a plausible explanation for the decline. Although modelled numbers followed the observed pattern, a discrepancy in one year was carried forward in subsequent years, so that the fit with the observed numbers was parallel rather than similar. However, it seems that the decline in numbers was largely due to poorer recruitment. We discuss whether breeding success had declined, whether the population had responded to changes in the local sewage treatment systems, which could affect invertebrate food for Purple Sandpipers, or whether fewer birds chose to winter in Scotland. The Moray Firth population is derived from Norway and possibly Canada, and there is evidence that the Norwegian population was disproportionately affected. The reason for poor recruitment requires further study, and other wader species require examination to test if poor recruitment is a common feature of decline in numbers.

  15. An anterior medial cell population with an apical-organ-like transcriptional profile that pioneers the central nervous system in the centipede Strigamia maritima.

    PubMed

    Hunnekuhl, Vera S; Akam, Michael

    2014-12-01

    The apical plate of primary marine larvae is characterized by a common set of transcription factors comprising six3, rx, hbn, nk2.1 and FoxQ2. It harbours the apical organ, a neural and ciliary structure with neurosecretory properties. Recent studies in lophotrochozoans have found that apical organ cells form the anterior tip of the developing central nervous system. We identify an anterior medial tissue in the embryonic centipede head that shares the transcriptional profile of the apical plate of marine larvae, including nested domains of FoxQ2 and six3 expression. This domain gives rise to an anterior medial population of neural precursors distinct from those arising within the segmental neuroectoderm. These medial cells do not express achaete scute homologue in proneural clusters, but express collier, a marker for post mitotic cells committed to a neural fate, while they are still situated in the surface ectodermal layer. They then sink under the surface to form a compact cell cluster. Once internalized these cells extend axons that pioneer the primary axonal scaffold of the central nervous system. The same cells express phc2, a neural specific prohormone convertase, which suggests that they form an early active neurosecretory centre. Some also express markers of hypothalamic neurons, including otp, vtn and vax1. These medial neurosecretory cells of the centipede are distinct from those of the pars intercerebralis, the anterior neurosecretory part of the insect brain. The pars intercerebralis derives from vsx positive placodal-like invagination sites. In the centipede, vsx expressing invaginating ectoderm is situated bilaterally adjacent to the medial pioneer cell population. Hence the pars intercerebralis is present in both insect and centipede brains, whereas no prominent anterior medial cluster of pioneer neurons is present in insects. These observations suggest that the arthropod brain retained ancestrally an anterior medial population of neurosecretory cells homologous to those of the apical plate in other invertebrate phyla, but that this cell population has been lost or greatly reduced in insects. PMID:25263198

  16. The feasibility and efficacy of early-season releases of a generalist predator (Forficula auricularia L.) to control populations of the RAA (Dysaphis plantaginea Passerini) in Southeastern France.

    PubMed

    Dib, H; Jamont, M; Sauphanor, B; Capowiez, Y

    2016-04-01

    Augmentative biological control is not commonly used in commercial orchards. We used an exclusion system to evaluate the potential of early-season releases of the European earwig (Forficula auricularia L., Dermaptera: Forficulidae) for control of the rosy apple aphid (Dysaphis plantaginea Passerini, Hemiptera: Aphididae) in the spring of 2009 in two pesticide-free apple orchards. In order to conduct this experiment we successfully reared earwigs with a high survival rate of nymphs (more than 96%) which may have commercial application. There were three treatments in the study: (i) a 'release treatment' where we confined the released earwigs in the canopy by using a barrier system; (ii) an 'exclusion treatment' where we blocked free access of earwigs into the canopy using the same barrier system; and (iii) a 'control treatment' that represented the natural situation. Contrary to expectations, earwig releases did not reduce D. plantaginea populations. In general, the abundance of natural enemies and their groups did not differ significantly among treatments, except for earwigs. We observed that the exclusion systems we used successfully kept both earwigs and ants away from tree canopies; total numbers on trees in the 'exclusion treatment' were significantly lower than on the other two treatments. Due to the complexity and difficulty of evaluating augmentative releases of natural enemies in open orchard conditions, we conclude that new technical approaches to control site conditions are needed when conducting such studies. PMID:26780826

  17. 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.

  18. 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

  19. An Insight into the Interaction Mode Between CheB and Chemoreceptor from Two Crystal Structures of CheB Methylesterase Catalytic Domain

    SciTech Connect

    K Cho; B Crane; S Park

    2011-12-31

    We have determined 2.2 {angstrom} resolution crystal structure of Thermotoga maritima CheB methylesterase domain to provide insight into the interaction mode between CheB and chemoreceptors. T. maritima CheB methylesterase domain has identical topology of a modified doubly-wound {alpha}/{beta} fold that was observed from the previously reported Salmonella typhimurium counterpart, but the analysis of the electrostatic potential surface near the catalytic triad indicated considerable charge distribution difference. As the CheB demethylation consensus sites of the chemoreceptors, the CheB substrate, are not uniquely conserved between T. maritima and S. typhimurium, such surfaces with differing electrostatic properties may reflect CheB regions that mediate protein-protein interaction. Via the computational docking of the two T. maritima and S. typhimurium CheB structures to the respective T. maritima and Escherichia coli chemoreceptors, we propose a CheB:chemoreceptor interaction mode.

  20. 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…

  1. A floral-derived compound attractive to the tephritid fruit fly parasitoid Diachasmimorpha longicaudata (Hymenoptera: Braconidae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Many adult hymenopteran parasitoids, even host-feeding species, consume the nectar of flowering plants. Previous field studies had identified plants attractive (Lobularia maritima L.) and unattractive (Spermacoce verticillata L) to certain opiine braconids (Hymenoptera). Under laboratory conditions,...

  2. Agronomy of strip intercropping broccoli with alyssum for biological control of aphids

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Organic broccoli growers in California typically control aphids by intercropping broccoli with strips of alyssum (Lobularia maritima (L.) Desv.) which attracts hoverflies (Diptera: Syrphidae) that are important predators of aphids. A three year study with transplanted organic broccoli in Salinas, ...

  3. An offspring signal of quality affects the timing of future parental reproduction

    PubMed Central

    Mas, Flore; Kölliker, Mathias

    2011-01-01

    Solicitation signals by offspring are well known to influence parental behaviour, and it is commonly assumed that this behavioural effect translates into an effect on residual reproduction of parents. However, this equivalence assumption concerning behavioural and reproductive effects caused by offspring signals remains largely untested. Here, we tested the effect of a chemical offspring signal of quality on the relative timing and amount of future reproduction in the European earwig (Forficula auricularia). We manipulated the nutritional condition of earwig nymphs and exposed females to their extract, or to solvent as a control. There were no significant main effects of exposure treatment on 2nd clutch production, but exposure to extracts of well-fed nymphs induced predictable timing of the 2nd relative to the 1st clutch. This result demonstrates for the first time that an offspring signal per se, in the absence of any maternal behaviour, affects maternal reproductive timing, possibly through an effect on maternal reproductive physiology. PMID:21208942

  4. An offspring signal of quality affects the timing of future parental reproduction.

    PubMed

    Mas, Flore; Kölliker, Mathias

    2011-06-23

    Solicitation signals by offspring are well known to influence parental behaviour, and it is commonly assumed that this behavioural effect translates into an effect on residual reproduction of parents. However, this equivalence assumption concerning behavioural and reproductive effects caused by offspring signals remains largely untested. Here, we tested the effect of a chemical offspring signal of quality on the relative timing and amount of future reproduction in the European earwig (Forficula auricularia). We manipulated the nutritional condition of earwig nymphs and exposed females to their extract, or to solvent as a control. There were no significant main effects of exposure treatment on 2nd clutch production, but exposure to extracts of well-fed nymphs induced predictable timing of the 2nd relative to the 1st clutch. This result demonstrates for the first time that an offspring signal per se, in the absence of any maternal behaviour, affects maternal reproductive timing, possibly through an effect on maternal reproductive physiology. PMID:21208942

  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. 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.

  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. Discontinuous Occurrence of the hsp70 (dnaK) Gene among Archaea and Sequence Features of HSP70 Suggest a Novel Outlook on Phylogenies Inferred from This Protein

    PubMed Central

    Gribaldo, Simonetta; Lumia, Valentina; Creti, Roberta; Conway de Macario, Everly; Sanangelantoni, Annamaria; Cammarano, Piero

    1999-01-01

    Occurrence of the hsp70 (dnaK) gene was investigated in various members of the domain Archaea comprising both euryarchaeotes and crenarchaeotes and in the hyperthermophilic bacteria Aquifex pyrophilus and Thermotoga maritima representing the deepest offshoots in phylogenetic trees of bacterial 16S rRNA sequences. The gene was not detected in 8 of 10 archaea examined but was found in A. pyrophilus and T. maritima, from which it was cloned and sequenced. Comparative analyses of the HSP70 amino acid sequences encoded in these genes, and others in the databases, showed that (i) in accordance with the vicinities seen in rRNA-based trees, the proteins from A. pyrophilus and T. maritima form a thermophilic cluster with that from the green nonsulfur bacterium Thermomicrobium roseum and are unrelated to their counterparts from gram-positive bacteria, proteobacteria/mitochondria, chlamydiae/spirochetes, deinococci, and cyanobacteria/chloroplasts; (ii) the T. maritima HSP70 clusters with the homologues from the archaea Methanobacterium thermoautotrophicum and Thermoplasma acidophilum, in contrast to the postulated unique kinship between archaea and gram-positive bacteria; and (iii) there are exceptions to the reported association between an insert in HSP70 and gram negativity, or vice versa, absence of insert and gram positivity. Notably, the HSP70 from T. maritima lacks the insert, although T. maritima is phylogenetically unrelated to the gram-positive bacteria. These results, along with the absence of hsp70 (dnaK) in various archaea and its presence in others, suggest that (i) different taxa retained either one or the other of two hsp70 (dnaK) versions (with or without insert), regardless of phylogenetic position; and (ii) archaea are aboriginally devoid of hsp70 (dnaK), and those that have it must have received it from phylogenetically diverse bacteria via lateral gene transfer events that did not involve replacement of an endogenous hsp70 (dnaK) gene. PMID:9882656

  10. Genome Sequence of Thermotoga sp Strain RQ2, a Hyperthermophilic Bacterium Isolated from a Geothermally Heated Region of the Seafloor near Ribeira Quente, the Azores

    SciTech Connect

    Swithers, Kristen S; DiPippo, Jonathan L; Bruce, David; Detter, J. Chris; Tapia, Roxanne; Han, Cliff; Woyke, Tanja; Pitluck, Sam; Pennacchio, Len; Nolan, Matt; Mikhailova, Natalia; Lykidis, A; Land, Miriam L; Stetter, Karl O; Nelson, Karen E; Gogarten, Peter; Noll, Kenneth M

    2011-01-01

    Thermotoga sp. strain RQ2 is probably a strain of Thermotoga maritima. Its complete genome sequence allows for an examination of the extent and consequences of gene flow within Thermotoga species and strains. Thermotoga sp. RQ2 differs from T. maritima in its genes involved in myo-inositol metabolism. Its genome also encodes an apparent fructose phosphotransferase system (PTS) sugar transporter. This operon is also found in Thermotoga naphthophila strain RKU-10 but no other Thermotogales. These are the first reported PTS transporters in the Thermotogales.

  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. Rhizoctonia Crown and Root Rot Resistance of Beta Plant Introductions from the USDA, Agricultural Research Service's National Plant Germplasm System, 2010

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Thirty wild beet (Beta vulgaris subsp. maritima (L.) Arcang) plant introduction (PI) accessions from the Beta collection of the USDA-ARS National Plant Germplasm System were screened for resistance to Rhizoctonia root and crown rot, at the USDA-ARS Fort Collins, CO Research Farm. The Rhizoctonia sc...

  14. 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...

  15. Genetic structure and immigation in French sea beet

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this study we examined accessions of sea beet (Beta vulgaris subsp. maritima (L.) Arcang.), collected along the Mediterranean Sea up the Atlantic coast of France. The aim was to identify the scale and magnitude of differentiation and diversity in these accessions using both molecular and quantita...

  16. Beta genetic resources: North American activities.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The main activity is with Beta genetic resources in North America evaluation and pre-breeding. There are 2513 accessions conserved, including lines, old varieties and 571 B. vulgaris subsp. maritima. Much research is based on pathology, ranging from epidemiology to the detection of markers. An ong...

  17. Genome evolution: groping in the soil interstices.

    PubMed

    Minelli, Alessandro

    2015-03-01

    Centipedes are a very old lineage of terrestrial animals. The first completely sequenced myriapod genome reveals that the blind centipede Strigamia maritima has no gene for light-sensory proteins, lacks the canonical circadian clock and possesses unusual features related to chemosensory perception. PMID:25734267

  18. A CLEAVED AMPLIFIED POLYMORPHIC SEQUENCE (CAPS) MARKER ASSOCIATED WITH ROOT-KNOT NEMATODE IN SUGAR BEET (BETA VULGARIS L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Resistance to root-knot nematode (Meloidogyne spp.) was introgressed into sugarbeet (Beta vulgaris L.) from wild beet [B. vulgaris ssp. maritima (L.) Arcang] and was demonstrated to be dominant and simply inherited. Since resistance conferred by this gene was effective against six different species...

  19. Beet curly top resistance in USDA-ARS Plant Introductions, 2012

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Thirty sea beet (Beta vulgaris subsp. maritima (L.) Arcang) and beet (Beta vulgaris subsp. vulgaris L.) plant introduction (PI) accessions from the Beta collection of the USDA-ARS National Plant Germplasm System were screened for resistance to Beet severe curly top virus (BSCTV) and other closely re...

  20. Screening Rhizoctonia crown and root rot resistance of Beta PIs from the USDA-ARS, National Plant Germplasm System, 2011

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Thirty beet (Beta vulgaris subsp. maritima (L.) Arcang and Beta vulgaris subsp. vulgaris L.) plant introduction (PI) accessions from the Beta collection of the USDA-ARS National Plant Germplasm System were screened for resistance to Rhizoctonia root and crown rot, at the USDA-ARS Fort Collins, CO Re...

  1. Evaluation of Beta PIs from the USDA-ARS, NPGS for Rhizoctonia crown and root rot resistance, 2013

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Thirty sea beet (Beta vulgaris subsp. maritima (L.) Arcang accessions from the Beta collection of the USDA-ARS National Plant Germplasm System were screened for resistance to Rhizoctonia root and crown rot, at the USDA-ARS Fort Collins, CO Research Farm. The Rhizoctonia screening nursery in 2013 wa...

  2. Release of EL54 Sugarbeet Germplasm Derived from WB879 Wild Germplasm With Resistance to Aphanomyces and Excellent Stand Establishment

    Technology Transfer Automated Retrieval System (TEKTRAN)

    EL54 (PI 654357) is a sugarbeet germplasm derived from wild beet (Beta vulgaris ssp. maritima) accession WB879 (PI 540625). EL54 is being released in the interest of broadening the genetic base of sugar beet. The parent accession WB879, collected in 1989 from Port-de-Houet, France (3 m elevation), w...

  3. Evaluation of genetic diversity and root traits of sea beet accessions of the Adriatic Sea coast

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Thirty nine sea beet [Beta vulgaris L. subsp. maritima (L.) Arcang.] accessions of the Adriatic coast were screened genetically and for their adaptive morpho-functional root traits in order to identify new sources of abiotic resistances for sugar beet breeding programs. Genetic diversity was evaluat...

  4. Registration of EL54 and EL55 sugarbeet germplasms

    Technology Transfer Automated Retrieval System (TEKTRAN)

    EL54 (PI 654357) is a sugarbeet germplasm derived from wild beet (Beta vulgaris ssp. maritima) accession WB879 (PI 540625), released in the interest of broadening the genetic base of sugar beet. The parent accession WB879, collected in 1989 from Port-de-Houet, France. EL54 has shown excellent Aphan...

  5. 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...

  6. 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

  7. A tale of two spartinas: Climatic, photobiological and isotopic insights on the fitness of non-indigenous versus native species

    NASA Astrophysics Data System (ADS)

    Duarte, B.; Baeta, A.; Rousseau-Gueutin, M.; Ainouche, M.; Marques, J. C.; Caçador, I.

    2015-12-01

    Salt marshes are facing a new threat: the invasion by non-indigenous species (NIS), Although its introduction time is not established yet, in 1999 Spartina versicolor was already identified as a NIS in the Mediterranean marshes, significantly spreading its area of colonization. Using the Mediterranean native Spartina maritima as a reference, the present research studied the ecophysiological fitness of this NIS in its new environment, as a tool to understand its potential invasiveness. It was found that Spartina versicolor had a stable photobiological pattern, with only minor fluctuations during an annual cycle, and lower efficiencies comparated to S. maritima. The NIS seems to be rather insensitive to the observed abiotic factors fluctuations (salinity and pH of the sediment), and thus contrasts with the native S. maritima, known to be salinity dependent with higher productivity values in higher salinity environments. Most of the differences observed between the photobiology of these species could be explained by their nitrogen nutrition (here evaluated by the δ15N stable isotope) and directly related with the Mediterranean climate. Enhanced by a higher N availability during winter, the primary production of S. maritima which lead to dilution of the foliar δ15N concentration in the newly formed biomass, similarly to what is observed along a rainfall gradient. On the other hand, S. versicolor showed an increased δ15N in its tissues along the annual rainfall gradient, probably due to a δ15N concentration effect during low biomass production periods (winter and autumn). Together with the photobiological traits, these isotopic data point out to a climatic misfit of S. versicolor to the Mediterranean climate compared to the native S. maritima. This appears to be the major constrain shaping the ecophysiological fitness of this NIS, its primary production and consequently, its spreading rate along the Mediterranean marshes.

  8. Matters of scale: positive allometry and the evolution of male dimorphisms.

    PubMed

    Tomkins, Joseph L; Kotiaho, Janne S; LeBas, Natasha R

    2005-03-01

    The developmental independence of alternative phenotypes is key to evolutionary theories of phenotypic plasticity and the origins of diversity. Male dimorphisms associated with alternative reproductive tactics are widely cited examples of such facultative expression of divergent fitness optima. Current models for the evolution of male dimorphisms invoke a size-dependent threshold at which the phenotype is reprogrammed. We use predictions derived from allometric modeling to test for the existence of reprogramming thresholds in two species of beetle, Onthophagus taurus and Onthophagus binodis, and the European earwig Forficula auricularia. We also compare the allometry of a number of morphological traits to determine whether minor males suppress their secondary sexual traits. The intercept of the horn allometry was suppressed, but there was no evidence of reprogramming of horn growth in either beetle species. There was reprogramming in the earwig. In the beetles, the horn length in all males can be explained largely in terms of exponential horn growth following an extraordinarily steep power function. The asymptote in O. taurus can be explained by exponential growth meeting the constraint of resource exhaustion. These findings question the currently held view that beetle horn dimorphisms showcase the importance of developmental independence in the evolution of diversity. PMID:15729668

  9. Inbreeding depression in an insect with maternal care: influences of family interactions, life stage and offspring sex.

    PubMed

    Meunier, J; Kölliker, M

    2013-10-01

    Although inbreeding is commonly known to depress individual fitness, the severity of inbreeding depression varies considerably across species. Among the factors contributing to this variation, family interactions, life stage and sex of offspring have been proposed, but their joint influence on inbreeding depression remains poorly understood. Here, we demonstrate that these three factors jointly shape inbreeding depression in the European earwig, Forficula auricularia. Using a series of cross-breeding, split-clutch and brood size manipulation experiments conducted over two generations, we first showed that sib mating (leading to inbred offspring) did not influence the reproductive success of earwig parents. Second, the presence of tending mothers and the strength of sibling competition (i.e. brood size) did not influence the expression of inbreeding depression in the inbred offspring. By contrast, our results revealed that inbreeding dramatically depressed the reproductive success of inbred adult male offspring, but only had little effect on the reproductive success of inbred adult female offspring. Overall, this study demonstrates limited effects of family interactions on inbreeding depression in this species and emphasizes the importance of disentangling effects of sib mating early and late during development to better understand the evolution of mating systems and population dynamics. PMID:23981229

  10. 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

  11. Paternal signature in kin recognition cues of a social insect: concealed in juveniles, revealed in adults

    PubMed Central

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

    2014-01-01

    Kin recognition is a key mechanism to direct social behaviours towards related individuals or avoid inbreeding depression. In insects, recognition is generally mediated by cuticular hydrocarbon (CHC) compounds, which are partly inherited from parents. However, in social insects, potential nepotistic conflicts between group members from different patrilines are predicted to select against the expression of patriline-specific signatures in CHC profiles. Whereas this key prediction in the evolution of insect signalling received empirical support in eusocial insects, it remains unclear whether it can be generalized beyond eusociality to less-derived forms of social life. Here, we addressed this issue by manipulating the number of fathers siring clutches tended by females of the European earwig, Forficula auricularia, analysing the CHC profiles of the resulting juvenile and adult offspring, and using discriminant analysis to estimate the information content of CHC with respect to the maternal and paternal origin of individuals. As predicted, if paternally inherited cues are concealed during family life, increases in mating number had no effect on information content of CHC profiles among earwig juveniles, but significantly decreased the one among adult offspring. We suggest that age-dependent expression of patriline-specific cues evolved to limit the risks of nepotism as family-living juveniles and favour sibling-mating avoidance as group-living adults. These results highlight the role of parental care and social life in the evolution of chemical communication and recognition cues. PMID:25165768

  12. Paternal signature in kin recognition cues of a social insect: concealed in juveniles, revealed in adults.

    PubMed

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

    2014-10-22

    Kin recognition is a key mechanism to direct social behaviours towards related individuals or avoid inbreeding depression. In insects, recognition is generally mediated by cuticular hydrocarbon (CHC) compounds, which are partly inherited from parents. However, in social insects, potential nepotistic conflicts between group members from different patrilines are predicted to select against the expression of patriline-specific signatures in CHC profiles. Whereas this key prediction in the evolution of insect signalling received empirical support in eusocial insects, it remains unclear whether it can be generalized beyond eusociality to less-derived forms of social life. Here, we addressed this issue by manipulating the number of fathers siring clutches tended by females of the European earwig, Forficula auricularia, analysing the CHC profiles of the resulting juvenile and adult offspring, and using discriminant analysis to estimate the information content of CHC with respect to the maternal and paternal origin of individuals. As predicted, if paternally inherited cues are concealed during family life, increases in mating number had no effect on information content of CHC profiles among earwig juveniles, but significantly decreased the one among adult offspring. We suggest that age-dependent expression of patriline-specific cues evolved to limit the risks of nepotism as family-living juveniles and favour sibling-mating avoidance as group-living adults. These results highlight the role of parental care and social life in the evolution of chemical communication and recognition cues. PMID:25165768

  13. [Does sea-grass biomass control the density of peracarids (Crustacea: Peracarida) in tropical lagoons?].

    PubMed

    Winfield, Ignacio; Cházaro-Olvera, Sergio; Alvarez, Fernando

    2007-03-01

    We analyzed the time-space variation of the peracarid crustaceans that inhabit seagrasses of the Alvarado Lagoon System, Veracruz, Gulf of Mexico. The organisms were collected from 108 samples in six sites with Ruppia maritima beds (December 1992 to November 1994). The assemblage was composed of 11 species. Eight species of Amphipoda (Hourstonius laguna, Cerapus benthophilus, Apocorophium louisianum, Grandidierella bonnieroides, Leptocheirus rhizophorae, Gammarus mucronatus, Melita longisetosa and Haustorius sp.), one of Isopoda (Cassidinidea ovalis) and two of Tanaidacea (Discapseudes holthuisi and Leptochelia savignyi) were identified. Taxocoenosis, density and biomass of peracarids showed seasonal pulses related to R. maritima biomass, salinity variation, epicontinental affluent and inlets. The species C. ovalis, G. mucronatus, A. louisianum and D. holthuisi were dominant. PMID:18457113

  14. 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.

  15. 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.

  16. 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.

    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.

  17. Structure of a tryptophanyl-tRNA synthetase containing an iron–sulfur cluster

    PubMed Central

    Han, Gye Won; Yang, Xiang-Lei; McMullan, Daniel; Chong, Yeeting E.; Krishna, S. Sri; Rife, Christopher L.; Weekes, Dana; Brittain, Scott M.; Abdubek, Polat; Ambing, Eileen; Astakhova, Tamara; Axelrod, Herbert L.; Carlton, Dennis; Caruthers, Jonathan; Chiu, Hsiu-Ju; Clayton, Thomas; Duan, Lian; Feuerhelm, Julie; Grant, Joanna C.; Grzechnik, Slawomir K.; Jaroszewski, Lukasz; Jin, Kevin K.; Klock, Heath E.; Knuth, Mark W.; Kumar, Abhinav; Marciano, David; Miller, Mitchell D.; Morse, Andrew T.; Nigoghossian, Edward; Okach, Linda; Paulsen, Jessica; Reyes, Ron; van den Bedem, Henry; White, Aprilfawn; Wolf, Guenter; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Elsliger, Marc-André; Schimmel, Paul; Wilson, Ian A.

    2010-01-01

    A novel aminoacyl-tRNA synthetase that contains an iron–sulfur cluster in the tRNA anticodon-binding region and efficiently charges tRNA with tryptophan has been found in Thermotoga maritima. The crystal structure of TmTrpRS (tryptophanyl-tRNA synthetase; TrpRS; EC 6.1.1.2) reveals an iron–sulfur [4Fe–­4S] cluster bound to the tRNA anticodon-binding (TAB) domain and an l-­tryptophan ligand in the active site. None of the other T. maritima aminoacyl-tRNA synthetases (AARSs) contain this [4Fe–4S] cluster-binding motif (C-x 22-C-x 6-C-x 2-C). It is speculated that the iron–sulfur cluster contributes to the stability of TmTrpRS and could play a role in the recognition of the anticodon. PMID:20944229

  18. Susceptibility of plant selections to Heterodera schachtii and a race of H. trifolii parasitic on Sugarbeet in The Netherlands

    PubMed Central

    Steele, A. E.; Toxopeus, H.; Heijbroek, W.

    1983-01-01

    Similar host ranges were found for Heterodera schachtii and a race of H. trifolii parasitic on sugarbeet in The Netherlands. Twenty-nine of 41 plant accessions evaluated were susceptible to H. trifolii. Five breeding lines of the interspecific hybrid Beta vulgaris-B. procumbens which are resistant to H. schachtii were highly susceptible to H. trifolii. An accession of B. maritima with partial resistance to H. schachtii was resistant to H. trifolii. PMID:19295803

  19. Spectral reflectance properties of mangrove species of the Muthupettai mangrove environment, Tamil Nadu.

    PubMed

    Ajithkumar, T T; Thangaradjou, T; Kannan, L

    2008-09-01

    In the Muthupettai mangrove environment, spectral properties of six mangrove species viz. Avicennia marina, Aegiceras corniculatum, Excoecaria agallocha, Acanthus ilicifolius, Suaeda monoica and S. maritima was studied using Multi band Ground Truth Radiometer (Model-041). The study found that the chlorophyll concentration of different mangrove leaves varies between 0.05 and 0.36 mg g(-1), registering the minimum in S. maritima and maximum in E. agallocha. Interestingly species with higher chlorophyll concentration showed lower reflectance values alteast in the spectral bands 1 and 2. E. agallocha registered 0.36 mg g(-1) of chlorophyll while it recorded only 2.18 and 2.43% reflectance where as S. maritima recorded 3.16 and 3.27% of reflectance in bands 1 and 2. This indicates chlorophyll concentration is one of major factors responsible in determining the reflectance pattern of the pant communities. The spectral properties of mangroves were largely differed with that of the water and soil samples collected from the same locations, these results favourd the utilization of remotely sensed data for depicting various water and soil quality parameters from that of mangrove species in the mangrove environment. This study also found that the difference in reflectance of mangroves at canopy level is not only influenced by the chlorophyll content of species but also by the prevailing environmental condition and background reflectance of soil and water as well. PMID:19295083

  20. Salt marsh vegetation as a carbonyl sulfide (COS) source to the atmosphere

    NASA Astrophysics Data System (ADS)

    Whelan, Mary E.; Min, Dong-Ha; Rhew, Robert C.

    2013-07-01

    Carbonyl sulfide (COS) is the most abundant and longest-lived reduced sulfur compound in the atmosphere; changes in its atmospheric concentration could significantly affect global climate and the biogeochemical sulfur cycle. The largest sink of COS in the troposphere is its destruction in plant leaves by the enzymes involved in photosynthesis. In this study, net fluxes of COS were measured from a coastal salt marsh on a subtropical barrier island on the Texas shore of the Gulf of Mexico. We find net emissions from sites with the common salt marsh plant Batis maritima compared to the net uptake from vegetated plots of most previously investigated biomes. The magnitude of the COS production from vegetated plots in this study was twice the emissions of soil-only salt marsh plots. This is the first time that emissions of COS have been found to be significantly enhanced by the presence of vegetation compared to soil alone. COS fluxes exceeded +110 pmol m-2 s-1 for non-inundated plots during daytime hours and were correlated with soil temperature at the depth of 5 cm. Tidal flooding inhibited soil COS exchange; however, we found continued net emissions from emergent B. maritima. This study suggests that emissions of COS resulted from interactions with the plants themselves, which would mean that B. maritima can mediate the production of atmospheric COS.

  1. Selection of a halophytic plant for assessing the phytotoxicity of dredged seaport sediment stored on land.

    PubMed

    Bedell, J-P; Ferro, Y; Bazin, C; Perrodin, Y

    2014-01-01

    The filling of dry quarries in coastal areas with sediments dredged in seaports represents a potentially interesting method of recycling of these materials. However, this recycling requires the prior carrying out of an Environmental Risk Assessment of the scenario concerned. For this, the question arose as to the type of plants capable of developing on the surface of such a deposit and the method to implement for assessing the possible phytotoxicity of dredged sediments. To answer this question, we chose to work with halophytic plants to be free from the salt-related effect and to assess only the effect related to the toxic compounds present. Based on the objectives set, these works led to the use of common plants of the French coast, with direct seeding, and with pollution-sensitive plants. Three species of angiosperms, Armeria maritima, Anthemis maritima and Plantago coronopus, were finally tested. As a result of this work, Armeria maritima was retained as the most suitable plant for testing the possible phytotoxic effect of dredged marine sediments stored on land. The results obtained with this plant are as follows: germination of 40 % of the seeds in 31 days, produced biomass of 493 mg FW in 6 months and a capacity to bioaccumulate metal pollutants in roots with 350 and 720 mg/kg DW for Zn and Cu, respectively. PMID:23955497

  2. 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

  3. Structural insights into a key carotenogenesis related enzyme phytoene synthase of P. falciparum: a novel drug target for malaria.

