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Sample records for atividade exploratoria maritima

  1. 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...

  2. The Halophyte Cakile maritima Reduces Phenanthrene Phytotoxicity.

    PubMed

    Shiri, Moez; Rabhi, Mokded; El Amrani, Abdelhak; Abdelly, Chedly

    2015-01-01

    In a previous study, we showed that the halophyte plant model Thellungiella salsuginea was more tolerant to phenanthrene (Polycyclic Aromatic Hydrocarbon: PAH) than its relative glycophyte Arabidopsis thaliana. In the present work, we investigated the potential of another halophyte with higher biomass production, Cakile maritma, to reduce phenanthrene phytotoxicity. Sand was used instead of arable soil with the aim to avoid pollutant degradation by microorganisms or their interaction with the plant. After 6 weeks of treatment by 500 ppm phenanthrene (Phe), stressed plants showed a severe reduction (-73%) in their whole biomass, roots being more affected than leaves and stems. In parallel, Guaiacol peroxidase (GPX) activity was increased by 185 and 62% in leaves and roots, respectively. Non-enzymatic antioxidant capacity (assayed by ABTS test) was maintained unchanged in all plant organs. The model halophytic plant Thellungiella salsuginea was used as a biomarker of phenanthrene stress severity and was grown at 0 (control), 125, 250, and 375 ppm. T. salsuginea plants grown on the sand previously contaminated by 500 ppm Phe then treated by C. maritma culture (phytoremediation culture) showed similar biomass production as plants subjected to 125 ppm Phe. This suggests that the phytotoxic effects of phenanthrene were reduced by 75% by the 6-week treatment by C. maritima. Our findings indicate that C. maritima can constitute a potentially good candidate for PAH phytoremediation.

  3. Three new flavonol glycosides from Suaeda maritima.

    PubMed

    Abd El-Latif, Rasha R; Mansour, Ragaa M A; Sharaf, Mohamed; Farag, Ahmad

    2014-01-01

    Three new flavonol glycosides isolated from the 70% methanol extract of Suaeda maritima (Chenopodiaceae) were characterized based on spectroscopic and chemical methods as quercetin 3-O-α-l-rhamnopyranosyl(1″' → 6″)-β-d-galactopyranoside-7-O-β-d-glucopyranosyl(1″″' → 2″″)-glucopyranoside, kaempferol 3-O-α-l-rhamnopyranosyl(1″' → 6″)-β-d-galactopyranoside-7-O-β-d-glucopyranosyl(1″″' → 2″″)-glucopyranoside, and kaempferol 3-O-α-l-rhamnopyranosyl(1″' → 6″)-β-d-galactopyranoside-7-O-(2″″'-O-trans-feruloyl)-β-d-glucopyranosyl-(1″″' → 2″″)-β-d-glucopyranoside. In addition, four known compounds, namely, quercetin and kaempferol, methyl cis, trans-ferulate, and methyl trans-ferulate were identified. The plant extract and these compounds showed cytotoxic activity against the human tumor cell lines MCF7, HCT116, and HEPG2.

  4. 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

  5. Toxicity and mutagenicity of the molluscicidal plant Ambrosia maritima L.

    PubMed

    Alard, F; Stievenart, C; Vanparys, P; Thilemans, L; Geerts, S

    1991-01-01

    The acute and subchronic toxicity of the molluscicidal plant, Ambrosia maritima L., has been tested on rats. No toxic signs could be detected neither after oral administration of 5 g/kg of dried leaves of the plant as a powder or as a methanolic extract, nor after the incorporation of 50,000 ppm powdered leaves in the feed during 4 weeks. Using an aqueous extract of the plant material of A. maritima or using ambrosin, one of the active molluscicidal components of the plant, no mutagenic activity could be detected in the S. typhimurium strains TA97, TA 98, TA1538, TA100 and TA1535.

  6. Wigeongrass (Ruppia maritima): a literature review

    USGS Publications Warehouse

    Kantrud, Harold 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

  7. Development of microsatellite markers for Suriana maritima (Surianaceae) using next-generation sequencing technology.

    PubMed

    Chen, W S; Zhao, G; Jian, S G; Wang, Z F

    2015-10-30

    Our objective was to develop microsatellite markers for use in assessing genetic variation in the small shrub or tree species Suriana maritima (Surianaceae). In China, this species is found only as a few fragmented populations and individuals on the Paracel Islands. Using next-generation genome sequencing methodology, we developed 17 novel microsatellite markers for S. maritima. Fifty-four individuals from six populations of S. maritima were examined for polymorphisms; only one allele was detected for each of the markers. Microsatellite loci developed indicate a complete absence of genetic diversity for S. maritima on the Paracel Islands in China. These markers will be useful for examining genetic variation among S. maritima populations in other areas of the world.

  8. Effects of tributyltin (TBT) on the seagrass Ruppia maritima.

    PubMed

    Jensen, H F; Holmer, M; Dahllöf, I

    2004-10-01

    The effects of tributyltin (TBT) on the seagrass Ruppia maritima were studied in two growth experiments. Plants were sampled at stations in Odense Fjord and Lunkebugten, Denmark, and replanted in reference sediment without TBT, reference sediment spiked with TBT, and in impacted sediment sampled in the highly TBT contaminated (7-57 microg kg (-1) dw) Odense Fjord. Plant performance was studied at weekly intervals for 3-4 weeks, by measuring net photosynthetic activity, respiration, relative growth rate (RGR) and number of leaves. Net photosynthetic activity in plants from spiked and impacted sediment was reduced by up to 60% relative to reference plants. Respiration both increased and decreased in response to TBT exposure, while RGR was generally lower in plants from contaminated sediments (reduced by 8-25%). The effects of spiked and impacted sediment differed between the experiments, which could be partly explained by the bioavailability of TBT in the two treatments, but also by adaptation of the plants from Odense Fjord to TBT. Measurements of enhanced TBT concentrations in the sediments in Odense Fjord suggest an impact of TBT on R. maritima is possible under in situ conditions.

  9. Low-affinity Na+ uptake in the halophyte Suaeda maritima.

    PubMed

    Wang, Suo-Min; Zhang, Jin-Lin; Flowers, Timothy J

    2007-10-01

    Na(+) uptake by plant roots has largely been explored using species that accumulate little Na(+) into their shoots. By way of contrast, the halophyte Suaeda maritima accumulates, without injury, concentrations of the order of 400 mM NaCl in its leaves. Here we report that cAMP and Ca(2+) (blockers of nonselective cation channels) and Li(+) (a competitive inhibitor of Na(+) uptake) did not have any significant effect on the uptake of Na(+) by the halophyte S. maritima when plants were in 25 or 150 mM NaCl (150 mM NaCl is near optimal for growth). However, the inhibitors of K(+) channels, TEA(+) (10 mM), Cs(+) (3 mM), and Ba(2+) (5 mM), significantly reduced the net uptake of Na(+) from 150 mM NaCl over 48 h, by 54%, 24%, and 29%, respectively. TEA(+) (10 mM), Cs(+) (3 mM), and Ba(2+) (1 mm) also significantly reduced (22)Na(+) influx (measured over 2 min in 150 mM external NaCl) by 47%, 30%, and 31%, respectively. In contrast to the situation in 150 mm NaCl, neither TEA(+) (1-10 mM) nor Cs(+) (0.5-10 mM) significantly reduced net Na(+) uptake or (22)Na(+) influx in 25 mM NaCl. Ba(2+) (at 5 mm) did significantly decrease net Na(+) uptake (by 47%) and (22)Na(+) influx (by 36% with 1 mM Ba(2+)) in 25 mM NaCl. K(+) (10 or 50 mM) had no effect on (22)Na(+) influx at concentrations below 75 mM NaCl, but the influx of (22)Na(+) was inhibited by 50 mM K(+) when the external concentration of NaCl was above 75 mM. The data suggest that neither nonselective cation channels nor a low-affinity cation transporter are major pathways for Na(+) entry into root cells. We propose that two distinct low-affinity Na(+) uptake pathways exist in S. maritima: Pathway 1 is insensitive to TEA(+) or Cs(+), but sensitive to Ba(2+) and mediates Na(+) uptake under low salinities (25 mM NaCl); pathway 2 is sensitive to TEA(+), Cs(+), and Ba(2+) and mediates Na(+) uptake under higher external salt concentrations (150 mM NaCl). Pathway 1 might be mediated by a high-affinity K transporter

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

    PubMed Central

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

    2015-01-01

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

  11. Unusual fatty acid compositions of the hyperthermophilic archaeon Pyrococcus furiosus and the bacterium Thermotoga maritima.

    PubMed Central

    Carballeira, N M; Reyes, M; Sostre, A; Huang, H; Verhagen, M F; Adams, M W

    1997-01-01

    The fatty acid compositions of the hyperthermophilic microorganisms Thermotoga maritima and Pyrococcus furiosus were studied and compared. A total of 37 different fatty acids were identified in T. maritima, including the novel 13,14-dimethyloctacosanedioic acid. In contrast, a total of 18 different fatty acids were characterized, as minor components, in P. furiosus, and these included saturated, monounsaturated, and dicarboxylic acids. This is the first report of fatty acids from an archaeon. PMID:9098079

  12. Fluid dynamics of two-dimensional pollination in Ruppia maritima

    NASA Astrophysics Data System (ADS)

    Musunuri, Naga; Bunker, Daniel; Pell, Susan; Pell, Fischer; Singh, Pushpendra

    2016-11-01

    The aim of this work is to understand the physics underlying the mechanisms of two-dimensional aquatic pollen dispersal, known as hydrophily. We observed two mechanisms by which the pollen released from male inflorescences of Ruppia maritima is adsorbed on a water surface: (i) inflorescences rise above the surface and after they mature their pollen mass falls onto the surface as clumps and disperses on the surface; (ii) inflorescences remain below the surface and produce air bubbles which carry their pollen mass to the surface where it disperses. In both cases dispersed pollen masses combined under the action of capillary forces to form pollen rafts. This increases the probability of pollination since the capillary force on a pollen raft towards a stigma is much larger than on a single pollen grain. The presence of a trace amount of surfactant can disrupt the pollination process so that the pollen is not transported or captured on the water surface. National Science Foundation.

  13. 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

  14. Suppressive Subtractive Hybridization Detects Extensive Genomic Diversity in Thermotoga maritima

    PubMed Central

    Nesbø, Camilla L.; Nelson, Karen E.; Doolittle, W. Ford

    2002-01-01

    Comparisons between genomes of closely related bacteria often show large variations in gene content, even between strains of the same species. Such studies have focused mainly on pathogens; here, we examined Thermotoga maritima, a free-living hyperthermophilic bacterium, by using suppressive subtractive hybridization. The genome sequence of T. maritima MSB8 is available, and DNA from this strain served as a reference to obtain strain-specific sequences from Thermotoga sp. strain RQ2, a very close relative (∼96% identity for orthologous protein-coding genes, 99.7% identity in the small-subunit rRNA sequence). Four hundred twenty-six RQ2 subtractive clones were sequenced. One hundred sixty-six had no DNA match in the MSB8 genome. These differential clones comprise, in sum, 48 kb of RQ2-specific DNA and match 72 genes in the GenBank database. From the number of identical clones, we estimated that RQ2 contains 350 to 400 genes not found in MSB8. Assuming a similar genome size, this corresponds to 20% of the RQ2 genome. A large proportion of the RQ2-specific genes were predicted to be involved in sugar transport and polysaccharide degradation, suggesting that polysaccharides are more important as nutrients for this strain than for MSB8. Several clones encode proteins involved in the production of surface polysaccharides. RQ2 encodes multiple subunits of a V-type ATPase, while MSB8 possesses only an F-type ATPase. Moreover, an RQ2-specific MutS homolog was found among the subtractive clones and appears to belong to a third novel archaeal type MutS lineage. Southern blot analyses showed that some of the RQ2 differential sequences are found in some other members of the order Thermotogales, but the distribution of these variable genes is patchy, suggesting frequent lateral gene transfer within the group. PMID:12142418

  15. Local variability of the phosphoglycerate kinase-triosephosphate isomerase fusion protein from Thermotoga maritima MSB 8.

    PubMed

    Wassenberg, D; Wuhrer, M; Beaucamp, N; Schurig, H; Wozny, M; Reusch, D; Fabry, S; Jaenicke, R

    2001-04-01

    The pgk-tpi gene locus of Thermotoga maritima encodes both phosphoglycerate kinase (PGK) and a bienzyme complex consisting of a fusion protein of PGK with triosephosphate isomerase (TIM). No separate tpi gene for TIM is present in T. maritima. A frame-shift at the end of the pgk gene has been previously proposed as a mechanism to regulate the expression of the two protein variants [Schurig et al., EMBO J. 14 (1995), 442-451]. Surprisingly, the complete T. maritima genome was found to contain a pgk-tpi sequence not requiring the proposed frameshift mechanism. To clarify the apparent discrepancy, a variety of DNA sequencing techniques were applied, disclosing an anomalous local variability in the pgk-tpi fusion region. The comparison of different DNA samples and the mass spectrometric analysis of the amino acid sequence of the natural fusion protein from T. maritima MSB8 confirmed the local variability of the DNA variants. Since not all peptide masses could be assigned, further variations are conceivable, suggesting an even higher heterogeneity of the T. maritima MSB8 strain.

  16. 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.

  17. Monoterpenoids glycosides content from two Mediterranean populations of Crucianella maritima L.

    PubMed

    Venditti, A; Altieri, A; Bianco, A

    2014-01-01

    In this study, the iridoidic content of two accessions of Crucianella maritima L., one from Sardinia and the second from Latium, was examined and compared. From a qualitative point of view, the iridoidic pattern of the two samples was similar, since the same compounds (asperuloside, asperulosidic acid and deacetyl asperulosidic acid) were isolated. Asperuloside was the main compound in both accessions. Asperulosidic acid was the second compound in the accession from Sardinia, while the accession from Latium exhibited a similar amount of asperulosidic acid and deacetyl asperulosidic acid. These iridoids can be considered as chemotaxonomic markers for parts of the Rubiaceae family, in particular for the Rubioideae subfamily to which C. maritima belongs.

  18. Hydride transfer during catalysis by dihydrofolate reductase from Thermotoga maritima.

    PubMed Central

    Maglia, Giovanni; Javed, Masood H; Allemann, Rudolf K

    2003-01-01

    DHFR (dihydrofolate reductase) catalyses the metabolically important reduction of 7,8-dihydrofolate by NADPH. DHFR from the hyperthermophilic bacterium Thermotoga maritima (TmDHFR), which shares similarity with DHFR from Escherichia coli, has previously been characterized structurally. Its tertiary structure is similar to that of DHFR from E. coli but it is the only DHFR characterized so far that relies on dimerization for stability. The midpoint of the thermal unfolding of TmDHFR was at approx. 83 degrees C, which was 30 degrees C higher than the melting temperature of DHFR from E. coli. The turnover and the hydride-transfer rates in the kinetic scheme of TmDHFR were derived from measurements of the steady-state and pre-steady-state kinetics using absorbance and stopped-flow fluorescence spectroscopy. The rate constant for hydride transfer was found to depend strongly on the temperature and the pH of the solution. Hydride transfer was slow (0.14 s(-1) at 25 degrees C) and at least partially rate limiting at low temperatures but increased dramatically with temperature. At 80 degrees C the hydride-transfer rate of TmDHFR was 20 times lower than that observed for the E. coli enzyme at its physiological temperature. Hydride transfer depended on ionization of a single group in the active site with a p K(a) of 6.0. While at 30 degrees C, turnover of substrate by TmDHFR was almost two orders of magnitude slower than by DHFR from E. coli; the steady-state rates of the two enzymes differed only 8-fold at their respective working temperatures. PMID:12765545

  19. The embryonic development of the centipede Strigamia maritima.

    PubMed

    Brena, Carlo; Akam, Michael

    2012-03-01

    The geophilomorph centipede Strigamia maritima is an emerging model for studies of development and evolution among the myriapods. A draft genome sequence has recently been completed, making it also an important reference for comparative genomics, and for studies of myriapod physiology more generally. Here we present the first detailed description of myriapod development using modern techniques. We describe a timeline for embryonic development, with a detailed staging system based on photographs of live eggs and fixed embryos. We show that the early, cleavage and nuclear migration, stages of development are remarkably prolonged, accounting for nearly half of the total developmental period (approx 22 of 48 days at 13 °C). Towards the end of this period, cleavage cells migrate to the egg periphery to generate a uniform blastoderm. Asymmetry quickly becomes apparent as cells in the anterior half of the egg condense ventrally to form the presumptive head. Five anterior segments, the mandibular to the first leg-bearing segment (1st LBS) become clearly visible through the chorion almost simultaneously. Then, after a short pause, the next 35 leg-bearing segments appear at a uniform rate of 1 segment every 3.2 h (at 13 °C). Segment addition then slows to a halt with 40-45 LBS, shortly before the dramatic movements of germ band flexure, when the left and right halves of the embryo separate and the embryo folds deeply into the yolk. After flexure, segment morphogenesis and organogenesis proceed for a further 10 days, before the egg hatches. The last few leg-bearing segments are added during this period, much more slowly, at a rate of 1-2 segments/day. The last leg-bearing segment is fully defined only after apolysis of the embryonic cuticle, so that at hatching the embryo displays the final adult number of leg-bearing segments (typically 47-49 in our population).

  20. 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...

  1. 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 northern...

  2. 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...

  3. 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.

  4. Early effects of salt stress on the physiological and oxidative status of Cakile maritima (halophyte) and Arabidopsis thaliana (glycophyte).

    PubMed

    Ellouzi, Hasna; Hamed, Karim Ben; Cela, Jana; Munné-Bosch, Sergi; Abdelly, Chedly

    2011-06-01

    Early changes in physiological and oxidative status induced by salt stress were monitored in two Brassicaceae plants differing in their tolerance to salinity, Cakile maritima (halophyte) and Arabidopsis thaliana (glycophyte). Growth response and antioxidant defense of C. maritima under 400 mM NaCl were compared with those of A. thaliana exposed to 100 mM NaCl. Salinity induced early growth reduction that is less pronounced in C. maritima than in A. thaliana. Maximum hydrogen peroxide (H₂O₂) level occurred in the leaves of both species 4 h after the onset of salt treatment. A rapid decline in H₂O₂ concentration was observed thereafter in C. maritima, whereas it remained high in A. thaliana. Correlatively, superoxide dismutase, catalase and peroxidase activities increased at 4 h of treatment in C. maritima and decreased thereafter. However, the activity of these enzymes remained higher in treated plants than that in controls, regardless of the duration of treatment, in A. thaliana. The concentrations of malondialdehyde (MDA) reached maximum values at 24 h of salt stress in both species. Again, MDA levels decreased later in C. maritima, but remained high in A. thaliana. The contents of α-tocopherol remained constant during salt stress in C. maritima and decreased during the first 24 h of salt stress and then remained low in A. thaliana. The results clearly showed that C. maritima, in contrast to A. thaliana, can rapidly evolve physiological and antioxidant mechanisms to adapt to salt and manage the oxidative stress. This may explain, at least partially, the difference in salt tolerance between halophytes and glycophytes.

  5. Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH(2)).

    PubMed

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

    2011-07-01

    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 sequencing because of its isolated phylogenetic location, as a distant next neighbor of the genus Desulfurella. Strain MH(2) (T) is the first type strain from the order Desulfurellales with a completely 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.

  6. 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.

  7. Ferredoxin from the hyperthermophile Thermotoga maritima is stable beyond the boiling point of water.

    PubMed

    Pfeil, W; Gesierich, U; Kleemann, G R; Sterner, R

    1997-10-03

    Heat-stable proteins from hyperthermophilic microorganisms are ideally suited for investigating protein stability and evolution. We measured with differential scanning calorimetry and optical absorption spectroscopy the thermal stability of [4Fe-4S] ferredoxin from Thermotoga maritima (tfdx), which is a small electron transfer protein. The results are consistent with two-state unfolding at the record denaturation temperature of 125 degrees C. According to the crystal structure at 1.75 A resolution, T. maritima ferredoxin contains a significantly increased number of hydrogen bonds that involve charged amino acid side-chains, compared to thermolabile ferredoxins. Thus, our results suggest that polar interactions substantially contribute to protein stability at very high temperatures. Moreover, because small [4Fe-4S] ferredoxins seem to have occurred early in evolution, the extreme thermostability of tfdx supports the hypothesis that life originated at high temperatures.

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

    SciTech Connect

    Martinez-Hackert,E.; Hendrickson, W.

    2007-01-01

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

  9. 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

  10. Comparative assessment of LECA and Spartina maritima to remove emerging organic contaminants from wastewater.

    PubMed

    Ferreira, Ana Rita; Guedes, Paula; Mateus, Eduardo P; Ribeiro, Alexandra B; Couto, Nazaré

    2017-01-18

    The present work aimed to evaluate the capacity of constructed wetlands (CWs) to remove three emerging organic contaminants with different physicochemical properties: caffeine (CAF), oxybenzone (MBPh), and triclosan (TCS). The simulated CWs were set up with a matrix of light expanded clay aggregates (LECA) and planted with Spartina maritima, a salt marsh plant. Controlled experiments were carried out in microcosms using deionized water and wastewater collected at a wastewater treatment plant (WWTP), with different contaminant mass ranges, for 3, 7, and 14 days. The effects of variables were tested isolatedly and together (LECA and/or S. maritima). The presence of LECA and/or S. maritima has shown higher removal (around 61-97%) of lipophilic compounds (MBPh and TCS) than the hydrophilic compound (CAF; around 19-85%). This was attributed to the fact that hydrophilic compounds are dissolved in the water column, whereas the lipophilic ones suffer sorption processes promoting their removal by plant roots and/or LECA. In the control (only wastewater), a decrease in the three contaminant levels was observed. Adsorption and bio/rhizoremediation are the strongest hypothesis to explain the decrease in contaminants in the tested conditions.

  11. 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.

  12. 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.

  13. Structure of a NAD kinase from Thermotoga maritima at 2.3 Å resolution

    SciTech Connect

    Oganesyan, Vaheh; Huang, Candice; Adams, Paul D.; Jancarik, Jaru; Yokota, Hisao A.; Kim, Rosalind; Kim, Sung-Hou

    2005-07-01

    The expression, purification, crystallization, and structure determination of NAD-kinase from T. maritima are reported. Similarity to other NAD-kinases as well as homo-oligomrization state of the enzyme from T. maritima are discussed. NAD kinase is the only known enzyme that catalyzes the formation of NADP, a coenzyme involved in most anabolic reactions and in the antioxidant defense system. Despite its importance, very little is known regarding the mechanism of catalysis and only recently have several NAD kinase structures been deposited in the PDB. Here, an independent investigation of the crystal structure of inorganic polyphosphate/ATP-NAD kinase, PPNK-THEMA, a protein from Thermotoga maritima, is reported at a resolution of 2.3 Å. The crystal structure was solved using single-wavelength anomalous diffraction (SAD) data collected at the Se absorption-peak wavelength in a state in which no cofactors or substrates were bound. It revealed that the 258-amino-acid protein is folded into two distinct domains, similar to recently reported NAD kinases. The N-terminal α/β-domain spans the first 100 amino acids and the last 30 amino acids of the polypeptide and has several topological matches in the PDB, whereas the other domain, which spans the middle 130 residues, adopts a unique β-sandwich architecture and only appreciably matches the recently deposited PDB structures of NAD kinases.

  14. 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

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

    PubMed Central

    Al-Dosary, Mona Mohammed

    2009-01-01

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

  16. Identification of two conserved aspartic acid residues required for DNA digestion by a novel thermophilic Exonuclease VII in Thermotoga maritima

    PubMed Central

    Larrea, Andres A.; Pedroso, Ilene M.; Malhotra, Arun; Myers, Richard S.

    2008-01-01

    Exonuclease VII was first identified in 1974 as a DNA exonuclease that did not require any divalent cations for activity. Indeed, Escherichia coli ExoVII was identified in partially purified extracts in the presence of EDTA. ExoVII is comprised of two subunits (XseA and XseB) that are highly conserved and present in most sequenced prokaryotic genomes, but are not seen in eukaryotes. To better understand this exonuclease family, we have characterized an ExoVII homolog from Thermotoga maritima. Thermotoga maritima XseA/B homologs TM1768 and TM1769 were co-expressed and purified, and show robust nuclease activity at 80°C. This activity is magnesium dependent and is inhibited by phosphate ions, which distinguish it from E. coli ExoVII. Nevertheless, both E. coli and T. maritima ExoVII share a similar putative active site motif with two conserved aspartate residues in the large (XseA/TM1768) subunit. We show that these residues, Asp235 and Asp240, are essential for the nuclease activity of T. maritima ExoVII. We hypothesize that the ExoVII family of nucleases can be sub-divided into two sub-families based on EDTA resistance and that T. maritima ExoVII is the first member of the branch that is characterized by EDTA sensitivity and inhibition by phosphate. PMID:18812402

  17. 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.

  18. 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.

  19. Seed germination responses to varying environmental conditions and provenances in Crucianella maritima L., a threatened coastal species.

    PubMed

    Del Vecchio, Silvia; Mattana, Efisio; Acosta, Alicia T R; Bacchetta, Gianluigi

    2012-01-01

    Seed germination (effects of light, temperature, NaCl and KNO(3)) of the coastal endangered species Crucianella maritima was investigated by testing seeds from three different populations. Data were analyzed by means of Generalized Linear Mixed Model (GLMM). The principal results showed that germination of C. maritima seeds was characterized by photoinhibition, absence of primary dormancy and salt-induced secondary dormancy, with no need for high nutrient availability (KNO(3)). Intraspecific differences in germination pattern emerged, apparently due to a different seed mass. These results show important germination traits of C. maritima which should be taken into account in possible reintroduction attempts aimed at restoring threatened populations of this species.

  20. 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

  1. 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

  2. Growth and photosynthetic responses of the cordgrass Spartina maritima to CO2 enrichment and salinity.

    PubMed

    Mateos-Naranjo, E; Redondo-Gómez, S; Andrades-Moreno, L; Davy, A J

    2010-10-01

    Future climatic scenarios combine increasing concentrations of atmospheric CO(2) and rising sea levels. Spartina maritima is a C(4) halophyte that is an important pioneer and ecosystem engineer in salt marshes of the Atlantic coast of southern Europe. A glasshouse experiment investigated the combined effects on its growth and photosynthetic apparatus of approximately doubling CO(2) concentration (from 380 to 700 μmol mol(-1)) at a range of salinity (0, 171 and 510 mM NaCl). We measured relative growth rates, gas exchange, chlorophyll fluorescence parameters, photosynthetic pigment concentrations, and total ash, Na(+), K(2+), Ca(2+) and N concentrations. Elevated CO(2) stimulated growth of S. maritima by c. 65% at all external salinities; this growth enhancement was associated with greater net photosynthetic rate (A) and improved leaf water relations. A increased despite a drop in stomatal conductance in response to 700 μmol mol(-1) CO(2). CO(2) and salinity had a marked overall effect on the photochemical (PSII) apparatus and the synthesis of photosynthetic pigments. Φ(PSII) values at midday decreased significantly with external salinity in plants grown at 380 μmol mol(-1) CO(2); and F(v)/F(m) and Φ(PSII) values were higher at 700 μmol mol(-1) CO(2) in presence of NaCl. Plant nutrient concentrations declined under elevated CO(2), which can be ascribed to the dilution effect caused by an increase in biomass. The results suggest that the productivity S. maritima and the ecosystem services it provides will increase in likely future climatic scenarios.

  3. 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

  4. Computational prediction and experimental validation of a novel miRNA in Suaeda maritima, a halophyte.

    PubMed

    Gharat, S A; Shaw, B P

    2016-01-22

    The lack of available transcriptome data for plants of no economic or agronomic importance limits the identification of miRNAs in many species. Considering the possible similarity of the transcriptome between related species, the present study used expressed sequence tags (ESTs) of Suaeda salsa and Suaeda glauca to identify conserved miRNAs, which were validated in a halophyte, Suaeda maritima, with the aim of identifying salt-responsive miRNAs from naturally salt-tolerant plants, information on which is limited. In this study, computational analysis predicted three miRNA sequences by mapping non-redundant miRNA sequences from miRBase 16.0 on 1534 ESTs of S. salsa and S. glauca. The expression of one could be validated in S. maritima, and was named sma-miR1867. This miRNA was downregulated in response to NaCl treatment. It was predicted to target ferredoxin-thioredoxin reductase (FTR), cell division control protein 6 (CDC6), and ubiquitin-protein ligase (UPL) in S. salsa and/or S. glauca. However, only UPL could be amplified in S. maritima, and RT-qPCR showed that it was upregulated in response to NaCl treatment. These results indicate that, in halophytes, FTR and CDC6 may promote carbon metabolism and cell division, respectively, in the presence of salt, while UPL may regulate the abundance of proteins that are important for salt tolerance in halophytes. Thus, sma-miR1867 could be an essential component of salt resistance in halophytes.

  5. 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.

  6. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

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

  8. 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.

  9. The crystal structure of dihydrofolate reductase from Thermotoga maritima: molecular features of thermostability.

    PubMed

    Dams, T; Auerbach, G; Bader, G; Jacob, U; Ploom, T; Huber, R; Jaenicke, R

    2000-03-31

    Two high-resolution structures have been obtained for dihydrofolate reductase from the hyperthermophilic bacterium Thermotoga maritima in its unliganded state, and in its ternary complex with the cofactor NADPH and the inhibitor, methotrexate. While the overall fold of the hyperthermophilic enzyme is closely similar to monomeric mesophilic dihydrofolate reductase molecules, its quaternary structure is exceptional, in that T. maritima dihydrofolate reductase forms a highly stable homodimer. Here, the molecular reasons for the high intrinsic stability of the enzyme are elaborated and put in context with the available data on the physical parameters governing the folding reaction. The molecule is extremely rigid, even with respect to structural changes during substrate binding and turnover. Subunit cooperativity can be excluded from structural and biochemical data. Major contributions to the high intrinsic stability of the enzyme result from the formation of the dimer. Within the monomer, only subtle stabilizing interactions are detectable, without clear evidence for any of the typical increments of thermal stabilization commonly reported for hyperthermophilic proteins. The docking of the subunits is optimized with respect to high packing density in the dimer interface, additional salt-bridges and beta-sheets. The enzyme does not show significant structural changes upon binding its coenzyme, NADPH, and the inhibitor, methotrexate. The active-site loop, which is known to play an important role in catalysis in mesophilic dihydrofolate reductase molecules, is rearranged, participating in the association of the subunits; it no longer participates in catalysis.

  10. 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)

  11. 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.

  12. Quinone- and nitroreductase reactions of Thermotoga maritima peroxiredoxin-nitroreductase hybrid enzyme.

    PubMed

    Anusevičius, Žilvinas; Misevičienė, Lina; Šarlauskas, Jonas; Rouhier, Nicolas; Jacquot, Jean-Pierre; Čėnas, Narimantas

    2012-12-01

    Thermotoga maritima peroxiredoxin-nitroreductase hybrid enzyme (Prx-NR) consists of a FMN-containing nitroreductase (NR) domain fused to a peroxiredoxin (Prx) domain. These domains seem to function independently as no electron transfer occurs between them. The reduction of quinones and nitroaromatics by NR proceeded in a two-electron manner, and follows a 'ping-pong' scheme with sometimes pronounced inhibition by quinone substrate. The comparison of steady- and presteady-state kinetic data shows that in most cases, the oxidative half-reaction may be rate-limiting in the catalytic cycle of NR. The enzyme was inhibited by dicumarol, a classical inhibitor of oxygen-insensitive nitroreductases. The reduction of quinones and nitroaromatic compounds by Prx-NR was characterized by the linear dependence of their reactivity (logk(cat)/K(m)) on their single-electron reduction potentials E(7)(1), while the reactivity of quinones markedly exceeded the one with nitroaromatics. It shows that NR lacks the specificity for the particular structure of these oxidants, except their single-electron accepting potency and the rate of electron self-exchange. It points to the possibility of a single-electron transfer step in a net two-electron reduction of quinones and nitroaromatics by T. maritima Prx-NR, and to a significant diversity of the structures of flavoenzymes which may perform the two-electron reduction of quinones and nitroaromatics.

  13. Potential of Spartina maritima in restored salt marshes for phytoremediation of metals in a highly polluted estuary.

    PubMed

    Curado, G; Rubio-Casal, A E; Figueroa, E; Castillo, J M

    2014-01-01

    Sedimentary abiotic environment, and concentration and stock of nine metals were analyzed in vegetation and sediments to evaluate the phytoremediation capacity of restored Spartina maritima prairies in the highly polluted Odiel Marshes (SW Iberian Peninsula). Samples were collected in two 10 -m long rows parallel to the tidal line at two sediments depths (0-2 cm and 2-20 cm). Metal concentrations were measured by inductively coupled plasma spectroscopy. Iron, aluminum, copper, and zinc were the most concentrated metals. Every metal, except nickel, showed higher concentration in the root zone than at the sediment surface, with values as high as ca. 70 g Fe kg(-1). The highest metal concentrations in S. maritima tissues were recorded in its roots (maximum for iron in Spartina roots: 4160.2 +/- 945.3 mg kg(-1)). Concentrations of aluminum and iron in leaves and roots were higher than in superficial sediments. Rhizosediments showed higher concentrations of every metal than plant tissues, except for nickel. Sediment metal stock in the first 20 cm deep was ca. 170.89 t ha(-1). Restored S. maritima prairies, with relative cover of 62 +/- 6%, accumulated ca. 22 kg metals ha(-1). Our results show S. maritima to be an useful biotool for phytoremediation projects in European salt marshes.

  14. 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/...

  15. 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.

  16. 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.

  17. Recombinant S-adenosylhomocysteine hydrolase from Thermotoga maritima: cloning, overexpression, characterization, and thermal purification studies.

    PubMed

    Lozada-Ramírez, J D; Sánchez-Ferrer, A; García-Carmona, F

    2013-06-01

    S-Adenosylhomocysteine hydrolase (SAHase) encoded by sahase gene is a determinant when catalyzing the reversible conversion of adenosine and homocysteine to S-adenosylhomocysteine in most living organisms. The sahase gene was isolated from the genome of the highly thermostable anaerobic bacteria Thermotoga maritima, and then it was cloned, characterized, overexpressed using Escherichia coli, and partially purified by thermal precipitation. The thermal purification of the recombinant SAHase resulted in changes in the circular dichroism spectra. As a result of this analysis, it was possible to determine the structural changes in the composition of the α-helix and β-sheet content of the recombinant enzyme after purification. Moreover, a predicted secondary structure and 3D structural model was rendered by comparative molecular modeling to further understand the molecular function of this protein including its attractive biotechnological use.

  18. Engineering of TM1459 from Thermotoga maritima for Increased Oxidative Alkene Cleavage Activity

    PubMed Central

    Fink, Matthias; Trunk, Sarah; Hall, Mélanie; Schwab, Helmut; Steiner, Kerstin

    2016-01-01

    Oxidative cleavage of alkenes is a widely employed process allowing oxyfunctionalization to corresponding carbonyl compounds. Recently, a novel biocatalytic oxidative alkene cleavage activity on styrene derivatives was identified in TM1459 from Thermotoga maritima. In this work we engineered the enzyme by site-saturation mutagenesis of active site amino acids to increase its activity and to broaden its substrate scope. A high-throughput assay for the detection of the ketone products was successfully developed. Several variants with up to twofold improved conversion level of styrene derivatives were successfully identified. Especially, changes in or removal of the C-terminus of TM1459 increased the activity most significantly. These best variants also displayed a slightly enlarged substrate scope. PMID:27713741

  19. Structure of thermotoga maritima stationary phase survival protein SurE : a novel acid phosphatase.

    SciTech Connect

    Zhang, R.-G; Skarina, T.; Katz, J. E.; Khachatryan, A; Vyas, S.; Arrowsmith, C. H.; Clarke, S.; Edwards, A.; Joachimiak, A.; Savchenko, A.; Biosciences Division; Univ. of Toronto; Univ. of California; Clinical Genomics Centre /Proteomics, Univ. Health Network

    2001-11-01

    Background: The rpoS, nlpD, pcm, and surE genes are among many whose expression is induced during the stationary phase of bacterial growth. rpoS codes for the stationary-phase RNA polymerase {sigma} subunit, and nlpD codes for a lipoprotein. The pcm gene product repairs damaged proteins by converting the atypical isoaspartyl residues back to L-aspartyls. The physiological and biochemical functions of surE are unknown, but its importance in stress is supported by the duplication of the surE gene in E. coli subjected to high-temperature growth. The pcm and surE genes are highly conserved in bacteria, archaea, and plants. Results: The structure of SurE from Thermotoga maritima was determined at 2.0 Angstroms. The SurE monomer is composed of two domains; a conserved N-terminal domain, a Rossman fold, and a C-terminal oligomerization domain, a new fold. Monomers form a dimer that assembles into a tetramer. Biochemical analysis suggests that SurE is an acid phosphatase, with an optimum pH of 5.5-6.2. The active site was identified in the N-terminal domain through analysis of conserved residues. Structure-based site-directed point mutations abolished phosphatase activity. T. maritima SurE intra- and intersubunit salt bridges were identified that may explain the SurE thermostability. Conclusions: The structure of SurE provided information about the protein's fold, oligomeric state, and active site. The protein possessed magnesium-dependent acid phosphatase activity, but the physiologically relevant substrate(s) remains to be identified. The importance of three of the assigned active site residues in catalysis was confirmed by site-directed mutagenesis.

  20. Two Extremely Thermostable Xylanases of the Hyperthermophilic Bacterium Thermotoga maritima MSB8

    PubMed Central

    Winterhalter, C.; Liebl, W.