    PubMed

    Agarwal, Shalini; Sharma, Vijeta; Phulera, Swastik; Abdin, M Z; Ayana, R; Singh, Shailja

    2015-12-01

    Carotenoids represent a diverse group of pigments derived from the common isoprenoid precursors and fulfill a variety of critical functions in plants and animals. Phytoene synthase (PSY), a transferase enzyme that catalyzes the first specific step in carotenoid biosynthesis plays a central role in the regulation of a number of essential functions mediated via carotenoids. PSYs have been deeply investigated in plants, bacteria and algae however in apicomplexans it is poorly studied. In an effort to characterize PSY in apicomplexans especially the malaria parasite Plasmodium falciparum (P. falciparum), a detailed bioinformatics analysis is undertaken. We have analysed the Phylogenetic relationship of PSY also referred to as octaprenyl pyrophosphate synthase (OPPS) in P. falciparum with other taxonomic groups. Further, we in silico characterized the secondary and tertiary structures of P. falciparum PSY/OPPS and compared the tertiary structures with crystal structure of Thermotoga maritima (T. maritima) OPPS. Our results evidenced the resemblance of P. falciparum PSY with the active site of T. maritima OPPS. Interestingly, the comparative structural analysis revealed an unconserved unique loop in P. falciparum OPPS/PSY. Such structural insights might contribute novel accessory functions to the protein thus, offering potential drug targets. PMID:26702306

  4. Recent horizontal transfer of mellifera subfamily mariner transposons into insect lineages representing four different orders shows that selection acts only during horizontal transfer.

    PubMed

    Lampe, David J; Witherspoon, David J; Soto-Adames, Felipe N; Robertson, Hugh M

    2003-04-01

    We report the isolation and sequencing of genomic copies of mariner transposons involved in recent horizontal transfers into the genomes of the European earwig, Forficula auricularia; the European honey bee, Apis mellifera; the Mediterranean fruit fly, Ceratitis capitata; and a blister beetle, Epicauta funebris, insects from four different orders. These elements are in the mellifera subfamily and are the second documented example of full-length mariner elements involved in this kind of phenomenon. We applied maximum likelihood methods to the coding sequences and determined that the copies in each genome were evolving neutrally, whereas reconstructed ancestral coding sequences appeared to be under selection, which strengthens our previous hypothesis that the primary selective constraint on mariner sequence evolution is the act of horizontal transfer between genomes. PMID:12654937

  5. Structure of ovaries and oogenesis in dermapterans. II. The nurse cells, nuage aggregates and sponge bodies.

    PubMed

    Tworzyd?o, Wac?aw; Kisiel, Elzbieta

    2010-01-01

    In three studied dermapteran species, Doru lineare, Opisthocosmia silvestris and Forficula auricularia, ovarian follicles are composed of two cells only, the oocyte and a single nurse cell. The nuclei of the nurse cells are large, ameboid and contain highly active nucleoli. RER elements, ribosomes, mitochondria and electron-dense aggregations of nuage material are present in the cytoplasm. Immunolocalization analysis revealed that in earwigs the nuage does not contain snRNAs. In one of the studied species, Doru lineare, apart from "canonical" nuage aggregations, characteristic RER/nuage complexes were found. These structures are morphologically similar to the sponge bodies present in the cytoplasm of the Drosophila germline cells. We suggest that RER/nuage complexes in Doru, as sponge bodies in Drosophila, are implicated in mRNA translocation. PMID:20420198

  6. Woolly apple aphid Eriosoma lanigerum Hausmann ecology and its relationship with climatic variables and natural enemies in Mediterranean areas.

    PubMed

    Lordan, Jaume; Alegre, Simó; Gatius, Ferran; Sarasúa, M José; Alins, Georgina

    2015-02-01

    A multilateral approach that includes both biotic and climatic data was developed to detect the main variables that affect the ecology and population dynamics of woolly apple aphid Eriosoma lanigerum (Hausmann). Crawlers migrated up and down the trunk mainly from spring to autumn and horizontal migration through the canopy was observed from May to August. Winter temperatures did not kill the canopy colonies, and both canopy and root colonies are the source of reinfestations in Mediterranean areas. Thus, control measures should simultaneously address roots and canopy. European earwigs Forficula auricularia (Linnaeus) were found to reduce the survival of overwintering canopy colonies up to June, and this can allow their later control by the parasitoid Aphelinus mali (Haldeman) from summer to fall. Preliminary models to predict canopy infestations were developed. PMID:25335497

  7. 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

  8. The influence of prolonged mouth closure on selected components of the hyperbenthos in the littoral zone of the temporarily open/closed Kasouga Estuary, South Africa

    NASA Astrophysics Data System (ADS)

    Froneman, P. W.; Henninger, T. O.

    2009-07-01

    The influence of prolonged mouth closure on the population dynamics of the caridian shrimp, Palaemon peringueyi and the estuarine isopod, Exosphaeroma hylocoetes, in the littoral zone of temporarily open/closed Kasouga Estuary located on the south-eastern coastline of southern Africa was assessed monthly over the period October 2007 to September 2008. Prolonged mouth closure of the estuary contributed to hypersaline conditions (psu > 35) prevailing throughout the estuary for the last four months of the study. The high salinities coincided with a decrease in the areal extent (up to 80%) of the submerged macrophytes, mainly Ruppia maritima, within the littoral zone of the estuary. Total abundance and biomass values of the shrimp and isopod over the period of investigation ranged from 0 to 14.6 ind m -2, from 0 to 13.3 mg dwt m -2, from 12 to 1540 ind m -2 and from 0.1 to 2.16 mg dwt m -2, respectively. Maximum values of both the shrimp and isopod were recorded in the upper reaches of the estuary in close association with R. maritima. Over the course of the investigation, both the abundance and biomass values of the shrimp decreased significantly ( P < 0.05 in both cases) which could be related to reduced habitat availability, R. maritima, that acts as a refuge against fish predation. Additionally, the decrease in abundance and biomass values could be attributed to reduced recruitment opportunities for the shrimp and the cessation of reproduction in the estuarine isopod. The establishment of a link to the marine environment following an overtopping event in September 2008 contributed to a decrease in salinity within the system although no recruitment of either the isopod or shrimp was recorded.

  9. 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.

  10. 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.

  11. Opening a can of centipedes: new insights into mechanisms of body segmentation.

    PubMed

    Valentin, Guillaume; Oates, Andrew C

    2013-01-01

    The search for a common developmental genetic mechanism of body segmentation appears to become more difficult, and more interesting, as new segmented organisms are added to the roster. Recent work in this journal by Brena and Akam on segmentation of the geophilomorph centipede Strigamia maritima, an arthropod distantly related to the standard insect models, contains developmental and evolutionary surprises that highlight the importance of a wider sampling of phyla.See research article: http://www.biomedcentral.com/1741-7007/11/112. PMID:24289333

  12. Antimicrobial activity of fatty acid methyl esters of some members of Chenopodiaceae.

    PubMed

    Chandrasekaran, Manivachagam; Kannathasan, Krishnan; Venkatesalu, Venugopalan

    2008-01-01

    Fatty acid methyl ester (FAME) extracts of four halophytic plants, viz. Arthrocnemum indicum, Salicornia brachiata, Suaeda maritima and Suaeda monoica belonging to the family Chenopodiaceae, were prepared and their composition was analyzed by GC-MS. The FAME extracts were also screened for antibacterial and antifungal activities. The GC-MS analysis revealed the presence of more saturated fatty acids than unsaturated fatty acids. Among the fatty acids analyzed, the relative percentage of lauric acid was high in S. brachiata (61.85%). The FAME extract of S. brachiata showed the highest antibacterial and antifungal activities among the extracts tested. The other three extracts showed potent antibacterial and moderate anticandidal activities. PMID:18669016

  13. 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

  14. 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.

  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. Organism traits determine the strength of scale-dependent bio-geomorphic feedbacks: A flume study on three intertidal plant species

    NASA Astrophysics Data System (ADS)

    Bouma, T. J.; Temmerman, S.; van Duren, L. A.; Martini, E.; Vandenbruwaene, W.; Callaghan, D. P.; Balke, T.; Biermans, G.; Klaassen, P. C.; van Steeg, P.; Dekker, F.; van de Koppel, J.; de Vries, M. B.; Herman, P. M. J.

    2013-01-01

    There is a growing recognition of the important role of scale-dependent feedback for biogeomorphological landscape formation, where organisms locally improve survival and growth but at the same time negatively affect organisms at larger distance. However, little is known on how scale-dependent bio-geomorphic feedback is influenced by organism traits in combination with abiotic forcing. This was studied by measuring in a flume, the flow patterns around patches of three contrasting marsh species (Spartina anglica, Puccinellia maritima and Salicornia procumbens), using the flow acceleration around vegetation patches and deceleration within vegetation patches as quantitative proxy for the negative and positive feedback to the vegetation performance. The importance of external forcing was assessed by comparing three realistic current velocities: 0.1, 0.2 and 0.3 m s- 1. Our results showed that the dense clonal growth of stiff Spartina anglica shoots caused strongest flow deviations, irrespective of the applied current velocity. In contrast, the more sparsely growing, shorter stiff shoots of Salicornia procumbens induced much less flow deviation, allowing more water to pass through and over the vegetation canopy. The dense but highly flexible shoots of Puccinellia maritima caused strong flow deviations at low velocities, which diminished at higher velocities due to bending of the vegetation. Overall, these hydrodynamic results demonstrate that plant species traits interact with environmental conditions in creating scale-dependent feedbacks explaining why the effects of vegetation on landscape formation in saltmarshes are species specific.

  17. Distribution and migration of seaside sparrows

    USGS Publications Warehouse

    Robbins, C.S.

    1983-01-01

    The majority of the nine presently recognized races of the Seaside Sparrow (Ammospiza maritima) are so similar to neighboring races that individual birds outside their known breeding range cannot be subspecifically identified with certainty. The northern race, A. m. maritima, is partially migratory, with most individuals departing in autumn from Chesapeake Bay and from all the coastal marshes that lie to the north of the mouth of this bay. No banded bird has been recaptured in winter south of its breeding locality, however, so even the major wintering ground of this subspecies cannot be defined. The other subspecies are presumed to be primarily sedentary. Median arrival and departure dates at Fairfield, Connecticut, are 18 May and 19 September. On Long Island, New York, the spring peak occurs in the third week of May, and the autumn peak in mid-October. Postbreeding wanderers of unknown origin move north and east in August and September to the coastal marshes of Maine, New Brunswick, and Nova Scotia. The remarkably few records away from tidewater are from North Carolina, eastern Pennsylvania, the lower Hudson River, and eastern Massachusetts.

  18. The role of macrophytes as a refuge and food source for the estuarine isopod Exosphaeroma hylocoetes (Barnard, 1940)

    NASA Astrophysics Data System (ADS)

    Henninger, Tony O.; Froneman, P. William; Richoux, Nicole B.; Hodgson, Alan N.

    2009-04-01

    The role of submerged macrophytes as refugia from fish predation and as possible food sources for the estuarine isopod Exosphaeroma hylocoetes ( Barnard, K.H., 1940) was investigated. Laboratory experiments tested the effectiveness of artificial vegetation, replicating submerged vegetation, in enabling isopods to elude selected fish predators Rhabdosargus holubi, Glossogobius callidus, Monodactylus falciformis and Clinus cottoides. Isopods preferentially hid in the vegetation (>90%), even in absence of fish. The predatory fish had varying success in finding isopods within the vegetation. Isopod mortality ranged from 2% ( R. holubi) to a maximum of 87% ( C. cottoides) within vegetation, depending on the fish predator present. Stable isotope and fatty acid analyses ruled out the submerged macrophyte Ruppia maritima and inundated fringing grasses as direct food sources, but highlighted the epiphytic biota (mainly diatoms) found on the submerged vegetation and sediments as more likely food sources. These findings are consistent with gut content analyses. The results suggest that the close association of E. hylocoetes with R. maritima is the result of the vegetation providing the isopod with a refuge against fish predation as well as areas of increased food availability.

  19. Structure-based activity prediction for an enzyme of unknown function

    PubMed Central

    Hermann, Johannes C.; Marti-Arbona, Ricardo; Fedorov, Alexander A.; Fedorov, Elena; Almo, Steven C.; Shoichet, Brian K.; Raushel, Frank M.

    2008-01-01

    With many genomes sequenced, a pressing challenge in biology is predicting the function of the proteins that the genes encode. When proteins are unrelated to others of known activity, bioinformatics inference for function becomes problematic. It would thus be useful to interrogate protein structures for function directly. Here, we predict the function of an enzyme of unknown activity, Tm0936 from Thermotoga maritima, by docking high-energy intermediate forms of thousands of candidate metabolites. The docking hit list was dominated by adenine analogues, which appeared to undergo C6-deamination. Four of these, including 5-methylthioadenosine and S-adenosylhomocysteine (SAH), were tested as substrates, and three had substantial catalytic rate constants (105 M?1s?1). The X-ray crystal structure of the complex between Tm0936 and the product resulting from the deamination of SAH, S-inosylhomocysteine, was determined, and it corresponded closely to the predicted structure. The deaminated products can be further metabolized by T. maritima in a previously uncharacterized SAH degradation pathway. Structure-based docking with high-energy forms of potential substrates may be a useful tool to annotate enzymes for function. PMID:17603473

  20. Structure-Based Activity Prediction for an Enzyme of Unknown Function

    SciTech Connect

    Hermann,J.; Marti-Arbona, R.; Fedorov, A.; Fedorov, E.; Almo, S.; Shoichet, B.; Raushel, F.

    2007-01-01

    With many genomes sequenced, a pressing challenge in biology is predicting the function of the proteins that the genes encode. When proteins are unrelated to others of known activity, bioinformatics inference for function becomes problematic. It would thus be useful to interrogate protein structures for function directly. Here, we predict the function of an enzyme of unknown activity, Tm0936 from Thermotoga maritima, by docking high-energy intermediate forms of thousands of candidate metabolites. The docking hit list was dominated by adenine analogues, which appeared to undergo C6-deamination. Four of these, including 5-methylthioadenosine and S-adenosylhomocysteine (SAH), were tested as substrates, and three had substantial catalytic rate constants (10{sup 5} M{sup -1} s{sup -1}). The X-ray crystal structure of the complex between Tm0936 and the product resulting from the deamination of SAH, S-inosylhomocysteine, was determined, and it corresponded closely to the predicted structure. The deaminated products can be further metabolized by T. maritima in a previously uncharacterized SAH degradation pathway. Structure-based docking with high-energy forms of potential substrates may be a useful tool to annotate enzymes for function.

  1. Antioxidant activity of raw, cooked and Rhizopus oligosporus fermented beans of Canavalia of coastal sand dunes of Southwest India.

    PubMed

    Niveditha, Vedavyas R; Sridhar, Kandikere R

    2014-11-01

    The raw and processed (cooked and cooked + solid-state fermented with Rhizopus oligosporus) split beans of two landraces of coastal sand dune wild legumes (Canavalia cathartica and Canavalia maritima) of the southwest coast of India were examined for bioactive compounds (total phenolics, tannins and vitamin C) and antioxidant potential (total antioxidant activity, ferrous-ion chelating capacity, DPPH free radical-scavenging activity and reducing activity). One-way ANOVA revealed significant elevation of bioactive compounds as well as antioxidant activities in fermented beans compared to raw and cooked beans in both legumes (p?maritima were clustered. The present study demonstrated that split beans of coastal sand dune Canavalia fermented by R. oligosporus endowed with high bioactive principles as well as antioxidant potential and thus serve as future nutraceutical source. PMID:26396318

  2. The effects of soil amendments on heavy metal bioavailability in two contaminated Mediterranean soils.

    PubMed

    Walker, David J; Clemente, Rafael; Roig, Asuncion; Bernal, M Pilar

    2003-01-01

    Two heavy metal contaminated calcareous soils from the Mediterranean region of Spain were studied. One soil, from the province of Murcia, was characterised by very high total levels of Pb (1572 mg kg(-1)) and Zn (2602 mg kg(-1)), whilst the second, from Valencia, had elevated concentrations of Cu (72 mg kg(-1)) and Pb (190 mg kg(-1)). The effects of two contrasting organic amendments (fresh manure and mature compost) and the chelate ethylenediaminetetraacetic acid (EDTA) on soil fractionation of Cu, Fe, Mn, Pb and Zn, their uptake by plants and plant growth were determined. For Murcia soil, Brassica juncea (L.) Czern. was grown first, followed by radish (Raphanus sativus L.). For Valencia soil, Beta maritima L. was followed by radish. Bioavailability of metals was expressed in terms of concentrations extractable with 0.1 M CaCl2 or diethylenetriaminepentaacetic acid (DTPA). In the Murcia soil, heavy metal bioavailability was decreased more greatly by manure than by the highly-humified compost. EDTA (2 mmol kg(-1) soil) had only a limited effect on metal uptake by plants. The metal-solubilising effect of EDTA was shorter-lived in the less contaminated, more highly calcareous Valencia soil. When correlation coefficients were calculated for plant tissue and bioavailable metals, the clearest relationships were for Beta maritima and radish. PMID:12531318

  3. 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

  4. Conformational Flexibility and Peptide Interaction of the Translocation ATPase SecA

    SciTech Connect

    Zimmer, Jochen; Rapoport, Tom A.; Harvard-Med

    2010-09-21

    The SecA ATPase forms a functional complex with the protein-conducting SecY channel to translocate polypeptides across the bacterial cell membrane. SecA recognizes the translocation substrate and catalyzes its unidirectional movement through the SecY channel. The recent crystal structure of the Thermotoga maritima SecA-SecYEG complex shows the ATPase in a conformation where the nucleotide-binding domains (NBDs) have closed around a bound ADP-BeFx complex and SecA's polypeptide-binding clamp is shut. Here, we present the crystal structure of T. maritima SecA in isolation, determined in its ADP-bound form at 3.1 {angstrom} resolution. SecA alone has a drastically different conformation in which the nucleotide-binding pocket between NBD1 and NBD2 is open and the preprotein cross-linking domain has rotated away from both NBDs, thereby opening the polypeptide-binding clamp. To investigate how this clamp binds polypeptide substrates, we also determined a structure of Bacillus subtilis SecA in complex with a peptide at 2.5 {angstrom} resolution. This structure shows that the peptide augments the highly conserved {beta}-sheet at the back of the clamp. Taken together, these structures suggest a mechanism by which ATP hydrolysis can lead to polypeptide translocation.

  5. An ecological approach to measuring the evolutionary consequences of gene flow from crops to wild or weedy relatives1

    PubMed Central

    Campbell, Lesley G.; Lee, David; Shukla, Kruti; Waite, Thomas A.; Bartsch, Detlef

    2016-01-01

    Premise of the study: Agricultural practices routinely create opportunities for crops to hybridize with wild relatives, leading to crop gene introgression into wild genomes. Conservationists typically worry this introgression could lead to genetic homogenization of wild populations, over and above the central concern of transgene escape. Alternatively, viewing introgression as analogous to species invasion, we suggest that increased genetic diversity may likewise be an undesirable outcome. Methods: Here, we compare the sensitivity of conventional population genetic metrics with species diversity indices as indicators of the impact of gene flow on genetic diversity. We illustrate this novel approach using multilocus genotype data (12 allozyme loci) from 10 wild (Beta vulgaris subsp. maritima) and eight putative crop–wild hybrid beet populations (B. vulgaris subsp. vulgaris × B. vulgaris subsp. maritima) scattered throughout Europe. Results: Conventional population genetic metrics mostly failed to detect shifts in genetic composition of putative hybrid populations. By contrast, species diversity indices unambiguously revealed increased genetic diversity in putative hybrid populations. Discussion: We encourage other workers to explore the utility of our more sensitive approach for risk assessment prior to the release of transgenic crops, with a view toward widespread adoption of our method in studies aimed at detecting allelic invasion. PMID:27011898

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

    PubMed Central

    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

  7. Structural Insights into the Catalytic Mechanism of Bacterial Guanosine-diphospho-d-mannose Pyrophosphorylase and Its Regulation by Divalent Ions*

    PubMed Central

    Pelissier, Marie-Cécile; Lesley, Scott A.; Kuhn, Peter; Bourne, Yves

    2010-01-01

    GMP catalyzes the formation of GDP-Man, a fundamental precursor for protein glycosylation and bacterial cell wall and capsular polysaccharide biosynthesis. Crystal structures of GMP from the thermophilic bacterium Thermotoga maritima in the apo form, in complex with the substrates mannose-1-phosphate or GTP and bound with the end product GDP-Man in the presence of the essential divalent cation Mg2+, were solved in the 2.1–2.8 ? resolution range. The T. maritima GMP molecule is organized in two separate domains: a N-terminal Rossman fold-like domain and a C-terminal left-handed ?-helix domain. Two molecules associate into a dimer through a tail-to-tail arrangement of the C-terminal domains. Comparative analysis of the structures along with characterization of enzymatic parameters reveals the bases of substrate specificity of this class of sugar nucleotidyltransferases. In particular, substrate and product binding are associated with significant changes in the conformation of loop regions lining the active center and in the relative orientation of the two domains. Involvement of both the N- and C-terminal domains, coupled to the catalytic role of a bivalent metal ion, highlights the catalytic features of bacterial GMPs compared with other members of the pyrophosphorylase superfamily. PMID:20573954

  8. Distance to semi-natural grassland influences seed production of insect-pollinated herbs.

    PubMed

    Jakobsson, Anna; Ågren, Jon

    2014-05-01

    Marginal grassland fragments, such as road verges and field margins, may act as important supplemental habitats for grassland plants in the modern agricultural landscape. However, abundance of pollinators in such fragments has been found to decline with distance to larger natural and semi-natural habitats, and this could have corresponding effects on plant pollination. In this study, we performed a field experiment on road verges with three insect-pollinated grassland herbs to examine the relationship between distance to semi-natural grassland and plant reproductive success in two landscapes with contrasting farming intensities. In Lychnis viscaria and Lotus corniculatus, seed production tended to decrease with increasing distance to semi-natural grassland, but only in the landscape with high farming intensity. Seed production in Armeria maritima spp. maritima decreased with distance in both landscapes. Although many studies have investigated effects of natural habitat on crop pollination, little is known about the impact on pollination in native plants. The results from this study indicate that management of semi-natural grasslands improves not only biodiversity within the actual grassland but also pollination of native plants in the surrounding agricultural landscape. PMID:24562471

  9. 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

  10. Phenotypic plasticity in the developmental integration of morphological trade-offs and secondary sexual trait compensation.

    PubMed

    Tomkins, Joseph L; Kotiaho, Janne S; Lebas, Natasha R

    2005-03-01

    Trait exaggeration through sexual selection will tale place alongside other changes in phenotype. Exaggerated morphology might be compensated by parallel changes in traits that support, enhance or facilitate exaggeration: 'secondary sexual trait compensation' (SSTC). Alternatively, exaggeration might be realized at the expense of other traits through morphological trade-offs. For the most part, SSTC has only been examined interspecifically. For these phenomena to be important intraspecifically, the sexual trait must be developmentally integrated with the compensatory or competing trait. We studied developmental integration in two species with different development: the holometabolous beetle Onthophagus taurus and the hemimetabolous earwig Forficula auricularia. Male-dimorphic variation in trait exaggeration was exploited to expose both trade-offs and SSTC. We found evidence for morphological trade-offs in O. taurus, but no F. auricularia, supporting the notion that trade-offs are more likely in closed developmetal systems. However, we found these trade-offs were not limited solely to traits growing close together. Developmental integration of structures involved in SSTC were detected in both species. The developmental integration of SSTC was phenotypically plastic, such that the compensation for relatively larger sexual traits was greater in the exasperated male morphs. Evidence of intraspecific SSTC demands studies of the selective, genetic and developmental architecture of phenotypic integration. PMID:15799950

  11. 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

  12. Electron microscopic localization of chitin using colloidal gold labelled with wheat germ agglutinin.

    PubMed

    Peters, W; Latka, I

    1986-01-01

    The lectin wheat germ agglutinin (WGA) has a binding site which is able to bind a sequence of three N-acetyl-glucosamine residues. Therefore, it has a very strong affinity for the polymers of this sugar, especially chitin. Colloidal gold can be labelled with WGA and used as a specific electron-dense marker for the electron-microscopic localization of chitin. The specificity of the WGA-gold binding can be checked by competitive inhibition with 5-10 mM triacetyl chitotriose. The reliability of this method was tested in three species. In the formation zone of the radula of the snail, Biomphalaria glabrata Say, chitin or chitin precursors were localized in vesicles of the odontoblasts, outside the extremely long microvilli of odontoblasts and in the newly formed teeth. The inner peritrophic envelope of the earwig, Forficula auricularia L., is characterized by an orthogonal texture of bundles of microfibrils that are thought to contain chitin. The presence of chitin was proved using the present method. In the peritrophic membranes of the blowfly, Calliphora erythrocephala Meigen, it was possible to differentiate between chitin and glycoproteins which have N-acetylglucosamine residues. PMID:3754855

  13. 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

  14. Phenotypic plasticity in the developmental integration of morphological trade-offs and secondary sexual trait compensation

    PubMed Central

    Tomkins, Joseph L; Kotiaho, Janne S; LeBas, Natasha R

    2005-01-01

    Trait exaggeration through sexual selection will take place alongside other changes in phenotype. Exaggerated morphology might be compensated by parallel changes in traits that support, enhance or facilitate exaggeration: ‘secondary sexual trait compensation’ (SSTC). Alternatively, exaggeration might be realized at the expense of other traits through morphological trade-offs. For the most part, SSTC has only been examined interspecifically. For these phenomena to be important intraspecifically, the sexual trait must be developmentally integrated with the compensatory or competing trait. We studied developmental integration in two species with different development: the holometabolous beetle Onthophagus taurus and the hemimetabolous earwig Forficula auricularia. Male-dimorphic variation in trait exaggeration was exploited to expose both trade-offs and SSTC. We found evidence for morphological trade-offs in O. taurus, but not F. auricularia, supporting the notion that trade-offs are more likely in closed developmental systems. However, we found these trade-offs were not limited solely to traits growing close together. Developmental integration of structures involved in SSTC were detected in both species. The developmental integration of SSTC was phenotypically plastic, such that the compensation for relatively larger sexual traits was greater in the exaggerated male morphs. Evidence of intraspecific SSTC demands studies of the selective, genetic and developmental architecture of phenotypic integration. PMID:15799950

  15. Patterns of threshold evolution in polyphenic insects under different developmental models.

    PubMed

    Tomkins, Joseph L; Moczek, Armin P

    2009-02-01

    Two hypotheses address the evolution of polyphenic traits in insects. Under the developmental reprogramming model, individuals exceeding a threshold follow a different developmental pathway from individuals below the threshold. This decoupling is thought to free selection to independently hone alternative morphologies, increasing phenotypic plasticity and morphological diversity. Under the alternative model, extreme positive allometry explains the existence of alternative phenotypes and divergent phenotypes are developmentally coupled by a continuous reaction norm, such that selection on either morph acts on both. We test the hypothesis that continuous reaction norm polyphenisms, evolve through changes in the allometric parameters of even the smallest males with minimal trait expression, whereas threshold polyphenisms evolve independent of the allometric parameters of individuals below the threshold. We compare two polyphenic species; the dung beetle Onthophagus taurus, whose allometry has been modeled both as a threshold polyphenism and a continuous reaction norm and the earwig Forficula auricularia, whose allometry is best modeled with a discontinuous threshold. We find that across populations of both species, variation in forceps or horn allometry in minor males are correlated to the population's threshold. These findings suggest that regardless of developmental mode, alternative morphs do not evolve independently of one another. PMID:19154360

  16. [Pests at Baltic Sea coast. II. Summary of most important groups on insects besides Coleoptera and Diptera].

    PubMed

    Eichler, W

    1976-05-01

    In the special holiday situations at the Baltic coast of GDR, species of very different insect groups may become annoying to man. Own experiences in this field are reported (excepting Coleoptera and Diptera). The earwig, Forficula auricularia, has many varying aspects of a health pest (also in the respect of social hygiene). This species, too, may pinch painfully with his pincers. The lice species Pediculus capitis and Pthirus pubis are met with sometimes. Limothrips cerealium may be annoying not only when swarming in mass, but also individual specimens (crawling on the skin or piercing it). Ants may be a pest in varying manners. A special example of this is if they invade sand castles [sun bathing places on the beaches surrounded by sand walls]. Wasps are attracted by different ways to childrens' holiday camps. In 1973, they were even aggressive on the beach of Hiddensee. Caterpillars of Thaumatopaea pinivora may become a serious health pest in individual cases. The real cause is not always detected by laymen. Fleas occur more or less regularly. Sometimes they are incorrectly diagnosed or reported. PMID:984495

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

    PubMed

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

    2009-08-01

    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

  18. Elastic joints in dermapteran hind wings: materials and wing folding.

    PubMed

    Haas, F; Gorb, S; Wootton, R J

    2000-04-01

    Representatives of Dermaptera probably have the most unusual hind wing venation and folding pattern among insects. Both correlate with unusual wing folding mechanics, in which folding is achieved from within the wing and unfolding is done by the cerci. In this account, the hind wings of the earwig Forficula auricularia were studied by means of bright field and fluorescence microscopy. Resilin, a rubber-like protein, was revealed in several, clearly defined patches. It occurs dorsally in the radiating veins, but ventrally in the intercalary vein. This distribution determines the folding direction, and resilin is the major driving mechanism for wing folding. Resilin stores elastic energy in broadened vein patches and along the folds. At the other locations, the mid-wing mechanism and central area, the primary function of resilin is suggested to be prevention of material failure. The arrangement of resilin patches is such that the wing cannot be unfolded from the thorax proper but must be unfolded by the cerci. In Dermaptera, the antagonistic movements of folding and unfolding are achieved in two different ways, resilin and cerci. To our knowledge this is unique. PMID:18088922

  19. Population density drives the local evolution of a threshold dimorphism.

    PubMed

    Tomkins, Joseph L; Brown, Gordon S

    2004-10-28

    Evolution can favour more than one reproductive tactic among conspecifics of the same sex. Under the conditional evolutionarily stable strategy, individuals adopt the tactic that generates the highest fitness return for their status: large males guard females, whereas small males sneak copulations. Tactics change at the status at which fitness benefits switch from favouring one tactic to favouring the alternative. This 'switchpoint' is expressed in many species as a threshold between divergent morphologies. Environmental and demographic parameters that influence the relative fitness of male tactics are predicted to determine a population's switchpoint and consequently whether the population is monomorphic or dimorphic. Here we show threshold evolution in the forceps dimorphism of the European earwig Forficula auricularia and document the transition from completely monomorphic to classical male-dimorphic populations over a distance of only 40 km. Because the superior fighting ability of the dominant morph will be more frequently rewarded at high encounter rates, population density is likely to be a key determinant of the relative fitness of the alternative tactics, and consequently the threshold. We show that, as predicted, population density correlates strongly with the shift in threshold, and that this factor drives the local evolution of the male dimorphism in these island populations. Our data provide evidence for the origin of phenotypic diversity within populations, through the evolution of a switchpoint in a conditional strategy that has responded to local population density. PMID:15510148

  20. Insect phylogenomics: results, problems and the impact of matrix composition.

    PubMed

    Letsch, Harald O; Meusemann, Karen; Wipfler, Benjamin; Schütte, Kai; Beutel, Rolf; Misof, Bernhard

    2012-08-22

    In this study, we investigated the relationships among insect orders with a main focus on Polyneoptera (lower Neoptera: roaches, mantids, earwigs, grasshoppers, etc.), and Paraneoptera (thrips, lice, bugs in the wide sense). The relationships between and within these groups of insects are difficult to resolve because only few informative molecular and morphological characters are available. Here, we provide the first phylogenomic expressed sequence tags data ('EST': short sub-sequences from a c(opy) DNA sequence encoding for proteins) for stick insects (Phasmatodea) and webspinners (Embioptera) to complete published EST data. As recent EST datasets are characterized by a heterogeneous distribution of available genes across taxa, we use different rationales to optimize the data matrix composition. Our results suggest a monophyletic origin of Polyneoptera and Eumetabola (Paraneoptera + Holometabola). However, we identified artefacts of tree reconstruction (human louse Pediculus humanus assigned to Odonata (damselflies and dragonflies) or Holometabola (insects with a complete metamorphosis); mayfly genus Baetis nested within Neoptera), which were most probably rooted in a data matrix composition bias due to the inclusion of sequence data of entire proteomes. Until entire proteomes are available for each species in phylogenomic analyses, this potential pitfall should be carefully considered. PMID:22628473

  1. Signals of Supersymmetry in Top Quark Decays at Positron-Electron and Hadron-Hadron Colliders

    NASA Astrophysics Data System (ADS)

    Haim, Dan

    1990-01-01

    As the search for 'new physics' intensified in the past decade, phenomenological consequences of non-standard theories, such as supersymmetry, became highly important to the future of high energy physics. We examined the possibility of detecting supersymmetry in existing and future e^+ e^- and hadron -hadron colliders. We have focussed on the influence of supersymmetry on the search for the top quark (as yet, undiscovered) by studying the two specific processes: e^+ e^- to Theta to g ~{g}~{k}, where ~{k} is either a ~{g} or ~{gamma}, and pp to t|{t}X followed by t to b+l^{+}+nu_{ rm l}+~gamma+~gamma . The Webber Marchesini Monte Carlo programs, EARWIG and HERWIG, were used to generate 1000 events of each type at center of mass energies of 2m_{ rm t} for the e^+ e^ - machines, and 40 TeV, for the SSC, respectively. We find that although it is possible to observe supersymmetry, we need machines of higher luminosity to detect it. We also find that there is a major background in the hadron -hadron colliders (both the Tevatron and the SSC) from the initial state bremsstrahlung radiation which, at top quark mass of 100 GeV, can obscure the true nature of the jets from the hard subprocess itself.

  2. Insect phylogenomics: results, problems and the impact of matrix composition

    PubMed Central

    Letsch, Harald O.; Meusemann, Karen; Wipfler, Benjamin; Schütte, Kai; Beutel, Rolf; Misof, Bernhard

    2012-01-01

    In this study, we investigated the relationships among insect orders with a main focus on Polyneoptera (lower Neoptera: roaches, mantids, earwigs, grasshoppers, etc.), and Paraneoptera (thrips, lice, bugs in the wide sense). The relationships between and within these groups of insects are difficult to resolve because only few informative molecular and morphological characters are available. Here, we provide the first phylogenomic expressed sequence tags data (‘EST’: short sub-sequences from a c(opy) DNA sequence encoding for proteins) for stick insects (Phasmatodea) and webspinners (Embioptera) to complete published EST data. As recent EST datasets are characterized by a heterogeneous distribution of available genes across taxa, we use different rationales to optimize the data matrix composition. Our results suggest a monophyletic origin of Polyneoptera and Eumetabola (Paraneoptera + Holometabola). However, we identified artefacts of tree reconstruction (human louse Pediculus humanus assigned to Odonata (damselflies and dragonflies) or Holometabola (insects with a complete metamorphosis); mayfly genus Baetis nested within Neoptera), which were most probably rooted in a data matrix composition bias due to the inclusion of sequence data of entire proteomes. Until entire proteomes are available for each species in phylogenomic analyses, this potential pitfall should be carefully considered. PMID:22628473

  3. Short-term benefits, but transgenerational costs of maternal loss in an insect with facultative maternal care.

    PubMed

    Thesing, Julia; Kramer, Jos; Koch, Lisa K; Meunier, Joël

    2015-10-22

    A lack of parental care is generally assumed to entail substantial fitness costs for offspring that ultimately select for the maintenance of family life across generations. However, it is unknown whether these costs arise when parental care is facultative, thus questioning their fundamental importance in the early evolution of family life. Here, we investigated the short-term, long-term and transgenerational effects of maternal loss in the European earwig Forficula auricularia, an insect with facultative post-hatching maternal care. We showed that maternal loss did not influence the developmental time and survival rate of juveniles, but surprisingly yielded adults of larger body and forceps size, two traits associated with fitness benefits. In a cross-breeding/cross-fostering experiment, we then demonstrated that maternal loss impaired the expression of maternal care in adult offspring. Interestingly, the resulting transgenerational costs were not only mediated by the early-life experience of tending mothers, but also by inherited, parent-of-origin-specific effects expressed in juveniles. Orphaned females abandoned their juveniles for longer and fed them less than maternally-tended females, while foster mothers defended juveniles of orphaned females less well than juveniles of maternally-tended females. Overall, these findings reveal the key importance of transgenerational effects in the early evolution of family life. PMID:26490790

  4. Estimation of climate change impacts on river flow and catchment hydrological connectivity incorporating uncertainty from multiple climate models, stochastic downscaling and hydrological model parameterisation error sources

    NASA Astrophysics Data System (ADS)

    Reaney, S. M.; Fowler, H. J.

    2008-12-01

    When estimating climate change impacts, there are many sources of uncertainty which must be considered. The main sources of uncertainty arise from the structure and parameterisation of physically based simulation models, downscaling methods, stochastic realisations of future weather time series and the underlying emission scenarios. This work focuses on the uncertainties resulting from the use of multiple climate models and the joint impact of the stochastic realisations of future weather time series from a weather generator, EARWIG, and from parameter estimation uncertainty of a hydrological model, CAS-Hydro. These tools have been applied to the River Rye, Yorkshire. A suite of model parameter sets and weather realisations have been used to project likely changes to the hydrological functioning under climate change. Results are presented on the projected changes in flow duration curves and the potential changes in the hydrological connectivity by overland flow within the catchment. The statistical sensitivity of the impact predictions to these sources of uncertainty and the use of a multi-model ensemble to enable the production of probabilistic estimates of change is assessed. These estimates of potential changes in flow can then be used to inform the adaptation of water resources design and management.

  5. Differential ant exclusion from canopies shows contrasting top-down effects on community structure.

    PubMed

    Mestre, Laia; Piñol, J; Barrientos, J A; Espadaler, X

    2016-01-01

    Predators have far-reaching effects on communities by triggering top-down trophic cascades that influence ecosystem functioning. Omnivory and intraguild interactions between predators give rise to reticulate food webs and may either strengthen or dampen trophic cascades depending on context. Disentangling the effects of multiple predator species is therefore crucial for predicting the influence of predators on community structure. We focused on ants as dominant generalist predators in arthropod communities and set up a differential ant exclusion from canopies to examine its effects on assemblage species composition and densities of five arthropod groups (psocopterans, aphids, spiders, heteropterans and beetles). We coupled a glue band with tubes allowing only the ant Lasius grandis to reach the canopies to isolate its effect from the rest of crawling predators (ants, earwigs) and compared it against a full exclusion and a control. L. grandis alone had widespread effects on assemblage species composition, with contrasting species-specific responses within groups, where some species affected by L. grandis presence were not further affected by the presence of the whole crawling predator assemblage, and vice versa. Overall, L. grandis caused two- to threefold decreases of generalist predators and a threefold increase of aphids. However, it lacked further top-down effects on primary consumers, which only emerged when all crawling predators were present. This differential exclusion demonstrates the distinctive and widespread intraguild effects on community structure of a single ant species that contrast with the top-down effects exerted by the whole crawling predator assemblage. PMID:26376660

  6. 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.

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

    PubMed Central

    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

  8. 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.

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

    PubMed Central

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

    2012-01-01

    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 Omp?) and the porin OmpB (or Omp?). 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 ?-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 ?-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. PMID:22768259

  10. 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.

  11. La?q: A Sustained-Release Dosage Form for Respiratory Disorders in Traditional Persian Medicine.

    PubMed

    Karegar-Borzi, Hossein; Salehi, Mehdi; Rahimi, Roja

    2016-01-01

    La?q is a pharmaceutical dosage form that had been mainly used for the treatment of various respiratory disorders in traditional Persian medicine. It is important from 2 aspects: a dosage form with efficient and optimum delivery of drugs to the respiratory tract and biological effects of its ingredients. Natural medicine in la?q has been demonstrated to act in respiratory disorders by their antitussive, antiallergic, anti-inflammatory, antioxidant, spasmolytic, and antibacterial activities. Some of these natural remedies act by most of the mentioned mechanisms such as Cydonia oblonga, Glycyrrhiza glabra, Crocus sativus, Hyssopus officinalis, Foeniculum vulgare, and honey. However, the evidence is limited including Cassia fistula, Papaver somniferum, and Drimia maritima. According to positive pharmacokinetic and pharmacodynamic aspects of la?qs, they may be considered as efficient dosage forms for delivery of drugs to the respiratory tract. For better compatibility of patients, it could be substituted la?qs with newer drug delivery systems like lozenges. PMID:26008751

  12. Radical scavenging, antioxidant and antimicrobial activities of halophytic species.

    PubMed

    Meot-Duros, Laetitia; Le Floch, Gaëtan; Magné, Christian

    2008-03-01

    For the first time, both antioxidant and antimicrobial activities are simultaneously reported in halophytic plants, particularly on polar fractions. Chloroformic and methanolic extracts of the halophytes Eryngium maritimum L., Crithmum maritimum L. and Cakile maritima Scop. were tested for their antimicrobial activities against 12 bacterial and yeast strains. In addition, radical scavenging and antioxidant activities were assessed, as well as total phenol contents. Only one bacterial strain (Listeria monocytogenes) was not inhibited by plants extracts, and apolar (chloroformic) fractions were generally more active than polar (methanolic) ones. Eryngium maritimum presented the weakest radical scavenging activity (ABTS IC(50)=0.28 mg ml(-1)), as well as the lowest total phenol content (16.4 mg GAE g(-1) DW). However, the three halophytic species had relatively strong total antioxidant activities (from 32.7 to 48.6 mg ascorbate equivalents g (-1) DW). Consequences on the potential use of these plants in food or cosmetic industry are discussed. PMID:18164885

  13. Food habits of mute swans in the Chesapeake Bay

    USGS Publications Warehouse

    Perry, M.C.; Osenton, P.C.; Lohnes, E.J.R.

    2004-01-01

    Unlike the tundra swan (Cygnus columbianus) that migrate to the Bay for the winter, the mute swan (Cygnus olor) is a year long resident and therefore has raised concerns among research managers over reports of conflicts with nesting native water birds and the consumption of submerged aquatic vegetation (SAV). Although data on the reduction of SAV by nesting mute swans and their offspring during the spring and summer are limited, food-habits data show that mute swans rely heavily on SAV during these months. Analyses of the gullet and gizzard of mute swans indicate that widgeon grass (Ruppia maritima) and eelgrass (Zostera marina) were the most important food items to mute swans during the winter and spring. Other organisms were eaten by mute swans, but represent small percentages of food. Corn (Zea mays) fed to the swans by Bay residents in late winter probably supplements their limited vegetative food resources at that time of year.

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

    SciTech Connect

    Kelly, R.J.; Guerin, T.F.

    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.

  15. 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.

  16. 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

  17. Biochemical characterization and structural analysis of a bifunctional cellulase/xylanase from Clostridium thermocellum.

    PubMed

    Yuan, Shuo-Fu; Wu, Tzu-Hui; Lee, Hsiao-Lin; Hsieh, Han-Yu; Lin, Wen-Ling; Yang, Barbara; Chang, Chih-Kang; Li, Qian; Gao, Jian; Huang, Chun-Hsiang; Ho, Meng-Chiao; Guo, Rey-Ting; Liang, Po-Huang

    2015-02-27

    We expressed an active form of CtCel5E (a bifunctional cellulase/xylanase from Clostridium thermocellum), performed biochemical characterization, and determined its apo- and ligand-bound crystal structures. From the structures, Asn-93, His-168, His-169, Asn-208, Trp-347, and Asn-349 were shown to provide hydrogen-bonding/hydrophobic interactions with both ligands. Compared with the structures of TmCel5A, a bifunctional cellulase/mannanase homolog from Thermotoga maritima, a flexible loop region in CtCel5E is the key for discriminating substrates. Moreover, site-directed mutagenesis data confirmed that His-168 is essential for xylanase activity, and His-169 is more important for xylanase activity, whereas Asn-93, Asn-208, Tyr-270, Trp-347, and Asn-349 are critical for both activities. In contrast, F267A improves enzyme activities. PMID:25575592

  18. Biohydrogenesis in the Thermotogales

    SciTech Connect

    Kelly, Robert M

    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 α-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.

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

    PubMed Central

    Lerman, Joshua A.; Hyduke, Daniel R.; Latif, Haythem; Portnoy, Vasiliy A.; Lewis, nathan E.; Orth, Jeffrey D.; Schrimpe-Rutledge, Alexandra C.; Smith, Richard D.; Adkins, Joshua n.; Zengler, Karsten; Palsson, Bernhard O.

    2013-01-01

    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. PMID:22760628

  20. RNA-activated DNA cleavage by the Type III-B CRISPR-Cas effector complex.

    PubMed

    Estrella, Michael A; Kuo, Fang-Ting; Bailey, Scott

    2016-02-15

    The CRISPR (clustered regularly interspaced short palindromic repeat) system is an RNA-guided immune system that protects prokaryotes from invading genetic elements. This system represents an inheritable and adaptable immune system that is mediated by multisubunit effector complexes. In the Type III-B system, the Cmr effector complex has been found to cleave ssRNA in vitro. However, in vivo, it has been implicated in transcription-dependent DNA targeting. We show here that the Cmr complex from Thermotoga maritima can cleave an ssRNA target that is complementary to the CRISPR RNA. We also show that binding of a complementary ssRNA target activates an ssDNA-specific nuclease activity in the histidine-aspartate (HD) domain of the Cmr2 subunit of the complex. These data suggest a mechanism for transcription-coupled DNA targeting by the Cmr complex and provide a unifying mechanism for all Type III systems. PMID:26848046

  1. Which plant for which skin disease? Part 2: Dermatophytes, chronic venous insufficiency, photoprotection, actinic keratoses, vitiligo, hair loss, cosmetic indications.

    PubMed

    Reuter, Juliane; Wölfle, Ute; Korting, Hans Christian; Schempp, Christoph

    2010-11-01

    This paper continues our review of scientifically evaluated plant extracts in dermatology. After plants effective against dermatophytes, botanicals with anti-edema effects in chronic venous insufficiency are discussed. There is good evidence from randomized clinical studies that plant extracts from grape vine leaves (Vitis vinifera), horse chestnut (Aesculus hippocastanum), sea pine (Pinus maritima) and butcher's broom (Ruscus aculeatus) can reduce edema in chronic venous insufficiency. Plant extracts from witch hazel (Hamamelis virginiana), green tea (Camellia sinensis), the fern Polypodium leucotomos and others contain antioxidant polyphenolic compounds that may protect the skin from sunburn and photoaging when administered topically or systemically. Extracts from the garden spurge (Euphorbia peplus) and from birch bark (Betula alba) have been shown to be effective in the treatment of actinic keratoses in phase II studies. Some plant extracts have also been investigated in the treatment of vitiligo, various forms of hair loss and pigmentation disorders, and in aesthetic dermatology. PMID:20707877

  2. Biochemical Characterization and Structural Analysis of a Bifunctional Cellulase/Xylanase from Clostridium thermocellum*

    PubMed Central

    Yuan, Shuo-Fu; Wu, Tzu-Hui; Lee, Hsiao-Lin; Hsieh, Han-Yu; Lin, Wen-Ling; Yang, Barbara; Chang, Chih-Kang; Li, Qian; Gao, Jian; Huang, Chun-Hsiang; Ho, Meng-Chiao; Guo, Rey-Ting; Liang, Po-Huang

    2015-01-01

    We expressed an active form of CtCel5E (a bifunctional cellulase/xylanase from Clostridium thermocellum), performed biochemical characterization, and determined its apo- and ligand-bound crystal structures. From the structures, Asn-93, His-168, His-169, Asn-208, Trp-347, and Asn-349 were shown to provide hydrogen-bonding/hydrophobic interactions with both ligands. Compared with the structures of TmCel5A, a bifunctional cellulase/mannanase homolog from Thermotoga maritima, a flexible loop region in CtCel5E is the key for discriminating substrates. Moreover, site-directed mutagenesis data confirmed that His-168 is essential for xylanase activity, and His-169 is more important for xylanase activity, whereas Asn-93, Asn-208, Tyr-270, Trp-347, and Asn-349 are critical for both activities. In contrast, F267A improves enzyme activities. PMID:25575592

  3. 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.

  4. Influence of biological, environmental and technical factors on phenolic content and antioxidant activities of Tunisian halophytes.

    PubMed

    Ksouri, Riadh; Megdiche, Wided; Falleh, Hanen; Trabelsi, Nejla; Boulaaba, Mondher; Smaoui, Abderrazak; Abdelly, Chedly

    2008-11-01

    Halophyte ability to withstand salt-triggered oxidative stress is governed by multiple biochemical mechanisms that facilitate retention and/or acquisition of water, protect chloroplast functioning, and maintain ion homeostasis. Most essential traits include the synthesis of osmolytes, specific proteins, and antioxidant molecules. This might explain the utilization of some halophytes as traditional medicinal and dietary plants. The present study aimed at assessing the phenolic content and antioxidant activities of some Tunisian halophytes (Cakile maritima, Limoniastrum monopetalum, Mesembryanthemum crystallinum, M. edule, Salsola kali, and Tamarix gallica), depending on biological (species, organ and developmental stage), environmental, and technical (extraction solvent) factors. The total polyphenol contents and antioxidant activities (DPPH and superoxide radicals scavenging activities, and iron chelating and reducing powers) were strongly affected by the above-cited factors. Such variability might be of great importance in terms of valorising these halophytes as a source of naturally secondary metabolites, and the methods for phenolic and antioxidant production. PMID:18940702

  5. In situ nitrogen generation removes wax from flowlines

    SciTech Connect

    Khalil, C.N.

    1996-07-01

    Formation of paraffin (wax) in cold deepwater flowlines is a major problem for offshore operators of such facilities. Petrobras faces this problem continuously in its deepwater operations in the Campos basin, offshore Brazil. Since 1990, through its Petrobras Research Center (CENPES), the company has developed, extensively field tested, and recently commercialized, a novel technique for chemically removing such wax depositions. The process involves mixing and introducing to the line, two inorganic salts and organic solvents. The ensuing chemical reaction--which both generates nitrogen and heats the inside of the blocked flowline--allows the solvent to dissolve and dislodge the buildup, which is then flushed from the line. The process is called the Nitrogen Generation System (SGN). Petrobras/CENPES has recently formed a joint venture with the Brazilian service company Maritima Navegacao e Engenharia Ltda. to offer SGN services worldwide.

  6. 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.

  7. Evaluation of phytotoxicity of seaport sediments aged artificially by rotary leaching in the framework of a quarry deposit scenario.

    PubMed

    Bedell, J-P; Ferro, Y; Bazin, C; Perrodin, Y

    2014-09-15

    In the framework of an ecological risk assessment of seaport sediments for terrestrial ecosystems when deposited in quarries, we simulated the "ageing" of sediments exposed to rain. This experiment highlighted an inflection point at the solid/liquid ratio 1/25, after which the extraction of pollutants increases moderately. The raw sediments studied inhibited the germination of Lolium perenne and Armeria maritima (a halophytic species) seeds. Furthermore, they affected the early development of L.perenne. The same sediments, leached at a ratio of 1/25, presented a reduction of acute (germination) and chronic (growth) phytotoxicity. The bioconcentration factors of the metals studied decreased with the leached sediment, except for Cu which was still clearly identified in root parts. Thus rotary leaching tests and phytotoxicity bioassays can be used to provide an initial assessment of the ability of plants, particularly halophytes, to colonize deposits of dredged seaport sediments. PMID:25110051

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

    USGS Publications Warehouse

    Perry, M.C.; Uhler, F.M.

    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 (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 food volume. These results contrast with historical records of food habits of canvasbacks in Chesapeake Bay. Canvasback population estimates during the 1970?s were examined to detect annual and seasonal changes in distribution. Linear regression analyses of winter canvasback populations in the bay showed a significant decline in the upper-bay and middle-bay populations, but no significant changes in the lower-bay and Potomac River populations. The changes in winter distribution and abundance of the canvasback appear related to changes in natural food availability, which is the result of altered environmental conditions.

  9. 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

  10. Different Dynamical Effects in Mesophilic and Hyperthermophilic Dihydrofolate Reductases

    PubMed Central

    2014-01-01

    The role of protein dynamics in the reaction catalyzed by dihydrofolate reductase from the hyperthermophile Thermotoga maritima (TmDHFR) has been examined by enzyme isotope substitution (15N, 13C, 2H). In contrast to all other enzyme reactions investigated previously, including DHFR from Escherichia coli (EcDHFR), for which isotopic substitution led to decreased reactivity, the rate constant for the hydride transfer step is not affected by isotopic substitution of TmDHFR. TmDHFR therefore appears to lack the coupling of protein motions to the reaction coordinate that have been identified for EcDHFR catalysis. Clearly, dynamical coupling is not a universal phenomenon that affects the efficiency of enzyme catalysis. PMID:24779446

  11. Proteolysis in hyperthermophilic microorganisms

    DOE PAGESBeta

    Ward, Donald E.; Shockley, Keith R.; Chang, Lara S.; Levy, Ryan D.; Michel, Joshua K.; Conners, Shannon B.; Kelly, Robert M.

    2002-01-01

    Proteases are found in every cell, where they recognize and break down unneeded or abnormal polypeptides or peptide-based nutrients within or outside the cell. Genome sequence data can be used to compare proteolytic enzyme inventories of different organisms as they relate to physiological needs for protein modification and hydrolysis. In this review, we exploit genome sequence data to compare hyperthermophilic microorganisms from the euryarchaeotal genus Pyrococcus , the crenarchaeote Sulfolobus solfataricus , and the bacterium Thermotoga maritima . An overview of the proteases in these organisms is given based on those proteases that have been characterized and on putativemore » proteases that have been identified from genomic sequences, but have yet to be characterized. The analysis revealed both similarities and differences in the mechanisms utilized for proteolysis by each of these hyperthermophiles and indicated how these mechanisms relate to proteolysis in less thermophilic cells and organisms.« less

  12. 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.

  13. Structural basis of a rationally rewired protein-protein interface critical to bacterial signaling

    PubMed Central

    Podgornaia, Anna I.; Casino, Patricia; Marina, Alberto; Laub, Michael T.

    2013-01-01

    Summary Two-component signal transduction systems typically involve a sensor histidine kinase that specifically phosphorylates a single, cognate response regulator. This protein-protein interaction relies on molecular recognition via a small set of residues in each protein. To better understand how these residues determine the specificity of kinase-substrate interactions, we rationally rewired the interaction interface of a Thermotoga maritima two-component system, HK853-RR468, to match that found in a different two-component system, E. coli PhoR-PhoB. The rewired proteins interacted robustly with each other, but no longer interacted with the parent proteins. Analysis of the crystal structures of the wild-type and mutant protein complexes, along with a systematic mutagenesis study, reveals how individual mutations contribute to the rewiring of interaction specificity. Our approach and conclusions have implications for studies of other protein-protein interactions, protein evolution, and the design of novel protein interfaces. PMID:23954504

  14. 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

  15. Diversity of beet curly top Iran virus isolated from different hosts in Iran.

    PubMed

    Gharouni Kardani, Sara; Heydarnejad, Jahangir; Zakiaghl, Mohammad; Mehrvar, Mohsen; Kraberger, Simona; Varsani, Arvind

    2013-06-01

    Beet curly top Iran virus (BCTIV) is a major pathogen of sugar beet in Iran. In order to study diversity of BCTIV, we sampled 68 plants in Iran during the summer of 2010 with curly top disease symptoms on beans (Phaseolus vulgaris), cowpeas (Vigna unguiculata), tomatoes (Solanum lycopersicum L.), sea beets (Beta vulgaris subsp. maritima), and sugar beets (Beta vulgaris). Plant samples showing leaf curling, yellowing, and/or swelling of veins on the lower leaf surfaces were collected from various fields in Khorasan Razavi, Northern Khorasan (north-eastern Iran), East Azarbayejan, West Azarbayejan (north-western Iran), and Fars (southern Iran) provinces. Using rolling circle amplification coupled with restriction digests, cloning, and Sanger sequencing, we determined the genomes of nine new BCTIV isolates from bean, cowpea, tomato, sea beet, and sugar beet in Iran. Our analysis reveals ~11 % diversity amongst BCTIV isolates and we detect evidence of recombination within these genomes. PMID:23329008

  16. 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

  17. Inorganic pyrophosphatases: one substrate, three mechanisms.

    PubMed

    Kajander, Tommi; Kellosalo, Juho; Goldman, Adrian

    2013-06-27

    Soluble inorganic pyrophosphatases (PPases) catalyse an essential reaction, the hydrolysis of pyrophosphate to inorganic phosphate. In addition, an evolutionarily ancient family of membrane-integral pyrophosphatases couple this hydrolysis to Na(+) and/or H(+) pumping, and so recycle some of the free energy from the pyrophosphate. The structures of the H(+)-pumping mung bean PPase and the Na(+)-pumping Thermotoga maritima PPase solved last year revealed an entirely novel membrane protein containing 16 transmembrane helices. The hydrolytic centre, well above the membrane, is linked by a charged "coupling funnel" to the ionic gate about 20Å away. By comparing the active sites, fluoride inhibition data and the various models for ion transport, we conclude that membrane-integral PPases probably use binding of pyrophosphate to drive pumping. PMID:23684653

  18. 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.

  19. Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: Assessment in two blind tests

    PubMed Central

    O?dziej, S.; Czaplewski, C.; Liwo, A.; Chinchio, M.; Nanias, M.; Vila, J. A.; Khalili, M.; Arnautova, Y. A.; Jagielska, A.; Makowski, M.; Schafroth, H. D.; Ka?mierkiewicz, R.; Ripoll, D. R.; Pillardy, J.; Saunders, J. A.; Kang, Y. K.; Gibson, K. D.; Scheraga, H. A.

    2005-01-01

    Recent improvements in the protein-structure prediction method developed in our laboratory, based on the thermodynamic hypothesis, are described. The conformational space is searched extensively at the united-residue level by using our physics-based UNRES energy function and the conformational space annealing method of global optimization. The lowest-energy coarse-grained structures are then converted to an all-atom representation and energy-minimized with the ECEPP/3 force field. The procedure was assessed in two recent blind tests of protein-structure prediction. During the first blind test, we predicted large fragments of ? and ?+? proteins [60–70 residues with C? rms deviation (rmsd) <6 Å]. However, for ?+? proteins, significant topological errors occurred despite low rmsd values. In the second exercise, we predicted whole structures of five proteins (two ? and three ?+?, with sizes of 53–235 residues) with remarkably good accuracy. In particular, for the genomic target TM0487 (a 102-residue ?+? protein from Thermotoga maritima), we predicted the complete, topologically correct structure with 7.3-Å C? rmsd. So far this protein is the largest ?+? protein predicted based solely on the amino acid sequence and a physics-based potential-energy function and search procedure. For target T0198, a phosphate transport system regulator PhoU from T. maritima (a 235-residue mainly ?-helical protein), we predicted the topology of the whole six-helix bundle correctly within 8 Å rmsd, except the 32 C-terminal residues, most of which form a ?-hairpin. These and other examples described in this work demonstrate significant progress in physics-based protein-structure prediction. PMID:15894609

  20. Structure of the ribosomal interacting GTPase YjeQ from the enterobacterial species Salmonella typhimurium

    SciTech Connect

    Nichols, C. E.; Johnson, C.; Lamb, H. K.; Lockyer, M.; Charles, I. G.; Hawkins, A. R.; Stammers, D. K.

    2007-11-01

    The X-ray crystal structure of the GTPase YjeQ from S. typhimurium is presented and compared with those of orthologues from T. maritima and B. subtilis. The YjeQ class of P-loop GTPases assist in ribosome biogenesis and also bind to the 30S subunit of mature ribosomes. YjeQ ribosomal binding is GTP-dependent and thought to specifically direct protein synthesis, although the nature of the upstream signal causing this event in vivo is as yet unknown. The attenuating effect of YjeQ mutants on bacterial growth in Escherichia coli makes it a potential target for novel antimicrobial agents. In order to further explore the structure and function of YjeQ, the isolation, crystallization and structure determination of YjeQ from the enterobacterial species Salmonella typhimurium (StYjeQ) is reported. Whilst the overall StYjeQ fold is similar to those of the previously reported Thematoga maritima and Bacillus subtilis orthologues, particularly the GTPase domain, there are larger differences in the three OB folds. Although the zinc-finger secondary structure is conserved, significant sequence differences alter the nature of the external surface in each case and may reflect varying signalling pathways. Therefore, it may be easier to develop YjeQ-specific inhibitors that target the N- and C-terminal regions, disrupting the metabolic connectivity rather than the GTPase activity. The availability of coordinates for StYjeQ will provide a significantly improved basis for threading Gram-negative orthologue sequences and in silico compound-screening studies, with the potential for the development of species-selective drugs.

  1. 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

  2. A comparative study of the early osmotic, ionic, redox and hormonal signaling response in leaves and roots of two halophytes and a glycophyte to salinity.

    PubMed

    Ellouzi, Hasna; Ben Hamed, Karim; Hernández, Iker; Cela, Jana; Müller, Maren; Magné, Christian; Abdelly, Chedly; Munné-Bosch, Sergi

    2014-12-01

    Salt stress is one of the most important abiotic stress factors affecting plant growth and productivity in natural ecosystems. In this study, we aimed at determining possible differences between salt tolerant and salt sensitive species in early (within 72 h) salt stress response in leaves and roots. To this purpose, we subjected three Brassicaceae species, namely two halophytes-Cakile maritima and Thellungiella salsuginea--and a glycophyte--Arabidopsis thaliana- to short-term salt stress (400 mM NaCl). The results indicate that the halophytes showed a differential osmotic and ionic response together with an early and transient oxidative burst, which was characterized by enhanced hydrogen peroxide levels and subsequent activation of antioxidant defenses in both leaves and roots. In addition, the halophytes displayed enhanced accumulation of abscisic acid, jasmonic acid (JA) and ACC (aminocyclopropane-1-carboxylic acid, the precursor of ethylene) in leaves and roots, as compared to A. thaliana under salt stress. Moreover, the halophytes showed enhanced expression of ethylene response factor1 (ERF1), the convergence node of the JA and ethylene signaling pathways in both leaves and roots upon exposure to salt stress. In conclusion, we show that the halophytes C. maritima and T. salsuginea experience an early oxidative burst, improved antioxidant defenses and hormonal response not only in leaves but also in roots, in comparison to the glycophyte A. thaliana. This differential signaling response converging, at least in part, into increased ERF1 expression in both above- and underground tissues seems to underlay, at least in part, the enhanced tolerance of the two studied halophytes to salt stress. PMID:25156490

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

    SciTech Connect

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

    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.

  4. 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

  5. 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.

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

    SciTech Connect

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

    2006-11-01

    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 P3{sub 2} and those with Man(?1-2)Man(?1)OMe crystallized in space group I222], which differed from those of the native proteins (P2{sub 1}2{sub 1}2 for CML and C222 for CGL), are reported. 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 P3{sub 2} and those with Man(?1-2)Man(?1)OMe crystallized in space group I222], which differed from those of the native proteins (P2{sub 1}2{sub 1}2 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.