    1995-01-01

    During growth with xylose or xylan as the source of carbon, xylanase production by Thermotoga maritima MSB8 was enhanced about 10-fold compared with growth with glucose or starch. Two extremely thermostable endoxylanases (1,4-(beta)-d-xylan-xylanohydrolase, EC 3.2.1.8), designated XynA and XynB, were identified and purified from cells of this organism. XynA and XynB occurred as proteins with apparent molecular masses of about 120 and 40 kDa, respectively, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Maximum activity at the optimal pH (pH 6.2 and pH 5.4 for XynA and XynB, respectively) was measured at about 92(deg)C for XynA (10-min assay) and at about 105(deg)C for XynB (5-min assay). XynB activity was stimulated twofold by the addition of 500 mM NaCl, while XynA displayed maximum activity without the addition of salt. Both xylanases were tolerant of relatively high salt concentrations. At 2 M (about 12% wt/vol) NaCl, XynA and XynB retained 49 and 65%, respectively, of their maximum activities. In contrast to XynB, XynA was able to adsorb to microcrystalline cellulose. Antibodies raised against a recombinant truncated XynA protein cross-reacted with XynB, indicating that the enzymes may have sequence or structural similarities. Part of the xylanase activity appeared to be associated with the outer membrane of T. maritima cells, since more than 40% of the total xylanase activity present in the crude cellular extract was found in the membrane fraction after high-speed centrifugation. Most of the membrane-bound activity appeared to be due to the 120-kDa xylanase XynA. PMID:16535021

  1. 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

  2. Triacylated cyanidin 3-(3X-glucosylsambubioside)-5-glucosides from the flowers of Malcolmia maritima.

    PubMed

    Tatsuzawa, Fumi; Saito, Norio; Toki, Kenjiro; Shinoda, Koichi; Shigihara, Atsushi; Honda, Toshio

    2008-02-01

    Three acylated cyanidin 3-(3(X)-glucosylsambubioside)-5-glucosides (1-3) and one non-acylated cyanidin 3-(3(X)-glucosylsambubioside)-5-glucoside (4) were isolated from the purple-violet or violet flowers and purple stems of Malcolmia maritima (L.) R. Br (the Cruciferae), and their structures were determined by chemical and spectroscopic methods. In the flowers of this plant, pigment 1 was determined to be cyanidin 3-O-[2-O-(2-O-(trans-sinapoyl)-3-O-(beta-D-glucopyranosyl)-beta-D-xylopyranosyl)-6-O-(trans-p-coumaroyl)-beta-D-glucopyranoside]-5-O-[6-O-(malonyl)-(beta-D-glucopyranoside) as a major pigment, and a minor pigment 2 was determined to be the cis-p-coumaroyl isomer of pigment 1. In the stems, pigment 3 was determined to be cyanidin 3-O-[2-O-(2-O-(trans-sinapoyl)-3-O-(beta-D-glucopyranosyl)-beta-D-xylopyranosyl)-6-O-(trans-p-coumaroyl)-beta-d-glucopyranoside]-5-O-(beta-D-glucopyranoside) as a major anthocyanin, and also a non-acylated anthocyanin, cyanidin 3-O-[2-O-(3-O-(beta-D-glucopyranosyl)-beta-D-xylopyranosyl)-beta-D-glucopyranoside]-5-O-(beta-D-glucopyranoside) was determined to be a minor pigment (pigment 4). In this study, it was established that the acylation-enzymes of malonic acid has important roles for the acylation of 5-glucose residues of these anthocyanins in the flower-tissues of M. maritima; however, the similar enzymatic reactions seemed to be inhibited or lacking in the stem-tissues.

  3. 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.

  4. 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.

  5. 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.

  6. Factors associated with determination of root ²²Na (+) influx in the salt accumulation halophyte Suaeda maritima.

    PubMed

    Zhang, Jin-Lin; Wetson, Anne M; Wang, Suo-Min; Gurmani, Ali R; Bao, Ai-Ke; Wang, Chun-Mei

    2011-01-01

    Salinity is an increasing problem for agricultural production worldwide. The result of low-affinity Na(+) uptake is toxic to the cytoplasm of most crop plants. Nevertheless, the pathways for this low-affinity Na(+) uptake are still uncertain. In this work we used ²²Na(+) isotope tracing technology to investigate factors associated with determination of root ²²Na(+) influx in the salt accumulation halophyte Suaeda maritima. We found that a 2 min of exposure to the ²²Na(+) labeled uptake solution was optimal for determining ²²Na(+) influx into excised roots of S. maritima and that 7 min of blotting is suitable in ²²Na(+) influx experiments. ²²Na(+) influx did not increase linearly with the increasing external Na(+) concentration, in the range tested, of 2 to 300 mM NaCl. But root ²²Na(+) influx and root Na(+) concentration were well correlated. ²²Na(+) influx into excised roots of S. maritima was not, however, well correlated with the plant size. All the above results indicated further that this ²²Na(+) isotope influx procedure is a good method for quantify Na(+) uptake rate by the roots of the salt accumulation halophyte.

  7. Similarity and divergence between the RNA polymerase alpha subunits from hyperthermophilic Thermotoga maritima and mesophilic Escherichia coli bacteria.

    PubMed

    Braun, Frederique; Marhuenda, Fanny B; Morin, Amelie; Guevel, Laetitia; Fleury, Fabrice; Takahashi, Masayuki; Sakanyan, Vehary

    2006-10-01

    The alpha subunit (alphaTm) of Thermotoga maritima RNA polymerase has been characterized to investigate its role in transcriptional regulation in one of the few known anaerobic hyperthermophilic bacteria. The highly thermostable alphaTm shares 54% similarity with its Escherichia coli analogue (alphaEc). The T. maritima rpoA gene coding the alpha subunit does not complement the thermosensitive rpoA112 mutation of E. coli. However, alphaTm and alphaEc show similar folding patterns as determined by circular dichroism. Purified alphaTm binds to the T. maritima PargGo promoter region (probably to a UP-element) and Arg282 appears to be crucial for DNA binding. The thermostable protein is also able to interact with transcription regulatory proteins, like ArgR from T. neapolitana or CRP from E. coli. These data indicate that the RNA polymerase alpha subunit might play a crucial role in the modulation of gene expression in hyperthermophiles.

  8. 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

  9. MiaB protein from Thermotoga maritima. Characterization of an extremely thermophilic tRNA-methylthiotransferase.

    PubMed

    Pierrel, Fabien; Hernandez, Heather L; Johnson, Michael K; Fontecave, Marc; Atta, Mohamed

    2003-08-08

    In Escherichia coli, the MiaB protein catalyzes the methylthiolation of N-6-isopentenyl adenosine in tRNAs, the last reaction step during biosynthesis of 2-methylthio-N-6-isopentenyl adenosine (ms2i6A-37). For the first time the thermophilic bacterium Thermotoga maritima is shown here to contain such a MiaB tRNA-modifying enzyme, named MiaBTm, and to synthesize ms2i6A-37 as demonstrated by an analysis of modified nucleosides from tRNA hydrolysates. The corresponding gene (TM0653) was identified by sequence similarity to the miaB gene cloned and expressed in E. coli. MiaBTm was purified to homogeneity and thoroughly characterized by biochemical and spectroscopic methods. It is a monomer of 443 residues with a molecular mass of 50,710 kilodaltons. Its amino acid sequence shares the CysXXX-CysXXCys sequence with MiaB from E. coli as well as with biotin synthase and lipoate synthase. This sequence was shown to be essential for chelation of an iron-sulfur center and for activity in these enzymes. As isolated, MiaBTm contains both iron and sulfide and an apoprotein form can coordinate up to 4 iron and 4 sulfur atoms per polypeptide chain. UV-visible absorption, resonance Raman, variable temperature magnetic circular dichroism, and EPR spectroscopy of MiaBTm indicate the presence of a [4Fe-4S]+2/+1 cluster under reducing and anaerobic conditions, whereas [3Fe-4S]+1 and [2Fe-2S]+2 forms are generated under aerobic conditions. The redox potential of the [4Fe-4S]+2/+1 transition is -495 +/- 10 mV (versus the normal hydrogen electrode). Finally, the expression of MiaBTm from T. maritima in an E. coli mutant strain lacking functional miaB gene allowed production of ms2i6A-37. These results provide further information on the enzymes involved in methylthiolation of tRNAs.

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

    PubMed

    McCall, Donna Drury; Rakocinski, Chet F

    2007-03-01

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

  11. Food and feeding ecology of purple sandpipers Calidris maritima on rocky intertidal habitats (Helgoland, German Bight)

    NASA Astrophysics Data System (ADS)

    Dierschke, Volker

    On the island of Helgoland (German Bight) Purple Sandpipers Calidris maritima feed mainly in the intertidal of piers and rocky shores. The main prey species are Littorina saxatilis and Mytilus edulis, complemented by crustaceans, polychaetes, other molluscs and green algae. Beach habitats are used as alternative feeding sites during storms. Feeding sites seem to be selected according to rates of assimilated energy intake. The most profitable habitat (wrack beds on the high-tide line with kelp-fly larvae, 16.8 W) is used after arrival in October but is not available during winter. Because of high intake rates in rocky habitats (13.1 W on piers, 5.5 W on mussel beds), which allow short daily feeding times, and available alternative feeding sites during storms, Purple Sandpipers do not need to carry fat reserves in winter like other waders wintering in central and Western Europe. This, and the ever accessible food supply of epibenthic macrofauna on rocky shores, may enable Purple Sandpipers to winter further north than other wader species.

  12. 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

  13. 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

  14. Expression and Characterization of a Novel Thermo-Alkalistable Lipase from Hyperthermophilic Bacterium Thermotoga maritima.

    PubMed

    Tian, Rui; Chen, Huayou; Ni, Zhong; Zhang, Qing; Zhang, Zhongge; Zhang, Tianxi; Zhang, Chunxia; Yang, Shengli

    2015-07-01

    A gene coding for lipase (Tm1350) from the hyperthermophilic bacterium Thermotoga maritima MSB8 was cloned and overexpressed by Escherichia coli. The enzyme can degrade substrates with both short and long acyl chain lengths. The apparent Km and Vmax values for p-nitrophenyl butyrate were 8 mM and 333 U/mg, respectively. The enzyme displayed optimal activity at pH 7.5 and 70 °C, maintained 66 % of the original activity after 8 h of incubation, and its half-lives at pHs 9 and 10 were 8 and 1 h. The activity of Tm1350 was stimulated up to 131 or 151 % of the original activity by incubating with 4 M urea or 20 % (v/v) methanol, and 90.1 or 70.2 % of the activity was maintained after 8 h incubation of the enzyme in 20 or 75 % (v/v) of the methanol, showing potential for biodiesel production. The activity of the enzyme without cysteine residue was stimulated up to 618 and 550 % of the original activity by incubating with dithiothreitol (DTT) and reduced glutathione (GSH) at a concentration of 1 mM. However, the circular dichroism spectra of the enzyme have no obvious change after DTT treatment. It is speculated that DTT interacts with potential residues in some key active sites without influence of structure.

  15. 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.

  16. 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.

  17. 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.

  18. The crystal structure of indoleglycerol-phosphate synthase from Thermotoga maritima. Kinetic stabilization by salt bridges.

    PubMed

    Knöchel, Thorsten; Pappenberger, Astrid; Jansonius, Johan N; Kirschner, Kasper

    2002-03-08

    The crystal structure of the thermostable indoleglycerol-phosphate synthase from Thermotoga maritima (tIGPS) was determined at 2.5 A resolution. It was compared with the structures of the thermostable sIGPS from Sulfolobus solfataricus and of the thermolabile eIGPS from Escherichia coli. The main chains of the three (beta alpha)(8)-barrel proteins superimpose closely, and the packing of side chains in the beta-barrel cores, as well as the architecture of surface loops, is very similar. Both thermostable proteins have, however, 17 strong salt bridges, compared with only 10 in eIGPS. The number of additional salt bridges in tIGPS and sIGPS correlates well with their reduced rate of irreversible thermal inactivation at 90 degrees C. Only 3 of 17 salt bridges in tIGPS and sIGPS are topologically conserved. The major difference between the two proteins is the preference for interhelical salt bridges in sIGPS and intrahelical ones in tIGPS. The different implementation of salt bridges in the closely related proteins suggests that the stabilizing effect of salt bridges depends rather on the sum of their individual contributions than on their location. This observation is consistent with a protein unfolding mechanism where the simultaneous breakdown of all salt bridges is the rate-determining step.

  19. Amorphus suaedae sp. nov., isolated from the root of a tidal flat plant, Suaeda maritima.

    PubMed

    Hwang, Jung Moon; Chung, Eu Jin; Park, Jeong Ae; Jeong, Jae Heon; Jeon, Che Ok; Chung, Young Ryun

    2013-10-01

    A novel bacterial strain, YC6899(T), was isolated from the root of Suaedae maritima growing on a tidal flat of Namhae Island, Korea. Cells were Gram-reaction-negative, rod-shaped, non-motile, slightly halophilic and heterotrophic. Strain YC6899(T) grew optimally at a salinity of 2-4 %, at 25-37 °C and at pH 6.5-8.0. Phylogenetic analysis of 16S rRNA gene sequences demonstrated that strain YC6899(T) was closely related to Amorphus orientalis YIM D10(T) (96.1 % similarity) and Amorphus coralli RS.Sph.026(T) (95.9 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unknown aminolipids, an unknown aminophospholipid, an unknown aminoglycolipid, unknown glycolipids and unknown lipids. The major fatty acids of strain YC6899(T) were C19 : 0 cyclo ω8c and C18 : 1ω7c. The G+C content of the genomic DNA was 61.3 mol%. Strain YC6899(T) contained ubiquinone-10 (Q-10) as the major respiratory quinone system. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain YC6899(T) represents a novel species within the genus Amorphus, for which the name Amorphus suaedae sp. nov. is proposed. The type strain is YC6899(T) ( = KACC 14912(T) = NBRC 107845(T)).

  20. 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.

  1. 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.

  2. Thermotoga maritima NusG: domain interaction mediates autoinhibition and thermostability

    PubMed Central

    Drögemüller, Johanna; Schneider, Christin; Schweimer, Kristian; Strauß, Martin; Wöhrl, Birgitta M.; Rösch, Paul; Knauer, Stefan H.

    2017-01-01

    NusG, the only universally conserved transcription factor, comprises an N- and a C-terminal domain (NTD, CTD) that are flexibly connected and move independently in Escherichia coli and other organisms. In NusG from the hyperthermophilic bacterium Thermotoga maritima (tmNusG), however, NTD and CTD interact tightly. This closed state stabilizes the CTD, but masks the binding sites for the interaction partners Rho, NusE and RNA polymerase (RNAP), suggesting that tmNusG is autoinhibited. Furthermore, tmNusG and some other bacterial NusGs have an additional domain, DII, of unknown function. Here we demonstrate that tmNusG is indeed autoinhibited and that binding to RNAP may stabilize the open conformation. We identified two interdomain salt bridges as well as Phe336 as major determinants of the domain interaction. By successive weakening of this interaction we show that after domain dissociation tmNusG-CTD can bind to Rho and NusE, similar to the Escherichia coli NusG-CTD, indicating that these interactions are conserved in bacteria. Furthermore, we show that tmNusG-DII interacts with RNAP as well as nucleic acids with a clear preference for double stranded DNA. We suggest that tmNusG-DII supports tmNusG recruitment to the transcription elongation complex and stabilizes the tmNusG:RNAP complex, a necessary adaptation to high temperatures. PMID:27899597

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

    PubMed

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

    1992-07-01

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

  4. Enzymatic synthesis of rare sugars with L-rhamnulose-1-phosphate aldolase from Thermotoga maritima MSB8.

    PubMed

    Li, Zijie; Wu, Xiaoru; Cai, Li; Duan, Shenglin; Liu, Jia; Yuan, Peng; Nakanishi, Hideki; Gao, Xiao-Dong

    2015-09-15

    L-Rhamnulose-1-phosphate aldolase from a thermophilic source (Thermotoga maritima MSB8) (RhaDT.mari) was heterologously overexpressed in Escherichia coli and the stereoselectivity of this enzyme with or without Nus tag was investigated. We also applied this enzyme to the synthesis of rare sugars D-psicose, D-sorbose, L-tagatose and L-fructose using our one-pot four-enzyme system. To the best of our knowledge, this is the first use of RhaD from a thermophilic source for rare sugar synthesis and the temperature tolerance of this enzyme paves the path for large scale fermentation.

  5. Microsatellite markers for the tetraploid halophyte Suaeda maritima (L.) Dumort. (Chenopodiaceae) and cross-species amplification in related taxa.

    PubMed

    Prinz, Kathleen; Hensen, Isabell; Schie, Stephan; Debener, Thomas; Weising, Kurt

    2009-07-01

    We developed 12 polymorphic microsatellite markers for the tetraploid halophyte Suaeda maritima (Chenopodiaceae). Population genetic parameters were estimated for three populations from different habitats (coastal and inland), using the program Tetrasat. Between two and 15 alleles per locus were observed. Mean expected heterozygosities (H(E) ) and Shannon-Wiener Diversity Indices (H') per locus and population ranged from zero to 0.852, and from zero to 2.990, respectively. The two inland populations were less diverse than the coastal one at most of the loci. All markers cross-amplified in the closely related Suaeda salsa, and all but one were transferable to Suaeda spicata and Suaeda salinaria.

  6. 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

    2004-10-04

    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.

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

    NASA Astrophysics Data System (ADS)

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

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

  8. Hoeflea suaedae sp. nov., an endophytic bacterium isolated from the root of the halophyte Suaeda maritima.

    PubMed

    Chung, Eu Jin; Park, Jeong Ae; Pramanik, Prabhat; Bibi, Fehmida; Jeon, Che Ok; Chung, Young Ryun

    2013-06-01

    A Gram-negative, aerobic, short rod-shaped bacterium, designated strain YC6898(T), was isolated from the surface-sterilized root of a halophyte (Suaeda maritima) inhabiting tidal flat of Namhae Island, Korea. Strain YC6898(T) grew optimally at 30-37 °C and pH 6.5-7.5. The strain inhibited mycelial growth of Pythium ultimum and Phytophthora capsici. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain YC6898(T) belongs to the genus Hoeflea in the family Phyllobacteriaceae. Its closest relatives were Hoeflea alexandrii AM1V30(T) (96.7% 16S rRNA gene sequence similarity), Hoeflea anabaenae WH2K(T) (95.7%), Hoeflea phototrophica DFL-43(T) (95.5%) and Hoeflea marina LMG 128(T) (94.8%). Strain YC6898(T) contained Q-10 as the major ubiquinone. The major fatty acids of strain YC6898(T) were C18:1ω7c (61.1%), C16:0 (11.9%), 11-methyl C18:1ω7c (9.6%) and C19:0 cyclo ω8c (8.0%). The polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, unknown lipids and an unknown glycolipid. The total genomic DNA G+C content was 53.7 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic analysis, strain YC6898(T) represents a novel species of the genus Hoeflea, for which the name Hoeflea suaedae sp. nov. is proposed. The type strain is YC6898(T) (=KACC 14911(T)=NBRC 107700(T)).

  9. 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.

  10. 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.

  11. 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.

  12. Development and evolution of segmentation assessed by geometric morphometrics: The centipede Strigamia maritima as a case study.

    PubMed

    Savriama, Yoland; Gerber, Sylvain; Baiocco, Matteo; Debat, Vincent; Fusco, Giuseppe

    2017-03-21

    Using the centipede model species Strigamia maritima as a subject of study, we illustrate the potential of geometric morphometrics for investigating the development and evolution of segmentation, with a specific focus on post-embryonic segmental patterning. We show how these techniques can contribute detailed descriptive data for comparative purposes, but also precious information on some features of the developmental system that are considered relevant for the evolvability of a segmented body architecture, such as developmental stability and canalization. Morphometric analyses allow to separately investigate several sources of phenotypic variation along a segmented body axis, like constitutive and random segment heteronomy, both within and among individuals. Specifically, in S. maritima, the segmental pattern of ventral sclerite shapes mirrors that of their bilateral fluctuating asymmetry and among-individual variation in associating the most anterior and most posterior segments in diverging from the central ones. Also, among segments, there seems to be a correlation between fluctuating asymmetry and shape variation among individuals, suggesting that canalization and developmental stability are somehow associated. Overall, these associations might stem from a joint influence of the segmental position on the two processes of developmental buffering.

  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. [The construction of Thermotoga maritima endoglucanase Cel12B fused with CBD and the characterization of chimeric enzyme].

    PubMed

    Li, Xiang-Qian; Shao, Wei-Lan

    2006-10-01

    Thermotoga maritima is strictly anaerobic and extremely thermophilic bacteria. The endoglucanase found in T. maritima showed extremely high thermostability and considerable potential in industrial application. Endoglucanase (Tm) Cel12B is extracellular enzyme. Tm Cel12B did not contain a cellulose-binding domain (CBD)and lacked activity on crystalline cellulose. Tm XynA is composed of catalytic domain (CD) and cellulose-binding domain (CBD). As such, the gene of CBD from Tm XynA was fused at the carboxyl-terminus of Tm Cel12B and recombinant plasmid pET-20b- Cel 12B- CBD was obtained. The recombinant plasmid pET-20b- Cel 12 B- CBD was transformed to E. coli JM109 (DE3), induced by IPTG. The properties of chimeric enzyme were determined. The chimeric enzyme displayed pH activity and stability profiles similar to those of parental enzyme with optimal pH 5.8. The optimal activity of the chimera was observed at 100 degrees C and the enzyme kept 87% of original enzyme activity after incubated at 90 degrees C for 2h. A notable feature on substrate specificity is that the chimeric enzyme has the capacity to hydrolases crystalline cellulose.

  15. 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.

  16. Hepatoprotective and antioxidant properties of Suaeda maritima (L.) dumort ethanolic extract on concanavalin-A induced hepatotoxicity in rats.

    PubMed

    Ravikumar, S; Gnanadesigan, M; Inbaneson, S Jacob; Kalaiarasi, A

    2011-06-01

    Hepatoprotective and antioxidant properties of Suaeda maritima (L.) Dumort on concanavalin-A induced stress in Wistar albino rats have been reported. Rats were administered with ethanolic extract of Suaeda maritimna at the concentration of 75, 150 and 300 mg/kg of body wt. for 9 days and concanavalin-A was administrated (iv) 12 mg/kg on 9th day. Rats in concanavalin-A administered group showed elevated levels of AST, ALT, ALP and bilurubin. Pretreatment of rats with ethanolic extract (300 mg/kg) significantly reduced these serum parameters compared to concavalin-A administered group. Histopathological examination of liver sections showed that, normal liver architecture was disturbed by hepatotoxin intoxication. The extract treated group and silymarin treated group retained the normal cell architecture, although less visible changes were observed. Preliminary phytochemical analysis showed the presence of triterpenioids and may be responsible for the hepatoprotective activity. The LD50 was calculated as 3 g/kg of the body weight. IC50 values of hydroxyl (52.21+/-1.32 microg/ml) and nitric oxide radicals (09.14+/-0.94 microg/ml) scavenging results showed comparable activity with vitamin-C. Results of this study may be useful for the development of herbal medicine from Suaeda maritima for the treatment of hepatitis.

  17. 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-Łysoniewska, 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.

  18. Modulation of superoxide dismutase (SOD) isozymes by organ development and high long-term salinity in the halophyte Cakile maritima.

    PubMed

    Houmani, Hayet; Rodríguez-Ruiz, Marta; Palma, José M; Abdelly, Chedly; Corpas, Francisco J

    2016-05-01

    Superoxide dismutase (SOD) activity catalyzes the disproportionation of superoxide radicals into hydrogen peroxide and oxygen. This enzyme is considered to be a first line of defense for controlling the production of reactive oxygen species (ROS). In this study, the number and type of SOD isozymes were identified in the principal organs (roots, stems, leaves, flowers, and seeds) of Cakile maritima. We also analyzed the way in which the activity of these SOD isozymes is modulated during development and under high long-term salinity (400 mM NaCl) stress conditions. The data indicate that this plant contains a total of ten SOD isozymes: two Mn-SODs, one Fe-SOD, and seven CuZn-SODs, with the Fe-SOD being the most prominent isozyme in the different organs analyzed. Moreover, the modulation of SOD isozymes, particularly CuZn-SODs, was only detected during development and under severe salinity stress conditions. These data suggest that, in C. maritima, the occurrence of these CuZn-SODs in roots and leaves plays an adaptive role since this CuZn-SOD isozyme might replace the diminished Fe-SOD activity under salinity stress to overcome this adverse environmental condition.

  19. H2O2 seed priming improves tolerance to salinity; drought and their combined effect more than mannitol in Cakile maritima when compared to Eutrema salsugineum.

    PubMed

    Ellouzi, Hasna; Sghayar, Souhir; Abdelly, Chedly

    2017-03-01

    The effect of H2O2 and mannitol seed priming was investigated on plant growth, oxidative stress biomarkers and activities of antioxidant enzymes in leaves of Cakile maritima and Eutrema salsugineum, when exposed to drought and salt stress, either separately applied or combined. Under unprimed conditions, drought severely restricted growth (40% as compared to the control) and redox balance of C. maritima seedlings, whereas E. salsugineum showed these drastic effects under individual salinity (33% as compared to the control). Combined salinity and drought maintained and even stimulated the antioxidant defense of both plants from unprimed seeds. Both priming agents (mannitol and H2O2) significantly ameliorated growth and antioxidant defense of both species grown under salinity, drought and their combined effect. However, H2O2 priming appeared to be more beneficial in C. maritima seedlings. Indeed, oxidative injuries were significantly reduced, together with significantly higher concentrations of ascorbic acid (36%), glutathione (2-fold) and proline production (2-fold), leading to a greater redox balance that was closely associated with enhanced antioxidant enzyme activities, specifically under salt stress. Overall, our results indicate that it is very likely that H2O2 priming, due to its signal role, improves C. maritima tolerance to both osmotic stresses and enables the plant to memorize and to decode early signals that are rapidly activated when plants are later exposed to stress.

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

    PubMed Central

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

    2013-01-01

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

  1. In vivo selection for the enhancement of Thermotoga maritima exopolygalacturonase activity at neutral pH and low temperature.

    PubMed

    Drone, Jullien; Dion, Michel; Tellier, Charles; Rabiller, Claude

    2007-01-01

    The aim of this study was to develop an Escherichia coli-based metabolic selection system for the uncovering of new oligogalacturonate-active enzymes. Based on the expression of the specific permease TogMNAB, this system enabled the entry of oligogalacturonates into the cytoplasm of E. coli thus providing a modified strain usable for this purpose. This tool was used for the metabolic selection of Thermotoga maritima exopolygalacturonase (TmGalU) mutants enabling the uptake of sodium trigalacturonate as the sole carbon source by the bacterium. In only one round of error-prone PCR and selection, mutants of TmGalU with a 4-fold increased turnover at pH 7.0 and 2-fold more active at 37 degrees C than wild-type enzyme were isolated. These results show the versatility of this strain for the evolution of oligogalacturonate-active enzymes.

  2. Autonomous folding of the excised coenzyme-binding domain of D-glyceraldehyde 3-phosphate dehydrogenase from Thermotoga maritima.

    PubMed Central

    Jecht, M.; Tomschy, A.; Kirschner, K.; Jaenicke, R.

    1994-01-01

    An important question in protein folding is whether compact substructures or domains are autonomous units of folding and assembly. The protomer of the tetrameric D-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima has a complex coenzyme-binding domain, in which residues 1-146 form a compact substructure with the last 31 residues (313-333). Here it is shown that the gene of a single-chain protein can be expressed in Escherichia coli after deleting the 163 codons corresponding to the interspersed catalytic domain (150-312). The purified gene product is a soluble, monomeric protein that binds both NAD+ and NADH strongly and possesses the same unfolding transition induced by guanidinium chloride as the native tetramer. The autonomous folding of the coenzyme-binding domain has interesting implications for the folding, assembly, function, and evolution of the native enzyme. PMID:8019412

  3. Drought and cadmium may be as effective as salinity in conferring subsequent salt stress tolerance in Cakile maritima.

    PubMed

    Ellouzi, Hasna; Ben Hamed, Karim; Asensi-Fabado, Maria Amparo; Müller, Maren; Abdelly, Chedly; Munné-Bosch, Sergi

    2013-05-01

    Plants are often exposed to a combination of stresses, which can occur simultaneously or at different times throughout their life. In this study, the effects of salinity, drought and cadmium pre-treatments were evaluated on the subsequent response of Cakile maritima, a halophytic species, to various levels of salinity (from 100 to 800 mM NaCl) after a recovery time of 2 weeks. Studies were performed in two sets of experiments in a glasshouse under short and long photoperiod (November and July, respectively). In both experiments and in contrast to control plants (not exposed to any previous stress), plants previously exposed to drought, salt or cadmium stress showed lower levels of hydrogen peroxide and malondialdehyde, an indicator of lipid peroxidation, upon salt treatment, particularly at high NaCl concentrations. Oxidative stress alleviation was not only observed at 800 mM NaCl under short photoperiod, but also at 600 and 800 mM NaCl under long photoperiod in terms of reduced salt-induced increases in hydrogen peroxide and malondialdehyde levels in plants previously exposed to drought, salt or cadmium stress. Previous exposure of plants to all stresses additionally caused decreased levels of jasmonic acid, which might be associated with a lower oxidative stress, differences being observed again at 800 mM NaCl only under short photoperiod and at 600 and 800 mM NaCl under long photoperiod. In conclusion, a relatively long-term stress memory was found in C. maritima pre-exposed to salinity, drought or cadmium, which resulted in a lower oxidative stress when subsequently exposed to salinity. The positive effects of drought and cadmium were of similar magnitude to those provided by salt pre-exposure, which indicated an effective cross-tolerance response in this species.

  4. Subunit exchange by CheA histidine kinases from the mesophile Escherichia coli and the thermophile Thermotoga maritima.

    PubMed

    Park, Sang-Youn; Quezada, Cindy M; Bilwes, Alexandrine M; Crane, Brian R

    2004-03-02

    Dimerization of the chemotaxis histidine kinase CheA is required for intersubunit autophosphorylation [Swanson, R. V., Bourret, R. B., and Simon, M. I. (1993) Mol. Microbiol. 8, 435-441]. Here we show that CheA dimers exchange subunits by the rate-limiting dissociation of a central four-helix bundle association domain (P3), despite the high stability of P3 versus unfolding. P3 alone determines the stability and exchange properties of the CheA dimer. For CheA proteins from the mesophile Escherichia coli and the thermophile Thermotoga maritima, subunit dissociation activates at temperatures where the respective organisms live (37 and 80 degrees C). Under destabilizing conditions, P3 dimer dissociation is cooperative with unfolding. Chemical denaturation is reversible for both EP3 and TP3. Aggregation accompanies thermal unfolding for both proteins under most conditions, but thermal unfolding is reversible and two-state for EP3 at low protein concentrations. Residue differences within interhelical loops may account for the contrasted thermodynamic properties of structurally similar EP3 and TP3 (41% sequence identity). Under stabilizing conditions, greater correlation between activation energy for dimer dissociation and P3 stability suggests more unfolding in the dissociation of EP3 than TP3. Furthermore, destabilization of extended conformations by glycerol slows relative dissociation rates more for EP3 than for TP3. Nevertheless, at physiological temperatures, neither protein likely unfolds completely during subunit exchange. EP3 and TP3 will not exchange subunits with each other. The receptor coupling protein CheW reduces the subunit dissociation rate of the T. maritima CheA dimer by interacting with the regulatory domain P5.

  5. 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

  6. 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

  7. 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.

  8. 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

  9. Salt-inducible isoform of plasma membrane H+ATPase gene in rice remains constitutively expressed in natural halophyte, Suaeda maritima.

    PubMed

    Sahu, Binod Bihari; Shaw, Birendra Prasad

    2009-07-01

    To look into a possible involvement of plasma membrane H+ATPase (PM-H+ATPase, EC 3.6.3.6) in mitigation of physiological disturbances imposed by salt stress, response of the enzyme was studied in two Oryza sativa Indica cultivars, salt-tolerant Lunishri and non-tolerant Badami, and a natural halophyte Suaeda maritima after challenge of the young plants with NaCl. Significant increase in activity of the enzyme was observed in response to NaCl in all the test plants with S. maritima showing maximum increase. Protein blot analysis, however, did not show any increase in the amount of the enzyme (protein). RNA blot analysis, on the other hand, revealed significant increase in transcript level of the enzyme upon NaCl treatment. In the rice cultivars, salt treatment also induced expression of a new isoform of PM-H+ATPase gene, not reported so far. The induced transcript showed maximum homology to OSA7 (O. sativa PM-H+ATPase isoform 7). Similar transcript message, however, remained constitutively present in S. maritima, along with the transcript of another isoform of PM-H+ATPase showing resemblance to OSA3 (O. sativa PM-H+ATPase isoform 3). The latter was the only PM-H+ATPase isoform expressed in both the rice cultivars not exposed to NaCl. In the salt-treated test plants, both rice and S. maritima, the salt-inducible PM-H+ATPase isoform resembling OSA7 was expressed in much greater amount than that resembling OSA3. Appearance of a new PM-H+ATPase transcript, besides increase in the enzyme activity, indicates the important role of the enzyme in maintaining ion-homeostasis in plants under salt stress, enabling them to survive under saline conditions.

  10. 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.

  11. 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

  12. Evolutionary optimization of life-history traits in the sea beet Beta vulgaris subsp. maritima: Comparing model to data

    NASA Astrophysics Data System (ADS)

    Hautekèete, N.-C.; Van Dijk, H.; Piquot, Y.; Teriokhin, A.

    2009-01-01

    At evolutionary equilibrium, ecological factors will determine the optimal combination of life-history trait values of an organism. This optimum can be assessed by assuming that the species maximizes some criterion of fitness such as the Malthusian coefficient or lifetime reproductive success depending on the degree of density-dependence. We investigated the impact of the amount of resources and habitat stability on a plant's age at maturity and life span by using an evolutionary optimization model in combination with empirical data. We conducted this study on sea beet, Beta vulgaris subsp. maritima, because of its large variation in life span and age at first reproduction along a latitudinal gradient including considerable ecological variation. We also compared the consequence in our evolutionary model of maximizing either the Malthusian coefficient or the lifetime reproductive success. Both the data analysis and the results of evolutionary modeling pointed to habitat disturbance and resources like length of the growing season as factors negatively related to life span and age at maturity in sea beet. Resource availability had a negative theoretical influence with the Malthusian coefficient as the chosen optimality criterion, while there was no influence in the case of lifetime reproductive success. As suggested by previous theoretical work the final conclusion on what criterion is more adequate depends on the assumptions of how in reality density-dependence restrains population growth. In our case of sea beet data R0 seems to be less appropriate than λ.

  13. Sex-specific fitness variation in gynodioecious Beta vulgaris ssp. maritima: do empirical observations fit theoretical predictions?

    PubMed

    De Cauwer, I; Arnaud, J-F; Courseaux, A; Dufay, M

    2011-11-01

    In gynodioecious species, in which hermaphroditic and female plants co-occur, the maintenance of sexual polymorphism relies on the genetic determination of sex and on the relative fitness of the different phenotypes. Flower production, components of male fitness (pollen quantity and pollen quality) and female fitness (fruit and seed set) were measured in gynodioecious Beta vulgaris spp. maritima, in which sex is determined by interactions between cytoplasmic male sterility (CMS) genes and nuclear restorers of male fertility. The results suggested that (i) female had a marginal advantage over hermaphrodites in terms of flower production only, (ii) restored CMS hermaphrodites (carrying both CMS genes and nuclear restorers) suffered a slight decrease in fruit production compared to non-CMS hermaphrodites and (iii) restored CMS hermaphrodites were poor pollen producers compared to non-CMS hermaphrodites, probably as a consequence of complex determination of restoration. These observations potentially have important consequences for the conditions of maintenance of sexual polymorphism in B. vulgaris and are discussed in the light of existing theory on evolutionary dynamics of gynodioecy.

  14. 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.

  15. 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 48 h 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.

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

    PubMed

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

    2015-06-10

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

  17. Cytotoxic and antimicrobial constituents of the bark of Diospyros maritima collected in two geographical locations in Indonesia.

    PubMed

    Gu, Jian-Qiao; Graf, Tyler N; Lee, Dongho; Chai, Hee-Byung; Mi, Qiuwen; Kardono, Leonardus B S; Setyowati, Fransisca M; Ismail, Rachman; Riswan, Soedarsono; Farnsworth, Norman R; Cordell, Geoffrey A; Pezzuto, John M; Swanson, Steven M; Kroll, David J; Falkinham, Joseph O; Wall, Monroe E; Wani, Mansukh C; Kinghorn, A Douglas; Oberlies, Nicholas H

    2004-07-01

    Bioactivity-directed fractionation of extracts of two Diospyros maritima bark samples from Indonesia,one collected at sea level in a beach forest in Java and the other collected at a slight elevation away from the sea shore on the island of Lombok, yielded a diverse set of secondary metabolites. The naphthoquinone plumbagin (1), although found in extracts of both specimens, constituted a much larger percentage of the former sample, which also yielded a series of plumbagin dimers, maritinone (2), chitranone (3), and zeylanone (4). The latter sample yielded a new naphthoquinone derivative, (4S)-shinanolone (5), and a new natural product coumarin, 7,8-dimethoxy-6-hydroxycoumarin (6), along with three other analogues of plumbagin, 2-methoxy-7-methyljuglone (7), 3-methoxy-7-methyljuglone (8), and 7-methyljuglone (9). The structures of compounds 5 and 6 were elaborated by physical, spectral, and chemical methods. All of the isolates were evaluated in both cytotoxicity and antimicrobial assays, and structure-activity relationships of these naphthoquinones are proposed. Plumbagin (1) and maritinone (2) were evaluated also for in vivo antitumor activity in the hollow fiber assay, but both were found to be inactive.

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

    PubMed

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

    2015-04-01

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

  19. 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.

  20. Transcriptome Analysis of the Response to NaCl in Suaeda maritima Provides an Insight into Salt Tolerance Mechanisms in Halophytes

    PubMed Central

    Tambat, Subodh; Vasudevan, Madavan

    2016-01-01

    Although salt tolerance is a feature representative of halophytes, most studies on this topic in plants have been conducted on glycophytes. Transcriptome profiles are also available for only a limited number of halophytes. Hence, the present study was conducted to understand the molecular basis of salt tolerance through the transcriptome profiling of the halophyte Suaeda maritima, which is an emerging plant model for research on salt tolerance. Illumina sequencing revealed 72,588 clustered transcripts, including 27,434 that were annotated using BLASTX. Salt application resulted in the 2-fold or greater upregulation of 647 genes and downregulation of 735 genes. Of these, 391 proteins were homologous to proteins in the COGs (cluster of orthologous groups) database, and the majorities were grouped into the poorly characterized category. Approximately 50% of the genes assigned to MapMan pathways showed homology to S. maritima. The majority of such genes represented transcription factors. Several genes also contributed to cell wall and carbohydrate metabolism, ion relation, redox responses and G protein, phosphoinositide and hormone signaling. Real-time PCR was used to validate the results of the deep sequencing for the most of the genes. This study demonstrates the expression of protein kinase C, the target of diacylglycerol in phosphoinositide signaling, for the first time in plants. This study further reveals that the biochemical and molecular responses occurring at several levels are associated with salt tolerance in S. maritima. At the structural level, adaptations to high salinity levels include the remodeling of cell walls and the modification of membrane lipids. At the cellular level, the accumulation of glycinebetaine and the sequestration and exclusion of Na+ appear to be important. Moreover, this study also shows that the processes related to salt tolerance might be highly complex, as reflected by the salt-induced enhancement of transcription factor

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

    PubMed Central

    Boucher, Nathalie; Noll, Kenneth M.

    2011-01-01

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

  2. 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

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

    PubMed Central

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

    2010-01-01

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

  4. NMR structure of the conserved hypothetical protein TM0487 from Thermotoga maritima: implications for 216 homologous DUF59 proteins.