  7. 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

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

    PubMed

    Meunier, Joël; Kölliker, Mathias

    2012-10-01

    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

  9. Effects of food restriction across stages of juvenile and early adult development on body weight, survival and adult life history.

    PubMed

    Wong, J W Y; Kölliker, M

    2014-11-01

    Organisms have to allocate limited resources among multiple life-history traits, which can result in physiological trade-offs, and variation in environmental conditions experienced during ontogeny can influence reproduction later in life. Food restriction may lead to an adaptive reallocation of the limited resources among traits as a phenotypically plastic adjustment, or it can act as an overall constraint with detrimental effects throughout reproductive life. In this study, we investigated experimentally the effects of food restriction during different stages of the juvenile and early adult development on body weight, survival and reproductive success in females and males of the European earwig Forficula auricularia. Individuals either received limited or unlimited access to food across three different stages of development (fully crossed) allowing us to identify sensitive periods during development and to test both additive and interactive effects of food limitation across stages on development and reproduction. Food restriction during the early and late juvenile stage had additive negative effects on juvenile survival and adult body weight. With regard to reproductive success of females which produce up to two clutches in their lifetime, restriction specifically in the late juvenile stage led to smaller first and second clutch size, lower probability of second clutch production and reduced hatching success in the second clutch. Reproductive success of females was not significantly affected when their male mates experienced food restriction during their development. Our findings in general support the 'silver-spoon' hypothesis in that food restriction during juvenile development poses constraints on development and reproduction throughout life. PMID:25263828

  10. Structure of ovaries and oogenesis in dermapterans. I. Origin and functioning of the ovarian follicles.

    PubMed

    Tworzyd?o, Wac?aw; Bili?ski, Szczepan M

    2008-07-01

    The ovaries of the studied earwig species (Forficula auricularia, Chelidurella acanthopygia, Doru lineare and Opisthocosmia silvestris) are meroistic-polytrophic and composed of numerous short ovarioles that consist of a terminal filament, germarium and vitellarium. The germaria of adult females comprise meiotic (pachytene) and postmeiotic (differentiating) germ cell clusters, as well as small prefollicular cells. All germ cell clusters consist of two cells that are connected by a single intercellular bridge. In the vitellarium there are usually 2 ovarian follicles only. The individual follicle consists of a transcriptionally dormant oocyte and a single, polyploid nurse cell and is surrounded by a layer of somatic follicular cells (FCs). During previtellogenesis the nurse cell enlarges and becomes highly transcriptionally active. Concurrently its nucleus attains a characteristic, irregular shape. In the nurse cell nucleus of one studied species, F. auricularia, in addition to chromatin aggregations and RNA- and Ag-NOR-positive nucleoli, a single compact DNA-positive body is present. During advanced vitellogenesis the molecules synthesized in the nurse cells (RNAs, proteins, as well as nurse cell organelles) are transferred to the ooplasm via the intercellular bridge. During this transfer the nurse cell nucleus is retained in the cell centre and does not occlude the intercellular bridge. The results of our studies indicate that such position of the nurse cell nucleus is maintained solely by its extended shape. In other words, the rigid extensions keep the nucleus in the cell centre while the cytoplasm flows, in between these extensions, towards the intercellular bridge connecting the nurse cell with the oocyte. PMID:18396462

  11. Investigating the genetic architecture of conditional strategies using the environmental threshold model.

    PubMed

    Buzatto, Bruno A; Buoro, Mathieu; Hazel, Wade N; Tomkins, Joseph L

    2015-12-22

    The threshold expression of dichotomous phenotypes that are environmentally cued or induced comprise the vast majority of phenotypic dimorphisms in colour, morphology, behaviour and life history. Modelled as conditional strategies under the framework of evolutionary game theory, the quantitative genetic basis of these traits is a challenge to estimate. The challenge exists firstly because the phenotypic expression of the trait is dichotomous and secondly because the apparent environmental cue is separate from the biological signal pathway that induces the switch between phenotypes. It is the cryptic variation underlying the translation of cue to phenotype that we address here. With a 'half-sib common environment' and a 'family-level split environment' experiment, we examine the environmental and genetic influences that underlie male dimorphism in the earwig Forficula auricularia. From the conceptual framework of the latent environmental threshold (LET) model, we use pedigree information to dissect the genetic architecture of the threshold expression of forceps length. We investigate for the first time the strength of the correlation between observable and cryptic 'proximate' cues. Furthermore, in support of the environmental threshold model, we found no evidence for a genetic correlation between cue and the threshold between phenotypes. Our results show strong correlations between observable and proximate cues and less genetic variation for thresholds than previous studies have suggested. We discuss the importance of generating better estimates of the genetic variation for thresholds when investigating the genetic architecture and heritability of threshold traits. By investigating genetic architecture by means of the LET model, our study supports several key evolutionary ideas related to conditional strategies and improves our understanding of environmentally cued decisions. PMID:26674955

  12. Cover cropping alters the diet of arthropods in a banana plantation: a metabarcoding approach.

    PubMed

    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

  13. A taste for exotic food: Neotropical land planarians feeding on an invasive flatworm

    PubMed Central

    Boll, Piter K.; Rossi, Ilana; Amaral, Silvana V.

    2015-01-01

    Invasive species establish successfully in new habitats especially due to their ability to include new species in their diet and due to the freedom from natural enemies. However, native species may also adapt to the use of new elements in their ecosystem. The planarian Endeavouria septemlineata, first recorded in Hawaii, was later found in Brazil. Recently, we found it in human-disturbed areas in southern Brazil and here we investigate its interactions with other invertebrates both in the field and in the laboratory. We observed the species in the field during collecting activities and hence maintained some specimens alive in small terraria in the laboratory, where we offered different invertebrate species as potential prey and also put them in contact with native land planarians in order to examine their interaction. Both in the field and in the laboratory, E. septemlineata showed a gregarious behavior and was found feeding on woodlice, millipedes, earwigs and gastropods. In the laboratory, specimens often did not attack live prey, but immediately approached dead specimens, indicating a scavenging behavior. In an experiment using the slug Deroceras laeve and the woodlouse Atlantoscia floridana, there was a higher consumption of dead specimens of woodlice and slugs compared to live specimens, as well as a higher consumption of dead woodlice over dead slugs. Four native land planarians of the genus Obama and one of the genus Paraba attacked and consumed E. septemlineata, which, after the beginning of the attack, tried to escape by tumbling or using autotomy. As a scavenger, E. septemlineata would have no impact on the populations of species used as food, but could possibly exclude native scavengers by competition. On the other hand, its consumption by native land planarians may control its spread and thus reduce its impact on the ecosystem. PMID:26500817

  14. 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

  15. A taste for exotic food: Neotropical land planarians feeding on an invasive flatworm.

    PubMed

    Boll, Piter K; Rossi, Ilana; Amaral, Silvana V; Leal-Zanchet, Ana

    2015-01-01

    Invasive species establish successfully in new habitats especially due to their ability to include new species in their diet and due to the freedom from natural enemies. However, native species may also adapt to the use of new elements in their ecosystem. The planarian Endeavouria septemlineata, first recorded in Hawaii, was later found in Brazil. Recently, we found it in human-disturbed areas in southern Brazil and here we investigate its interactions with other invertebrates both in the field and in the laboratory. We observed the species in the field during collecting activities and hence maintained some specimens alive in small terraria in the laboratory, where we offered different invertebrate species as potential prey and also put them in contact with native land planarians in order to examine their interaction. Both in the field and in the laboratory, E. septemlineata showed a gregarious behavior and was found feeding on woodlice, millipedes, earwigs and gastropods. In the laboratory, specimens often did not attack live prey, but immediately approached dead specimens, indicating a scavenging behavior. In an experiment using the slug Deroceras laeve and the woodlouse Atlantoscia floridana, there was a higher consumption of dead specimens of woodlice and slugs compared to live specimens, as well as a higher consumption of dead woodlice over dead slugs. Four native land planarians of the genus Obama and one of the genus Paraba attacked and consumed E. septemlineata, which, after the beginning of the attack, tried to escape by tumbling or using autotomy. As a scavenger, E. septemlineata would have no impact on the populations of species used as food, but could possibly exclude native scavengers by competition. On the other hand, its consumption by native land planarians may control its spread and thus reduce its impact on the ecosystem. PMID:26500817

  16. Tidal events and salt-marsh structure influence black mangrove (Avicennia germinans) recruitment across an ecotone.

    PubMed

    Peterson, Jennifer M; Bell, Susan S

    2012-07-01

    Field experiments were conducted at a black mangrove-salt-marsh ecotone in southwest Florida (U.S.A.) to investigate retention of propagules of the black mangrove, Avicennia germinans, by salt-marsh plants as a mechanism of facilitation operating on recruitment success at landward boundaries. Buoyant A. germinans propagules are dispersed by tides, and stranding is required for establishment; therefore, processes that enable stranding should facilitate mangrove recruitment. We expected the physical structure of salt-marsh vegetation to define propagule retention capacity, and we predicted that salt-marsh plants with distinct growth forms would differentially retain propagules. Experimental monoculture plots (1 m2) of salt-marsh plants with different growth forms (Sporobolus virginicus [grass], Sesuvium portulacastrum [succulent forb], and Batis maritima [succulent scrub]) were created, and A. germinans propagules were emplaced into these plots and monitored over time. For comparison, propagules were also placed into natural polyculture plots (1 m2). Polyculture plots contained at least two of the salt-marsh plant taxa selected for monoculture treatments, and S. virginicus was always present within these polyculture plots. Natural polyculture plots retained 59.3% +/- 11.0% (mean +/- SE) of emplaced propagules. Monocultures varied in their propagule retention capacities with plots of S. virginicus retaining on average 65.7% +/- 11.5% of transplanted propagules compared to 7.2% +/- 1.8% by B. maritima and 5.0% +/- 1.9% by S. portulacastrum. Plots containing S. virginicus retained a significantly greater percentage of emplaced propagules relative to the two succulent salt-marsh taxa. Furthermore, propagule entrapment, across all treatments, was strongly correlated with salt-marsh structure (r2 = 0.6253, P = 0.00001), which was estimated using an indirect quantitative metric (lateral obstruction) calculated from digital images of plots. Overall, our findings imply that entrapment of propagules by salt-marsh plants may be facilitative if propagules are dispersed beyond the established tree line by spring or storm tides, and that facilitation may be sustained over time. We conclude that salt-marsh ecotone permeability may modulate landward encroachment by A. germinans, and that interactions among the early life history stages of black mangroves and neighboring plants may direct community responses to climate change. PMID:22919911

  17. USE OF GREEN MANURE CROPS AND SUGAR BEET VARIETIES TO CONTROL HETERODERA BETAE.

    PubMed

    Raaijmakers, E

    2014-01-01

    Although it is less studied than the white beet cyst nematode (Heterodera schachtii), the yellow beet cyst nematode (H. betae) has been found in many countries in Europe. For example in The Netherlands, France and Spain. H. betae causes yield losses on sandy soils. A high infestation can result in loss of complete plants. In The Netherlands, this nematode is especially found in the south eastern and north eastern part, where it occurs on 18% and 5% of the fields, respectively. From a project of the Dutch Sugar beet Research Institute IRS (SUSY) on factors explaining differences in sugar yield, this nematode was one of the most important factors reducing sugar yields on sandy soils. Until 2008, the only way to control H. betae was by reducing the number of host crops in the crop rotation. Host crops are crops belonging to the families of Cruciferae, Chenopodiaceae, Polygonaceae, Caryophyllaceae and Leguminosea. In order to find more control measures, research was done to investigate the host status of different green manure crops and the resistance and tolerance of different sugar beet varieties to H. betae. White mustard (Sinapis alba) and oil seed radish (Raphanus sativus spp. oleiferus) varieties resistant to H. schachtii were investigated for their resistance against H. betae. A climate room trial and a field trial with white mustard and oil seed radish were conducted in 2007 and 2008, respectively. Results show that H. betae could multiply on susceptible white mustard and susceptible oil seed radish, but not on the H. schachtii resistant varieties. In climate room trials in 2009, 2010 and 2011 and field trials in 2010, 2011 and 2012, the effect of different sugar beet varieties on the multiplication of H. betae and the effect of H. betae on yield at different infestation levels was investigated. Sugar beet varieties with resistance genes to H. schachtii (from Beta procumbens or B. maritima) were selected. Varieties with resistance genes from these sources were not totally resistant to H. betae, but limited the multiplication of this nematode in comparison with susceptible varieties considerably. Only the varieties with resistance genes from B. maritima gave higher yields in comparison with susceptible varieties. Growing these varieties was already profitable from very light infestation levels (75 eggs and larvae/100 ml soil) of H. betae. Therefore, resistant cruciferous green manure crops and resistant and tolerant sugar beet varieties are good tools for growers to control H. betae. PMID:26084110

  18. Spatial and temporal habitat partitioning by zooplankton in the Bornholm Basin (central Baltic Sea)

    NASA Astrophysics Data System (ADS)

    Schulz, Jan; Peck, Myron A.; Barz, Kristina; Schmidt, Jörn Oliver; Hansen, Frank C.; Peters, Janna; Renz, Jasmin; Dickmann, Miriam; Mohrholz, Volker; Dutz, Jörg; Hirche, Hans-Jürgen

    2012-12-01

    The deep basins in the Baltic Sea such as the Bornholm Basin (BB) are subject to seasonal changes in the strength of physico-chemical stratification. These depth-related changes in key abiotic factors are strong drivers of habitat partitioning by the autochthonous zooplankton community. Species-specific ecophysiological preferences often result in both seasonal and inter-annual changes in vertical abundance that, when combined with depth-specific water currents, also lead to horizontal differences in spatial distribution. The present study documented the seasonal and depth-specific changes in the abundance and species composition of zooplankton in the BB based upon broad-scale survey data: 832 vertically-resolved (10 m) multinet samples collected at nine stations between March 2002 and May 2003. Changes in the zooplankton community were significantly correlated with changes in ambient hydrography. Each of five taxa (Bosmina coregoni maritima, Acartia spp., Pseudocalanus spp., Temora longicornis, Synchaeta spp.) contributed >10% to the zooplankton community composition. The appearance of cladocerans was mainly correlated with the phenology of thermocline development in the spring. The cladoceran B. coregoni maritima was a dominant member of this community during the warmest periods, preferring the surface waters above the thermocline. Copepods exhibited distinct, ontogenetic and seasonal changes in their distribution. The rotifers (Synchaeta sp.) were the most abundant zooplankton in May. Based on a multivariate approach and the evaluation of vertical distribution patterns, five major habitat utilisation modes were identified that were based, to a large extent, on the dynamics of thermal and haline stratification of the Baltic Sea. Our statistical analysis of one of the most thorough datasets collected on Baltic zooplankton in recent decades reveals some of the factors that make this stratified system highly dynamic with respect to the spatial overlap between predators and prey. As fish and gelatinous plankton often feed in distinct layers and/or exhibit feeding migrations, the inhomogeneous distribution of potential prey can result in a spatial mismatch. Based on the five modes identified at the community level for zooplankton, we discuss how climate-driven hydrographic variability may influence the strength of trophic coupling within the Bornholm Basin.

  19. Effect of tidal flooding on metal distribution in pore waters of marsh sediments and its transport to water column (Tagus estuary, Portugal).

    PubMed

    Santos-Echeandía, Juan; Vale, Carlos; Caetano, Miguel; Pereira, Patrícia; Prego, Ricardo

    2010-12-01

    Sediment cores and flooding water were collected at 0, 5, 10 and 50 min of tidal inundation in two sites of the Rosário salt marsh located in the proximity of a heavy industrialised zone of Tagus estuary colonised by pure stands of Spartina maritima (low marsh) and Sarcocornia fruticosa (high marsh). The cores were sliced in 5 cm layers and sediment solids, pore water, and belowground biomass were separated in order to measure Fe, Mn, Zn, Cu, Pb and Cd. The pore waters and sediments colonised by S. fruticosa, as well as belowground biomass presented high concentrations of Zn, Cu, Pb and Cd. Belowground biomass exceeded in one order of magnitude the metal levels in sediments. Abundant belowground biomass and small dimension of S. fruticosa roots facilitates the root-sediment interactions and presumably the metal retention in the higher marsh. The novelty of this work is the result of tidal inundation on pore water concentrations of metals in salt marsh sediments and their exportation to the water column. Concentrations in pore waters varied at minute scales, but 50 min after inundation levels were comparable to the initial values. The metal levels in flooding water increased abruptly during the first 10-20 min of inundation. The concentration peaks (Fe = 60 ?M, Mn = 7.5 ?M, Zn = 1.7 ?M, Cu = 550 nM, Pb = 100 nM, Cd = 1.7 nM) reached one to two orders of magnitude above the values found in subsequent periods of inundation. The advective transports during the 50 min inundation during two daily pulses of inundation were: Fe (9520 and 1640), Mn (24), Zn (220 and 82), Cu (74 and 16), Pb (13 and 15) and Cd (0.3 and 0.08) for S. maritima and S. fruticosa, respectively. These quantities exceeded three to four orders of magnitude of the corresponding predicted diffusive fluxes (Fick 1st law) on a daily basis. This work emphasizes the importance of tidal flooding over salt marsh sediments to the metal exportation to the water column. PMID:20727578

  20. Biosynthesis, Translocation, and Accumulation of Betaine in Sugar Beet and Its Progenitors in Relation to Salinity 12

    PubMed Central

    Hanson, Andrew D.; Wyse, Roger

    1982-01-01

    Like other halophytic chenopods, sugar beet (Beta vulgaris L.) can accumulate high betaine levels in shoots and roots. N,N,N-trimethylglycine impedes sucrose crystallization and so lowers beet quality. The objective of this research was to examine the genetic variability and physiological significance of betaine accumulation in sugar beet and its relatives. Three cultivated genotypes of B. vulgaris and two genotypes of the wild progenitor B. maritima L. were grown with and without gradual salinization (final NaCl concentration = 150 millimolar). At 6 weeks old, all five genotypes had moderately high betaine levels in shoots and roots when unsalinized (averages for all genotypes: shoots = 108 micromoles per gram dry weight; roots = 99 micromoles per gram dry weight). Salinization raised betaine levels of shoots and roots 2- to 3-fold, but did not greatly depress shoot or root growth. The genotype WB-167—an annual B. maritima type—always had approximately 40% lower betaine levels in roots than the other four genotypes, although the betaine levels in the shoots were not atypically low. The site and pathway of betaine synthesis were investigated in young, salinized sugar beet plants by: (a) supplying 1 micromole [14C]ethanolamine to young leaf blades or to the taproot sink of intact plants; (b) supplying tracer [14C]formate to discs of leaf, hypocotyl, and taproot tissues in darkness. Conversion of both 14C precursors to betaine was active only in leaf tissue. Very little 14C appeared in the phospholipid phosphatidylcholine before betaine was heavily labeled; this was in marked contrast to the labeling patterns in salinized barley. Phosphorylcholine was a prominent early 14C metabolite of both [14C]ethanolamine and [14C]formate in all tissues of sugar beet. Betaine translocation was examined in young plants of sugar beet and WB-167 by applying tracer [methyl-14C]betaine to a young expanded leaf and determining the distribution of 14C after 3 days. In all cases, extensive 14C translocation to young leaves and taproot sink occurred; neither in the fed leaf nor in sink organs were any 14C metabolites of betaine detected. PMID:16662637

  1. Crystal structure of human L-isoaspartyl-O-methyl-transferase with S-adenosyl homocysteine at 1.6-A resolution and modeling of an isoaspartyl-containing peptide at the active site.

    PubMed

    Smith, Craig D; Carson, Mike; Friedman, Alan M; Skinner, Matthew M; Delucas, Lawrence; Chantalat, Laurent; Weise, Lance; Shirasawa, Takuji; Chattopadhyay, Debashish

    2002-03-01

    Spontaneous formation of isoaspartyl residues (isoAsp) disrupts the structure and function of many normal proteins. Protein isoaspartyl methyltransferase (PIMT) reverts many isoAsp residues to aspartate as a protein repair process. We have determined the crystal structure of human protein isoaspartyl methyltransferase (HPIMT) complexed with adenosyl homocysteine (AdoHcy) to 1.6-A resolution. The core structure has a nucleotide binding domain motif, which is structurally homologous with the N-terminal domain of the bacterial Thermotoga maritima PIMT. Highly conserved residues in PIMTs among different phyla are placed at positions critical to AdoHcy binding and orienting the isoAsp residue substrate for methylation. The AdoHcy is completely enclosed within the HPIMT and a conformational change must occur to allow exchange with adenosyl methionine (AdoMet). An ordered sequential enzyme mechanism is supported because C-terminal residues involved with AdoHcy binding also form the isoAsp peptide binding site, and a change of conformation to allow AdoHcy to escape would preclude peptide binding. Modeling experiments indicated isoAsp groups observed in some known protein crystal structures could bind to the HPIMT active site. PMID:11847284

  2. Use of digital multispectral videography to assess seagrass distribution in San Quintin Bay, Baja California, Mexico

    USGS Publications Warehouse

    Ward, D.H.; Tibbitts, T.L.; Morton, Alexandra; Carrera-Gonzalez, Eduardo; 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.

  3. From bacterial to human dihydrouridine synthase: automated structure determination

    SciTech Connect

    Whelan, Fiona Jenkins, Huw T.; Griffiths, Samuel C.; Byrne, Robert T.; Dodson, Eleanor J.; Antson, Alfred A.

    2015-06-30

    The crystal structure of a human dihydrouridine synthase, an enzyme associated with lung cancer, with 18% sequence identity to a T. maritima enzyme, has been determined at 1.9 Å resolution by molecular replacement after extensive molecular remodelling of the template. The reduction of uridine to dihydrouridine at specific positions in tRNA is catalysed by dihydrouridine synthase (Dus) enzymes. Increased expression of human dihydrouridine synthase 2 (hDus2) has been linked to pulmonary carcinogenesis, while its knockdown decreased cancer cell line viability, suggesting that it may serve as a valuable target for therapeutic intervention. Here, the X-ray crystal structure of a construct of hDus2 encompassing the catalytic and tRNA-recognition domains (residues 1–340) determined at 1.9 Å resolution is presented. It is shown that the structure can be determined automatically by phenix.mr-rosetta starting from a bacterial Dus enzyme with only 18% sequence identity and a significantly divergent structure. The overall fold of the human Dus2 is similar to that of bacterial enzymes, but has a larger recognition domain and a unique three-stranded antiparallel β-sheet insertion into the catalytic domain that packs next to the recognition domain, contributing to domain–domain interactions. The structure may inform the development of novel therapeutic approaches in the fight against lung cancer.

  4. Isolation, characterization, and survival strategies of Thermotoga sp. strain PD524, a hyperthermophile from a hot spring in Northern Thailand.

    PubMed

    Kanoksilapatham, Wirojne; Keawram, Porranee; Gonzalez, Juan M; Robb, Frank T

    2015-07-01

    A hyperthermophilic Thermotoga sp. strain PD524 was isolated from a hot spring in Northern Thailand. Cells were long-curved rods (0.5-0.6 × 2.5-10 μm) surrounded by a typical outer membrane toga. Strain PD524 is aero-tolerant at 4 °C but is aero-sensitive at 80 °C. A heat resistant subpopulation was observed in late-stationary phase. Cells from late-stationary phase were revealed remarkably less sensitive to 0.001 % SDS treatment than cells from exponential phase. The temperature range for growth was 70-85 °C (opt. temp. 80 °C), pH range was 6-8.5 (opt. pH 7.5-8.0), and NaCl range of 0 to <10 g/L (opt. 0.5 g/L). Glucose, sucrose, maltose, fructose, xylose, mannose, arabinose, trehalose, starch, and cellobiose were utilized as growth substrates. Growth was inhibited by S(o). Growth yield was stimulated by SO 4 (=) but not by S2O 3 (=) and NO3 (-). Analysis of 16S rRNA gene sequence (KF164213) of strain PD524 revealed closest similarity (96 %) to Thermotoga maritima MSB8(T), T. neapolitana NES(T), T. petrophila RKU-1(T), and T. naphthophila RKU-10(T). PMID:26101016

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

    SciTech Connect

    Hamilton-Brehm, Scott; 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 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.

  6. Crystal structure of the RNA component of bacterial ribonuclease P

    SciTech Connect

    Torres-Larios, Alfredo; Swinger, Kerren K.; Krasilnikov, Andrey S.; Pan, Tao; Mondragon, Alfonso

    2010-03-08

    Transfer RNA (tRNA) is produced as a precursor molecule that needs to be processed at its 3' and 5' ends. Ribonuclease P is the sole endonuclease responsible for processing the 5' end of tRNA by cleaving the precursor and leading to tRNA maturation. It was one of the first catalytic RNA molecules identified and consists of a single RNA component in all organisms and only one protein component in bacteria. It is a true multi-turnover ribozyme and one of only two ribozymes (the other being the ribosome) that are conserved in all kingdoms of life. Here we show the crystal structure at 3.85 {angstrom} resolution of the RNA component of Thermotoga maritima ribonuclease P. The entire RNA catalytic component is revealed, as well as the arrangement of the two structural domains. The structure shows the general architecture of the RNA molecule, the inter- and intra-domain interactions, the location of the universally conserved regions, the regions involved in pre-tRNA recognition and the location of the active site. A model with bound tRNA is in agreement with all existing data and suggests the general basis for RNA-RNA recognition by this ribozyme.

  7. Composition, abundance, biomass, and production of macrofauna in a New England estuary: comparisons among eelgrass meadows and other nursery habitats

    USGS Publications Warehouse

    Heck, K.L., Jr.; Able, K.W.; Roman, C.T.; Fahay, M.P.

    1995-01-01

    Quantitative suction sampling was used to characterize and compare the species composition, abundance, biomass, and secondary production of macrofauna inhabiting intertidal mudflat and sandflat, eelgrass meadow, and saltmarshpool habitats in the Nauset Marsh complex, Cape Cod, Massachusetts (USA). Species richness and abundance were often greatest in eelgrass habitat, as was macroinvertebrate biomass and production. Most striking was the five to fifteen times greater rate of annual macrofaunal production in eelgrass habitat than elsewhere, with values ranging from approximately 23139 g AFDW m super(2) yr super(1). The marsh pool containing widgeon grass (Ruppia maritima) supported surprisingly low numbers of macroinvertebrates, probably due to stressfully low dissolved oxygen levels at night during the summer. Two species of macroinvertebrates, blue mussels (Mytilus edulis) and to a lesser extent bay scallops (Argopecten irradians), used eelgrass as 'nursery habitat.' Calculations showed that macroinvertebrate production is proportionally much greater than the amount of primary production attributable to eelgrass in the Nauset Marsh system, and that dramatic changes at all trophic levels could be expected if large changes in seagrass abundance should occur. This work further underscores the extraordinarily large impact that seagrass can have on both the structure and function of estuarine ecosystems.

  8. Temporal sampling helps unravel the genetic structure of naturally occurring populations of a phytoparasitic nematode. 1. Insights from the estimation of effective population sizes.

    PubMed

    Jan, Pierre-Loup; Gracianne, Cécile; Fournet, Sylvain; Olivier, Eric; Arnaud, Jean-François; Porte, Catherine; Bardou-Valette, Sylvie; Denis, Marie-Christine; Petit, Eric J

    2016-03-01

    The sustainability of modern agriculture relies on strategies that can control the ability of pathogens to overcome chemicals or genetic resistances through natural selection. This evolutionary potential, which depends partly on effective population size (N e ), is greatly influenced by human activities. In this context, wild pathogen populations can provide valuable information for assessing the long-term risk associated with crop pests. In this study, we estimated the effective population size of the beet cyst nematode, Heterodera schachtii, by sampling 34 populations infecting the sea beet Beta vulgaris spp. maritima twice within a one-year period. Only 20 populations produced enough generations to analyze the variation in allele frequencies, with the remaining populations showing a high mortality rate of the host plant after only 1 year. The 20 analyzed populations showed surprisingly low effective population sizes, with most having N e close to 85 individuals. We attribute these low values to the variation in population size through time, systematic inbreeding, and unbalanced sex-ratios. Our results suggest that H. schachtii has low evolutionary potential in natural environments. Pest control strategies in which populations on crops mimic wild populations may help prevent parasite adaptation to host resistance. PMID:26989440

  9. Structure and electrostatic property of cytoplasmic domain of ZntB transporter.

    SciTech Connect

    Tan, K.; Sather, A.; Robertson, J. L.; Moy, S.; Roux, B.; Joachimiak, A.; Biosciences Division; Cornell Univ.; Univ. of Chicago

    2009-10-01

    ZntB is the distant homolog of CorA Mg{sup 2+} transporter within the metal ion transporter superfamily. It was early reported that the ZntB from Salmonella typhimurium facilitated efflux of Zn{sup 2+} and Cd{sup 2+}, but not Mg{sup 2+}. Here, we report the 1.90 {angstrom} crystal structure of the intracellular domain of ZntB from Vibrio parahemolyticus. The domain forms a funnel-shaped homopentamer that is similar to the full-length CorA from Thermatoga maritima, but differs from two previously reported dimeric structures of truncated CorA intracellular domains. However, no Zn{sup 2+} or Cd{sup 2+} binding sites were identified in the high-resolution structure. Instead, 25 well-defined Cl{sup -} ions were observed and some of these binding sites are highly conserved within the ZntB family. Continuum electrostatics calculations suggest that the central pore of the funnel is highly attractive for cations, especially divalents. The presence of the bound Cl{sup -} ions increases the stability of cations along the pore suggesting they could be important in enhancing cation transport.