    PubMed

    Almeida, Marcius S; Herrmann, Torsten; Peti, Wolfgang; Wilson, Ian A; Wüthrich, Kurt

    2005-11-01

    The NMR structure of the conserved hypothetical protein TM0487 from Thermotoga maritima represents an alpha/beta-topology formed by the regular secondary structures alpha1-beta1-beta2-alpha2-beta3-beta4-alpha3- beta5-3(10)-alpha4, with a small anti-parallel beta-sheet of beta-strands 1 and 2, and a mixed parallel/anti-parallel beta-sheet of beta-strands 3-5. Similar folds have previously been observed in other proteins, with amino acid sequence identity as low as 3% and a variety of different functions. There are also 216 sequence homologs of TM0487, which all have the signature sequence of domains of unknown function 59 (DUF59), for which no three-dimensional structures have as yet been reported. The TM0487 structure thus presents a platform for homology modeling of this large group of DUF59 proteins. Conserved among most of the DUF59s are 13 hydrophobic residues, which are clustered in the core of TM0487. A putative active site of TM0487 consisting of residues D20, E22, L23, T51, T52, and C55 is conserved in 98 of the 216 DUF59 sequences. Asp20 is buried within the proposed active site without any compensating positive charge, which suggests that its pK(a) value may be perturbed. Furthermore, the DUF59 family includes ORFs that are part of a conserved chromosomal group of proteins predicted to be involved in Fe-S cluster metabolism.

  5. 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

  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. Directed evolution of the alpha-L-fucosidase from Thermotoga maritima into an alpha-L-transfucosidase.

    PubMed

    Osanjo, George; Dion, Michel; Drone, Jullien; Solleux, Claude; Tran, Vinh; Rabiller, Claude; Tellier, Charles

    2007-01-30

    The alpha-L-fucosidase from Thermotoga maritima (Tm alpha fuc) was converted into alpha-L-transfucosidase variants by directed evolution. The wild-type enzyme catalyzes oligosaccharide synthesis by transfer of a fucosyl residue from a pNP-fucoside donor to pNP-fucoside (self-condensation) with alpha-(1-->3) regioselectivity or pNP-galactoside (transglycosylation) with alpha-(1-->2) regioselectivity at low yields (7%). The wild-type enzyme was submitted to one cycle of mutagenesis, followed by rational recombination of the selected mutations, which allowed identification of variants with improved transferase activity. The transferase and hydrolytic kinetics of all the mutants were assessed by NMR methods and capillary electrophoresis. It was shown that the best mutant exhibited a dramatic 32-fold increase in the transferase/hydrolytic kinetic ratio, while keeping 60% of the overall wild-type enzyme activity. Accordingly, the maximum yield of a specific transglycosylation product [pNP-Gal-alpha-(1-->2)-Fuc] reached more than 60% compared to 7% with WT enzyme at equimolar and low concentrations of donor and acceptor (10 mM). Such an improvement was obtained with only three mutations (T264A, Y267F, L322P), which were all located in the second amino acid shell of the fucosidase active site. Molecular modeling suggested that some of these mutations (T264A, Y267F) cause a reorientation of the amino acids that are in direct contact with the substrates, resulting in a better docking energy. Such mutants with high transglycosidase activity may constitute novel enzymatic tools for the synthesis of fucooligosaccharides.

  8. 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

  9. Modification of granular corn starch with 4-alpha-glucanotransferase from Thermotoga maritima: effects on structural and physical properties.

    PubMed

    Oh, E J; Choi, S J; Lee, S J; Kim, C H; Moon, T W

    2008-04-01

    Corn starch was converted using alpha-1,4-glucanotransferase from Thermotoga maritima (Tm alpha GT), a hyperthermophilic bacterium, without inducing gelatinization, and the structural changes and physical properties of the modified starches were investigated. Enzyme modification was induced at 65 degrees C for 8, 16, or 24 h, and the morphology of the modified starches was observed with light and scanning electron microscopy. Granule integrity was mostly maintained after enzyme treatment, although some granules were partially fragmented as evidenced by enlarged surface pores and some cracks. The modified starches had lower apparent amylose levels than raw starch. The molecular weights of amylose and amylopectin molecules in the treated starches were lower than those of raw starch, and the amount of branched molecules, which had much lower molecular weights, also increased in the treated starches. The chain-length distribution of amylopectin showed an increased number of shorter branched chains. The modified starches showed a wider melting temperature range and a lower melting enthalpy than that of raw starch. The X-ray diffraction pattern of the modified starches showed typical A-type starch peaks, but the relative crystallinities were lower than that of raw starch. The solubility and paste clarity of the modified starches were much higher than those of raw starch. The modified starch gels maintained their rigidity over the whole frequency range tested and showed thermoreversibility between 4 and 75 degrees C. These results suggest that Tm alpha GT can be used to produce granular corn starch, which contains amylose and amylopectin having lower molecular weights and a thermoreversible gelation property.

  10. Crystal structure of butyrate kinase 2 from Thermotoga maritima, a member of the ASKHA superfamily of phosphotransferases.

    PubMed

    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-A 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.

  11. Genetic structure of coastal and inland populations of the annual halophyte Suaeda maritima (L.) dumort. in Central Europe, inferred from amplified fragment length polymorphism markers.

    PubMed

    Prinz, K; Weising, K; Hensen, I

    2009-11-01

    Naturally occurring inland salt habitats are highly threatened due to increasing fragmentation and area reduction, while the surroundings of former potash mining dumps have experienced a massive invasion by halophytes over the last 20 years. We reconstructed colonisation patterns of these purely anthropogenic inland salt sites using molecular markers in the obligate halophyte Suaeda maritima (L.) dumort. (Chenopodiaceae), a typical plant in such areas. In the present study, 120 individual plants from 40 coastal and inland populations in Central Europe were subjected to AFLP analysis with nine primer combinations. A total of 243 AFLP band positions were scored as presence/absence characters. Genetic diversity values were not significantly different in populations from natural and anthropogenic inland salt sites as compared to coastal habitats. Results from principal coordinate analysis, neighbour-joining analysis and analysis of molecular variance (amova) all indicated that most of the genetic variation is preserved within populations, while genetic differentiation among populations is comparatively low. We conclude that S. maritima has repeatedly and independently colonised the surroundings of former potash mining dumps in Central Germany. However, the absence of founder effects and the lack of phylogeographic structure prevented us from identifying putative donor populations.

  12. Genetic Diversity and Physiological Performance of Portuguese Wild Beet (Beta vulgaris spp. maritima) from Three Contrasting Habitats.

    PubMed

    Ribeiro, Isa C; Pinheiro, Carla; Ribeiro, Carla M; Veloso, Maria M; Simoes-Costa, Maria C; Evaristo, Isabel; Paulo, Octávio S; Ricardo, Cândido P

    2016-01-01

    The establishment of stress resilient sugar beets (Beta vulgaris spp. vulgaris) is an important breeding goal since this cash crop is susceptible to drought and salinity. The genetic diversity in cultivated sugar beets is low and the beet wild relatives are useful genetic resources for tolerance traits. Three wild beet populations (Beta vulgaris spp. maritima) from contrasting environments, Vaiamonte (VMT, dry inland hill), Comporta (CMP, marsh) and Oeiras (OEI, coastland), and one commercial sugar beet (Isella variety, SB), are compared. At the genetic level, the use of six microsatellite allowed to detect a total of seventy six alleles. It was observed that CMP population has the highest value concerning the effective number of alleles and of expected heterozygosity. By contrast, sugar beet has the lowest values for all the parameters considered. Loci analysis with STRUCTURE allows defining three genetic clusters, the sea beet (OEI and CMP), the inland ruderal beet (VMT) and the sugar beet (SB). A screening test for progressive drought and salinity effects demonstrated that: all populations were able to recover from severe stress; drought impact was higher than that from salinity; the impact on biomass (total, shoot, root) was population specific. The distinct strategies were also visible at physiological level. We evaluated the physiological responses of the populations under drought and salt stress, namely at initial stress stages, late stress stages, and early stress recovery. Multivariate analysis showed that the physiological performance can be used to discriminate between genotypes, with a strong contribution of leaf temperature and leaf osmotic adjustment. However, the separation achieved and the groups formed are dependent on the stress type, stress intensity and duration. Each of the wild beet populations evaluated is very rich in genetic terms (allelic richness) and exhibited physiological plasticity, i.e., the capacity to physiologically adjust to

  13. Genetic Diversity and Physiological Performance of Portuguese Wild Beet (Beta vulgaris spp. maritima) from Three Contrasting Habitats

    PubMed Central

    Ribeiro, Isa C.; Pinheiro, Carla; Ribeiro, Carla M.; Veloso, Maria M.; Simoes-Costa, Maria C.; Evaristo, Isabel; Paulo, Octávio S.; Ricardo, Cândido P.

    2016-01-01

    The establishment of stress resilient sugar beets (Beta vulgaris spp. vulgaris) is an important breeding goal since this cash crop is susceptible to drought and salinity. The genetic diversity in cultivated sugar beets is low and the beet wild relatives are useful genetic resources for tolerance traits. Three wild beet populations (Beta vulgaris spp. maritima) from contrasting environments, Vaiamonte (VMT, dry inland hill), Comporta (CMP, marsh) and Oeiras (OEI, coastland), and one commercial sugar beet (Isella variety, SB), are compared. At the genetic level, the use of six microsatellite allowed to detect a total of seventy six alleles. It was observed that CMP population has the highest value concerning the effective number of alleles and of expected heterozygosity. By contrast, sugar beet has the lowest values for all the parameters considered. Loci analysis with STRUCTURE allows defining three genetic clusters, the sea beet (OEI and CMP), the inland ruderal beet (VMT) and the sugar beet (SB). A screening test for progressive drought and salinity effects demonstrated that: all populations were able to recover from severe stress; drought impact was higher than that from salinity; the impact on biomass (total, shoot, root) was population specific. The distinct strategies were also visible at physiological level. We evaluated the physiological responses of the populations under drought and salt stress, namely at initial stress stages, late stress stages, and early stress recovery. Multivariate analysis showed that the physiological performance can be used to discriminate between genotypes, with a strong contribution of leaf temperature and leaf osmotic adjustment. However, the separation achieved and the groups formed are dependent on the stress type, stress intensity and duration. Each of the wild beet populations evaluated is very rich in genetic terms (allelic richness) and exhibited physiological plasticity, i.e., the capacity to physiologically adjust to

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

    PubMed Central

    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

    2014-01-01

    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

  15. Pollen limitation of female reproductive success at fine spatial scale in a gynodioecious and wind-pollinated species, Beta vulgaris ssp. maritima.

    PubMed

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

    2010-12-01

    In sexually polymorphic plants, the spatial distribution of sexes is usually not random. Local variation in phenotype frequencies is expected to affect individual fitness of the different phenotypes. For gynodioecious species, with co-occurrence of hermaphrodites and females, if sexual phenotypes are structured in space and pollen flow is spatially restricted, local pollen availability should vary among patches. Female fitness may thus be low when hermaphrodites are locally rare. To test this hypothesis, we analysed how the reproductive output of females varied among patches within two natural study sites of the gynodioecious wind-pollinated Beta vulgaris ssp. maritima. Plants growing in female-biased areas and experiencing pollen limitation were found to have low fruit and seed sets but did not reallocate resources towards better offspring. Our results show that fine-scale processes influence individual fitness and the evolution of sex ratio in sexually polymorphic plants.

  16. Potential for evolutionary change in the seasonal timing of germination in sea beet (Beta vulgaris ssp. maritima) mediated by seed dormancy.

    PubMed

    Wagmann, Kristen; Hautekèete, Nina-Coralie; Piquot, Yves; Van Dijk, Henk

    2010-07-01

    In sea beet (Beta vulgaris ssp. maritima), germination occurs in autumn or spring and is mediated by dormancy which can be released by cold or dry periods. Environmental change such as current climate change may require evolutionary response in seasonal timing. Here, we explore the potential for such evolutionary change. Seed dormancy was studied in a composite population based on seeds from all over the species range in France together with several generations of reciprocal crosses. We found high, repeatable variability for dormancy rate among individuals under greenhouse conditions and confirmed its relevance for germination phenology in the field. Our data fitted best with an exclusively maternal determination of the dormancy phenotype. Narrow-sense heritability, h(2) approximately 0.5 in the composite population and approximately 0.4 in the original local populations, was such that rapid evolutionary change in the relative proportions of autumn and spring germination may be possible.

  17. 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

  18. Extremely thermostable L(+)-lactate dehydrogenase from Thermotoga maritima: cloning, characterization, and crystallization of the recombinant enzyme in its tetrameric and octameric state.

    PubMed Central

    Ostendorp, R.; Auerbach, G.; Jaenicke, R.

    1996-01-01

    L(+)-lactate dehydrogenase (LDH; E.C.1.1.1.27) from the hyperthermophilic bacterium Thermotoga maritima has been shown to represent the most stable LDH isolated so far (Wrba A, Jaenicke R, Huber R, Stetter KO, 1990, Eur J Biochem 188:195-201). In order to obtain the enzyme in amounts sufficient for physical characterization, and to analyze the molecular basis of its intrinsic stability, the gene was cloned and expressed functionally in Escherichia coli. Growth of the cells and purification of the enzyme were performed aerobically at 26 degrees C, i.e., ca. 60 degrees below the optimal growth temperature of Thermotoga. Two enzyme species with LDH activity were purified to homogeneity. Crystals of the enzyme obtained at 4 degrees C show satisfactory diffraction suitable for X-ray analysis up to a resolution of 2.8 A. As shown by gel-permeation chromatography, chemical crosslinking, light scattering, analytical ultracentrifugation, and electron microscopy, the two LDH species represent homotetramers and homooctamers (i.e., dimers of tetramers), with a common subunit molecular mass of 35 kDa. The spectroscopic characteristics (UV absorption, fluorescence emission, near- and far-UV CD) of the two species are indistinguishable. The calculated alpha-helix content is 45%, in accordance with the result of homology modeling. Compared to the tetrameric enzyme, the octamer exhibits reduced specific activity, whereas KM is unalatered. The extreme intrinsic stability of the protein is reflected by its unaltered catalytic activity over 4 h at 85 degrees C; irreversible thermal denaturation becomes significant at approximately 95 degrees C. The anomalous resistance toward chemical denaturation using guanidinium chloride and urea confirms this observation. Both the high optimal temperature and the pH optimum of the catalytic activity correspond to the growth conditions of T. maritima in its natural habitat. PMID:8732758

  19. TM0486 from the hyperthermophilic anaerobe Thermotoga maritima is a thiamin-binding protein involved in response of the cell to oxidative conditions.

    PubMed

    Dermoun, Zorah; Foulon, Amélie; Miller, Mitchell D; Harrington, Daniel J; Deacon, Ashley M; Sebban-Kreuzer, Corinne; Roche, Philippe; Lafitte, Daniel; Bornet, Olivier; Wilson, Ian A; Dolla, Alain

    2010-07-16

    The COG database was used for a comparative genome analysis with genomes from anaerobic and aerobic microorganisms with the aim of identifying proteins specific to the anaerobic way of life. A total of 33 COGs were identified, five of which correspond to proteins of unknown function. We focused our study on TM0486 from Thermotoga maritima, which belongs to one of these COGs of unknown function, namely COG0011. The crystal structure of the protein was determined at 2 A resolution. The structure adopts a beta alpha beta beta alpha beta ferredoxin-like fold and assembles as a homotetramer. The structure also revealed the presence of a pocket in each monomer that bound an unidentified ligand. NMR and calorimetry revealed that TM0486 specifically bound thiamin with a K(d) of 1.58 microM, but not hydroxymethyl pyrimidine (HMP), which has been implicated as a potential ligand. We demonstrated that the TM0486 gene belongs to the same multicistronic unit as TM0483, TM0484 and TM0485. Although these three genes have been assigned to the transport of HMP, with TM0484 being the periplasmic thiamin/HMP-binding protein and TM0485 and TM0483 the transmembrane and the ATPase components, respectively, our results led us to conclude that this operon encodes an ABC transporter dedicated to thiamin, with TM0486 transporting charged thiamin in the cytoplasm. Given that this transcriptional unit was up-regulated when T. maritima was exposed to oxidative conditions, we propose that, by chelating cytoplasmic thiamin, TM0486 and, by extension, proteins belonging to COG0011 are involved in the response mechanism to stress that could arise during aerobic conditions.

  20. 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.

  1. 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

  2. Structure of Thermotoga maritima TM0439: implications for the mechanism of bacterial GntR transcription regulators with Zn{sup 2+}-binding FCD domains

    SciTech Connect

    Zheng, Meiying; Cooper, David R.; Grossoehme, Nickolas E.; Yu, Minmin; Hung, Li-Wei; Cieslik, Marcin; Derewenda, Urszula; Lesley, Scott A.; Wilson, Ian A.; Giedroc, David P.; Derewenda, Zygmunt S.

    2009-04-01

    Here, the crystal structure of TM0439, a GntR regulator with an FCD domain found in the Thermotoga maritima genome, is described. The GntR superfamily of dimeric transcription factors, with more than 6200 members encoded in bacterial genomes, are characterized by N-terminal winged-helix 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-α-helical regulatory domains classified into two related Pfam families: FadR-C and FCD. Only two crystal structures of FadR-family members, those of Escherichia coli FadR protein and LldR from Corynebacterium glutamicum, have been described to date in the literature. Here, the crystal structure of TM0439, a GntR regulator with an FCD domain found in the Thermotoga maritima genome, is described. 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, it is shown that the recombinant protein contains bound Ni{sup 2+} ions but that it is able to bind Zn{sup 2+} with K{sub d} < 70 nM. It is concluded that Zn{sup 2+} is the likely physiological metal and that it may perform either structural or regulatory roles or both. Finally, the TM0439 structure is compared with 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.

  3. 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.

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

    PubMed

    Nadwodnik, Jan; Lohaus, Gertrud

    2008-04-01

    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.

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

    PubMed

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

    2016-12-15

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

  6. 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

  7. Structural role of a conserved active site cis proline in the Thermotoga maritima acetyl esterase from the carbohydrate esterase family 7.

    PubMed

    Singh, Mrityunjay K; Manoj, Narayanan

    2017-04-01

    A conserved cis proline residue located in the active site of Thermotoga maritima acetyl esterase (TmAcE) from the carbohydrate esterase family 7 (CE7) has been substituted by alanine. The residue was known to play a crucial role in determining the catalytic properties of the enzyme. To elucidate the structural role of the residue, the crystal structure of the Pro228Ala variant (TmAcEP228A ) was determined at 2.1 Å resolution. The replacement does not affect the overall secondary, tertiary, and quaternary structures and moderately decreases the thermal stability. However, the wild type cis conformation of the 227-228 peptide bond adopts a trans conformation in the variant. Other conformational changes in the tertiary structure are restricted to residues 222-226, preceding this peptide bond and are located away from the active site. Overall, the results suggest that the conserved proline residue is responsible for the cis conformation of the peptide and shapes the geometry of the active site. Elimination of the pyrrolidine ring results in the loss of van der Waals and hydrophobic interactions with both the alcohol and acyl moeities of the ester substrate, leading to significant impairment of the activity and perturbation of substrate specificity. Furthermore, a cis-to-trans conformational change arising out of residue changes at this position may be associated with the evolution of divergent activity, specificity, and stability properties of members constituting the CE7 family. Proteins 2017; 85:694-708. © 2016 Wiley Periodicals, Inc.

  8. Spatial analysis of nuclear and cytoplasmic DNA diversity in wild sea beet (Beta vulgaris ssp. maritima) populations: do marine currents shape the genetic structure?

    PubMed

    Fievet, Virgil; Touzet, Pascal; Arnaud, Jean-François; Cuguen, Joël

    2007-05-01

    Patterns of seed dispersal in the wild sea beet (Beta vulgaris ssp. maritima) are predicted to be influenced by marine currents because populations are widely distributed along the European Atlantic coast. We investigated the potential influence of marine currents on the pattern of spatial genetic structuring in natural populations of sea beet. Populations were located along the French coasts of the Anglo-Norman gulf that features peculiar marine currents in the Channel. Thirty-three populations were sampled, among which 23 were continental and 10 were insular populations located in Jersey, Guernsey and Chausey, for a total of 1224 plants genotyped. To validate the coastal topography influence and the possibility of marine current orientated gene flow on the genetic features of sea beet populations, we assessed patterns of genetic structuring of cytoplasmic and nuclear diversity by: (i) searching for an isolation-by-distance (IBD) pattern using spatial autocorrelation tools; (ii) using the Monmonier algorithm to identify genetic boundaries in the area studied; and (iii) performing assignment tests that are based on multilocus genotype information to ascertain population membership of individuals. Our results showed a highly contrasted cytoplasmic and nuclear genetic differentiation and highlighted the peculiar situation of island populations. Beyond a classical isolation-by-distance due to short-range dispersal, genetic barriers fitting the orientation of marine currents were clearly identified. This suggests the occurrence of long-distance seed dispersal events and an asymmetrical gene flow separating the eastern and western part of the Anglo-Norman gulf.

  9. 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

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

    PubMed Central

    Zheng, Meiying; Cooper, David R.; Grossoehme, Nickolas E.; Yu, Minmin; Hung, Li-Wei; Cieslik, Marcin; Derewenda, Urszula; Lesley, Scott A.; Wilson, Ian A.; Giedroc, David P.; Derewenda, Zygmunt S.

    2009-01-01

    The GntR superfamily of dimeric transcription factors, with more than 6200 members encoded in bacterial genomes, are characterized by N-terminal winged-helix 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-α-helical regulatory domains classified into two related Pfam families: FadR_C and FCD. Only two crystal structures of FadR-family members, those of Escherichia coli FadR protein and LldR from Corynebacterium glutamicum, have been described to date in the literature. Here, the crystal structure of TM0439, a GntR regulator with an FCD domain found in the Thermotoga maritima genome, is described. 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, it is shown that the recombinant protein contains bound Ni2+ ions but that it is able to bind Zn2+ with K d < 70 nM. It is concluded that Zn2+ is the likely physiological metal and that it may perform either structural or regulatory roles or both. Finally, the TM0439 structure is compared with 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. PMID:19307717

  11. Structural and biochemical characterization of the β-N-acetylglucosaminidase from Thermotoga maritima: toward rationalization of mechanistic knowledge in the GH73 family.

    PubMed

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

    2015-03-01

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

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

    PubMed Central

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

    1992-01-01

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

  13. The N-terminal hybrid binding domain of RNase HI from Thermotoga maritima is important for substrate binding and Mg2+-dependent activity.

    PubMed

    Jongruja, Nujarin; You, Dong-Ju; Kanaya, Eiko; Koga, Yuichi; Takano, Kazufumi; Kanaya, Shigenori

    2010-11-01

    Thermotoga maritima ribonuclease H (RNase H) I (Tma-RNase HI) contains a hybrid binding domain (HBD) at the N-terminal region. To analyze the role of this HBD, Tma-RNase HI, Tma-W22A with the single mutation at the HBD, the C-terminal RNase H domain (Tma-CD) and the N-terminal domain containing the HBD (Tma-ND) were overproduced in Escherichia coli, purified and biochemically characterized. Tma-RNase HI prefers Mg(2+) to Mn(2+) for activity, and specifically loses most of the Mg(2+)-dependent activity on removal of the HBD and 87% of it by the mutation at the HBD. Tma-CD lost the ability to suppress the RNase H deficiency of an E. coli rnhA mutant, indicating that the HBD is responsible for in vivo RNase H activity. The cleavage-site specificities of Tma-RNase HI are not significantly changed on removal of the HBD, regardless of the metal cofactor. Binding analyses of the proteins to the substrate using surface plasmon resonance indicate that the binding affinity of Tma-RNase HI is greatly reduced on removal of the HBD or the mutation. These results indicate that there is a correlation between Mg(2+)-dependent activity and substrate binding affinity. Tma-CD was as stable as Tma-RNase HI, indicating that the HBD is not important for stability. The HBD of Tma-RNase HI is important not only for substrate binding, but also for Mg(2+)-dependent activity, probably because the HBD affects the interaction between the substrate and enzyme at the active site, such that the scissile phosphate group of the substrate and the Mg(2+) ion are arranged ideally.

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

    PubMed

    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.

  15. Dissection of the gene of the bifunctional PGK-TIM fusion protein from the hyperthermophilic bacterium Thermotoga maritima: design and characterization of the separate triosephosphate isomerase.

    PubMed Central

    Beaucamp, N.; Hofmann, A.; Kellerer, B.; Jaenicke, R.

    1997-01-01

    Triosephosphate isomerase (TIM), from the hyperthermophilic bacterium Thermotoga maritima, has been shown to be covalently linked to phosphoglycerate kinase (PGK) forming a bifunctional fusion protein with TIM as the C-terminal portion of the subunits of the tetrameric protein (Schurig et al., EMBO J 14:442-451, 1995). To study the effect of the anomalous state of association on the structure, stability, and function of Thermotoga TIM, the isolated enzyme was cloned and expressed in Escherichia coli, and compared with its wild-type structure in the PGK-TIM fusion protein. After introducing a start codon at the beginning of the tpi open reading frame, the gene was expressed in E.c.BL21(DE3)/ pNBTIM. The nucleotide sequence was confirmed and the protein purified as a functional dimer of 56.5 kDa molecular mass. Spectral analysis, using absorption, fluorescence emission, near- and far-UV circular dichroism spectroscopy were used to compare the separated Thermotoga enzyme with its homologs from mesophiles. The catalytic properties of the enzyme at approximately 80 degrees C are similar to those of its mesophilic counterparts at their respective physiological temperatures, in accordance with the idea that under in vivo conditions enzymes occupy corresponding states. As taken from chaotropic and thermal denaturation transitions, the separated enzyme exhibits high intrinsic stability, with a half-concentration of guanidinium-chloride at 3.8 M, and a denaturation half-time at 80 degrees C of 2 h. Comparing the properties of the TIM portion of the PGK-TIM fusion protein with those of the isolated recombinant TIM, it is found that the fusion of the two enzymes not only enhances the intrinsic stability of TIM but also its catalytic efficiency. PMID:9336838

  16. 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.

  17. Effect of dietary supplementation with Suaeda maritima on blood physiology, innate immune response, and disease resistance in olive flounder against Miamiensis avidus.

    PubMed

    Harikrishnan, Ramasamy; Kim, Ju-Sang; Kim, Man-Chul; Dharaneedharan, Subramanian; Kim, Dong-Hwi; Hong, Seung-Hyun; Song, Chang-Young; Balasundaram, Chellam; Heo, Moon-Soo

    2012-06-01

    The effect of Suaeda maritima enriched diet on blood physiology, innate immune response, and disease resistance in olive flounder Paralichythys olivaceus against Miamiensis avidus on weeks 1, 2, and 4 was investigated. Feeding with any enriched diet and then challenging with M. avidus significantly increased white blood cells (WBC) on weeks 2 and 4; the red blood cells (RBC) significantly increased with 0.1% and 1.0% enriched diets on week 4. The hemoglobin (Hb) and hematocrit (Ht) levels significantly increased when fed with 0.1% and 1.0% supplementation diets on weeks 2 and 4. The mean corpuscular volume (MCV) did not significantly vary with any diet and time; however the mean corpuscular hemoglobin (MCH) and mean corpuscular hemoglobin concentration (MCHC) significantly increased with 0.1% and 1.0% supplementation diets on weeks 2 and 4. The leukocytes such as lymphocytes (Lym), monocytes (Mon), neutrophils (Neu) and biochemical parameters such as total protein (TP), glucose (GLU), and calcium (CAL) levels significantly increased in 0.1% and 1.0% supplementation diet fed groups on weeks 2 and 4. The serum lysozyme activity was significantly enhanced in 0.1% and 1.0% supplementation diet fed groups from weeks 1 to 4 when compared to the control (0% herbal extract enriched diet). The scuticocidal activity and respiratory burst activity were significantly enhanced when fish were fed with 0.1% and 1.0% supplementation diets from weeks 2 and 4. The protective effect in terms of cumulative mortality (50% and 40%) was low in groups on being fed with 0.1% and 1.0% supplemented diet. Therefore the present study suggested that 0.1% and 1.0% S. maritime-supplemented diets protect the hematological and biochemical parameters, improving the innate immunity, affording protection disease from M. avidus infection in olive flounder.

  18. Importance of Hydrogen Bonding in Fine Tuning the [2Fe-2S] Cluster Redox Potential of HydC from Thermotoga maritima.

    PubMed

    Birrell, James A; Laurich, Christoph; Reijerse, Edward J; Ogata, Hideaki; Lubitz, Wolfgang

    2016-08-09

    Iron-sulfur clusters form one of the largest and most diverse classes of enzyme cofactors in nature. They may serve as structural factors, form electron transfer chains between active sites and external redox partners, or form components of enzyme active sites. Their specific role is a consequence of the cluster type and the surrounding protein environment. The relative effects of these factors are not completely understood, and it is not yet possible to predict the properties of iron-sulfur clusters based on amino acid sequences or rationally tune their properties to generate proteins with new desirable functions. Here, we generate mutations in a [2Fe-2S] cluster protein, the TmHydC subunit of the trimeric [FeFe]-hydrogenase from Thermotoga maritima, to study the factors that affect its redox potential. Saturation mutagenesis of Val131 was used to tune the redox potential over a 135 mV range and revealed that cluster redox potential and electronic properties correlate with amino acid hydrophobicity and the ability to form hydrogen bonds to the cluster. Proline scanning mutagenesis between pairs of ligating cysteines was used to remove backbone amide hydrogen bonds to the cluster and decrease the redox potential by up to 132 mV, without large structural changes in most cases. However, substitution of Gly83 with proline caused a change of HydC to a [4Fe-4S] cluster protein with a redox potential of -526 mV. Together, these results confirm the importance of hydrogen bonding in tuning cluster redox potentials and demonstrate the versatility of iron-sulfur cluster protein folds at binding different types of clusters.

  19. Simultaneous determination of bufadienolides and phenolic compounds in sea squill (Drimia maritima (L.) Stearn) by HPLC-DAD-MSn as a means to differentiate individual plant parts and developmental stages.

    PubMed

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

    2014-09-01

    Mediterranean sea squill (Drimia maritima (L.) Stearn) is used in the production of medicinal products. Current HPLC methods comprise tedious sample clean-up and have been merely focused on the analysis of cardiac glycosides, whereas a thorough characterization of D. maritima considering both the latter compound class and more hydrophilic secondary metabolites in one HPLC run has not been performed so far. Consequently, a novel HPLC-DAD-MS(n) method has been developed allowing the simultaneous determination of both cardiac glycosides and phenolic compounds, which is characterized by simplified sample preparation. This method was applied to characterize sea squill, revealing a complex profile of its extractive compounds derived from the two classes. Furthermore, the potential of the method reported here to quantitate the predominant compounds, i.e., dihydroquercetin derivatives and bufadienolides, was demonstrated. The occurrence of phenolic compounds, not described for sea squill so far, and of characteristic compounds specific to individual plant parts or vegetation stages was further addressed. The data revealed that classification of various vegetation phases based on quantitative evaluation of bufadienolides and dihydroquercetin derivatives applying principal component analysis (PCA) appears possible. Thus, the methodology presented here forms the basis for future routine application in quality control of raw materials and pharmaceutical preparations derived from sea squill. This will allow systematic comparison of different plant parts, vegetation stages and origins based on an extended sample set.

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

    SciTech Connect

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

    2010-01-01

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

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

    SciTech Connect

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

    2010-01-01

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

  2. Ardenticatena maritima gen. nov., sp. nov., a ferric iron- and nitrate-reducing bacterium of the phylum 'Chloroflexi' isolated from an iron-rich coastal hydrothermal field, and description of Ardenticatenia classis nov.

    PubMed

    Kawaichi, Satoshi; Ito, Norihiro; Kamikawa, Ryoma; Sugawara, Tatsuya; Yoshida, Takashi; Sako, Yoshihiko

    2013-08-01

    A novel thermophilic, chemoheterotrophic, Gram-negative-staining, multicellular filamentous bacterium, designated strain 110S(T), was isolated from an iron-rich coastal hydrothermal field in Japan. The isolate is facultatively aerobic and chemoheterotrophic. Phylogenetic analysis using 16S rRNA gene sequences nested strain 110S(T) in a novel class-level clone cluster of the phylum 'Chloroflexi'. The isolate grows by dissimilatory iron- and nitrate-reduction under anaerobic conditions, which is the first report of these abilities in the phylum 'Chloroflexi'. The organism is capable of growth with oxygen, ferric iron and nitrate as a possible electron acceptor, has a wide range of growth temperatures, and tolerates higher NaCl concentrations for growth compared to the other isolates in the phylum. Using phenotypic and phylogenetic data, strain 110S(T) (= JCM 17282(T) = NBRC 107679(T) = DSM 23922(T) = KCTC 23289(T) = ATCC BAA-2145(T)) is proposed as the type strain of a novel species in a new genus, Ardenticatena maritima gen. nov., sp. nov. In addition, as strain 110S(T) apparently constitutes a new class of the phylum 'Chloroflexi' with other related uncultivated clone sequences, we propose Ardenticatenia classis nov. and the subordinate taxa Ardenticatenales ord. nov. and Ardenticatenaceae fam. nov.

  3. Prevendo a atividade solar através de redes neurais nebulosas

    NASA Astrophysics Data System (ADS)

    Martin, V. A. F.; Poppe, P. C. R.

    2003-08-01

    Atualmente, a integração de redes neurais com técnicas da Matemática Nebulosa (Fuzzy Sets), tem sido usada robustamente para fazer previsões em vários sistemas físicos. Este trabalho representa uma continuidade da contribuição apresentada anteriormente durante a XXVIIa Reunião Anual da SAB, onde exploramos a aplicação de redes neurais para previsões futuras de séries temporais. Para este, enfatizamos o uso da técnica ANFIS (Adaptative Neuro-Fuzzy Inference System), que consiste em uma rede do tipo back-propagation, onde os dados são processados em uma camada intermediária, tendo numa camada de saída, os dados numéricos. Para que a previsão seja feita com sucesso utilizando-se técnicas matemáticas adequadas, é fundamental a existência de uma série razoavelmente longa de modo que a dinâmica contida nesta possa ser melhor extraída pela rede neural. Nesse sentido, foram utilizados novamente os dados históricos das manchas do Sol (1818-2002) afim de verificar o comportamento futuro da atividade solar (Ciclos de Schawbe) a partir da técnica descrita acima. Previsões realizadas para o ciclo anterior (n.22, máximo de 158,5 em julho de 1989), bem como para o atual (n.23, máximo de 153 em setembro de 2000), apontam valores bastante coerentes com os publicados na literatura, levando em consideração, respectivamente, as barras de erros associadas: 166+/-18 e 160+/-14. Para o próximo ciclo de Schawbe (2006-2017), nossa previsão aponta o valor de 172+/-23 como máximo para o primeiro semestre de 2011 (Abril +/- 3 meses). A ANFIS acompanha de maneira satisfatória o movimento das séries estudadas durante o treinamento e durante a verificação (menor dispersão das funções de pertinência), com erro absoluto inferior a 20 por cento.

  4. Practical Astronomical Activities during Daytime. (Spanish Title: Actividades Astronómicas Prácticas Diurnas.) Atividades Astronômicas Práticas Diurnas

    NASA Astrophysics Data System (ADS)

    Jackson, Eric

    2009-12-01

    relacionadas al mal tiempo. El problema de no tener suficientes actividades prácticas, la sensación de poseer conocimientos inadecuados, la necesidad de disponer de equipamiento astronómico y experiencia suelen ser demasiado intimidantes para que los profesores introduzcan la materia en sus clases. Si la Astronomía iba a ser introducida, entonces era preciso encontrar una forma de resolver estas dificultades. Nuestro grupo, trabajando con maestros y alumnos dentro de un marco constructivista, encontró que los principios de la Astronomía pueden ser descubiertos durante el día, en cuanto los alumnos están en la escuela. Trabajando de forma cooperativa los alumnos midieron y registraron observaciones de sus propias sombras causadas por los movimientos de la estrella más próxima, el Sol, y nuestro planeta Tierra. Debido a que los alumnos se involucraran tan personalmente en las actividades, estuvieron mucho más interesados en los resultados del estudio. La Astronomía pasó a ser un desafío para el maestro y sus alumnos cuando aplicaron sus experiencias diurnas a la observación nocturna desde sus casas, reportada después en clase. Estas atividades astronômicas diurnas surgiram de uma investigação feita na Nova Zelândia por um grupo de professores e astrônomos a respeito dos problemas do ensino da Astronomia. Este trabalho mostrou que a Astronomia é geralmente considerada uma disciplina difícil de ensinar, tradicionalmente baseada em livros, filmes e modelos. Os mais afortunados podem ter feito alguma visita a um observatório ou planetário, e os mais avançados podem talvez ter tentado uma sessão de observação noturna, as quais sofrem às vezes de dificuldades relacionadas ao tempo. O problema de não dispor de suficientes atividades práticas, a sensação de possuir conhecimentos inadequados, a necessidade de dispor de equipamento astronômico e experiência tem sido, em geral, demasiado intimidante para que os professores introduzam a matéria nas suas

  5. A Proposed Activity for a Meaningful Learning about the Moon Phases. (Breton Title: Uma Proposta de Atividade Para a Aprendizagem Significativa sobre as Fases da Lua.) Una Actividad Propuesta Para EL Aprendizaje Significativo Acerca de Las Fases de la Luna

    NASA Astrophysics Data System (ADS)

    Martins, Bruno Andrade; Langhi, Rodolfo

    2012-12-01

    This paper presents one of the concepts of Astronomy and its consequent failure in teaching this topic in high school, even when the official documents point out the necessity of Astronomy teaching at this school level. Among the spontaneous conceptions in Astronomy that high school students carry with them, even after the end of the school, we emphasized in this research the Moon phases. The development of different strategies in relation to traditional methods, aimed to teaching-learning process on this topic was considered in this study. These strategies were devised based on the reference frame of the Meaningful Learning, as elaborated by Ausubel. The proposals presented here include the active participation of students in experimental activities and other didactic activities, for their continuous evaluation during the process. These activities finished with a Comics elaboration about the Moon phases. Therefore, the objective of this paper is to present a proposal for differentiated teaching activity about Moon phases supported by the theoretical principles of Meaningful Learning at Physics classes. Este texto foca um dos conteúdos de Astronomia e a consequente falha no ensino deste tema no ensino médio, apesar de os documentos oficiais apresentarem a necessidade de se trabalhar a Astronomia neste nível de ensino. Dentre as concepções alternativas em Astronomia que os alunos do ensino médio carregam consigo, mesmo após o término dos estudos, destacamos, nesta pesquisa, o fenômeno das fases da Lua. O desenvolvimento de estratégias diferenciadas em relação ao ensino tradicional, visando o processo de ensino-aprendizagem sobre este tema, foi contemplado neste trabalho como um dos resultados obtidos sob a luz dos referenciais da aprendizagem significativa, fundamentados em Ausubel. Segundo a proposta aqui apresentada, a participação ativa dos alunos na execução de uma atividade experimental e outras atividades didáticas, que visam sua cont

  6. 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, ...

  7. Membrane pyrophosphatases from Thermotoga maritima and Vigna radiata suggest a conserved coupling mechanism

    PubMed Central

    Li, Kun-Mou; Wilkinson, Craig; Kellosalo, Juho; Tsai, Jia-Yin; Kajander, Tommi; Jeuken, Lars J. C.; Sun, Yuh-Ju; Goldman, Adrian

    2016-01-01

    Membrane-bound pyrophosphatases (M-PPases), which couple proton/sodium ion transport to pyrophosphate synthesis/hydrolysis, are important in abiotic stress resistance and in the infectivity of protozoan parasites. Here, three M-PPase structures in different catalytic states show that closure of the substrate-binding pocket by helices 5–6 affects helix 13 in the dimer interface and causes helix 12 to move down. This springs a ‘molecular mousetrap', repositioning a conserved aspartate and activating the nucleophilic water. Corkscrew motion at helices 6 and 16 rearranges the key ionic gate residues and leads to ion pumping. The pumped ion is above the ion gate in one of the ion-bound structures, but below it in the other. Electrometric measurements show a single-turnover event with a non-hydrolysable inhibitor, supporting our model that ion pumping precedes hydrolysis. We propose a complete catalytic cycle for both proton and sodium-pumping M-PPases, and one that also explains the basis for ion specificity. PMID:27922000

  8. 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.