  10. Ritual plants of Muslim graveyards in northern Israel

    PubMed Central

    Dafni, Amots; Lev, Efraim; Beckmann, Sabine; Eichberger, Christian

    2006-01-01

    This article surveys the botanical composition of 40 Muslim graveyards in northern Israel, accompanied by an ethnobotanical study of the folkloristic traditions of the use of these plants in cemeteries. Three groups of plants were found to be repeated systematically and were also recognized for their ritual importance: aromatics herbs (especially Salvia fruticosa and Rosmarinus officinalis), white flowered plants (mainly Narcissus tazetta, Urginea maritima, Iris spp. and Pancratium spp.) and Cupressus sempervirens as the leading cemetery tree. As endemic use we can indicate the essential role of S. fruticosa as the main plant used in all human rites of passage symbolizing the human life cycle. The rosemary is of European origin while the use of basil is of Indian influence. The use of white flowers as cemeteries plants reflects an old European influence and almost the same species are used or their congeners. Most of the trees and shrubs that are planted in Muslim cemeteries in Israel have the same use in ancient as well in modern European cultures. In conclusion, our findings on the occurrence of plants in graveyards reflect the geographic situation of Israel as a crossroads in the cultural arena between Asia and Europe. Most of the traditions are common to the whole Middle East showing high relatedness to the classical world as well as to the present-day Europe. PMID:16961931

  11. A structural basis for Mg2+ homeostasis and the CorA translocation cycle

    PubMed Central

    Payandeh, Jian; Pai, Emil F

    2006-01-01

    We describe the CorA Mg2+ transporter homologue from Thermotoga maritima in complex with 12 divalent cations at 3.7 Å resolution. One metal is found near the universally conserved GMN motif, apparently stabilized within the transmembrane region. This portion of the selectivity filter might discriminate between the size and preferred coordination geometry of hydrated substrates. CorA may further achieve specificity by requiring the sequential dehydration of substrates along the length of its ?55 Å long pore. Ten metal sites identified within the cytoplasmic funnel domain are linked to long extensions of the pore helices and regulate the transport status of CorA. We have characterized this region as an intrinsic divalent cation sensor and provide evidence that it functions as a Mg2+-specific homeostatic molecular switch. A proteolytic protection assay, biophysical data, and comparison to a soluble domain structure from Archaeoglobus fulgidus have revealed the potential reaction coordinate for this diverse family of transport proteins. PMID:16902408

  12. Functional adaptations of the bacterial chaperone trigger factor to extreme environmental temperatures.

    PubMed

    Godin-Roulling, Amandine; Schmidpeter, Philipp A M; Schmid, Franz X; Feller, Georges

    2015-07-01

    Trigger factor (TF) is the first molecular chaperone interacting cotranslationally with virtually all nascent polypeptides synthesized by the ribosome in bacteria. Thermal adaptation of chaperone function was investigated in TFs from the Antarctic psychrophile Pseudoalteromonas haloplanktis, the mesophile Escherichia coli and the hyperthermophile Thermotoga maritima. This series covers nearly all temperatures encountered by bacteria. Although structurally homologous, these TFs display strikingly distinct properties that are related to the bacterial environmental temperature. The hyperthermophilic TF strongly binds model proteins during their folding and protects them from heat-induced misfolding and aggregation. It decreases the folding rate and counteracts the fast folding rate imposed by high temperature. It also functions as a carrier of partially folded proteins for delivery to downstream chaperones ensuring final maturation. By contrast, the psychrophilic TF displays weak chaperone activities, showing that these functions are less important in cold conditions because protein folding, misfolding and aggregation are slowed down at low temperature. It efficiently catalyses prolyl isomerization at low temperature as a result of its increased cellular concentration rather than from an improved activity. Some chaperone properties of the mesophilic TF possibly reflect its function as a cold shock protein in E. coli. PMID:25389111

  13. Starch self-processing in transgenic sweet potato roots expressing a hyperthermophilic ?-amylase.

    PubMed

    Santa-Maria, Monica C; Yencho, Craig G; Haigler, Candace H; Thompson, William F; Kelly, Robert M; Sosinski, Bryon

    2011-01-01

    Sweet potato is a major crop in the southeastern United States, which requires few inputs and grows well on marginal land. It accumulates large quantities of starch in the storage roots and has been shown to give comparable or superior ethanol yields to corn per cultivated acre in the southeast. Starch conversion to fermentable sugars (i.e., for ethanol production) is carried out at high temperatures and requires the action of thermostable and thermoactive amylolytic enzymes. These enzymes are added to the starch mixture impacting overall process economics. To address this shortcoming, the gene encoding a hyperthermophilic ?-amylase from Thermotoga maritima was cloned and expressed in transgenic sweet potato, generated by Agrobacterium tumefaciens-mediated transformation, to create a plant with the ability to self-process starch. No significant enzyme activity could be detected below 40°C, but starch in the transgenic sweet potato storage roots was readily hydrolyzed at 80°C. The transgene did not affect normal storage root formation. The results presented here demonstrate that engineering plants with hyperthermophilic glycoside hydrolases can facilitate cost effective starch conversion to fermentable sugars. Furthermore, the use of sweet potato as an alternative near-term energy crop should be considered. PMID:21365786

  14. Biosynthesis of D-xylulose 5-phosphate from D-xylose and polyphosphate through a minimized two-enzyme cascade.

    PubMed

    Kim, Jae-Eung; Zhang, Y-H Percival

    2016-02-01

    Sugar phosphates cannot be produced easily by microbial fermentation because negatively-charged compounds cannot be secreted across intact cell membrane. D-xylulose 5-phosphate (Xu5P), a very expensive sugar phosphate, was synthesized from D-xylose and polyphosphate catalyzed by enzyme cascades in one pot. The synthetic enzymatic pathway comprised of xylose isomerase and xylulokinase was designed to produce Xu5P, along with a third enzyme, polyphosphate kinase, responsible for in site ATP regeneration. Due to the promiscuous activity of the ATP-based xylulokinase from a hyperthermophilic bacterium Thermotoga maritima on polyphosphate, the number of enzymes in the pathway was minimized to two without polyphosphate kinase. The reactions catalyzed by the two-enzyme and three-enzyme pathways were compared for Xu5P production, and the reaction conditions were optimized by examining effects of reaction temperature, enzyme ratio and substrate concentration. The optimized two-enzyme system produced 32 mM Xu5P from 50 mM xylose and polyphosphate after 36 h at 45°C. Biosynthesis of less costly Xu5P from D-xylose and polyphosphate could be highly feasible via this minimized two-enzyme pathway. Biotechnol. Bioeng. 2016;113: 275-282. © 2015 Wiley Periodicals, Inc. PMID:26241217

  15. Structure and electrostatic property of cytoplasmic domain of ZntB transporter

    PubMed Central

    Tan, Kemin; Sather, Alicia; Robertson, Janice L; Moy, Shiu; Roux, Benoît; Joachimiak, Andrzej

    2009-01-01

    ZntB is the distant homolog of CorA Mg2+ transporter within the metal ion transporter superfamily. It was early reported that the ZntB from Salmonella typhimurium facilitated efflux of Zn2+ and Cd2+, but not Mg2+. Here, we report the 1.90 Å crystal structure of the intracellular domain of ZntB from Vibrio parahemolyticus. The domain forms a funnel-shaped homopentamer that is similar to the full-length CorA from Thermatoga maritima, but differs from two previously reported dimeric structures of truncated CorA intracellular domains. However, no Zn2+ or Cd2+ binding sites were identified in the high-resolution structure. Instead, 25 well-defined Cl? ions were observed and some of these binding sites are highly conserved within the ZntB family. Continuum electrostatics calculations suggest that the central pore of the funnel is highly attractive for cations, especially divalents. The presence of the bound Cl? ions increases the stability of cations along the pore suggesting they could be important in enhancing cation transport. PMID:19653298

  16. 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

  17. One-Pot Biosynthesis of High-Concentration ?-Glucose 1-Phosphate from Starch by Sequential Addition of Three Hyperthermophilic Enzymes.

    PubMed

    Zhou, Wei; You, Chun; Ma, Hongwu; Ma, Yanhe; Zhang, Y-H Percival

    2016-03-01

    ?-Glucose 1-phosphate (G1P) is synthesized from 5% (w/v) corn starch and 1 M phosphate mediated by ?-glucan phosphorylase (?GP) from the thermophilic bacterium Thermotoga maritima at pH 7.2 and 70 °C. To increase G1P yield from corn starch containing branched amylopectin, a hyper-thermostable isoamylase from Sulfolobus tokodaii was added for simultaneous starch gelatinization and starch-debranching hydrolysis at 85 °C and pH 5.5 before ?GP use. The pretreatment of isoamylase increased G1P titer from 120 mM to 170 mM. To increase maltose and maltotriose utilization, the third thermostable enzyme, 4-glucanotransferase (4GT) from Thermococcus litoralis, was added during the late stage of G1P biotransformation, further increasing G1P titer to 200 mM. This titer is the highest G1P level obtained on starch or its derived products (maltodextrin and soluble starch). This study suggests that in vitro multienzyme biotransformation has an advantage of great engineering flexibility in terms of space and time compared with microbial fermentation. PMID:26832825

  18. 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

  19. Structural and functional studies of a metallo-?-lactamase unveil a new type of structurally encoded nickel-containing heterodinuclear site.

    PubMed

    Choi, Hwajung; Kim, Hee Jung; Matsuura, Atsushi; Mikami, Bunzo; Yoon, Hye Jin; Lee, Hyung Ho

    2015-10-01

    The selection of correct metal ions with high fidelity against competing cellular cations is crucial for the function of many metalloenzymes; however, the understanding of the principles that govern metal selectivity is still incomplete. In this study, the crystal structure of the Tm1162 protein from Thermotoga maritima, a metallo-?-lactamase, is reported. Several crystal structures of wild-type Tm1162 and its mutants were solved. Homologues of Tm1162 are widely distributed in bacteria and archaea, including several human pathogens. The monomer possesses an ??/?? fold, with the core ?-strands having the ?-sheet sandwich structure common to the metallo-?-lactamase superfamily. Tm1162 exists as a trimer in the crystal and this trimeric unit is likely to be present in solution. In the trimer, three active sites reside at the interface between subunits, suggesting that the oligomeric assembly is crucial for catalysis. A new type of structurally encoded heterodinuclear site has been identified by confirming the identity of nickel-containing heteronuclear sites in Tm1162 via X-ray absorption spectroscopy and anomalous difference Fourier maps. The second coordination sphere, including His8 and Glu73, maintains the side-chain orientations of histidines and stabilizes the metal-binding site. Nickel coordination was crucial for the oligomerization of Tm1162. The nickel-dependent and manganese-dependent ?-lactamase and phosphodiesterase activities of Tm1162 have also been characterized. PMID:26457429

  20. Expression patterns of Wnt genes in the venom claws of centipedes.

    PubMed

    Hayden, Luke; Arthur, Wallace

    2013-01-01

    The venom claws of centipedes, also known as forcipules, represent an evolutionary novelty that must have arisen in the centipede stem species, as they are not found in any other myriapods. The developmental-genetic changes that are involved in the origin of novelties are of considerable interest. It has previously been shown that centipede forcipules have a unique Hox code. However, this is a combinatorial code: no single Hox gene has a forcipule-specific expression. Here, we focus on Wnt genes. Two genes of this family show forcipule-specific expression in the "model centipede" Strigamia maritima: Wnt7 and Wnt11. For Wnt7, this forcipular expression zone seems to be a new one, which has arisen in evolution subsequently to other expression zones of the same gene. However, for Wnt11, the forcipule-specific expression probably arose by reduction of a more general pattern that originally included most or all of the limbs of an ancestral myriapod. Thus the developmental-genetic basis of the evolutionary change that turned the first pair of walking legs into venom claws is complex, involving different types of change in expression pattern. This sort of complexity is likely to be the case regarding evolutionary changes in morphology in general. Whether the origins of those features that can be considered as novelties are different in terms of their developmental-genetic basis from more routine evolutionary changes remains an open question. PMID:24074281

  1. 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

  2. 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

  3. X-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound Fe4S4 clusters.

    PubMed

    Nicolet, Yvain; Rohac, Roman; Martin, Lydie; Fontecilla-Camps, Juan C

    2013-04-30

    Fe4S4 clusters are very common versatile prosthetic groups in proteins. Their redox property of being sensitive to O2-induced oxidative damage is, for instance, used by the cell to sense oxygen levels and switch between aerobic and anaerobic metabolisms, as exemplified by the fumarate, nitrate reduction regulator (FNR). Using the hydrogenase maturase HydE from Thermotoga maritima as a template, we obtained several unusual forms of FeS clusters, some of which are associated with important structural changes. These structures represent intermediate states relevant to both FeS cluster assembly and degradation. We observe one Fe2S2 cluster bound by two cysteine persulfide residues. This observation lends structural support to a very recent Raman study, which reported that Fe4S4-to-Fe2S2 cluster conversion upon oxygen exposure in FNR resulted in concomitant production of cysteine persulfide as cluster ligands. Similar persulfide ligands have been observed in vitro for several other Fe4S4 cluster-containing proteins. We have also monitored FeS cluster conversion directly in our protein crystals. Our structures indicate that the Fe4S4-to-Fe2S2 change requires large structural modifications, which are most likely responsible for the dimer-monomer transition in FNR. PMID:23596207

  4. A comparative molecular dynamics study of thermophilic and mesophilic ?-fructosidase enzymes.

    PubMed

    Mazola, Yuliet; Guirola, Osmany; Palomares, Sucel; Chinea, Glay; Menéndez, Carmen; Hernández, Lázaro; Musacchio, Alexis

    2015-09-01

    Arabidopsis thaliana cell wall invertase 1 (AtcwINV1) and Thermotoga maritima ?-fructosidase (BfrA) are among the best structurally studied members of the glycoside hydrolase family 32. Both enzymes hydrolyze sucrose as the main substrate but differ strongly in their thermal stability. Mesophilic AtcwINV1 and thermophilic BfrA have divergent sequence similarities in the N-terminal five bladed ?-propeller catalytic domain (31 %) and the C-terminal ?-sandwich domain (15 %) of unknown function. The two enzymes were subjected to 200 ns molecular dynamics simulations at 300 K (27 °C) and 353 K (80 °C). Regular secondary structure regions, but not loops, in AtcwINV1 and BfrA showed no significant fluctuation differences at both temperatures. BfrA was more rigid than AtcwINV1 at 300 K. The simulation at 353 K did not alter the structural stability of BfrA, but did increase the overall flexibility of AtcwINV1 exhibiting the most fluctuating regions in the ?-propeller domain. The simulated heat treatment also increased the gyration radius and hydrophobic solvent accessible surface area of the plant enzyme, consistent with the initial steps of an unfolding process. The preservation of the conformational rigidity of BfrA at 353 K is linked to the shorter size of the protein loops. Shortening of BfrA loops appears to be a key mechanism for thermostability. PMID:26267297

  5. 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

  6. Cloning of the Gene Encoding a Novel Thermostable α-Galactosidase from Thermus brockianus ITI360

    PubMed Central

    Fridjonsson, Olafur; Watzlawick, Hildegard; Gehweiler, Axel; Rohrhirsch, Thilo; Mattes, Ralf

    1999-01-01

    An α-galactosidase gene from Thermus brockianus ITI360 was cloned, sequenced, and expressed in Escherichia coli, and the recombinant protein was purified. The gene, designated agaT, codes for a 476-residue polypeptide with a calculated molecular mass of 53,810 Da. The native structure of the recombinant enzyme (AgaT) was estimated to be a tetramer. AgaT displays amino acid sequence similarity to the α-galactosidases of Thermotoga neapolitana and Thermotoga maritima and a low-level sequence similarity to α-galactosidases of family 36 in the classification of glycosyl hydrolases. The enzyme is thermostable, with a temperature optimum of activity at 93°C with para-nitrophenyl-α-galactopyranoside as a substrate. Half-lives of inactivation at 92 and 80°C are 100 min and 17 h, respectively. The pH optimum is between 5.5 and 6.5. The enzyme displayed high affinity for oligomeric substrates. The Kms for melibiose and raffinose at 80°C were determined as 4.1 and 11.0 mM, respectively. The α-galactosidase gene in T. brockianus ITI360 was inactivated by integrational mutagenesis. Consequently, no α-galactosidase activity was detectable in crude extracts of the mutant strain, and it was unable to use melibiose or raffinose as a single carbohydrate source. PMID:10473401

  7. Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins.

    PubMed

    Frye, R A

    2000-07-01

    Sirtuins (Sir2-like proteins) are present in prokaryotes and eukaryotes. Here, two new human sirtuins (SIRT6 and SIRT7) are found to be similar to a particular subset of insect, nematode, plant, and protozoan sirtuins. Molecular phylogenetic analysis of 60 sirtuin conserved core domain sequences from a diverse array of organisms (including archaeans, bacteria, yeasts, plants, protozoans, and metazoans) shows that eukaryotic Sir2-like proteins group into four main branches designated here as classes I-IV. Prokaryotic sirtuins include members of classes II and III. A fifth class of sirtuin is present in gram positive bacteria and Thermotoga maritima. Saccharomyces cerevisiae has five class I sirtuins. Caenorhabditis elegans and Drosophila melanogaster have sirtuin genes from classes I, II, and IV. The seven human sirtuin genes include all four classes: SIRT1, SIRT2, and SIRT3 are class I, SIRT4 is class II, SIRT5 is class III, and SIRT6 and SIRT7 are class IV. PMID:10873683

  8. A Structural Basis for Mg(2+) Homeostasis and the CorA Translocation Cycle

    SciTech Connect

    Payandeh,J.; Pai, E.

    2006-01-01

    We describe the CorA Mg{sup 2+} transporter homologue from Thermotoga maritima in complex with 12 divalent cations at 3.7 {angstrom} resolution. One metal is found near the universally conserved GMN motif, apparently stabilized within the transmembrane region. This portion of the selectivity filter might discriminate between the size and preferred coordination geometry of hydrated substrates. CorA may further achieve specificity by requiring the sequential dehydration of substrates along the length of its {approx}55 {angstrom} long pore. Ten metal sites identified within the cytoplasmic funnel domain are linked to long extensions of the pore helices and regulate the transport status of CorA. We have characterized this region as an intrinsic divalent cation sensor and provide evidence that it functions as a Mg{sup 2+}-specific homeostatic molecular switch. A proteolytic protection assay, biophysical data, and comparison to a soluble domain structure from Archaeoglobus fulgidus have revealed the potential reaction coordinate for this diverse family of transport proteins.

  9. Crystallization and preliminary X-ray diffraction analysis of the magnesium transporter CorA

    SciTech Connect

    Payandeh, Jian; Pai, Emil F.

    2006-02-01

    Full-length and soluble domains of the integral membrane protein CorA have been expressed, purified and crystallized. X-ray diffraction data have been collected and analyzed. The full-length integral membrane protein CorA from Thermotoga maritima (TmCorA{sub 1–351}) has been expressed in Escherichia coli and purified without membrane isolation. TmCorA{sub 1–351} crystallized in the monoclinic space group C2, with unit-cell parameters a = 214.25, b = 86.30, c = 181.53 Å, ? = 112.23°. Native crystals diffracted to 3.7 Å using synchrotron radiation, but selenomethionine-substituted crystals rarely diffracted to better than 5.0 Å. All full-length protein crystals were highly mosaic and produced anisotropic diffraction patterns. To aid in crystallographic phasing, soluble domain constructs were screened and the periplasmic domain of CorA from Archaeoglobus fulgidus (AfCorA{sub 1–263}) was crystallized in the hexagonal space group P6{sub 1}22, with unit-cell parameters a = b = 101.17, c = 142.87 Å. Native and SeMet-substituted AfCorA{sub 1–263} crystals diffracted to ?3.0 Å using synchrotron radiation.

  10. Crystallization and Preliminary X-ray Diffraction Analysis of the Magnesium Transporter CorA

    SciTech Connect

    Payandeh,J.; Pai, E.

    2006-01-01

    The full-length integral membrane protein CorA from Thermotoga maritima (TmCorA{sub 1-351}) has been expressed in Escherichia coli and purified without membrane isolation. TmCorA{sub 1-351} crystallized in the monoclinic space group C2, with unit-cell parameters a = 214.25, b = 86.30, c = 181.53 Angstroms, {beta} = 112.23 degrees . Native crystals diffracted to 3.7 Angstroms using synchrotron radiation, but selenomethionine-substituted crystals rarely diffracted to better than 5.0 Angstroms. All full-length protein crystals were highly mosaic and produced anisotropic diffraction patterns. To aid in crystallographic phasing, soluble domain constructs were screened and the periplasmic domain of CorA from Archaeoglobus fulgidus (AfCorA1-263) was crystallized in the hexagonal space group P6{sub 1}22, with unit-cell parameters a = b = 101.17, c = 142.87 Angstroms. Native and SeMet-substituted AfCorA{sub 1-263} crystals diffracted to {approx}3.0 Angstroms using synchrotron radiation.

  11. Crystal structure of the middle and C-terminal domains of the flagellar rotor protein FliG

    PubMed Central

    Brown, Perry N.; Hill, Christopher P.; Blair, David F.

    2002-01-01

    The FliG protein is essential for assembly, rotation and clockwise/counter-clockwise (CW/CCW) switching of the bacterial flagellum. About 25 copies of FliG are present in a large rotor-mounted assembly termed the ‘switch complex’, which also contains the proteins FliM and FliN. Mutational studies have identified the segments of FliG most crucial for flagellar assembly, rotation and switching. The structure of the C-terminal domain, which functions specifically in rotation, was reported previously. Here, we describe the crystal structure of a larger fragment of the FliG protein from Thermotoga maritima, which encompasses the middle and C-terminal parts of the protein (termed FliG-MC). The FliG-MC molecule consists of two compact globular domains, linked by an ?-helix and an extended segment that contains a well-conserved Gly–Gly motif. Mutational studies indicate that FliM binds to both of the globular domains, and given the flexibility of the linking segment, FliM is likely to determine the relative orientation of the domains in the flagellum. We propose a model for the organization of FliG-MC molecules in the flagellum, and suggest that CW/CCW switching might occur by movement of the C-terminal domain relative to other parts of FliG, under the control of FliM. PMID:12093724

  12. Weighted Implementation of Suboptimal Paths (WISP): An Optimized Algorithm and Tool for Dynamical Network Analysis.

    PubMed

    Van Wart, Adam T; Durrant, Jacob; Votapka, Lane; Amaro, Rommie E

    2014-02-11

    Allostery can occur by way of subtle cooperation among protein residues (e.g., amino acids) even in the absence of large conformational shifts. Dynamical network analysis has been used to model this cooperation, helping to computationally explain how binding to an allosteric site can impact the behavior of a primary site many ångstroms away. Traditionally, computational efforts have focused on the most optimal path of correlated motions leading from the allosteric to the primary active site. We present a program called Weighted Implementation of Suboptimal Paths (WISP) capable of rapidly identifying additional suboptimal pathways that may also play important roles in the transmission of allosteric signals. Aside from providing signal redundancy, suboptimal paths traverse residues that, if disrupted through pharmacological or mutational means, could modulate the allosteric regulation of important drug targets. To demonstrate the utility of our program, we present a case study describing the allostery of HisH-HisF, an amidotransferase from T. maritima thermotiga. WISP and its VMD-based graphical user interface (GUI) can be downloaded from http://nbcr.ucsd.edu/wisp. PMID:24803851

  13. Insights into Flavin-based Electron Bifurcation via the NADH-dependent Reduced Ferredoxin:NADP Oxidoreductase Structure.

    PubMed

    Demmer, Julius K; Huang, Haiyan; Wang, Shuning; Demmer, Ulrike; Thauer, Rudolf K; Ermler, Ulrich

    2015-09-01

    NADH-dependent reduced ferredoxin:NADP oxidoreductase (NfnAB) is found in the cytoplasm of various anaerobic bacteria and archaea. The enzyme reversibly catalyzes the endergonic reduction of ferredoxin with NADPH driven by the exergonic transhydrogenation from NADPH onto NAD(+). Coupling is most probably accomplished via the mechanism of flavin-based electron bifurcation. To understand this process on a structural basis, we heterologously produced the NfnAB complex of Thermotoga maritima in Escherichia coli, provided kinetic evidence for its bifurcating behavior, and determined its x-ray structure in the absence and presence of NADH. The structure of NfnAB reveals an electron transfer route including the FAD (a-FAD), the [2Fe-2S] cluster of NfnA and the FAD (b-FAD), and the two [4Fe-4S] clusters of NfnB. Ferredoxin is presumably docked onto NfnB close to the [4Fe-4S] cluster distal to b-FAD. NAD(H) binds to a-FAD and NADP(H) consequently to b-FAD, which is positioned in the center of the NfnAB complex and the site of electron bifurcation. Arg(187) is hydrogen-bonded to N5 and O4 of the bifurcating b-FAD and might play a key role in adjusting a low redox potential of the FADH(•)/FAD pair required for ferredoxin reduction. A mechanism of FAD-coupled electron bifurcation by NfnAB is proposed. PMID:26139605

  14. 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.

  15. Crystal structure of a two-subunit TrkA octameric gating ring assembly

    DOE PAGESBeta

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

    2015-03-31

    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 acrossmore » 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.« less

  16. Switching base preferences of mismatch cleavage in endonuclease V: an improved method for scanning point mutations.

    PubMed

    Gao, Honghai; Huang, Jianmin; Barany, Francis; Cao, Weiguo

    2007-01-01

    Endonuclease V (endo V) recognizes a broad range of aberrations in DNA such as deaminated bases or mismatches. It nicks DNA at the second phosphodiester bond 3' to a deaminated base or a mismatch. Endonuclease V obtained from Thermotoga maritima preferentially cleaves purine mismatches in certain sequence context. Endonuclease V has been combined with a high-fidelity DNA ligase to develop an enzymatic method for mutation scanning. A biochemical screening of site-directed mutants identified mutants in motifs III and IV that altered the base preferences in mismatch cleavage. Most profoundly, a single alanine substitution at Y80 position switched the enzyme to essentially a C-specific mismatch endonuclease, which recognized and cleaved A/C, C/A, T/C, C/T and even the previously refractory C/C mismatches. Y80A can also detect the G13D mutation in K-ras oncogene, an A/C mismatch embedded in a G/C rich sequence context that was previously inaccessible using the wild-type endo V. This investigation offers insights on base recognition and active site organization. Protein engineering in endo V may translate into better tools in mutation recognition and cancer mutation scanning. PMID:17130153

  17. 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

  18. 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.

  19. 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.

  20. 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

  1. A Robust and Versatile Method of Combinatorial Chemical Synthesis of Gene Libraries via Hierarchical Assembly of Partially Randomized Modules

    PubMed Central

    Popova, Blagovesta; Schubert, Steffen; Bulla, Ingo; Buchwald, Daniela; Kramer, Wilfried

    2015-01-01

    A major challenge in gene library generation is to guarantee a large functional size and diversity that significantly increases the chances of selecting different functional protein variants. The use of trinucleotides mixtures for controlled randomization results in superior library diversity and offers the ability to specify the type and distribution of the amino acids at each position. Here we describe the generation of a high diversity gene library using tHisF of the hyperthermophile Thermotoga maritima as a scaffold. Combining various rational criteria with contingency, we targeted 26 selected codons of the thisF gene sequence for randomization at a controlled level. We have developed a novel method of creating full-length gene libraries by combinatorial assembly of smaller sub-libraries. Full-length libraries of high diversity can easily be assembled on demand from smaller and much less diverse sub-libraries, which circumvent the notoriously troublesome long-term archivation and repeated proliferation of high diversity ensembles of phages or plasmids. We developed a generally applicable software tool for sequence analysis of mutated gene sequences that provides efficient assistance for analysis of library diversity. Finally, practical utility of the library was demonstrated in principle by assessment of the conformational stability of library members and isolating protein variants with HisF activity from it. Our approach integrates a number of features of nucleic acids synthetic chemistry, biochemistry and molecular genetics to a coherent, flexible and robust method of combinatorial gene synthesis. PMID:26355961

  2. Biomimetic assembly and activation of [FeFe]-hydrogenases.

    PubMed

    Berggren, G; Adamska, A; Lambertz, C; Simmons, T R; Esselborn, J; Atta, M; Gambarelli, S; Mouesca, J-M; Reijerse, E; Lubitz, W; Happe, T; Artero, V; Fontecave, M

    2013-07-01

    Hydrogenases are the most active molecular catalysts for hydrogen production and uptake, and could therefore facilitate the development of new types of fuel cell. In [FeFe]-hydrogenases, catalysis takes place at a unique di-iron centre (the [2Fe] subsite), which contains a bridging dithiolate ligand, three CO ligands and two CN(-) ligands. Through a complex multienzymatic biosynthetic process, this [2Fe] subsite is first assembled on a maturation enzyme, HydF, and then delivered to the apo-hydrogenase for activation. Synthetic chemistry has been used to prepare remarkably similar mimics of that subsite, but it has failed to reproduce the natural enzymatic activities thus far. Here we show that three synthetic mimics (containing different bridging dithiolate ligands) can be loaded onto bacterial Thermotoga maritima HydF and then transferred to apo-HydA1, one of the hydrogenases of Chlamydomonas reinhardtii algae. Full activation of HydA1 was achieved only when using the HydF hybrid protein containing the mimic with an azadithiolate bridge, confirming the presence of this ligand in the active site of native [FeFe]-hydrogenases. This is an example of controlled metalloenzyme activation using the combination of a specific protein scaffold and active-site synthetic analogues. This simple methodology provides both new mechanistic and structural insight into hydrogenase maturation and a unique tool for producing recombinant wild-type and variant [FeFe]-hydrogenases, with no requirement for the complete maturation machinery. PMID:23803769

  3. Comparison of Three Ionic Liquid-Tolerant Cellulases by Molecular Dynamics

    PubMed Central

    Jaeger, Vance; Burney, Patrick; Pfaendtner, Jim

    2015-01-01

    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

  4. 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 μg 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 μg/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

  5. Analysis of genetic structure and dispersal patterns in a population of sea beet.

    PubMed Central

    Tufto, J; Raybould, A F; Hindar, K; Engen, S

    1998-01-01

    A model of the migration pattern in a metapopulation of sea beet (Beta vulgaris L. ssp. maritima), based on the continuous distributions of seed and pollen movements, is fitted to gene frequency data at 12 isozyme and RFLP loci by maximum likelihood by using an approximation of the simultaneous equilibrium distribution of the gene frequencies generated by the underlying multivariate stochastic process of genetic drift in the population. Several alternative restrictions of the general model are fitted to the data, including the island model, a model of complete isolation, and a model in which the seed and pollen dispersal variances are equal. Several likelihood ratio tests between these alternatives are performed, and median bias in the estimated parameters is corrected by using parametric bootstrapping. To assess the fit of the selected model, the predicted covariances are compared with covariances computed from the data directly. The dependency of estimated parameters on the ratio between effective and absolute subpopulation sizes, which is treated as a known parameter in the analysis, is also examined. Finally, we note that the data also appear to contain some information about this ratio. PMID:9691051

  6. 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

  7. 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

  8. Binding and inhibition of human spermidine synthase by decarboxylated S-adenosylhomocysteine

    PubMed Central

    Še?kut?, Jolita; McCloskey, Diane E; Thomas, H Jeanette; Secrist, John A; Pegg, Anthony E; Ealick, Steven E

    2011-01-01

    Aminopropyltransferases are essential enzymes that form polyamines in eukaryotic and most prokaryotic cells. Spermidine synthase (SpdS) is one of the most well-studied enzymes in this biosynthetic pathway. The enzyme uses decarboxylated S-adenosylmethionine and a short-chain polyamine (putrescine) to make a medium-chain polyamine (spermidine) and 5?-deoxy-5?-methylthioadenosine as a byproduct. Here, we report a new spermidine synthase inhibitor, decarboxylated S-adenosylhomocysteine (dcSAH). The inhibitor was synthesized, and dose-dependent inhibition of human, Thermatoga maritima, and Plasmodium falciparum spermidine synthases, as well as functionally homologous human spermine synthase, was determined. The human SpdS/dcSAH complex structure was determined by X-ray crystallography at 2.0 Å resolution and showed consistent active site positioning and coordination with previously known structures. Isothermal calorimetry binding assays confirmed inhibitor binding to human SpdS with Kd of 1.1 ± 0.3 ?M in the absence of putrescine and 3.2 ± 0.1 ?M in the presence of putrescine. These results indicate a potential for further inhibitor development based on the dcSAH scaffold. PMID:21898642

  9. 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

  10. 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 σ70 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 α subunit, and then optimally-separated patterns of -35 and -10 boxes, required for interaction with the σ70 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

  11. Crystal structure of a two-subunit TrkA octameric gating ring assembly

    SciTech Connect

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

    2015-03-31

    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.

  12. Food habits of diving ducks in the Carolinas

    USGS Publications Warehouse

    Perry, M.C.; Uhler, F.M.