  9. 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

  10. French maritime pine bark (Pinus maritima Lam.) extract (Flavangenol) prevents chronic UVB radiation-induced skin damage and carcinogenesis in melanin-possessing hairless mice.

    PubMed

    Kimura, Yoshiyuki; Sumiyoshi, Maho

    2010-01-01

    A French maritime pine bark extract, Flavangenol, is widely used as a nutritional supplement for protection against atherosclerosis, hypertension, diabetes, etc. Chronic exposure to solar UV radiation damages skin, increasing cutaneous thickness, wrinkling and pigmentation, as well as reducing elasticity, and causes skin cancer. The aim of this study was to examine the effects of flavangenol on skin damage and the incidence of skin tumors caused by long-term UVB irradiation in melanin-possessing hairless mice. The oral administration of flavangenol (60, 200 or 600 mg kg(-1), twice daily) significantly inhibited increases in skin thickness, and the formation of wrinkles and melanin granules, as well as increases in the diameter and length of skin blood vessels. Furthermore, it prevented increases in numbers of apoptotic, Ki-67-positive and 8-hydroxy-2'-deoxyguanosine (8-OHdG)-positive cells, and the expression of skin vascular endothelial growth factor (VEGF) induced by chronic UVB irradiation. The effect on these biomarkers was associated with a reduction in the incidence of tumors in mice. The antiphotoaging and anticarcinogenetic activities of flavangenol may be due to inhibition of the expression of Ki-67, 8-OHdG and VEGF through a scavenging effect on reactive oxygen species.

  11. Low level of gene flow from cultivated beets (Beta vulgaris L. ssp. vulgaris) into Danish populations of sea beet (Beta vulgaris L. ssp. maritima (L.) Arcangeli).

    PubMed

    Andersen, N S; Siegismund, H R; Meyer, V; Jørgensen, R B

    2005-04-01

    Gene flow from sugar beets to sea beets occurs in the seed propagation areas in southern Europe. Some seed propagation also takes place in Denmark, but here the crop-wild gene flow has not been investigated. Hence, we studied gene flow to sea beet populations from sugar beet lines used in Danish seed propagation areas. A set of 12 Danish, two Swedish, one French, one Italian, one Dutch, and one Irish populations of sea beets, and four lines of sugar beet were analysed. To evaluate the genetic variation and gene flow, eight microsatellite loci were screened. This analysis revealed hybridization with cultivated beet in one of the sea beet populations from the centre of the Danish seed propagation area. Triploid hybrids found in this population were verified with flow cytometry. Possible hybrids or introgressed plants were also found in the French and Italian populations. However, individual assignment test using a Bayesian method provided 100% assignment success of diploid individuals into their correct subspecies of origin, and a Bayesian Markov chain Monte Carlo (MC MC) approach revealed clear distinction of individuals into groups according to their subspecies of origin, with a zero level of genetic admixture among subspecies. This underlines that introgression beyond the first hybridization is not extensive. The overall pattern of genetic distance and structure showed that Danish and Swedish sea beet populations were closely related to each other, and they are both more closely related to the population from Ireland than to the populations from France, the Netherlands, and Italy.

  12. 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.

  13. 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.

  14. 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.

  15. Environmental Assessment for Lock and Dam 22 Major Rehabilitation, Ralls County, Missouri and Pike County, Illinois.

    DTIC Science & Technology

    1987-02-01

    parvula rare - Wild sarsaparilla Aralia nudicaulis rare - Salt meadow grass Leptochloa panlcoides - endangered Jeweled shooting star Dodecatheon...lots rare - Ditch grass Ruppia maritima rare - Small spike-rush Eleocharis parvula rare - Wild sarsaparilla Aralia nudicaulis rare Salt meadow grass

  16. 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, ...

  17. Severe Weather Guide, Mediterranean Ports. 18. Ibiza

    DTIC Science & Technology

    1988-05-01

    two piers (Figure 2-3). A fuel pier extends southwest from the northern side of the port, while Estacion Maritima pier extends northeastward from the...side of the port, while Estacion Maritima (Maritime Station) pier extends northeastward from the southern side. The westernmost basin is used...wind velocity. At a given wind speed and a given state of wave development, each spectrum has a band of frequencies where most of the total energy is

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

    PubMed

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

    2013-10-01

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

  19. 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.

  20. 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.

  1. 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

  2. [The floristic diversity of the psammophyte vegetation in the region of Tlemcen (north-west Algeria)].

    PubMed

    Stambouli-Meziane, Hassiba; Bouazza, M; Thinon, Michel

    2009-08-01

    This study is devoted to the analysis of the psammophyte of the coastal and semi-continental dunes in Tlemcen. Interesting results have been obtained, in particular, on the biological and ecological aspects of the psammophyte. The interpretation from Factoriel analysis of correspondences enabled us to identify the different phytosociological classes (Cakiletea maritimae, Ammophiletea, Quercetea ilicis, Therobrachypodietea and Stellarietea mediae). Some of these classes (Cakiletea maritimae and Ammophiletea) inhabit, exceedingly well, the embryonic dunes. Some species (Therobrachypodietea) colonize the quickset dunes. Lastly, some others (Quercetea ilicis) settle in the more mature and stable dunes. By using the phytosociological and phytodynamical data, we have been able to understand the vegetation and its diversity.

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

    PubMed Central

    Swithers, Kristen S.; DiPippo, Jonathan L.; Bruce, David C.; Detter, Christopher; Tapia, Roxanne; Han, Shunsheng; Saunders, Elizabeth; Goodwin, Lynne A.; Han, James; Woyke, Tanja; Pitluck, Sam; Pennacchio, Len; Nolan, Matthew; Mikhailova, Natalia; Lykidis, Athanasios; Land, Miriam L.; Brettin, Thomas; Stetter, Karl O.; Nelson, Karen E.; Gogarten, J. 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. PMID:21952543

  4. Genome sequence of Thermotoga sp. strain RQ2, a hyperthermophilic bacterium isolated from a geothermally heated region of the seafloor near Ribeira Quente, the Azores.

    PubMed

    Swithers, Kristen S; DiPippo, Jonathan L; Bruce, David C; Detter, Christopher; Tapia, Roxanne; Han, Shunsheng; Saunders, Elizabeth; Goodwin, Lynne A; Han, James; Woyke, Tanja; Pitluck, Sam; Pennacchio, Len; Nolan, Matthew; Mikhailova, Natalia; Lykidis, Athanasios; Land, Miriam L; Brettin, Thomas; Stetter, Karl O; Nelson, Karen E; Gogarten, J Peter; Noll, Kenneth M

    2011-10-01

    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.

  5. Genome evolution: groping in the soil interstices.

    PubMed

    Minelli, Alessandro

    2015-03-02

    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.

  6. 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...

  7. Rhizoctonia crown and root rot resistance evaluation of Beta PIs in Fort Collins, CO, 2015

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Thirty beet accessions of either cultivated beet or sea beet (Beta vulgaris subsp. vulgaris or Beta vulgaris subsp. maritima (L.) Arcang) from the Beta collection of the USDA-Agricultural Research Service National Plant Germplasm System were screened for resistance to Rhizoctonia crown and root rot ...

  8. 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...

  9. 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...

  10. West European and East Asian Perspectives on Defense, Deterrence and Strategy. Volume 3. Spanish Perspectives on Defense, Deterrence and Strategy.

    DTIC Science & Technology

    1984-05-16

    Sociological Research of Madrid. The poll took into account previous public opinion polls conducted by the now defunct 𔃾. Instituto de la Opinion Publica . Among...PERIODICALS 10. de Espana, Juan, "Sobre la concepcion de la seguridad nacional," Ya, December 1982. 11. Jaudenes, Ramon, "La condicion maritima de Espana

  11. 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...

  12. Maritime Factors Affecting Iberian Security,

    DTIC Science & Technology

    1980-10-01

    afirme/ que para las sovie’ticas una campaiia en gran escala dirigida contra las comunicaciones marftimas del Atlantica Norte durante el perfada inicial...defender sus l ’neas de comunicacion maritima; y cuarta -- y a mi parecer la consideracion mas importante -- las otras tareas que la marina de guerra

  13. 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...

  14. Virginia Coast Reserve 2007 Remote Sensing Experiment

    DTIC Science & Technology

    2012-03-09

    SAV species in bold type. Submerged aquatic vegetation species studied in the VCR include Ruppia maritima (Widgeon grass ) and Zostera marina...Andropogon scoparius Cyperus odoratus Hypericum hypericoides Andropogon virginicus Danthonia compressa Ilex opaca Andropogon virginicus Diodea virginiana...Robinia pseudo-acacia Spiranthes Vernalis Panicum amarum Rubus argutus Strophostyles Helvola Panicum amarulum Rumex acetosella Strophostyles Umbellate

  15. Response of primary producers to nutrient enrichment in a shallow estuary

    USGS Publications Warehouse

    Kinney, E.H.; Roman, C.T.

    1998-01-01

    Shallow coastal systems worldwide are exhibiting increased algal growth in response to nutrient enrichment. This study evaluates primary production patterns in an estuarine system (Bass Harbor Marsh, ME, USA) receiving low levels of anthropogenic nitrogen. Biomass, areal coverage and in situ oxygen production of green macroalgae, Ruppia Maritima, and Phytoplankton were measured over a growing season to determine net ecosystem production. Macroalgae and R. maritima exhibited seasonal biomass curves with early summer peaks; however, peak biomass of macroalgae [150 g dry weight (wt) m-2] was substantially greater that R. maritima (33 g dry wt m-2) Phytoplankton biomass, measured as chlorophyll a, was low (<1 ??g 1-1) early in the season and peaked (11 ??g 1-1) following a mid-summer decline in macroalgal biomass, suggesting a competitive interaction with macroalgae. Instantaneous net production rates varied over the growing season for all 3 primary producers. R. maritima net production ranged from near zero to 2.7 mg C g-1 dry wt h-1, with higher rates during summer and much of the seasonal variability explained by temperature. Macroalgal (0.88 to 5.0 mg C g-1 dry wt h-1) and phytoplankton (0 to 28 mg C m-3 h-1) net production did not exhibit any clear seasonal signal. Net primary production calculated on an areal basis demonstrated macroalgae's dominance in the lower basin of Bass Harbor Marsh, with peak summer rates (400 mg C m-2 h-1) greatly exceeding maximum rates for both R maritima (70 mg C m-2h-1) and phytoplankton (12 mg C m-2 h-1). When compared to other New England estuarine sites with short residence times, nutrient loading and peak green macroalgal biomass in Bass Harbor Marsh are relatively low; however, the strong dominance of opportunistic green macroalgae is a pattern that is characteristic of shallow coastal systems undergoing eutrophication.

  16. Gene Transfer & Hybridization Studies in Hyperthermophilic Species

    SciTech Connect

    Nelson, Karen E.

    2005-10-14

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

  17. 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.

  18. Directed evolution of a pyruvate aldolase to recognize a long chain acyl substrate.

    PubMed

    Cheriyan, Manoj; Walters, Matthew J; Kang, Brian D; Anzaldi, Laura L; Toone, Eric J; Fierke, Carol A

    2011-11-01

    The use of biological catalysts for industrial scale synthetic chemistry is highly attractive, given their cost effectiveness, high specificity that obviates the need for protecting group chemistry, and the environmentally benign nature of enzymatic procedures. Here we evolve the naturally occurring 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolases from Thermatoga maritima and Escherichia coli, into enzymes that recognize a nonfunctionalized electrophilic substrate, 2-keto-4-hydroxyoctonoate (KHO). Using an in vivo selection based on pyruvate auxotrophy, mutations were identified that lower the K(M) value up to 100-fold in E. coli KDPG aldolase, and that enhance the efficiency of retro-aldol cleavage of KHO by increasing the value of k(cat)/K(M) up to 25-fold in T. maritima KDPG aldolase. These data indicate that numerous mutations distal from the active site contribute to enhanced 'uniform binding' of the substrates, which is the first step in the evolution of novel catalytic activity.

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

    PubMed

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

    2015-01-01

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

  20. 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

  1. (10E,12E,14E)-9,16-Dioxoocta-deca-10,12,14-trienoic acid.

    PubMed

    Bréant, Lise; Vonthron-Sénécheau, Catherine; Brelot, Lydia; Lobstein, Annelise

    2012-09-01

    The title octa-deca-trienoic acid derivative, C(18)H(26)O(4), was isolated from Silene maritima With. (Caryophyllaceae), the first time this natural compound has been found in the Caryophyllales order. This fatty acid has an 18-carbon backbone with three double bonds on trans (E) conformation and two carbonyl. In the crystal, molecules are linked via pairs of O-H⋯O hydrogen bonds, forming inversion dimers.

  2. Overview Environmental Assessment for the Space Based Infrared System (SBIRS)

    DTIC Science & Technology

    1996-12-01

    conditions. Stratospheric Ozone Quantifiable human health effects due to ozone depletion are less than one extra cancer case per million persons. Effects...curtissii Curtis milkweed - E o Chrysophyllum oliviforme Satinleaf - E o Ernodea littoratis Beach creeper - T o Glandularia maritima Coastal vervain - E o...Hydrazine is acutely toxic, a teratogen (causes developmental malformations), a neurotoxin (affects the nervous system), a carcinogen (causes cancer

  3. Barren Island Dredged Material Placement for Regional Sediment Management

    DTIC Science & Technology

    2012-09-01

    the island are extensive sea grass beds dominated by Ruppia maritima. Although geotextile tubes have been installed and some wetland restoration has...exceedingly costly, geotextile tubes were used at Bar- ren Island to contain the sediment as a less expensive alternative. Baltimore District desired...out of the placement site. After several discussions with various manufacturers of the geotextile tubes, Baltimore District ERDC/CHL CHETN-XIV-21

  4. Monterey Peninsula Water Supply Project. Supplemental Draft Environmental Impact Report/Statement II. Appendices

    DTIC Science & Technology

    1993-02-01

    bromeIBromus mollis soft chess Bromus rigidus ripgut grass Bromus rubens red bromeICalochortus albus var. albus white globe lily Calystegia purpurata ssp... Bromus diandrus Rip-gut Brome Bromus mollis Soft Chess Bromus sp. Brome Grass Cakile maritima Sea Rocket Camissonia cheiranthifolia Beach Evening...Seed for native grass species, primarily Stipa sp., Bromus carinatus, Elymus glaucus, and Danthonia califomica, would be collected within Garland

  5. Thermostable cellulases, and mutants thereof, capable of hydrolyzing cellulose in ionic liquid

    DOEpatents

    Sapra, Rajat; Datta, Supratim; Chen, Zhiwei; Holmes, Bradley M.; Simmons, Blake A.; Blanch, Harvey W.

    2016-04-26

    The present invention provides for a composition comprising an ionic liquid and a thermostable cellulose, and a method of hydrolyzing a cellulose, comprising: (a) providing a composition comprising a solution comprising an ionic liquid and a cellulose, and (b) introducing a thermostable cellulase to the solution, such that the cellulose is hydrolyzed by the cellulase. The present invention also provides for a Thermatoga maritima thermostable cellulase mutant with increased cellulase activity.

  6. Productivity and nutrient cycling in salt marshes: Contribution to ecosystem health

    NASA Astrophysics Data System (ADS)

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

    2010-05-01

    This study aimed to assess the contribution of different salt marsh halophytes ( Spartina maritima, Scirpus maritimus, Halimione portulacoides, Sarcocornia fruticosa, and Sarcocornia perennis) to nutrient cycling and sequestration in warm-temperate salt marshes. Carbon, nitrogen and phosphorus concentration in plant organs and rhizosediment, as well as plant biomass were monitored every two months during one year. Results show that the C retained in the rhizosediment does not seem to be species or site specific. However, some halophytes seem to have a higher contribution to retain C from external sources, namely S. perennis and S. maritima. Regarding N, halophytes colonizing the upper and middle marsh areas had the highest NBPP (net belowground primary production) as well as the retention of N in the rhizosediment. Yet, excluding S. maritimus, all halophytes seem to contribute to the retention of N from external sources. The P retained in the rhizosediment does not seem to be species or site specific. Still, only S. maritima colonizing the lower marsh areas, which also had comparatively lower NBPP, seem to have a higher contribution to retain P from external sources. Additionally, it seems that there is no relation between plants sequestration capacity for nutrients and plant photosynthetic pathway. This work shows that nutrient cycling and accumulation processes by salt marsh halophytes contribute to reduce eutrophication (N and P retention) and also to reduce atmospheric CO 2 (C retention), highlighting salt marsh ecosystems services and the crucial role of halophytes in maintaining ecosystem functions and health.

  7. Anatomical and ultrastructural adaptations of seagrass leaves: an evaluation of the southern Atlantic groups.

    PubMed

    Ferreira, Chirle; Horta, Paulo A; Almeida, Gabriela M; Zitta, Carmen S; de M Oliveira, Eliana; Gueye, Marietou B Y B; Rodrigues, Ana C

    2015-01-01

    Seagrasses, which form an integral part of the worldwide coastal habitat, are considered highly relevant from an ecological point of view. Due to the scarcity of anatomical information, the present study analyzed the morphoanatomy, histochemistry, and ultrastructure of Halophila decipiens, Halodule wrightii, and Ruppia maritima leaves, discussing their adaptations to the marine environments observed throughout the southwestern tropical and subtropical Atlantic coast. The leaves of these three species feature a uniseriate epidermis with the presence of chloroplasts in large quantities and absence of stomata. The vascular system consists of a central vascular bundle with sieve tube elements of the phloem and protoxylem lacunae, as well as small vascular bundles near the leaf margins. The leaves of H. decipiens possess trichomes, but no mesophyll in the leaf margins. The mesophyll of H. wrightii and R. maritima is homogeneous with chlorenchyma cells and air lacunae scattered throughout the leaf. The histochemistry analysis revealed the absence of amyloplasts and the presence of proteins in the outer periclinal walls of ordinary epidermal cells of the three species. It was also possible to detect the presence of idioblasts containing phenolic compounds in H. decipiens and R. maritima. The ultrastructural analysis of the three species revealed many elliptical chloroplasts, with organized thylakoids, expansion of the epidermal cell wall into the cytoplasm, and a thin cuticle. Hydropoten were also observed in the three specimens. The results show that the species analyzed have important adaptations which enable their survival in the marine environment.

  8. 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.