    1982-01-01

    Food habits analyses were conducted on 264 diving ducks (7 species) from North and South Carolina during the 1970'S. The Baltic clam (Macoma balthica) was the predominant food among canvasbacks (Aythya valisineria) from the Pamlico River area, whereas sago pondweed (Potamogeton pectinatus) predominated in birds from impoundments in North and South Carolina. Shoalgrass (Halodule beaudettei) formed 100% of the gullet food and 99% of the gizzard food in redheads (Aythya americana) from Pamlico Sound. Lesser scaup (Aythya affinis) in North Carolina had fed predominantly on mollusks (Mulinia lateralis and Rangia cuneata), whereas widgeon grass (Ruppia maritima) was the predominant food in birds from South Carolina. In North Carolina, ring-necked ducks (Aythya collaris) fed mainly on vegetation, and greater scaup (Aythya marila), bufflehead (Bucephala albeola), and ruddy ducks (Oxyura jamaicensis) fed mainly on Mulinia lateralis. Food habits data from this study when compared with historical food habits of these species indicate that most diving duck species were feeding more on invertebrates and less on submerged aquatic vegetation than in the past. North and South Carolina have a diverse food supply and appear to offer waterfowl adequate wintering habitat based on these food habits studies. Present trends in wintering habitat, however, could adversely affect diving duck populations in the future.

  13. Air pollution effects on the ultrastructure of Phlomis fruticosa mesophyll cells

    SciTech Connect

    Psaras, G.K.; Christodoulakis, N.S.

    1987-04-01

    Plant physiologists and environmental scientists suggest that a basic effect of air pollution on plants leads towards the minimization of their productivity. On the other hand the action of individual pollutants on intact plants has been studied from biochemical as well as structural viewpoint. Thus the study of plant responses to SO/sub 2/ exposure revealed that this agent causes acute and chronic injury. Chronic injury results in chlorosis and subsequent necrosis due to destruction of chlorophylls and final chloroplast lysis. It has been documented that ultrastructural characteristics of leaves are affected prior to any visible injury. Electron microscope examination of SO/sub 2/ fumigated plant-attached leaves of Vicia faba revealed chloroplast thylakoids starting to swell whilst photosynthesis rate was drastically reduced. The first light microscope-detected effects of air pollution on the leaf structure of plants common in natural ecosystems of Athens metropolitan area, have been reported. A chlorosis phenomenon in Urginea maritima leaves as well as an indication of detrimental effects of Phlomis fruticosa mesophyll chloroplasts were documented. In this work further investigation has been undertaken in order to elucidate the precise effects of air pollution on the ultrastructure of the photosynthesizing mesophyll cells.

  14. Surface display of the thermophilic lipase Tm1350 on the spore of Bacillus subtilis by the CotB anchor protein.

    PubMed

    Chen, Huayou; Tian, Rui; Ni, Zhong; Zhang, Qing; Zhang, Tianxi; Chen, Zhi; Chen, Keping; Yang, Shengli

    2015-07-01

    Lipases expressed in microbial hosts have great commercial value, but their applications are restricted by the high costs of production and harsh conditions used in industrial processes, such as high temperature and alkaline environment. In this study, an Escherichia coli-Bacillus subtilis shuttle vector (pHS-cotB-Tm1350) was constructed for the spore surface display of the lipase Tm1350 from hyperthermophilic bacterium Thermotoga maritima MSB8. Successful display of the CotB-Tm1350 fusion protein on spore surface was confirmed by Western blot analysis and activity measurements. The optimal catalytic temperature and pH of the spore surface-displayed Tm1350 were 80 °C and 9, respectively, which were higher than non-immobilized Tm1350 (70 °C and pH 7.5). Analysis of thermal and pH stability showed that spore surface-displayed Tm1350 retained 81 or 70 % of its original activity after 8 h of incubation at pH 8 or pH 9 (70 °C), which were 18 % higher than the retained activity of the non-immobilized Tm1350 under the same conditions. Meanwhile, recycling experiments showed that the recombinant spores could be used for up to three reaction cycles without a significant decrease in the catalytic rate (84 %). These results suggested that enzyme display on the surface of the B. subtilis spore could serve as an effective approach for enzyme immobilization, which has potential applications in the harsh biochemical industry. PMID:26026992

  15. Crystallization and preliminary X-ray analysis of the periplasmic domain of FliP, an integral membrane component of the bacterial flagellar type III protein-export apparatus.

    PubMed

    Fukumura, Takuma; Furukawa, Yukio; Kawaguchi, Tatsuya; Saijo-Hamano, Yumiko; Namba, Keiichi; Imada, Katsumi; Minamino, Tohru

    2014-09-01

    The bacterial flagellar proteins are transported via a specific export apparatus to the distal end of the growing structure for their self-assembly. FliP is an essential membrane component of the export apparatus. FliP has an N-terminal signal peptide and is predicted to have four transmembrane (TM) helices and a periplasmic domain (FliPP) between TM-2 and TM-3. In this study, FliPP from Thermotoga maritima (TmFliPP) and its selenomethionine derivative (SeMet-TmFliPP) were purified and crystallized. TmFliPP formed a homotetramer in solution. Crystals of TmFliPP and SeMet-TmFliPP were obtained by the hanging-drop vapour-diffusion technique with 2-methyl-2,4-pentanediol as a precipitant. These two crystals grew in the hexagonal space group P6222 or P6422, with unit-cell parameters a = b = 114.9, c = 193.8?Å. X-ray diffraction data were collected from crystals of TmFliPP and SeMet-TmFliPP to 2.4 and 2.8?Å resolution, respectively. PMID:25195894

  16. The two domains of Mycobacterium tuberculosis NusG protein are dynamically independent.

    PubMed

    Strauß, Martin; Schweimer, Kristian; Burmann, Björn M; Richter, Anne; Güttler, Stephanie; Wöhrl, Birgitta M; Rösch, Paul

    2016-02-01

    Transcription elongation factor NusG from Escherichia coli couples transcription and translation. It is the only conserved transcription factor in all three kingdoms of life, playing a variety of roles in gene expression. E. coli NusG consists of two non-interacting domains. While the N-terminal domain interacts with RNA polymerase, the C-terminal domain contacts NusE (S10), or the Rho transcription termination factor. The two corresponding domains of Thermotoga maritima NusG are mutually interacting. Therefore, NusG here forms an autoinhibited state, where the binding sites to RNAP, NusE, and the Rho factor are masked. Recent functional studies showed differences between NusG from E. coli and Mycobacterium tuberculosis. In contrast to E. coli NusG, M. tuberculosis NusG is able to stimulate intrinsic termination, but is not able to bind the Rho factor. To analyze whether this has structural reasons, we determined the solution structure of the carboxyterminal domain of M. tuberculosis NusG by nuclear magnetic resonance spectroscopy. Furthermore, we modeled the wild-type full-length protein, and present evidence that the two domains of this protein do not interact in solution by NMR dynamics measurements. PMID:25931133

  17. 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.

  18. Binding and inhibition of human spermidine synthase by decarboxylated S-adenosylhomocysteine

    SciTech Connect

    ?e; #269; kut; #279; , Jolita; McCloskey, Diane E.; Thomas, H. Jeanette; Secrist III, John A.; Pegg, Anthony E.; Ealick, Steven E.

    2011-11-17

    Aminopropyltransferases are essential enzymes that form polyamines in eukaryotic and most prokaryotic cells. Spermidine synthase (SpdS) is one of the most well-studied enzymes in this biosynthetic pathway. The enzyme uses decarboxylated S-adenosylmethionine and a short-chain polyamine (putrescine) to make a medium-chain polyamine (spermidine) and 5'-deoxy-5'-methylthioadenosine as a byproduct. Here, we report a new spermidine synthase inhibitor, decarboxylated S-adenosylhomocysteine (dcSAH). The inhibitor was synthesized, and dose-dependent inhibition of human, Thermatoga maritima, and Plasmodium falciparum spermidine synthases, as well as functionally homologous human spermine synthase, was determined. The human SpdS/dcSAH complex structure was determined by X-ray crystallography at 2.0 {angstrom} resolution and showed consistent active site positioning and coordination with previously known structures. Isothermal calorimetry binding assays confirmed inhibitor binding to human SpdS with K{sub d} of 1.1 {+-} 0.3 {mu}M in the absence of putrescine and 3.2 {+-} 0.1 {mu}M in the presence of putrescine. These results indicate a potential for further inhibitor development based on the dcSAH scaffold.

  19. The crystal structure of spermidine synthase with a multisubstrate adduct inhibitor.

    SciTech Connect

    Korolev, S.; Ikeguchi, Y.; Skarina, T.; Beasley, S.; Arrowsmith, C.; Edwards, A.; Joachimiak, A.; Pegg, A. E.; Savchenko, A.; Pennsylvania State Univ. Coll. of Medicine; Milton S. Hershey Medical Center; Banting and Best Department of Medical Research; Univ. of Health Network

    2002-01-01

    Polyamines are essential in all branches of life. Spermidine synthase (putrescine aminopropyltransferase, PAPT) catalyzes the biosynthesis of spermidine, a ubiquitous polyamine. The crystal structure of the PAPT from Thermotoga maritima (TmPAPT) has been solved to 1.5 Angstroms resolution in the presence and absence of AdoDATO (S-adenosyl-1,8-diamino-3-thiooctane), a compound containing both substrate and product moieties. This, the first structure of an aminopropyltransferase, reveals deep cavities for binding substrate and cofactor, and a loop that envelops the active site. The AdoDATO binding site is lined with residues conserved in PAPT enzymes from bacteria to humans, suggesting a universal catalytic mechanism. Other conserved residues act sterically to provide a structural basis for polyamine specificity. The enzyme is tetrameric; each monomer consists of a C-terminal domain with a Rossmann-like fold and an N-terminal {beta}-stranded domain. The tetramer is assembled using a novel barrel-type oligomerization motif.

  20. The Structure of a Soluble Chemoreceptor Suggests a Mechanism for Propagating Conformational Signals

    SciTech Connect

    Pollard, Abiola M.; Bilwes, Alexandrine M.; Crane, Brian R.; Cornell

    2009-09-02

    Transmembrane chemoreceptors, also known as methyl-accepting chemotaxis proteins (MCPs), translate extracellular signals into intracellular responses in the bacterial chemotaxis system. MCP ligand binding domains control the activity of the CheA kinase, situated {approx}200 {angstrom} away, across the cytoplasmic membrane. The 2.17 {angstrom} resolution crystal structure of a Thermotoga maritima soluble receptor (Tm14) reveals distortions in its dimeric four-helix bundle that provide insight into the conformational states available to MCPs for propagating signals. A bulge in one helix generates asymmetry between subunits that displaces the kinase-interacting tip, which resides more than 100 {angstrom} away. The maximum bundle distortion maps to the adaptation region of transmembrane MCPs where reversible methylation of acidic residues tunes receptor activity. Minor alterations in coiled-coil packing geometry translate the bulge distortion to a >25 {angstrom} movement of the tip relative to the bundle stalks. The Tm14 structure discloses how alterations in local helical structure, which could be induced by changes in methylation state and/or by conformational signals from membrane proximal regions, can reposition a remote domain that interacts with the CheA kinase.

  1. Reconstruction of the Chemotaxis Receptor-Kinase Assembly

    SciTech Connect

    Park,S.; Borbat, P.; Gonzalez-Bonet, G.; Bhatnagar, J.; Pollard, A.; Freed, J.; Bilwes, A.; Crane, B.

    2006-01-01

    In bacterial chemotaxis, an assembly of transmembrane receptors, the CheA histidine kinase and the adaptor protein CheW processes environmental stimuli to regulate motility. The structure of a Thermotoga maritima receptor cytoplasmic domain defines CheA interaction regions and metal ion-coordinating charge centers that undergo chemical modification to tune receptor response. Dimeric CheA-CheW, defined by crystallography and pulsed ESR, positions two CheWs to form a cleft that is lined with residues important for receptor interactions and sized to clamp one receptor dimer. CheW residues involved in kinase activation map to interfaces that orient the CheW clamps. CheA regulatory domains associate in crystals through conserved hydrophobic surfaces. Such CheA self-contacts align the CheW receptor clamps for binding receptor tips. Linking layers of ternary complexes with close-packed receptors generates a lattice with reasonable component ratios, cooperative interactions among receptors and accessible sites for modification enzymes.

  2. A ConA-like lectin from Dioclea guianensis Benth. has antifungal activity against Colletotrichum gloeosporioides, unlike its homologues, ConM and ConA.

    PubMed

    Araújo-Filho, José H; Vasconcelos, Ilka M; Martins-Miranda, Aparecida S; Gondim, Darcy M F; Oliveira, José T A

    2010-04-14

    This study reports on the antifungal activity of Dgui, a ConA-like lectin from Dioclea guianensis seeds. Dgui inhibited conidial germination but not mycelial growth of Colletotrichum gloeosporioides. The lectins ConA and ConM from Canavalia ensiformis and Canavalia maritima, respectively, share high levels of amino acid sequence similarity (>84%) with Dgui and have the same specificity toward glucose/mannose but had no effect on the fungus. Fluorescence microscopy showed that both Dgui and ConM bind to C. gloeosporioides ungerminated conidia. However, Dgui did not bind to C. gloeosporioides germinated conidia and germ tubes and was not inhibitory to mycelial growth. Because only Dgui inhibited germination of the fungus, C. gloeosporioides conidia might have surface-specific germination targets recognized by Dgui but not by its homologues, ConM and ConA. Therefore, Dgui is a candidate for biotechnological approaches for improving the resistance of various nutritionally and commercially important crops that are affected by C. gloeosporioides. PMID:20201549

  3. Rapid refinement of crystallographic protein construct definition employing enhanced hydrogen/deuterium exchange MS.

    PubMed

    Pantazatos, Dennis; Kim, Jack S; Klock, Heath E; Stevens, Raymond C; Wilson, Ian A; Lesley, Scott A; Woods, Virgil L

    2004-01-20

    Crystallographic efforts often fail to produce suitably diffracting protein crystals. Unstructured regions of proteins play an important role in this problem and considerable advantage can be gained in removing them. We have developed a number of enhancements to amide hydrogen/high-throughput and high-resolution deuterium exchange MS (DXMS) technology that allow rapid identification of unstructured regions in proteins. To demonstrate the utility of this approach for improving crystallization success, DXMS analysis was attempted on 24 Thermotoga maritima proteins with varying crystallization and diffraction characteristics. Data acquisition and analysis for 21 of these proteins was completed in 2 weeks and resulted in the localization and prediction of several unstructured regions within the proteins. When compared with those targets of known structure, the DXMS method correctly localized even small regions of disorder. DXMS analysis was then correlated with the propensity of such targets to crystallize and was further used to define truncations that improved crystallization. Truncations that were defined solely on DXMS analysis demonstrated greatly improved crystallization and have been used for structure determination. This approach represents a rapid and generalized method that can be applied to structural genomics or other targets in a high-throughput manner. PMID:14715906

  4. Recognition of the Helical Structure of β-1,4-Galactan by a New Family of Carbohydrate-binding Modules*

    PubMed Central

    Cid, Melissa; Pedersen, Henriette Lodberg; Kaneko, Satoshi; Coutinho, Pedro M.; Henrissat, Bernard; Willats, William G. T.; Boraston, Alisdair B.

    2010-01-01

    The microbial enzymes that depolymerize plant cell wall polysaccharides, ultimately promoting energy liberation and carbon recycling, are typically complex in their modularity and often contain carbohydrate-binding modules (CBMs). Here, through analysis of an unknown module from a Thermotoga maritima endo-β-1,4-galactanase, we identify a new family of CBMs that are most frequently found appended to proteins with β-1,4-galactanase activity. Polysaccharide microarray screening, immunofluorescence microscopy, and biochemical analysis of the isolated module demonstrate the specificity of the module, here called TmCBM61, for β-1,4-linked galactose-containing ligands, making it the founding member of family CBM61. The ultra-high resolution x-ray crystal structures of TmCBM61 (0.95 and 1.4 Å resolution) in complex with β-1,4-galactotriose reveal the molecular basis of the specificity of the CBM for β-1,4-galactan. Analysis of these structures provides insight into the recognition of an unexpected helical galactan conformation through a mode of binding that resembles the recognition of starch. PMID:20826814

  5. Transcriptional Regulation of Central Carbon and Energy Metabolism in Bacteria by Redox-Responsive Repressor Rex

    PubMed Central

    Ravcheev, Dmitry A.; Li, Xiaoqing; Latif, Haythem; Zengler, Karsten; Leyn, Semen A.; Korostelev, Yuri D.; Kazakov, Alexey E.; Novichkov, Pavel S.; Osterman, Andrei L.

    2012-01-01

    Redox-sensing repressor Rex was previously implicated in the control of anaerobic respiration in response to the cellular NADH/NAD+ levels in Gram-positive bacteria. We utilized the comparative genomics approach to infer candidate Rex-binding DNA motifs and assess the Rex regulon content in 119 genomes from 11 taxonomic groups. Both DNA-binding and NAD-sensing domains are broadly conserved in Rex orthologs identified in the phyla Firmicutes, Thermotogales, Actinobacteria, Chloroflexi, Deinococcus-Thermus, and Proteobacteria. The identified DNA-binding motifs showed significant conservation in these species, with the only exception detected in Clostridia, where the Rex motif deviates in two positions from the generalized consensus, TTGTGAANNNNTTCACAA. Comparative analysis of candidate Rex sites revealed remarkable variations in functional repertoires of candidate Rex-regulated genes in various microorganisms. Most of the reconstructed regulatory interactions are lineage specific, suggesting frequent events of gain and loss of regulator binding sites in the evolution of Rex regulons. We identified more than 50 novel Rex-regulated operons encoding functions that are essential for resumption of the NADH:NAD+ balance. The novel functional role of Rex in the control of the central carbon metabolism and hydrogen production genes was validated by in vitro DNA binding assays using the TM0169 protein in the hydrogen-producing bacterium Thermotoga maritima. PMID:22210771

  6. Structure-Guided Discovery of New Deaminase Enzymes

    PubMed Central

    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.

    2013-01-01

    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 Sinosylhomocysteine (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 was 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

  7. Integration of an [FeFe]-hydrogenase into the anaerobic metabolism of Escherichia coli

    PubMed Central

    Kelly, Ciarán L.; Pinske, Constanze; Murphy, Bonnie J.; Parkin, Alison; Armstrong, Fraser; Palmer, Tracy; Sargent, Frank

    2015-01-01

    Biohydrogen is a potentially useful product of microbial energy metabolism. One approach to engineering biohydrogen production in bacteria is the production of non-native hydrogenase activity in a host cell, for example Escherichia coli. In some microbes, hydrogenase enzymes are linked directly to central metabolism via diaphorase enzymes that utilise NAD+/NADH cofactors. In this work, it was hypothesised that heterologous production of an NAD+/NADH-linked hydrogenase could connect hydrogen production in an E. coli host directly to its central metabolism. To test this, a synthetic operon was designed and characterised encoding an apparently NADH-dependent, hydrogen-evolving [FeFe]-hydrogenase from Caldanaerobacter subterranus. The synthetic operon was stably integrated into the E. coli chromosome and shown to produce an active hydrogenase, however no H2 production was observed. Subsequently, it was found that heterologous co-production of a pyruvate::ferredoxin oxidoreductase and ferredoxin from Thermotoga maritima was found to be essential to drive H2 production by this system. This work provides genetic evidence that the Ca.subterranus [FeFe]-hydrogenase could be operating in vivo as an electron-confurcating enzyme. PMID:26839796

  8. 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

  9. Fusion of a family 9 cellulose-binding module improves catalytic potential of Clostridium thermocellum cellodextrin phosphorylase on insoluble cellulose.

    PubMed

    Ye, Xinhao; Zhu, Zhiguang; Zhang, Chenming; Zhang, Y-H Percival

    2011-11-01

    Clostridium thermocellum cellodextrin phosphorylase (CtCDP), a single-module protein without an apparent carbohydrate-binding module, has reported activities on soluble cellodextrin with a degree of polymerization (DP) from two to five. In this study, CtCDP was first discovered to have weak activities on weakly water-soluble celloheptaose and insoluble regenerated amorphous cellulose (RAC). To enhance its activity on solid cellulosic materials, four cellulose binding modules, e.g., CBM3 (type A) from C. thermocellum CbhA, CBM4-2 (type B) from Rhodothermus marinus Xyn10A, CBM6 (type B) from Cellvibrio mixtus Cel5B, and CBM9-2 (type C) from Thermotoga maritima Xyn10A, were fused to the C terminus of CtCDP. Fusion of any selected CBM with CtCDP did not influence its kinetic parameters on cellobiose but affected the binding and catalytic properties on celloheptaose and RAC differently. Among them, addition of CBM9 to CtCDP resulted in a 2.7-fold increase of catalytic efficiency for degrading celloheptaose. CtCDP-CBM9 exhibited enhanced specific activities over 20% on the short-chain RAC (DP = 14) and more than 50% on the long-chain RAC (DP = 164). The chimeric protein CtCDP-CBM9 would be the first step to construct a cellulose phosphorylase for in vitro hydrogen production from cellulose by synthetic pathway biotransformation (SyPaB). PMID:21630044

  10. Improving small-angle X-ray scattering data for structural analyses of the RNA world.

    PubMed

    Rambo, Robert P; Tainer, John A

    2010-03-01

    Defining the shape, conformation, or assembly state of an RNA in solution often requires multiple investigative tools ranging from nucleotide analog interference mapping to X-ray crystallography. A key addition to this toolbox is small-angle X-ray scattering (SAXS). SAXS provides direct structural information regarding the size, shape, and flexibility of the particle in solution and has proven powerful for analyses of RNA structures with minimal requirements for sample concentration and volumes. In principle, SAXS can provide reliable data on small and large RNA molecules. In practice, SAXS investigations of RNA samples can show inconsistencies that suggest limitations in the SAXS experimental analyses or problems with the samples. Here, we show through investigations on the SAM-I riboswitch, the Group I intron P4-P6 domain, 30S ribosomal subunit from Sulfolobus solfataricus (30S), brome mosaic virus tRNA-like structure (BMV TLS), Thermotoga maritima asd lysine riboswitch, the recombinant tRNA(val), and yeast tRNA(phe) that many problems with SAXS experiments on RNA samples derive from heterogeneity of the folded RNA. Furthermore, we propose and test a general approach to reducing these sample limitations for accurate SAXS analyses of RNA. Together our method and results show that SAXS with synchrotron radiation has great potential to provide accurate RNA shapes, conformations, and assembly states in solution that inform RNA biological functions in fundamental ways. PMID:20106957

  11. The Structural Basis of Sirtuin Substrate Affinity

    SciTech Connect

    Cosgrove,M.; Bever, K.; Avalos, J.; Muhammad, S.; Zhang, X.; Wolberger, C.

    2006-01-01

    Sirtuins comprise a family of enzymes that catalyze the deacetylation of acetyllysine side chains in a reaction that consumes NAD+. Although several crystal structures of sirtuins bound to non-native acetyl peptides have been determined, relatively little about how sirtuins discriminate among different substrates is understood. We have carried out a systematic structural and thermodynamic analysis of several peptides bound to a single sirtuin, the Sir2 homologue from Thermatoga maritima (Sir2Tm). We report structures of five different forms of Sir2Tm: two forms bound to the p53 C-terminal tail in the acetylated and unacetylated states, two forms bound to putative acetyl peptide substrates derived from the structured domains of histones H3 and H4, and one form bound to polypropylene glycol (PPG), which resembles the apoenzyme. The structures reveal previously unobserved complementary side chain interactions between Sir2Tm and the first residue N-terminal to the acetyllysine (position -1) and the second residue C-terminal to the acetyllysine (position +2). Isothermal titration calorimetry was used to compare binding constants between wild-type and mutant forms of Sir2Tm and between additional acetyl peptide substrates with substitutions at positions -1 and +2. The results are consistent with a model in which peptide positions -1 and +2 play a significant role in sirtuin substrate binding. This model provides a framework for identifying sirtuin substrates.

  12. Castanea sativa Mill. leaves as new sources of natural antioxidant: an electronic spin resonance study.

    PubMed

    Calliste, Claude-Alain; Trouillas, Patrick; Allais, Daovy-Paulette; Duroux, Jean-Luc

    2005-01-26

    The antioxidant potential of Castanea sativa Mill. leaf (sweet chestnut) was explored as a new source of active extracts. The capacity of the different fractions issued from aqueous, methanol, and ethyl acetate extracts to inhibit the stable free radical 2,2-diphenyl-1-pycryl-hydrazyl, superoxide anion, and hydroxyl radical was measured by electronic spin resonance. Their scavenging potential was analyzed versus their amount of phenolic compounds. Among the active fractions, the most effective one was A6, an ethyl acetate fraction, which contained a high level of total phenolic compounds (29.1 g/100 g). Thus, a different extraction procedure was performed to concentrate the active compounds of A6 in the new C. sativa leaf extract (CSLE). Compared to reference antioxidants (quercetin and vitamin E) and standard extracts (Pycnogenol, from French Pinus maritima bark, and grape marc extract), it was observed that A6 and CSLE have high antioxidant potentials, equivalent to at least those of reference compounds. PMID:15656662

  13. Mapping of the SecA·SecY and SecA·SecG Interfaces by Site-directed in Vivo Photocross-linking

    PubMed Central

    Das, Sanchaita; Oliver, Donald B.

    2011-01-01

    The two major components of the Eubacteria Sec-dependent protein translocation system are the heterotrimeric channel-forming component SecYEG and its binding partner, the SecA ATPase nanomotor. Once bound to SecYEG, the preprotein substrate, and ATP, SecA undergoes ATP-hydrolytic cycles that drive the stepwise translocation of proteins. Although a previous site-directed in vivo photocross-linking study (Mori, H., and Ito, K. (2006) Proc. Natl. Acad. Sci. U.S.A. 103, 16159–16164) elucidated residues of SecY needed for interaction with SecA, no reciprocal study for SecA protein has been reported to date. In the present study we mapped residues of SecA that interact with SecY or SecG utilizing this approach. Our results show that distinct domains of SecA on two halves of the molecule interact with two corresponding SecY partners as well as with the central cytoplasmic domain of SecG. Our data support the in vivo relevance of the Thermotoga maritima SecA·SecYEG crystal structure that visualized SecYEG interaction for only one-half of SecA as well as previous studies indicating that SecA normally binds two molecules of SecYEG. PMID:21317284

  14. The structure of Aquifex aeolicus FtsH in the ADP-bound state reveals a C2-symmetric hexamer.

    PubMed

    Vostrukhina, Marina; Popov, Alexander; Brunstein, Elena; Lanz, Martin A; Baumgartner, Renato; Bieniossek, Christoph; Schacherl, Magdalena; Baumann, Ulrich

    2015-06-01

    The crystal structure of a truncated, soluble quadruple mutant of FtsH from Aquifex aeolicus comprising the AAA and protease domains has been determined at 2.96 Å resolution in space group I222. The protein crystallizes as a hexamer, with the protease domain forming layers in the ab plane. Contacts between these layers are mediated by the AAA domains. These are highly disordered in one crystal form, but are clearly visible in a related form with a shorter c axis. Here, adenosine diphosphate (ADP) is bound to each subunit and the AAA ring exhibits twofold symmetry. The arrangement is different from the ADP-bound state of an analogously truncated, soluble FtsH construct from Thermotoga maritima. The pore is completely closed and the phenylalanine residues in the pore line a contiguous path. The protease hexamer is very similar to those described for other FtsH structures. To resolve certain open issues regarding a conserved glycine in the linker between the AAA and protease domains, as well as the active-site switch ?-strand, mutations have been introduced in the full-length membrane-bound protein. Activity analysis of these point mutants reveals the crucial importance of these residues for proteolytic activity and is in accord with previous interpretation of the active-site switch and the importance of the linker glycine residue. PMID:26057670

  15. Novel α-L-Fucosidases from a Soil Metagenome for Production of Fucosylated Human Milk Oligosaccharides.

    PubMed

    Lezyk, Mateusz; Jers, Carsten; Kjaerulff, Louise; Gotfredsen, Charlotte H; Mikkelsen, Maria D; Mikkelsen, Jørn D

    2016-01-01

    This paper describes the discovery of novel α-L-fucosidases and evaluation of their potential to catalyse the transglycosylation reaction leading to production of fucosylated human milk oligosaccharides. Seven novel α-L-fucosidase-encoding genes were identified by functional screening of a soil-derived metagenome library and expressed in E. coli as recombinant 6xHis-tagged proteins. All seven fucosidases belong to glycosyl hydrolase family 29 (GH 29). Six of the seven α-L-fucosidases were substrate-inhibited, moderately thermostable and most hydrolytically active in the pH range 6-7, when tested with para-nitrophenyl-α-L-fucopyranoside (pNP-Fuc) as the substrate. In contrast, one fucosidase (Mfuc6) exhibited a high pH optimum and an unusual sigmoidal kinetics towards pNP-Fuc substrate. When tested for trans-fucosylation activity using pNP-Fuc as donor, most of the enzymes were able to transfer fucose to pNP-Fuc (self-condensation) or to lactose. With the α-L-fucosidase from Thermotoga maritima and the metagenome-derived Mfuc5, different fucosyllactose variants including the principal fucosylated HMO 2'-fucosyllactose were synthesised in yields of up to ~6.4%. Mfuc5 was able to release fucose from xyloglucan and could also use it as a fucosyl-donor for synthesis of fucosyllactose. This is the first study describing the use of glycosyl hydrolases for the synthesis of genuine fucosylated human milk oligosaccharides. PMID:26800369

  16. Ecological correlates of variable organ sizes and fat loads in the most northerly-wintering shorebirds

    USGS Publications Warehouse

    Ruthrauff, Daniel R.; Dekinga, Anne; Gill, R.E., Jr.; Summers, R.W.; Piersma, Theunis

    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.

  17. Structural basis of ConM binding with resveratrol, an anti-inflammatory and antioxidant polyphenol.

    PubMed

    Rocha, Bruno A M; Teixeira, Claudener S; Silva-Filho, José C; Nóbrega, Raphael B; Alencar, Daniel B; Nascimento, Kyria S; Freire, Valder N; Gottfried, Carmem J S; Nagano, Celso S; Sampaio, Alexandre H; Saker-Sampaio, Silvana; Cavada, Benildo S; Delatorre, Plínio

    2015-01-01

    Resveratrol can also inhibit the activation of proinflammatory mediators and cytokines at the early gene expression stage. It is well known that lectins are sugar-binding proteins that act as both pro- and anti-inflammatory molecules. Thus, the objective of this work was to verify the binding of a polyphenol compound with a lectin of Canavalia maritima (ConM) based on their ability to inhibit pro-inflammatory processes. To accomplish this, ConM was purified and crystallized, and resveratrol was soaked at 5mM for 2h of incubation. The crystal belongs to the monoclinic space group C2, the final refinement resulted in an Rfactor of 16.0% and an Rfree of 25.5%. Resveratrol binds in the rigid ?-sheet through H-bonds and hydrophobic interaction with amino acids that compose the fifth and sixth ?-strands of the rigid ?-sheet of ConM. The ConM and resveratrol inhibited DPPH oxidation, showing synergic activity with the most effective ratio of 2:3 and carbohydrate binding site is not directly related to antioxidant activity. It is the interaction between ConM and resveratrol that indicates the synergism of these two molecules in acting as free radicals scavengers and in reducing the inflammatory process through the inhibition of many pro-inflammatory events. PMID:25192853

  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. 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

  20. Mercury in sediments and vegetation in a moderately contaminated salt marsh (Tagus Estuary, Portugal).

    PubMed

    Canário, João; Vale, Carlos; Poissant, Laurier; Nogueira, Marta; Pilote, Martin; Branco, Vasco

    2010-01-01

    Depth variations of total mercury (Hg) and methylmercury (MeHg) concentrations were studied in cores from non-colonized sediments, sediments colonized by Halimione portulacoides, Sarcocorniafruticosa and Spartina maritima and belowground biomass, in a moderately contaminated salt marsh (Tagus Estuary, Portugal). Concentrations in belowground biomass exceeded up to 3 (Hg) and 15 (MeHg) times the levels in sediments, and up to 198 (Hg) and 308 (MeHg) times those found in aboveground parts. Methylmercury in colonized sediments reached 3% of the total Hg, 50 times above the maximum values found in non-colonized sediments. The absence of correlations between total Hg concentrations in sediments and the corresponding MeHg levels suggested that methylation was only dependent on the environmental and microbiological factors. The analysis of belowground biomass at high-depth resolution (2 cm) provided evidence that Hg and MeHg were actively absorbed from sediments, with higher enrichment factors at layers where higher microbial activity was probably occurring. The results obtained in this study indicated that the biotransformation of Hg to the toxic MeHg could increase the toxicity of plant-colonized sediments. PMID:21179951

  1. Evidence for extensive gene flow and Thermotoga subpopulations in subsurface and marine environments.

    PubMed

    Nesbø, Camilla L; S Swithers, Kristen; Dahle, Håkon; Haverkamp, Thomas H A; Birkeland, Nils-Kåre; Sokolova, Tatiana; Kublanov, Ilya; Zhaxybayeva, Olga

    2015-07-01

    Oil reservoirs represent a nutrient-rich ecological niche of the deep biosphere. Although most oil reservoirs are occupied by microbial populations, when and how the microbes colonized these environments remains unanswered. To address this question, we compared 11 genomes of Thermotoga maritima-like hyperthermophilic bacteria from two environment types: subsurface oil reservoirs in the North Sea and Japan, and marine sites located in the Kuril Islands, Italy and the Azores. We complemented our genomes with Thermotoga DNA from publicly available subsurface metagenomes from North America and Australia. Our analysis revealed complex non-bifurcating evolutionary history of the isolates' genomes, suggesting high amounts of gene flow across all sampled locations, a conjecture supported by numerous recombination events. Genomes from the same type of environment tend to be more similar, and have exchanged more genes with each other than with geographically close isolates from different types of environments. Hence, Thermotoga populations of oil reservoirs do not appear isolated, a requirement of the 'burial and isolation' hypothesis, under which reservoir bacteria are descendants of the isolated communities buried with sediments that over time became oil reservoirs. Instead, our analysis supports a more complex view, where bacteria from subsurface and marine populations have been continuously migrating into the oil reservoirs and influencing their genetic composition. The Thermotoga spp. in the oil reservoirs in the North Sea and Japan probably entered the reservoirs shortly after they were formed. An Australian oil reservoir, on the other hand, was likely colonized very recently, perhaps during human reservoir development. PMID:25500512

  2. 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

  3. Functional characterization of two M42 aminopeptidases erroneously annotated as cellulases.

    PubMed

    Dutoit, Raphaël; Brandt, Nathalie; Legrain, Christianne; Bauvois, Cédric

    2012-01-01

    Several aminopeptidases of the M42 family have been described as tetrahedral-shaped dodecameric (TET) aminopeptidases. A current hypothesis suggests that these enzymes are involved, along with the tricorn peptidase, in degrading peptides produced by the proteasome. Yet the M42 family remains ill defined, as some members have been annotated as cellulases because of their homology with CelM, formerly described as an endoglucanase of Clostridium thermocellum. Here we describe the catalytic functions and substrate profiles CelM and of TmPep1050, the latter having been annotated as an endoglucanase of Thermotoga maritima. Both enzymes were shown to catalyze hydrolysis of nonpolar aliphatic L-amino acid-pNA substrates, the L-leucine derivative appearing as the best substrate. No significant endoglucanase activity was measured, either for TmPep1050 or CelM. Addition of cobalt ions enhanced the activity of both enzymes significantly, while both the chelating agent EDTA and bestatin, a specific inhibitor of metalloaminopeptidases, proved inhibitory. Our results strongly suggest that one should avoid annotating members of the M42 aminopeptidase family as cellulases. In an updated assessment of the distribution of M42 aminopeptidases, we found TET aminopeptidases to be distributed widely amongst archaea and bacteria. We additionally observed that several phyla lack both TET and tricorn. This suggests that other complexes may act downstream from the proteasome. PMID:23226342

  4. A model for the effect of submerged aquatic vegetation on turbulence induced by an oscillating grid

    NASA Astrophysics Data System (ADS)

    Pujol, Dolors; Colomer, Jordi; Serra, Teresa; Casamitjana, Xavier

    2012-12-01

    The aim of this study is to model, under controlled laboratory conditions, the effect of submerged aquatic vegetation (SAV) on turbulence generated in a water column by an oscillating grid turbulence (OGT). Velocity profiles have been measured by an acoustic Doppler velocimeter (MicroADV). Experimental conditions are analysed in two canopy models (rigid and semi-rigid), using nine plant-to-plant distances (ppd), three stem diameters (d), four types of natural SAV (Cladium mariscus, Potamogeton nodosus, Myriophyllum verticillatum and Ruppia maritima) and two oscillation grid frequencies (f). To quantify this response, we have developed a non-dimensional model, with a specific turbulent kinetic energy (TKE), f, stroke (s), d, ppd, distance from the virtual origin to the measurement (zm) and space between grid bars (M). The experimental data show that, at zm/zc < 1 the turbulent kinetic energy decays with zm, according to the well-known power law, zm-2, and does not depend on the vegetation characteristics. In contrast, at zm/zc > 1, TKE decreases faster with zm and scales to the model variables according to TKE/(f·s)?(·(. Therefore, at zm/zc > 1 the TKE is affected by the geometric characteristics of the plants (both diameter and plant-to-plant distance), an effect called sheltering. Results from semi-rigid canopies and natural SAV are found to scale with the non-dimensional model proposed for rigid canopies. We also discuss the practical implications for field conditions (wind and natural SAV).

  5. Paleobiology of the Sand Beneath the Valders Diamicton at Valders, Wisconsin

    USGS Publications Warehouse

    Maher, L.J., Jr.; Miller, N.G.; Baker, R.G.; Curry, B. Brandon; Mickelson, D.M.

    1998-01-01

    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 Picea and Artemisia, but the low percentages of many other types of longdistance 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 alpinum type, Silene acaulis, Sibbaldia procumbens, Dryas integrifolia, Vaccinium uliginosum var. 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. ?? 1998 University of Washington.

  6. 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.

  7. Structure of the Entire Cytoplasmic Portion of a Sensor Histidine-kinase Protein

    SciTech Connect

    Marina,A.; Waldburger, C.; Hendrickson, W.

    2005-01-01

    The large majority of histidine kinases (HKs) are multifunctional enzymes having autokinase, phosphotransfer and phosphatase activities, and most of these are transmembrane sensor proteins. Sensor HKs possess conserved cytoplasmic phosphorylation and ATP-binding kinase domains. The different enzymatic activities require participation by one or both of these domains, implying the need for different conformational states. The catalytic domains are linked to the membrane through a coiled-coil segment that sometimes includes other domains. We describe here the first crystal structure of the complete cytoplasmic region of a sensor HK, one from the thermophile Thermotoga maritima in complex with ADP{beta}N at 1.9 Angstrom resolution. The structure reveals previously unidentified functions for several conserved residues and reveals the relative disposition of domains in a state seemingly poised for phosphotransfer. The structure thereby inspires hypotheses for the mechanisms of autophosphorylation, phosphotransfer and response-regulator dephosphorylation, and for signal transduction through the coiled-coil segment. Mutational tests support the functional relevance of interdomain contacts.

  8. 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

  9. Metal speciation in salt marsh sediments: Influence of halophyte vegetation in salt marshes with different morphology

    NASA Astrophysics Data System (ADS)

    Pedro, Sílvia; Duarte, Bernardo; Raposo de Almeida, Pedro; Caçador, Isabel

    2015-12-01

    Salt marshes provide environmental conditions that are known to affect metal speciation in sediments. The elevational gradient along the marsh and consequent differential flooding are some of the major factors influencing halophytic species distribution and coverage due to their differential tolerance to salinity and submersion. Different species, in turn, also have distinct influences on the sediment's metal speciation, and its metal accumulation abilities. The present work aimed to evaluate how different halophyte species in two different salt marshes could influence metal partitioning in the sediment at root depth and how that could differ from bare sediments. Metal speciation in sediments around the roots (rhizosediments) of Halimione portulacoides, Sarcocornia fruticosa and Spartina maritima was determined by sequentially extracting operationally defined fractions with solutions of increasing strength and acidity. Rosário salt marsh generally showed higher concentrations of all metals in the rhizosediments. Metal partitioning was primarily related to the type of metal, with the elements' chemistry overriding the environment's influence on fractionation schemes. The most mobile elements were Cd and Zn, with greater availability being found in non-vegetated sediments. Immobilization in rhizosediments was predominantly influenced by the presence of Fe and Mn oxides, as well as organic complexes. In the more mature of both salt marshes, the differences between vegetated and non-vegetated sediments were more evident regarding S. fruticosa, while in the younger system all halophytes presented significantly different metal partitioning when compared to that of mudflats.

  10. 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.

  11. The effect of nitrogen loading on a brackish estuarine faunal community: A stable isotope approach

    USGS Publications Warehouse

    Keats, R.A.; Osher, L.J.; Neckles, H.A.

    2004-01-01

    Coastal ecosystems worldwide face increased nutrient enrichment from shoreline and watershed development and atmospheric pollution. We investigated the response of the faunal community of a small microtidal estuary dominated by Ruppia maritima (widgeon grass) in Maine, United States, to increased nitrogen loading using an in situ mesocosm enrichment experiment. Community response was characterized by assessing quantitative shifts in macroin-vertebrate community composition and identifying changes in food web structure using stable carbon and nitrogen isotope ratios of producers and consumers. The community was dominated by brackish water invertebrates including midge larvae, oligochaetes, damselfly larvae, amphipods, and ostracods. Experimental nutrient additions resulted in significantly lower densities of herbivorous chironomids and predatory damselflies and greater densities of deposit feeding oligochaetes. Grazing midge larvae (Chironomidae: Dicrotendipes, Cricotopus) consumed epiphytic algae under both natural and enriched conditions. Deposit feeding Chironomus was dependent on allochthonous sources of detritus under natural conditions and exhibited a shift to autochthonous sources of detritus under enriched conditions. Predatory Enallagma primarily consumed grazing chironomids under all but the highest loading conditions. Experimental nutrient loading resulted in an increase in generalist deposit feeders dependent on autochthonous sources of detritus.

  12. Determination of 5-methylcytosine from plant DNA by high-performance liquid chromatography.

    PubMed

    Wagner, I; Capesius, I

    1981-06-26

    The relative amounts of the five nucleosides (deoxycytidine, 5-methyldeoxycytidine, deoxyadenosine, deoxyguanosine and thymidine) in the DNA of nine plant species, one plant satellite DNA, and one animal species were determined by high performance liquid chromatography. The method allows the clean separation of the nucleosides from 10 microgram samples with 15 min. The following values for the proportion of methylated cytosines among all cytosines were obtained: Lobularia maritima 18.5%, Nicotiana tabacum 32.6%, Pisum sativum 23.2%, Rhinanthus minor 29.2%, Sinapsis alba 12.2%, Vicia faba 30.5%, Viscum album 23.2%, Cymbidium pumilum 18.8%, Cymbidium pumilum AT-rich satellite DNA 15.8%, Triticum aestivum 22.4%. DNA of an animal, the gerbil, Meriones unguiculatus, had a methylation percentage of 3.1%. An estimate of the GC content based on the buoyant density of DNA tends to be lower than the actual value, an estimate based on the melting temperature tends to be higher. This supports the finding by other authors that DNA methylation decreases the buoyant density and may increase the melting temperature at high m5C concentration. PMID:7272310

  13. Antioxidant Potential of Bark Extracts from Boreal Forest Conifers.

    PubMed

    Legault, Jean; Girard-Lalancette, Karl; Dufour, Dominic; Pichette, André

    2013-01-01

    The bark of boreal forest conifers has been traditionally used by Native Americans to treat various ailments and diseases. Some of these diseases involve reactive oxygen species (ROS) that can be prevented by the consumption of antioxidants such as phenolic compounds that can be found in medicinal plants. In this study, ultrasonic assisted extraction has been performed under various solvent conditions (water:ethanol mixtures) on the bark of seven boreal forest conifers used by Native Americans including: Pinus strobus, Pinus resinosa, Pinus banksiana, Picea mariana, Picea glauca, Larix laricina, and Abies balsamea. The total phenolic content, as well as ORACFL potency and cellular antioxidant activity (IC50), were evaluated for all bark extracts, and compared with the standardized water extract of Pinus maritima bark (Pycnogenol), which showed clinical efficiency to prevent ROS deleterious effects. The best overall phenolic extraction yield and antioxidant potential was obtained with Picea glauca and Picea mariana. Interestingly, total phenolic content of these bark extracts was similar to Pycnogenol but their antioxidant activity were higher. Moreover, most of the extracts did not inhibit the growth of human skin fibroblasts, WS1. A significant correlation was found between the total phenolic content and the antioxidant activity for water extracts suggesting that these compounds are involved in the activity. PMID:26784337

  14. CheY’s acetylation sites responsible for generating clockwise flagellar rotation in Escherichia coli

    PubMed Central

    Fraiberg, Milana; Afanzar, Oshri; Cassidy, C. Keith; Gabashvili, Alexandra; Schulten, Klaus; Levin, Yishai; Eisenbach, Michael

    2015-01-01

    Summary Stimulation of Escherichia coli with acetate elevates the acetylation level of the chemotaxis response regulator CheY. This elevation, in an unknown mechanism, activates CheY to generate clockwise rotation. Here, using quantitative selective reaction monitoring mass spectrometry and high-resolution targeted mass spectrometry, we identified K91 and K109 as the major sites whose acetylation level in vivo increases in response to acetate. Employing single and multiple lysine replacements in CheY, we found that K91 and K109 are also the sites mainly responsible for acetate-dependent clockwise generation. Furthermore, we showed that clockwise rotation is repressed when residue K91 is non-modified, as evidenced by an increased ability of CheY to generate clockwise rotation when K91 was acetylated or replaced by specific amino acids. Using molecular dynamics simulations we show that K91 repression is manifested in the conformational dynamics of the ?4?4 loop, shifted towards an active state upon mutation. Removal of ?4?4 loop repression may represent a general activation mechanism in CheY, pertaining also to the canonical phosphorylation activation pathway as suggested by crystal structures of active and inactive CheY from Thermotoga maritima. By way of elimination we further suggest that K109 acetylation is actively involved in generating clockwise rotation. PMID:25388160

  15. Transportable data from non-target arthropod field studies for the environmental risk assessment of genetically modified maize expressing an insecticidal double-stranded RNA.

    PubMed

    Ahmad, Aqeel; Negri, Ignacio; Oliveira, Wladecir; Brown, Christopher; Asiimwe, Peter; Sammons, Bernard; Horak, Michael; Jiang, Changjian; Carson, David

    2016-02-01

    As part of an environmental risk assessment, the potential impact of genetically modified (GM) maize MON 87411 on non-target arthropods (NTAs) was evaluated in the field. MON 87411 confers resistance to corn rootworm (CRW; Diabrotica spp.) by expressing an insecticidal double-stranded RNA (dsRNA) transcript and the Cry3Bb1 protein and tolerance to the herbicide glyphosate by producing the CP4 EPSPS protein. Field trials were conducted at 14 sites providing high geographic and environmental diversity within maize production areas from three geographic regions including the U.S., Argentina, and Brazil. MON 87411, the conventional control, and four commercial conventional reference hybrids were evaluated for NTA abundance and damage. Twenty arthropod taxa met minimum abundance criteria for valid statistical analysis. Nine of these taxa occurred in at least two of the three regions and in at least four sites across regions. These nine taxa included: aphid, predatory earwig, lacewing, ladybird beetle, leafhopper, minute pirate bug, parasitic wasp, sap beetle, and spider. In addition to wide regional distribution, these taxa encompass the ecological functions of herbivores, predators and parasitoids in maize agro-ecosystems. Thus, the nine arthropods may serve as representative taxa of maize agro-ecosystems, and thereby support that analysis of relevant data generated in one region can be transportable for the risk assessment of the same or similar GM crop products in another region. Across the 20 taxa analyzed, no statistically significant differences in abundance were detected between MON 87411 and the conventional control for 123 of the 128 individual-site comparisons (96.1 %). For the nine widely distributed taxa, no statistically significant differences in abundance were detected between MON 87411 and the conventional control. Furthermore, no statistically significant differences were detected between MON 87411 and the conventional control for 53 out of 56 individual-site comparisons (94.6 %) of NTA pest damage to the crop. In each case where a significant difference was observed in arthropod abundance or damage, the mean value for MON 87411 was within the reference range and/or the difference was not consistently observed across collection methods and/or sites. Thus, the differences were not representative of an adverse effect unfamiliar to maize and/or were not indicative of a consistent plant response associated with the GM traits. Results from this study support a conclusion of no adverse environmental impact of MON 87411 on NTAs compared to conventional maize and demonstrate the utility of relevant transportable data across regions for the ERA of GM crops. PMID:26433587

  16. Simulating the Spatial Distribution of Hydrological Connectivity Under Possible Future Climates - Impacts on River Flow Dynamics and Non-Point Source Pollution

    NASA Astrophysics Data System (ADS)

    Reaney, S. M.; Lane, S. N.; Heathwaite, L.

    2009-12-01

    Predicted changes to the climate have the potential to alter the hydrological dynamics of catchments in response to new rainfall and temperate patterns. Primary effect will be on soil moisture and river flow. However, an important secondary effect will be on hydrological connectivity within the landscape. This factor is important since the locations of critical source zones for non-point source pollution are determined by the pollutant source risk pattern and the structure of the surface hydrological connectivity. The surface hydrological connectivity is determined by the topography and the temporal structure of the rainfall, which is predicted to alter under climatic change. Using spatial connectivity statistics and a hydrological model, the potential for changes has been investigated. The hydrological simulations were performed using CRUM3, a fully distributed, physically based, model with a grid spatial structure. The simulated catchment hydrological connectivity was based on the Network Index, which describes the propensity for each point in the landscape to connect to the receiving waters. From the Network Index, two connectivity indices were calculated: 1 the percentage of time that a point is connected to the receiving waters; and 2 the average number of connection - disconnection cycles per year. The percentage of time that a point is connected for give information of the potential for the export of non-source limited pollutants, such as fine sediment. The number of connection-disconnection cycles is important for pollutants that require aerobic conditions to accumulate and saturated conditions to be exported, such as nitrate. Simulations were performed for a baseline period (1961 - 1990) and a climate change period (2071-2100) based on the medium-high emissions scenario from UKCIP02. The climate predictions were downscaled using the EARWIG weather generator. To gain insight into the uncertainty associated with the predictions, four realisations from the stochastic weather generator and four model parameter sets were used giving 16 simulations of 30 years per time period. The simulation results show that 1, there may be significant changes in the size of the areas that will readily connect to receiving waters; 2, the duration of connection will increase; and 3, the number of connection - disconnection cycles will increase. These changes have the potential both the hydrological dynamics of the catchment and the sources and export of non-point source pollutants. Due to the non-linear relationship between catchment runoff and connectivity, there is the potential for increased high flows. The predicted changes to the surface flow connectivity have the potential to alter the location of critical sources areas for non-point source pollution and the distribution of pollution of non-point sources across the year.

  17. Mother and offspring fitness in an insect with maternal care: phenotypic trade-offs between egg number, egg mass and egg care

    PubMed Central

    2014-01-01

    Background Oviparous females have three main options to increase their reproductive success: investing into egg number, egg mass and/or egg care. Although allocating resources to either of these three components is known to shape offspring number and size, potential trade-offs among them may have key impacts on maternal and offspring fitness. Here, we tested the occurrence of phenotypic trade-offs between egg number, egg mass and maternal expenditure on egg care in the European earwig, Forficula auricularia, an insect with pre- and post-hatching forms of maternal care. In particular, we used a series of laboratory observations and experiments to investigate whether these three components non-additively influenced offspring weight and number at hatching, and whether they were associated with potential costs to females in terms of future reproduction. Results We found negative associations between egg number and mass as well as between egg number and maternal expenditure on egg care. However, these trade-offs could only be detected after statistically correcting for female weight at egg laying. Hatchling number was not determined by single or additive effects among the three life-history traits, but instead by pairwise interactions among them. In particular, offspring number was positively associated with the number of eggs only in clutches receiving high maternal care or consisting of heavy eggs, and negatively associated with mean egg mass in clutches receiving low care. In contrast, offspring weight was positively associated with egg mass only. Finally, maternal expenditure on egg care reduced their future reproduction, but this effect was only detected when mothers were experimentally isolated from their offspring at egg hatching. Conclusions Overall, our study reveals simultaneous trade-offs between the number, mass and care of eggs. It also demonstrates that these factors interact in their impact on offspring production, and that maternal expenditure on egg care possibly shapes female future reproduction. These findings emphasize that studying reproductive success requires consideration of phenotypic trade-offs between egg-number, egg mass and egg care in oviparous species. PMID:24913927

  18. 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

  19. Masterplan to safeguard Venice and to restore the lagoon and conterminous areas

    NASA Astrophysics Data System (ADS)

    Bini, Claudio; Gallo, Alba; Nadimi-Goki, Mandana; Wahsha, Mohammad

    2015-04-01

    Venice and its lagoon constitute a complex system, well known all over the world for the peculiarity of the town and for the fragility of the lagoon ecosystem with its delicate equilibrium. The whole system has been, and is currently, affected by human activities (industry, agriculture, settlements, tourism) that impact severely the ecosystem. Discharge from the agricultural drainage basin affects particularly the area North of the city of Venice; the central and southern areas, instead, receive important pollutant inputs from the industrial zone of Porto Marghera since the early'50s. Additional sources of pollution are domestic sewage and waste disposal from the urban area, that is visited by more than 10M people every year. As a consequence of the increasing land contamination, significant amounts of contaminants (both organic and inorganic) are accumulated in soils of the borderline, in water and in lagoon sediments, which constitute a potential source of secondary pollution. Results of surveys carried out in recent years in the whole area show that contaminants concentration increased from the beginning of the industrial activities until the '90s, when Porto Marghera declined. Most of contaminants have concentrations above the background levels. The highest metal levels were found in an area between Porto Marghera and the city of Venice, where both industrial and urban sewage are discharged, provoking environmental and human health hazard. In order to safeguard the city of Venice, and to restore its lagoon and conterminous areas, a Master Plan of intervention has been developed since the early 2000s. The land currently interested by environmental analysis and/or restoration covers approximately 1350ha; 78% of these (1100ha) proved variously contaminated, with 85% of sites overcoming the National Reference Values. Contamination, besides being diffused, is quite complex, involving the co-existence of several contaminant families (PAH, PCB, dioxin, heavy metals). PAH and metals, in particular, present wide diffusion, both horizontal and vertical (until 5 m below the sea level), with As, Zn, Cd and Hg being the elements more represented in all the soil strata considered. The lagoon sediments inside industrial channels is higher than the other parts of the lagoon; major contaminants are metals (As, Cd, Hg, Pb) and organic micro-pollutants (PCB, PAH); ammonia and phosphate too are present with conspicuous concentrations, contributing to lagoon eutrophication. Groundwater contamination is diffused and complex, with As prevailing over Pb and Cr(VI). The primary objective of the Master Plan was to reduce/eliminate the risk associated to the contamination sources of past activities, and the consequent environmental and human health hazard. Restoration is still in progress, and concerns different intervention strategies: • Channel overbank containment to prevent contaminant migration to water; • Excavation, physical removal and re-distribution of channel sediments (A and B classes); • Landfilling of heavily contaminated sediments (C class); • Soil containment to impede contact with people and the environment; • Restoration of contaminated agricultural land with phytoremediation techniques. Concerning in particular the last item, restoration has been carried out with native or exotic vegetation (e.g. Fragmites australis, Juncus lacustris, Pterix vittata, Spartina maritima), or cultivated plants (e.g. Heliantus annuus, Zea mays, Brassica napus), with contrasting results. The exotic fern (Pterix vittata) proved highly effective to accumulate As, consistently with data from literature; Spartina maritima proved more effective than Fragmites australis to uptake metals, while cultivated plants could not survive to high heavy metal concentrations. At some sites, soil has been stored, selected and finally (the most contaminated part) delivered to landfill, while groundwater was remediated by bioremediation techniques.

  20. 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

  1. Ethnopharmacological survey of wild medicinal plants in Showbak, Jordan.

    PubMed

    Al-Qura'n, S

    2009-05-01

    Two main research questions are framing this investigation: (1) the main taxa of the medicinal importance value altered the Showbak forest stand and species composition? (2) The most safe species and what are the toxic ones (unsafe). These two research questions are the vital ones to draw a clear image about the wild medicinal plants of this investigated area of Showbak region in Jordan. 79 wild medicinal plant species were investigated in this study which are used in traditional medication for the treatment of various diseases. Most of the locals interviewed dealt with well-known safe medicinal plants such as Aaronsohnia factorovskyi Warb. et Eig., Achillea santolina L., Adiantum capillus-veneris L., Artemisia herba-alba L., Ceratonia siliqua L., Clematis recta L., Herniaria hirsuta L., Malva neglecta Wallr., Rosmarinus officinalis L., Ruta chalepensis L., Salvia triloba L., Sarcopoterium spinosa (L.) Spach., Thymbra capitata (L.) Hof, and Urginea maritima Barker. Many of the wild medicinal plants investigated were toxic and needed to be practiced by practitioners and herbalists rather than the local healers. These plants include Calotropis procera Willd R.Br., Citrullus colocynthis (L.) Sch., Datura stramonium L., Digitalis purpurea L., Ecballium elaterium (L.) A.Rich., Euphorbia helioscopia L., Euphorbia tinctoria Boiss., Glaucium corniculatum (L.) Curt., Hyoscyamus aureus L., Mandragora officinarum L., Nerium oleander L., Ricinus communis L., Solanum nigrum L., Withania somnifera (L.) Dunel. The conservation of medicinal plants and natural resources is becoming increasingly important, so this research is trying to collect information from local population concerning the use of medicinal plants in Showbak; identify the most important specie; determine the relative importance value of the species and calculate the informant consensus factor (ICF) for the medicinal plants. Obtaining results is relied on the interviewee's personal information and the medicinal use of specific plants. PMID:19429338

  2. Structural Analysis of a Periplasmic Binding Protein in the Tripartite ATP-Independent Transporter Family Reveals a Tetrameric Assembly That May Have a Role in Ligand Transport

    SciTech Connect

    Cuneo, M.; Changela, A; Miklos, A; Beese, L; Krueger, J; Hellinga, H

    2008-01-01

    Several bacterial solute transport mechanisms involve members of the periplasmic binding protein (PBP) superfamily that bind and deliver ligand to integral membrane transport proteins in the ATP-binding cassette, tripartite tricarboxylate transporter, or tripartite ATP-independent (TRAP) families. PBPs involved in ATP-binding cassette transport systems have been well characterized, but only a few PBPs involved in TRAP transport have been studied. We have measured the thermal stability, determined the oligomerization state by small angle x-ray scattering, and solved the x-ray crystal structure to 1.9 A resolution of a TRAP-PBP (open reading frame tm0322) from the hyperthermophilic bacterium Thermotoga maritima (TM0322). The overall fold of TM0322 is similar to other TRAP transport related PBPs, although the structural similarity of backbone atoms (2.5-3.1 A root mean square deviation) is unusually low for PBPs within the same group. Individual monomers within the tetrameric asymmetric unit of TM0322 exhibit high root mean square deviation (0.9 A) to each other as a consequence of conformational heterogeneity in their binding pockets. The gel filtration elution profile and the small angle x-ray scattering analysis indicate that TM0322 assembles as dimers in solution that in turn assemble into a dimer of dimers in the crystallographic asymmetric unit. Tetramerization has been previously observed in another TRAP-PBP (the Rhodobacter sphaeroides ?-keto acid-binding protein) where quaternary structure formation is postulated to be an important requisite for the transmembrane transport process.

  3. 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

  4. Conformational Changes of the Clamp of the Protein Translocation ATPase SecA.

    PubMed

    Chen, Yu; Bauer, Benedikt W; Rapoport, Tom A; Gumbart, James C

    2015-07-17

    Post-translational protein translocation across the bacterial plasma membrane is mediated by the interplay of the SecA ATPase and the protein-conducting SecY channel. SecA consists of several domains, including two nucleotide-binding domains (NBD1 and NBD2), a polypeptide cross-linking domain (PPXD), a helical scaffold domain (HSD), and a helical wing domain (HWD). PPXD, HSD, and NBD2 form a clamp that positions the polypeptide substrate above the channel so that it can be pushed into the channel by a two-helix finger of the HSD. How the substrate is accommodated in the clamp during translocation is unclear. Here, we report a crystal structure of Thermotoga maritima SecA at 1.9 Å resolution. Structural analysis and free-energy calculations indicate that the new structure represents an intermediate state during the transition of the clamp from an open to a closed conformation. Molecular dynamics simulations show that closure of the clamp occurs in two phases, an initial movement of PPXD, HSD, and HWD as a unit, followed by a movement of PPXD alone toward NBD2. Simulations in the presence of a polypeptide chain show that the substrate associates with the back of the clamp by dynamic hydrogen bonding and that the clamp is laterally closed by a conserved loop of the PPXD. Mutational disruption of clamp opening or closure abolishes protein translocation. These results suggest how conformational changes of SecA allow substrate binding and movement during protein translocation. PMID:25982945

  5. 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.

  6. 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.

  7. 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

  8. Evolution of the pair rule gene network: Insights from a centipede.

    PubMed

    Green, Jack; Akam, Michael

    2013-10-01

    Comparative studies have examined the expression and function of homologues of the Drosophila melanogaster pair rule and segment polarity genes in a range of arthropods. The segment polarity gene homologues have a conserved role in the specification of the parasegment boundary, but the degree of conservation of the upstream patterning genes has proved more variable. Using genomic resources we identify a complete set of pair rule gene homologues from the centipede Strigamia maritima, and document a detailed time series of expression during trunk segmentation. We find supportive evidence for a conserved hierarchical organisation of the pair rule genes, with a division into early- and late-activated genes which parallels the functional division into primary and secondary pair rule genes described in insects. We confirm that the relative expression of sloppy-paired and paired with respect to wingless and engrailed at the parasegment boundary is conserved between myriapods and insects; suggesting that functional interactions between these genes might be an ancient feature of arthropod segment patterning. However, we find that the relative expression of a number of the primary pair rule genes is divergent between myriapods and insects. This corroborates suggestions that the evolution of upper tiers in the segmentation gene network is more flexible. Finally, we find that the expression of the Strigamia pair rule genes in periodic patterns is restricted to the ectoderm. This suggests that any direct role of these genes in segmentation is restricted to this germ layer, and that mesoderm segmentation is either dependent on the ectoderm, or occurs through an independent mechanism. PMID:23810931

  9. 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

  10. 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

  11. Thermophilic anaerobic oxidation of methane by marine microbial consortia

    PubMed Central

    Holler, Thomas; Widdel, Friedrich; Knittel, Katrin; Amann, Rudolf; Kellermann, Matthias Y; Hinrichs, Kai-Uwe; Teske, Andreas; Boetius, Antje; Wegener, Gunter

    2011-01-01

    The anaerobic oxidation of methane (AOM) with sulfate controls the emission of the greenhouse gas methane from the ocean floor. AOM is performed by microbial consortia of archaea (ANME) associated with partners related to sulfate-reducing bacteria. In vitro enrichments of AOM were so far only successful at temperatures ?25?°C; however, energy gain for growth by AOM with sulfate is in principle also possible at higher temperatures. Sequences of 16S rRNA genes and core lipids characteristic for ANME as well as hints of in situ AOM activity were indeed reported for geothermally heated marine environments, yet no direct evidence for thermophilic growth of marine ANME consortia was obtained to date. To study possible thermophilic AOM, we investigated hydrothermally influenced sediment from the Guaymas Basin. In vitro incubations showed activity of sulfate-dependent methane oxidation between 5 and 70?°C with an apparent optimum between 45 and 60?°C. AOM was absent at temperatures ?75?°C. Long-term enrichment of AOM was fastest at 50?°C, yielding a 13-fold increase of methane-dependent sulfate reduction within 250 days, equivalent to an apparent doubling time of 68 days. The enrichments were dominated by novel ANME-1 consortia, mostly associated with bacterial partners of the deltaproteobacterial HotSeep-1 cluster, a deeply branching phylogenetic group previously found in a butane-amended 60?°C-enrichment culture of Guaymas sediments. The closest relatives (Desulfurella spp.; Hippea maritima) are moderately thermophilic sulfur reducers. Results indicate that AOM and ANME archaea could be of biogeochemical relevance not only in cold to moderate but also in hot marine habitats. PMID:21697963

  12. 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.

  13. 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

  14. A Diferrous-Dinitrosyl Intermediate in the N2O-Generating Pathway of a Deflavinated Flavo-Diiron Protein

    PubMed Central

    2015-01-01

    Flavo-diiron proteins (FDPs) function as anaerobic nitric oxide scavengers in some microorganisms, catalyzing reduction of nitric to nitrous oxide. The FDP from Thermotoga maritima can be prepared in a deflavinated form with an intact diferric site (deflavo-FDP). Hayashi et al. [(2010) Biochemistry 49, 7040–7049] reported that reaction of NO with reduced deflavo-FDP produced substoichiometric N2O. Here we report a multispectroscopic approach to identify the iron species in the reactions of deflavo-FDP with NO. Mössbauer spectroscopy identified two distinct ferrous species after reduction of the antiferromagnetically coupled diferric site. Approximately 60% of the total ferrous iron was assigned to a diferrous species associated with the N2O-generating pathway. This pathway proceeds through successive diferrous-mononitrosyl (S = 1/2 FeII{FeNO}7) and diferrous-dinitrosyl (S = 0 [{FeNO}7]2) species that form within ?100 ms of mixing of the reduced protein with NO. The diferrous-dinitrosyl intermediate converted to an antiferromagnetically coupled diferric species that was spectroscopically indistinguishable from that in the starting deflavinated protein. These diiron species closely resembled those reported for the flavinated FDP [Caranto et al. (2014) J. Am. Chem. Soc. 136, 7981–7992], and the time scales of their formation and decay were consistent with the steady state turnover of the flavinated protein. The remaining ?40% of ferrous iron was inactive in N2O generation but reversibly bound NO to give an S = 3/2 {FeNO}7 species. The results demonstrate that N2O formation in FDPs can occur via conversion of S = 0 [{FeNO}7]2 to a diferric form without participation of the flavin cofactor. PMID:25144650

  15. Conformational Transitions that Enable Histidine Kinase Autophosphorylation and Receptor Array Integration.

    PubMed

    Greenswag, Anna R; Muok, Alise; Li, Xiaoxiao; Crane, Brian R

    2015-12-01

    During bacterial chemotaxis, transmembrane chemoreceptor arrays regulate autophosphorylation of the dimeric histidine kinase CheA. The five domains of CheA (P1-P5) each play a specific role in coupling receptor stimulation to CheA activity. Biochemical and X-ray scattering studies of thermostable CheA from Thermotoga maritima determine that the His-containing substrate domain (P1) is sequestered by interactions that depend upon P1 of the adjacent subunit. Non-hydrolyzable ATP analogs (but not ATP or ADP) release P1 from the protein core (domains P3P4P5) and increase its mobility. Detachment of both P1 domains or removal of one within a dimer increases net autophosphorylation substantially at physiological temperature (55°C). However, nearly all activity is lost without the dimerization domain (P3). The linker length between P1 and P3 dictates intersubunit (trans) versus intrasubunit (cis) autophosphorylation, with the trans reaction requiring a minimum length of 47 residues. A new crystal structure of the most active dimerization-plus-kinase unit (P3P4) reveals trans directing interactions between the tether connecting P3 to P2-P1 and the adjacent ATP-binding (P4) domain. The orientation of P4 relative to P3 in the P3P4 structure supports a planar CheA conformation that is required by membrane array models, and it suggests that the ATP lid of CheA may be poised to interact with receptors and coupling proteins. Collectively, these data suggest that the P1 domains are restrained in the off-state as a result of cross-subunit interactions. Perturbations at the nucleotide-binding pocket increase P1 mobility and access of the substrate His to P4-bound ATP. PMID:26522934

  16. Ancestral patterning of tergite formation in a centipede suggests derived mode of trunk segmentation in trilobites.

    PubMed

    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

  17. Potassium Acts as a GTPase-Activating Element on Each Nucleotide-Binding Domain of the Essential Bacillus subtilis EngA

    PubMed Central

    Foucher, Anne-Emmanuelle; Reiser, Jean-Baptiste; Ebel, Christine; Housset, Dominique; Jault, Jean-Michel

    2012-01-01

    EngA proteins form a unique family of bacterial GTPases with two GTP-binding domains in tandem, namely GD1 and GD2, followed by a KH (K-homology) domain. They have been shown to interact with the bacterial ribosome and to be involved in its biogenesis. Most prokaryotic EngA possess a high GTPase activity in contrast to eukaryotic GTPases that act mainly as molecular switches. Here, we have purified and characterized the GTPase activity of the Bacillus subtilis EngA and two shortened EngA variants that only contain GD1 or GD2-KH. Interestingly, the GTPase activity of GD1 alone is similar to that of the whole EngA, whereas GD2-KH has a 150-fold lower GTPase activity. At physiological concentration, potassium strongly stimulates the GTPase activity of each protein construct. Interestingly, it affects neither the affinities for nucleotides nor the monomeric status of EngA or the GD1 domain. Thus, potassium likely acts as a chemical GTPase-activating element as proposed for another bacterial GTPase like MnmE. However, unlike MnmE, potassium does not promote dimerization of EngA. In addition, we solved two crystal structures of full-length EngA. One of them contained for the first time a GTP-like analogue bound to GD2 while GD1 was free. Surprisingly, its overall fold was similar to a previously solved structure with GDP bound to both sites. Our data indicate that a significant structural change must occur upon K+ binding to GD2, and a comparison with T. maritima EngA and MnmE structures allowed us to propose a model explaining the chemical basis for the different GTPase activities of GD1 and GD2. PMID:23056455

  18. Evolution of the pair rule gene network: Insights from a centipede☆

    PubMed Central

    Green, Jack; Akam, Michael

    2013-01-01

    Comparative studies have examined the expression and function of homologues of the Drosophila melanogaster pair rule and segment polarity genes in a range of arthropods. The segment polarity gene homologues have a conserved role in the specification of the parasegment boundary, but the degree of conservation of the upstream patterning genes has proved more variable. Using genomic resources we identify a complete set of pair rule gene homologues from the centipede Strigamia maritima, and document a detailed time series of expression during trunk segmentation. We find supportive evidence for a conserved hierarchical organisation of the pair rule genes, with a division into early- and late-activated genes which parallels the functional division into primary and secondary pair rule genes described in insects. We confirm that the relative expression of sloppy-paired and paired with respect to wingless and engrailed at the parasegment boundary is conserved between myriapods and insects; suggesting that functional interactions between these genes might be an ancient feature of arthropod segment patterning. However, we find that the relative expression of a number of the primary pair rule genes is divergent between myriapods and insects. This corroborates suggestions that the evolution of upper tiers in the segmentation gene network is more flexible. Finally, we find that the expression of the Strigamia pair rule genes in periodic patterns is restricted to the ectoderm. This suggests that any direct role of these genes in segmentation is restricted to this germ layer, and that mesoderm segmentation is either dependent on the ectoderm, or occurs through an independent mechanism. PMID:23810931

  19. Tuning protein mechanics through an ionic cluster graft from an extremophilic protein.

    PubMed

    Tych, Katarzyna M; Batchelor, Matthew; Hoffmann, Toni; Wilson, Michael C; Paci, Emanuele; Brockwell, David J; Dougan, Lorna

    2016-03-14

    Proteins from extremophilic organisms provide excellent model systems to determine the role of non-covalent interactions in defining protein stability and dynamics as well as being attractive targets for the development of robust biomaterials. Hyperthermophilic proteins have a prevalence of salt bridges, relative to their mesophilic homologues, which are thought to be important for enhanced thermal stability. However, the impact of salt bridges on the mechanical properties of proteins is far from understood. Here, a combination of protein engineering, biophysical characterisation, single molecule force spectroscopy (SMFS) and molecular dynamics (MD) simulations directly investigates the role of salt bridges in the mechanical stability of two cold shock proteins; BsCSP from the mesophilic organism Bacillus subtilis and TmCSP from the hyperthermophilic organism Thermotoga maritima. Single molecule force spectroscopy shows that at ambient temperatures TmCSP is mechanically stronger yet, counter-intuitively, its native state can withstand greater deformation before unfolding (i.e. it is mechanically soft) compared with BsCSP. MD simulations were used to identify the location and quantify the population of salt bridges, and reveal that TmCSP contains a larger number of highly occupied salt bridges than BsCSP. To test the hypothesis that salt-bridges endow these mechanical properties on the hyperthermophilic CSP, a charged triple mutant (CTM) variant of BsCSP was generated by grafting an ionic cluster from TmCSP into the BsCSP scaffold. As expected CTM is thermodynamically more stable and mechanically softer than BsCSP. We show that a grafted ionic cluster can increase the mechanical softness of a protein and speculate that it could provide a mechanical recovery mechanism and that it may be a design feature applicable to other proteins. PMID:26809452

  20. Vegetation change on a northeast tidal marsh: Interaction of sea-level rise and marsh accretion

    SciTech Connect

    Warren, R.S.; Niering, W.A. )

    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.

  1. Taxonomic revision of the spider genera Agyneta and Tennesseellum (Araneae, Linyphiidae) of North America north of Mexico with a study of the embolic division within Micronetinae sensu Saaristo & Tanasevitch 1996.

    PubMed

    Dupérré, Nadine

    2013-01-01

    The genera Agyneta Hull 1911 and Tennesseellum Petrunkevitch 1925 are revised for North America north of Mexico. The synonymy of Meioneta Hull 1920 with Agyneta Hull 1911 proposed by Saaristo 1973 is corroborated. The North American fauna north of Mexico of Agyneta now includes a total of 69 species, of which 31 are new species: A. watertoni n. sp., A. perspicua n. sp., A. aquila n. sp., A. yukona n. sp., A. darrelli n. sp., A. bucklei n. sp., A. erinacea n. sp., A. crawfordi n. sp., A. vinki n. sp., A. panthera n. sp., A. miniata n. sp., A. danielbelangeri n. sp., A. pistrix n. sp., A. flax n. sp., A. barfoot n. sp., A. sandia n. sp., A. spicula n. sp., A. grandcanyon n. sp., A. chiricahua n. sp., A. crista n. sp., A. tuberculata n. sp., A. catalina n. sp., A. ledfordi n. sp., A. platnicki n. sp., A. bronx n. sp., A. paquini n. sp., A. girardi n. sp., A. flibuscrocus n. sp., A. delphina n. sp., A. okefenokee n. sp. and A. issaqueena n. sp. The genus Tennesseellum includes two spe-cies, with one new species, T. gollum n. sp. Ten new synonyms are recognized: Meioneta grayi Barnes 1953 = Anibontes mimus Chamberlin 1924; Meioneta dactylata Chamberlin & Ivie 1944, Meioneta officiosa (Barrows 1940) = Meioneta micaria (Emerton 1882); Meioneta imitata Chamberlin & Ivie 1944 = Meioneta leucophora Chamberlin & Ivie 1944; Meioneta ferosa (Chamberlin & Ivie 1943) = Meioneta fillmorana (Chamberlin 1919); Meioneta fuscipes Chamberlin & Ivie 1944 = Meioneta floridana (Banks 1896); Meioneta alaskensis Holm 1960 = Meioneta maritima (Emerton 1919); Meioneta meridionalis (Crosby & Bishop 1936), Meioneta zebrina Chamberlin & Ivie, 1944 = Meioneta parva (Banks 1896); Meioneta zygia (Keyserling 1886) = Meioneta fabra (Keyserling 1886). Ten informal species groups are proposed based on the study on the male palpal conformation of the embolus and radical division; these groups are not intened to be phylogenetic hypotheses. The limits and composition of the subfamily Micronetinae sensu Saaristo & Tanasevitch 1996 are discussed. PMID:26146700

  2. 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.

  3. 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

  4. Photorespiration and carbon limitation determine productivity in temperate seagrasses.

    PubMed

    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

  5. Impacts of summer ozone exposure on the growth and overwintering of UK upland vegetation

    NASA Astrophysics Data System (ADS)

    Hayes, Felicity; Mills, Gina; Williams, Philip; Harmens, Harry; Büker, Patrick

    The effects of ozone exposure on species of an upland grassland were assessed. Thirty-three species from Snowdonia, North Wales, UK, were exposed for 10 weeks to a weekly episodic ozone regime in solardomes representing predicted future concentrations. Two solardomes were used as controls, with ozone added to charcoal-filtered air to give a continuous ozone concentration of 30 ppb (O 3(30)). A weekly episodic ozone regime was applied to two other solardomes, with concentrations rising for 8 h per day to 80 ppb on day 1, 100 ppb on days 2 and 3, and 80 ppb on day 4; ozone concentrations remained at 30 ppb at all other times (O 3(30+peaks)). The control and background ozone concentrations of 30 ppb were maintained throughout the night as well as during the daytime. During exposure to the episodic ozone regime, some species were sensitive to ozone and showed ozone-specific leaf injury symptoms (e.g . Carex echinata) and/or premature senescence (e.g. Festuca rubra) and/or changes in above-ground biomass (e.g. Armeria maritima), whereas other species (e.g Holcus lanatus and Carex demissa) showed no effects. Some species, although showing no effects during the 10-week ozone exposure, showed carry-over effects on biomass the following spring, after a winter period of ambient ozone exposure (e.g. Galium saxatile, Nardus stricta and Saxifraga stellaris). The carry-over effects shown in this study indicate the potential ecological impact of ozone on semi-natural vegetation species and indicate the importance of longer-term studies on the effects of ozone on plants.

  6. Diversity and Plant Growth Promoting Capacity of Endophytic Fungi Associated with Halophytic Plants from the West Coast of Korea

    PubMed Central

    Khalmuratova, Irina; Kim, Hyun; Nam, Yoon-Jong; Oh, Yoosun; Jeong, Min-Ji; Choi, Hye-Rim; You, Young-Hyun; Choo, Yeon-Sik; Lee, In-Jung; Shin, Jae-Ho

    2015-01-01

    Five halophytic plant species, Suaeda maritima, Limonium tetragonum, Suaeda australis, Phragmites australis, and Suaeda glauca Bunge, which are native to the Muan salt marsh of South Korea, were examined for fungal endophytes by sequencing the internal transcribed spacer (ITS) region containing ITS1, 5.8S rRNA, and ITS2. In total, 160 endophytic fungal strains were isolated and identified from the roots of the 5 plant species. Taxonomically, all 160 strains belonged to the phyla Ascomycota, Basidiomycota, and Zygomycota. The most dominant genus was Fusarium, followed by the genera Penicillium and Alternaria. Subsequently, using 5 statistical methods, the diversity indices of the endophytes were determined at genus level. Among these halophytic plants, P. australis was found to host the greatest diversity of endophytic fungi. Culture filtrates of endophytic fungi were treated to Waito-C rice seedlings for plant growth-promoting effects. The fungal strain Su-3-4-3 isolated from S. glauca Bunge provide the maximum plant length (20.1 cm) in comparison with wild-type Gibberella fujikuroi (19.6 cm). Consequently, chromatographic analysis of the culture filtrate of Su-3-4-3 showed the presence of physiologically active gibberellins, GA1 (0.465 ng/mL), GA3 (1.808 ng/mL) along with other physiologically inactive GA9 (0.054 ng/mL) and GA24 (0.044 ng/mL). The fungal isolate Su-3-4-3 was identified as Talaromyces pinophilus. PMID:26839496

  7. 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

  8. 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

  9. Exploring codon context bias for synthetic gene design of a thermostable invertase in Escherichia coli.

    PubMed

    Pek, Han Bin; Klement, Maximilian; Ang, Kok Siong; Chung, Bevan Kai-Sheng; Ow, Dave Siak-Wei; Lee, Dong-Yup

    2015-01-01

    Various isoforms of invertases from prokaryotes, fungi, and higher plants has been expressed in Escherichia coli, and codon optimisation is a widely-adopted strategy for improvement of heterologous enzyme expression. Successful synthetic gene design for recombinant protein expression can be done by matching its translational elongation rate against heterologous host organisms via codon optimization. Amongst the various design parameters considered for the gene synthesis, codon context bias has been relatively overlooked compared to individual codon usage which is commonly adopted in most of codon optimization tools. In addition, matching the rates of transcription and translation based on secondary structure may lead to enhanced protein folding. In this study, we evaluated codon context fitness as design criterion for improving the expression of thermostable invertase from Thermotoga maritima in Escherichia coli and explored the relevance of secondary structure regions for folding and expression. We designed three coding sequences by using (1) a commercial vendor optimized gene algorithm, (2) codon context for the whole gene, and (3) codon context based on the secondary structure regions. Then, the codon optimized sequences were transformed and expressed in E. coli. From the resultant enzyme activities and protein yield data, codon context fitness proved to have the highest activity as compared to the wild-type control and other criteria while secondary structure-based strategy is comparable to the control. Codon context bias was shown to be a relevant parameter for enhancing enzyme production in Escherichia coli by codon optimization. Thus, we can effectively design synthetic genes within heterologous host organisms using this criterion. PMID:26047917

  10. Cobalamin-Independent Methionine Synthase (MetE): A Face-to-Face Double Barrel That Evolved by Gene Duplication

    PubMed Central

    2005-01-01

    Cobalamin-independent methionine synthase (MetE) catalyzes the transfer of a methyl group from methyltetrahydrofolate to L-homocysteine (Hcy) without using an intermediate methyl carrier. Although MetE displays no detectable sequence homology with cobalamin-dependent methionine synthase (MetH), both enzymes require zinc for activation and binding of Hcy. Crystallographic analyses of MetE from T. maritima reveal an unusual dual-barrel structure in which the active site lies between the tops of the two (??)8 barrels. The fold of the N-terminal barrel confirms that it has evolved from the C-terminal polypeptide by gene duplication; comparisons of the barrels provide an intriguing example of homologous domain evolution in which binding sites are obliterated. The C-terminal barrel incorporates the zinc ion that binds and activates Hcy. The zinc-binding site in MetE is distinguished from the (Cys)3Zn site in the related enzymes, MetH and betaine–homocysteine methyltransferase, by its position in the barrel and by the metal ligands, which are histidine, cysteine, glutamate, and cysteine in the resting form of MetE. Hcy associates at the face of the metal opposite glutamate, which moves away from the zinc in the binary E·Hcy complex. The folate substrate is not intimately associated with the N-terminal barrel; instead, elements from both barrels contribute binding determinants in a binary complex in which the folate substrate is incorrectly oriented for methyl transfer. Atypical locations of the Hcy and folate sites in the C-terminal barrel presumably permit direct interaction of the substrates in a ternary complex. Structures of the binary substrate complexes imply that rearrangement of folate, perhaps accompanied by domain rearrangement, must occur before formation of a ternary complex that is competent for methyl transfer. PMID:15630480

  11. 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; Kaligarič, Mitja; Vavpetič, 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.

  12. MULCHES AND OTHER COVER MATERIALS TO REDUCE WEED GROWTH IN CONTAINER-GROWN NURSERY STOCK.

    PubMed

    Rys, F; Van Wesemael, D; Van Haecke, D; Mechant, E; Gobin, B

    2014-01-01

    Due to the recent EU-wide implementation of Integrated Pest Management (IPM), alternative methods to reduce weed growth in container-grown nursery stock are needed to cut back the use of herbicides. Covering the upper layer of the substrate is known as a potential method to prevent or reduce weed growth in plant containers. As a high variety of mulches and other cover materials are on the market, however, it is no longer clear for growers which cover material is most efficient for use in containers. Therefore, we examined the effect on weed growth of different mulches and other cover materials, including Pinus maritima, P. sylvestris, Bio-Top Basic, Bio-Top Excellent, coco chips fine, hemp fibres, straw pellets, coco disk 180LD and jute disk. Cover materials were applied immediately after repotting of Ligustrum ovalifolium or planting of Fagus sylvatica. At regular times, both weed growth and side effects (e.g., plant growth, water status of the substrate, occurrence of mushrooms, foraging of birds, complete cover of the substrate and fixation) were assessed. All examined mulches or other cover materials were able to reduce weed growth on the containers during the whole growing season. Weed suppression was even better than that of a chemical treated control. Although all materials showed some side effects, the impact on plant growth is most important to the grower and depends not only on material characteristics (e.g., biodegradation, nutrient leaching and N-immobilisation) but also on container size and climatic conditions. In conclusion, mulches and other cover materials can be a valuable tool within IPM to lower herbicide use. To enable a deliberate choice of which cover material is best used in a specific situation more research is needed on lifespan and stability as well as on economic characteristics of the materials. PMID:26084081

  13. Cobalamin-Independent Methionine Synthase (MetE): A Face-to-Face Double Barrel that Evolved by Gene Duplication

    SciTech Connect

    Pejcha, Robert; Ludwig, Martha L.

    2010-03-08

    Cobalamin-independent methionine synthase (MetE) catalyzes the transfer of a methyl group from methyltetrahydrofolate to L-homocysteine (Hcy) without using an intermediate methyl carrier. Although MetE displays no detectable sequence homology with cobalamin-dependent methionine synthase (MetH), both enzymes require zinc for activation and binding of Hcy. Crystallographic analyses of MetE from T. maritima reveal an unusual dual-barrel structure in which the active site lies between the tops of the two ({beta}{alpha}){sub 8} barrels. The fold of the N-terminal barrel confirms that it has evolved from the C-terminal polypeptide by gene duplication; comparisons of the barrels provide an intriguing example of homologous domain evolution in which binding sites are obliterated. The C-terminal barrel incorporates the zinc ion that binds and activates Hcy. The zinc-binding site in MetE is distinguished from the (Cys){sub 3}Zn site in the related enzymes, MetH and betaine-homocysteine methyltransferase, by its position in the barrel and by the metal ligands, which are histidine, cysteine, glutamate, and cysteine in the resting form of MetE. Hcy associates at the face of the metal opposite glutamate, which moves away from the zinc in the binary E {center_dot} Hcy complex. The folate substrate is not intimately associated with the N-terminal barrel; instead, elements from both barrels contribute binding determinants in a binary complex in which the folate substrate is incorrectly oriented for methyl transfer. Atypical locations of the Hcy and folate sites in the C-terminal barrel presumably permit direct interaction of the substrates in a ternary complex. Structures of the binary substrate complexes imply that rearrangement of folate, perhaps accompanied by domain rearrangement, must occur before formation of a ternary complex that is competent for methyl transfer.

  14. 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.

  15. Comparison of bulk and compound-specific ? 13C analyses and determination of carbon sources to salt marsh sediments using n-alkane distributions (Maine, USA)

    NASA Astrophysics Data System (ADS)

    Tanner, Benjamin R.; Uhle, Maria E.; Mora, Claudia I.; Kelley, Joseph T.; Schuneman, Patrick J.; Lane, Chad S.; Allen, Evan S.

    2010-01-01

    Sources of sedimentary organic matter to a Morse River, Maine (USA) salt marsh over the last 3390 ± 60 RCYBP (Radiocarbon Years Before Present) are determined using distribution patterns of n-alkanes, bulk carbon isotopic analysis, and compound-specific carbon isotopic analysis. Marsh foraminiferal counts suggest a ubiquitous presence of high marsh and higher-high marsh deposits (dominated by Trochammina macrescens forma macrescens, Trochammina comprimata, and Trochammina inflata), implying deposition from ˜0.2 m to 0.5 m above mean high water. Distributions of n-alkanes show a primary contribution from higher plants, confirmed by an average chain length value of 27.5 for the core sediments, and carbon preference index values all >3. Many sample depths are dominated by the C 25 alkane. Salicornia depressa and Ruppia maritima have similar n-alkane distributions to many of the salt marsh sediments, and we suggest that one or both of these plants is either an important source to the biomass of the marsh through time, or that another unidentified higher plant source is contributing heavily to the sediment pool. Bacterial degradation or algal inputs to the marsh sediments appear to be minor. Compound-specific carbon isotopic analyses of the C 27 alkane are on average 7.2‰ depleted relative to bulk values, but the two records are strongly correlated ( R2 = 0.89), suggesting that marsh plants dominate the bulk carbon isotopic signal. Our study underscores the importance of using caution when applying mixing models of plant species to salt marsh sediments, especially when relatively few plants are included in the model.

  16. 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

  17. 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

  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. Novel α-L-Fucosidases from a Soil Metagenome for Production of Fucosylated Human Milk Oligosaccharides

    PubMed Central

    Lezyk, Mateusz; Jers, Carsten; Kjaerulff, Louise; Gotfredsen, Charlotte H.; Mikkelsen, Maria D.; Mikkelsen, Jørn D.

    2016-01-01

    This paper describes the discovery of novel α-L-fucosidases and evaluation of their potential to catalyse the transglycosylation reaction leading to production of fucosylated human milk oligosaccharides. Seven novel α-L-fucosidase-encoding genes were identified by functional screening of a soil-derived metagenome library and expressed in E. coli as recombinant 6xHis-tagged proteins. All seven fucosidases belong to glycosyl hydrolase family 29 (GH 29). Six of the seven α-L-fucosidases were substrate-inhibited, moderately thermostable and most hydrolytically active in the pH range 6–7, when tested with para-nitrophenyl-α-L-fucopyranoside (pNP-Fuc) as the substrate. In contrast, one fucosidase (Mfuc6) exhibited a high pH optimum and an unusual sigmoidal kinetics towards pNP-Fuc substrate. When tested for trans-fucosylation activity using pNP-Fuc as donor, most of the enzymes were able to transfer fucose to pNP-Fuc (self-condensation) or to lactose. With the α-L-fucosidase from Thermotoga maritima and the metagenome-derived Mfuc5, different fucosyllactose variants including the principal fucosylated HMO 2’-fucosyllactose were synthesised in yields of up to ~6.4%. Mfuc5 was able to release fucose from xyloglucan and could also use it as a fucosyl-donor for synthesis of fucosyllactose. This is the first study describing the use of glycosyl hydrolases for the synthesis of genuine fucosylated human milk oligosaccharides. PMID:26800369

  20. Design of an α-l-transfucosidase for the synthesis of fucosylated HMOs.

    PubMed

    Saumonneau, Amélie; Champion, Elise; Peltier-Pain, Pauline; Molnar-Gabor, Dora; Hendrickx, Johann; Tran, Vinh; Hederos, Markus; Dekany, Gyula; Tellier, Charles

    2016-03-01

    Human milk oligosaccharides (HMOs) are recognized as benefiting breast-fed infants in multiple ways. As a result, there is growing interest in the synthesis of HMOs mimicking their natural diversity. Most HMOs are fucosylated oligosaccharides. α-l-Fucosidases catalyze the hydrolysis of α-l-fucose from the non-reducing end of a glucan. They fall into the glycoside hydrolase GH29 and GH95 families. The GH29 family fucosidases display a classic retaining mechanism and are good candidates for transfucosidase activity. We recently demonstrated that the α-l-fucosidase from Thermotoga maritima (TmαFuc) from the GH29 family can be evolved into an efficient transfucosidase by directed evolution ( Osanjo et al. 2007). In this work, we developed semi-rational approaches to design an α-l-transfucosidase starting with the α-l-fucosidase from commensal bacteria Bifidobacterium longum subsp. infantis (BiAfcB, Blon_2336). Efficient fucosylation was obtained with enzyme mutants (L321P-BiAfcB and F34I/L321P-BiAfcB) enabling in vitro synthesis of lactodifucotetraose, lacto-N-fucopentaose II, lacto-N-fucopentaose III and lacto-N-difucohexaose I. The enzymes also generated more complex HMOs like fucosylated para-lacto-N-neohexaose (F-p-LNnH) and mono- or difucosylated lacto-N-neohexaose (F-LNnH-I, F-LNnH-II and DF-LNnH). It is worth noting that mutation at these two positions did not result in a strong decrease in the overall activity of the enzyme, which makes these variants interesting candidates for large-scale transfucosylation reactions. For the first time, this work provides an efficient enzymatic method to synthesize the majority of fucosylated HMOs. PMID:26582607

  1. Crystal complexes of a predicted S-adenosylmethionine-dependent methyltransferase reveal a typical AdoMet binding domain and a substrate recognition domain

    SciTech Connect

    Miller, D.J.; Ouellette, N.; Evodokimova, E.; Savchenko, A.; Edwards, A.; Anderson, W.F.

    2010-03-08

    S-adenosyl-L-methionine-dependent methyltransferases (MTs) are abundant, and highly conserved across phylogeny. These enzymes use the cofactor AdoMet to methylate a wide variety of molecular targets, thereby modulating important cellular and metabolic activities. Thermotoga maritima protein 0872 (TM0872) belongs to a large sequence family of predicted MTs, ranging phylogenetically from relatively simple bacteria to humans. The genes for many of the bacterial homologs are located within operons involved in cell wall synthesis and cell division. Despite preliminary biochemical studies in E. coli and B. subtilis, the substrate specificity of this group of more than 150 proteins is unknown. As part of the Midwest Center for Structural Genomics initiative (www.mcsg.anl.gov), we have determined the structure of TM0872 in complexes with AdoMet and with S-adenosyl-L-homocysteine (AdoHcy). As predicted, TM0872 has a typical MT domain, and binds endogenous AdoMet, or co-crystallized AdoHcy, in a manner consistent with other known MT structures. In addition, TM0872 has a second domain that is novel among MTs in both its location in the sequence and its structure. The second domain likely acts in substrate recognition and binding, and there is a potential substrate-binding cleft spanning the two domains. This long and narrow cleft is lined with positively charged residues which are located opposite the S{sup +}-CH{sub 3} bond, suggesting that a negatively charged molecule might be targeted for catalysis. However, AdoMet and AdoHcy