  9. Activity of select dehydrogenases with Sepharose-immobilized N6-carboxymethyl-NAD

    PubMed Central

    Beauchamp, Justin; Vieille, Claire

    2015-01-01

    N6-carboxymethyl-NAD (N6-CM-NAD) can be used to immobilize NAD onto a substrate containing terminal primary amines. We previously immobilized N6-CM-NAD onto sepharose beads and showed that Thermotoga maritima glycerol dehydrogenase could use the immobilized cofactor with cofactor recycling. We now show that Saccharomyces cerevisiae alcohol dehydrogenase, rabbit muscle L-lactate dehydrogenase (type XI), bovine liver L-glutamic dehydrogenase (type III), Leuconostoc mesenteroides glucose-6-phosphate dehydro-genase, and Thermotoga maritima mannitol dehydrogenase are active with soluble N6-CM-NAD. The products of all enzymes but 6-phospho-D-glucono-1,5-lactone were formed when sepharose-immobilized N6-CM-NAD was recycled by T. maritima glycerol dehydrogenase, indicating that N6-immobilized NAD is suitable for use by a variety of different dehydrogenases. Observations of the enzyme active sites suggest that steric hindrance plays a greater role in limiting or allowing activity with the modified cofactor than do polarity and charge of the residues surrounding the N6-amine group on NAD. PMID:25611453

  10. Activity of select dehydrogenases with sepharose-immobilized N(6)-carboxymethyl-NAD.

    PubMed

    Beauchamp, Justin; Vieille, Claire

    2015-01-01

    N(6)-carboxymethyl-NAD (N(6)-CM-NAD) can be used to immobilize NAD onto a substrate containing terminal primary amines. We previously immobilized N(6)-CM-NAD onto sepharose beads and showed that Thermotoga maritima glycerol dehydrogenase could use the immobilized cofactor with cofactor recycling. We now show that Saccharomyces cerevisiae alcohol dehydrogenase, rabbit muscle L-lactate dehydrogenase (type XI), bovine liver L-glutamic dehydrogenase (type III), Leuconostoc mesenteroides glucose-6-phosphate dehydro-genase, and Thermotoga maritima mannitol dehydrogenase are active with soluble N(6)-CM-NAD. The products of all enzymes but 6-phospho-D-glucono-1,5-lactone were formed when sepharose-immobilized N(6)-CM-NAD was recycled by T. maritima glycerol dehydrogenase, indicating that N(6)-immobilized NAD is suitable for use by a variety of different dehydrogenases. Observations of the enzyme active sites suggest that steric hindrance plays a greater role in limiting or allowing activity with the modified cofactor than do polarity and charge of the residues surrounding the N(6)-amine group on NAD.

  11. Evolution of mal ABC transporter operons in the Thermococcales and Thermotogales

    PubMed Central

    2008-01-01

    Background The mal genes that encode maltose transporters have undergone extensive lateral transfer among ancestors of the archaea Thermococcus litoralis and Pyrococcus furiosus. Bacterial hyperthermophiles of the order Thermotogales live among these archaea and so may have shared in these transfers. The genome sequence of Thermotoga maritima bears evidence of extensive acquisition of archaeal genes, so its ancestors clearly had the capacity to do so. We examined deep phylogenetic relationships among the mal genes of these hyperthermophiles and their close relatives to look for evidence of shared ancestry. Results We demonstrate that the two maltose ATP binding cassette (ABC) transporter operons now found in Tc. litoralis and P. furiosus (termed mal and mdx genes, respectively) are not closely related to one another. The Tc. litoralis and P. furiosus mal genes are most closely related to bacterial mal genes while their respective mdx genes are archaeal. The genes of the two mal operons in Tt. maritima are not related to genes in either of these archaeal operons. They are highly similar to one another and belong to a phylogenetic lineage that includes mal genes from the enteric bacteria. A unique domain of the enteric MalF membrane spanning proteins found also in these Thermotogales MalF homologs supports their relatively close relationship with these enteric proteins. Analyses of genome sequence data from other Thermotogales species, Fervidobacterium nodosum, Thermosipho melanesiensis, Thermotoga petrophila, Thermotoga lettingae, and Thermotoga neapolitana, revealed a third apparent mal operon, absent from the published genome sequence of Tt. maritima strain MSB8. This third operon, mal3, is more closely related to the Thermococcales' bacteria-derived mal genes than are mal1 and mal2. F. nodosum, Ts. melanesiensis, and Tt. lettingae have only one of the mal1-mal2 paralogs. The mal2 operon from an unknown species of Thermotoga appears to have been horizontally

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

    USGS Publications Warehouse

    Zacheis, Amy B.; Hupp, J.W.; Ruess, Roger 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

  13. 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.

  14. Role of three different plants on simultaneous salt and nutrient reduction from saline synthetic wastewater in lab-scale constructed wetlands.

    PubMed

    Jesus, João M; Cassoni, A C; Danko, Anthony S; Fiúza, António; Borges, Maria-Teresa

    2017-02-01

    Constructed Wetlands (CWs) can be a valuable technology to treat high salinity wastewaters but it is not known their potential for removal of both nutrients and salt, and the type of plants to use. This study evaluated the effect of three plants on salt reduction and simultaneous nutrient removal in CWs microcosms with expanded clay and in hydroponic conditions. Initial values of the synthetic wastewater tested were EC=15dSm(-1), SAR=151; NH4(+)-N=24mgL(-1); PO4(3-)-P=30mgL(-1) and NO3(-)-N=34mgL(-1). With expanded clay CW removal efficiency for NH4(+)-N was 21, 88 and 85%, while for NO3(-)-N, it was 4, 56 and 68% for Spartina maritima, Juncus maritimus and Arundo donax, respectively. PO4(3-)-P was adsorbed completely in the expanded clay. However, in hydroponic system, removal efficiencies for NH4(+)-N were 53 and 50%, while PO4(3-)-P removal was 89 and -14% for Spartina maritima and Juncus maritimus, respectively. Nutrient removal in planted microcosms was statistically higher than unplanted controls for NH4(+)-N and PO4(3-)-P. However, salt removal was apparent in the hydroponic system only after 23days of HRT, despite clear salt excretion visible in both Spartina maritima and Juncus maritimus. This study demonstrates the potential of two halophytic plants for saline wastewater treatment. However, salt removal in such a scenario could not be well documented and might prove to be impractical in future work.

  15. Probing the functional tolerance of the b subunit of Escherichia coli ATP synthase for sequence manipulation through a chimera approach.

    PubMed

    Bi, Yumin; Watts, Joel C; Bamford, Pamela Krauss; Briere, Lee-Ann K; Dunn, Stanley D

    2008-01-01

    A dimer of 156-residue b subunits forms the peripheral stator stalk of eubacterial ATP synthase. Dimerization is mediated by a sequence with an unusual 11-residue (hendecad) repeat pattern, implying a right-handed coiled coil structure. We investigated the potential for producing functional chimeras in the b subunit of Escherichia coli ATP synthase by replacing parts of its sequence with corresponding regions of the b subunits from other eubacteria, sequences from other polypeptides having similar hendecad patterns, and sequences forming left-handed coiled coils. Replacement of positions 55-110 with corresponding sequences from Bacillus subtilis and Thermotoga maritima b subunits resulted in fully functional chimeras, judged by support of growth on nonfermentable carbon sources. Extension of the T. maritima sequence N-terminally to position 37 or C-terminally to position 124 resulted in slower but significant growth, indicating retention of some capacity for oxidative phosphorylation. Portions of the dimerization domain between 55 and 95 could be functionally replaced by segments from two other proteins having a hendecad pattern, the distantly related E subunit of the Chlamydia pneumoniae V-type ATPase and the unrelated Ag84 protein of Mycobacterium tuberculosis. Extension of such sequences to position 110 resulted in loss of function. None of the chimeras that incorporated the leucine zipper of yeast GCN4, or other left-handed coiled coils, supported oxidative phosphorylation, but substantial ATP-dependent proton pumping was observed in membrane vesicles prepared from cells expressing such chimeras. Characterization of chimeric soluble b polypeptides in vitro showed their retention of a predominantly helical structure. The T. maritima b subunit chimera melted cooperatively with a midpoint more than 20 degrees C higher than the normal E. coli sequence. The GCN4 construct melted at a similarly high temperature, but with much reduced cooperativity, suggesting a

  16. 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.

  17. Wetlands Research Program. Corps of Engineers Wetlands Delineation Manual. Appendix C. Sections 1 and 2. Region 2 - Southeast.

    DTIC Science & Technology

    1987-01-01

    cycZophylZa’Fernald Bacopa B 3. innominata (Gomez Maza) Alain Bacopa OBL B. monnieri (L.) Wettst. Coast bacopa OBL 3. repens (Swartz) Wettgt. Creeping bacopa ...OBL B. rctundifoiia (Michx.) Wettst. Roundleaf bacopa OBL Baiduina atropur’purea Harper Balduina FACW B. uniflora Nutt. One-flowered balduina FACW... Bacopa OBL Batis maritima Saltwort OBL .B.’., 5erchemia scanden8 Rattan vine FACW " " Fetula nigra River birch OBL -.. ¢2 ". FAC FA 3.eThre3er4Ztu

  18. Antioxidant activity of wild plants collected in Beni-Sueif governorate, Upper Egypt.

    PubMed

    Abouzid, S; Elshahaat, A; Ali, S; Choudhary, M I

    2008-10-01

    Antioxidant activity of a selection of commonly occurring wild plants growing in Beni-Sueif governorate, Upper Egypt, has been tested. The plants selected are Tamarix nilotica, Ambrosia maritima, Zygophyllum coccenium, Conyza dioscoridis, Chenopodium ambrosioides, and Calotropis procera. The in vitro antioxidant assays used in this study were 1,1-diphenyl-2-picryl hydrazyl (DPPH) radical scavenging activity, superoxide anion scavenging activity and iron chelating activity. Extracts prepared from the leaves and flowers of Tamarix nilotica have shown the highest antioxidant activity in the three kinds of assay.

  19. Recombinant expression and purification of "virus-like" bacterial encapsulin protein cages.

    PubMed

    Rurup, W Frederik; Cornelissen, Jeroen J L M; Koay, Melissa S T

    2015-01-01

    Ultracentrifugation, particularly the use of sucrose or cesium chloride density gradients, is a highly reliable and efficient technique for the purification of virus-like particles and protein cages. Since virus-like particles and protein cages have a unique size compared to cellular macromolecules and organelles, the rate of migration can be used as a tool for purification. Here we describe a detailed protocol for the purification of recently discovered virus-like assemblies called bacterial encapsulins from Thermotoga maritima and Brevibacterium linens.

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

    NASA Technical Reports Server (NTRS)

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

    1988-01-01

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

  1. Solar Physics Topics in High School: Analysis of a Course with Practical Activities at Dietrich Schiel Observatory. (Spanish Title: Temas de Física Solar Para Estudiantes de Escuelas Secundarias: un Análisis de un Curso con Enfoque Práctico en el Observatorio Dietrich Schiel.) Tópicos de Física Solar no Ensino Médio: Análise de um Curso com Atividades Práticas no Observatório Dietrich Schiel

    NASA Astrophysics Data System (ADS)

    Calbo Aroca, Silvia; Donizete Colombo, Pedro, Jr.; Celestino Silva, Cibelle

    2012-12-01

    This work analyses results obtained in a solar physics course for high school students promoted at the Dietrich Schiel Observatory of the University of São Paulo (USP). The course was elaborated by the authors with the intention of investigating student's concepts about the Sun, teaching topics of modern physics related to the Sun and providing students with knowledge about our star as well. The methodology of data gathering consisted of audio and video records of classes and of semi-structured interviews, and analysis of answers to written questionnaires. The results showed that most high school students conceived the Sun as made of fire, while sunspots were thought to be holes in the Sun. Even though some students did know that a spectrum is formed using a prism or diffraction grating, most of them ignored the nature of the observed spectral lines. Through the course, this topic was developed by means of a practical approach with solar and lamp spectra observations. The results obtained in the course point to the importance of science centers as partners in formal education. In this specific case, the Solar Room at the Dietrich Schiel Observatory is as a favorable environment for teaching modern physics in high school. Este artículo analiza los resultados obtenidos en un curso sobre la física solar, auspiciado por el Observatorio Dietrich Schiel de la USP para estudiantes de las escuelas secundarias. El curso fue diseñado por los autores con la intención de investigar las concepciones sobre el sol, enseñar temas relacionados con la física moderna del Sol y conocimientos generales sobre el astro rey. La metodología utilizada para la recolección de datos consistió en grabar, en audio y video, las clases, las entrevistas semi-estructuradas y las respuestas a los cuestionarios escritos. Los resultados mostraron que la mayoría de los participantes conciben el Sol como constituido por fuego y las manchas solares en la superficie solar como agujeros. Aunque algunos estudiantes sabían que un espectro puede estar formado por un prisma o red de difracción, la mayor parte de ellos desconocía la naturaleza de las líneas espectrales. A lo largo del curso, esta cuestión fue trabajada con un enfoque práctico mediante la observación del espectro solar y de las lámparas durante clases expositivas/dialogadas. Los resultados obtenidos en el curso mustran la importancia de los centros de ciencia como un apoyo en la educación formal. En este caso en particular, la Sala Solar del Observatorio Dietrich Schiel se destaca como un entorno favorable para la enseñanza de la física moderna en la escuela secundaria. Este trabalho analisa resultados obtidos em um curso sobre física solar para alunos do ensino médio promovido pelo Observatório Dietrich Schiel da USP. O curso foi elaborado pelos autores com a intenção de investigar concepções sobre o Sol, ensinar tópicos de física moderna relacionados ao Sol e conhecimentos gerais sobre o astro rei. A metodologia de coleta de dados consistiu em gravação em áudio e vídeo das aulas e das entrevistas semi-estruturadas, e respostas a questionários escritos. Os resultados mostraram que a maioria dos participantes concebeu o Sol como constituído por fogo e as manchas solares como buracos na superfície solar. Embora alguns alunos soubessem que um espectro pode ser formado por um prisma ou rede de difração, a maior parte deles desconhecia a natureza das linhas espectrais. Ao longo do curso, este tema foi trabalhado com uma abordagem prática com observação do espectro solar e de lâmpadas e em aulas expositivo-dialogadas. Os resultados obtidos no curso apontam para a importância dos centros de ciências como parceiros da educação formal. Neste caso específico, a Sala Solar do Observatório Dietrich Schiel é um ambiente propício para o ensino de física moderna no ensino médio.

  2. 'Blue Carbon' and Nutrient Stocks of Salt Marshes at a Temperate Coastal Lagoon (Ria de Aveiro, Portugal).

    PubMed

    Sousa, Ana I; Santos, Danielle B; Silva, Eduardo Ferreira da; Sousa, Lisa P; Cleary, Daniel F R; Soares, Amadeu M V M; Lillebø, Ana I

    2017-01-25

    Ria de Aveiro is a mesotidal coastal lagoon with one of the largest continuous salt marshes in Europe. The objective of this work was to assess C, N and P stocks of Spartina maritima (low marsh pioneer halophyte) and Juncus maritimus (representative of mid-high marsh halophytes) combined with the contribution of Halimione portulacoides, Sarcocornia perennis, and Bolbochenous maritimus to the lagoon ≈4400 ha marsh area. A multivariate analysis (PCO), taking into account environmental variables and the annual biomass and nutrient dynamics, showed that there are no clear seasonal or spatial differences within low or mid-high marshes, but clearly separates J. maritimus and S. maritima marshes. Calculations of C, N and P stocks in the biomass of the five most representative halophytes plus the respective rhizosediment (25 cm depth), and taking into account their relative coverage, represents 252053 Mg C, 38100 Mg N and 7563 Mg P. Over 90% of the stocks are found within mid-high marshes. This work shows the importance of this lagoon's salt marshes on climate and nutrients regulation, and defines the current condition concerning the 'blue carbon' and nutrient stocks, as a basis for prospective future scenarios of salt marsh degradation or loss, namely under SLR context.

  3. 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 < 0.001). The EC50 values in fermented beans of both legumes were significantly lowest compared to raw and cooked beans (p < 0.001). In principal component analysis, total phenolics along with antioxidant activities (total antioxidant, ferrous-ion chelating and free radical-scavenging activities) of fermented beans of C. cathartica, while total antioxidant and free radical-scavenging activities of fermented beans of C. 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.

  4. Hydrogen transfer between methanogens and fermentative heterotrophs in hyperthermophilic cocultures

    SciTech Connect

    Muralidharan, V.; Hirsh, I.S.; Bouwer, E.J.; Rinker, K.D.; Kelly, R.M.

    1997-11-05

    Interactions involving hydrogen transfer were studied in a coculture of two hyperthermophilic microorganisms: Thermotoga maritima, an anaerobic heterotroph, and Methanococcus jannaschii, a hydrogenotrophic methanogen. Cell densities of T. maritima increased 10-fold when cocultured with M. jannaschii at 85 C, and the methanogen was able to grow in the absence of externally supplied H{sub 2} and CO{sub 2}. The coculture could not be established if the two organisms were physically separated by a dialysis membrane, suggesting the importance of spatial proximity. The significance of spatial proximity was also supported by cell cytometry, where the methanogen was only found in cell sorts at or above 4.5 {micro}m in samples of the coculture in exponential phase. An unstructured mathematical model was used to compare the influence of hydrogen transport and metabolic properties on mesophilic and hyperthermophilic cocultures. Calculations suggest the increases in methanogenesis rates with temperature result from greater interactions between the methanogenic and fermentative organisms, as evidenced by the sharp decline in H{sub 2} concentration in the proximity of a hyperthermophilic methanogen. The experimental and modeling results presented here illustrate the need to consider the interactions within hyperthermophilic consortia when choosing isolation strategies and evaluating biotransformations at elevated temperatures.

  5. Seasonal Variation of the Macrozoobenthic Community Structure at Low Salinities in a Mediterranean Lagoon (Monolimni Lagoon, Northern Aegean)

    NASA Astrophysics Data System (ADS)

    Kevrekidis, Theodoros

    2004-09-01

    The macrozoobenthic community structure and dynamics at low salinities (0.3-6 psu) in a Mediterranean lagoon (Monolimni lagoon) were investigated. Samples were collected monthly from February 1998 to February 1999 at two sampling stations. Community structure was analyzed by means of uni- and multivariate methods. 21 taxa were collected; the amphipod Corophium orientale and the gastropod Ventrosia maritima dominated the assemblages. Total abundance peaked (50,000-60,000 individuals m-2) in mid or late autumn. Community structure showed an almost even seasonal periodicity; seasonal changes were mainly derived from the intense variation in abundance of most species and the non-occurrence of a few ones (e.g. Corophium insidiosum, Polydora ciliata) in spring and summer. Non- occurrence, which led to a depression of the most diversity indices, was possibly the only direct impact of the extremely low salinities (~0.3 psu) on community structure. The main structuring factors of the community in the deeper outer part of the lagoon were water temperature and depth, and in the innermost part, where a Ruppia maritima meadow occurred, were water temperature and predation pressure by crabs (Carcinus aestuarii) and gobies (Knipowitchia caucasica). A temporary decline in total abundance in summer followed an increase in abundance of these predators. (

  6. Crystal Structure of the First Eubacterial Mre11 Nuclease Reveals Novel Features that may Discriminate Substrates During DNA Repair

    PubMed Central

    Das, Debanu; Moiani, Davide; Axelrod, Herbert L.; Miller, Mitchell D.; McMullan, Daniel; Jin, Kevin K.; Abdubek, Polat; Astakhova, Tamara; Burra, Prasad; Carlton, Dennis; Chiu, Hsiu-Ju; Clayton, Thomas; Deller, Marc C.; Duan, Lian; Ernst, Dustin; Feuerhelm, Julie; Grant, Joanna C.; Grzechnik, Anna; Grzechnik, Slawomir K.; Han, Gye Won; Jaroszewski, Lukasz; Klock, Heath E.; Knuth, Mark W.; Kozbial, Piotr; Krishna, S. Sri; Kumar, Abhinav; Marciano, David; Morse, Andrew T.; Nigoghossian, Edward; Okach, Linda; Paulsen, Jessica; Reyes, Ron; Rife, Christopher L.; Sefcovic, Natasha; Tien, Henry J.; Trame, Christine B.; van den Bedem, Henry; Weekes, Dana; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Elsliger, Marc-André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Tainer, John A.; Wilson, Ian A.

    2010-01-01

    Mre11 nuclease plays a central role in the repair of cytotoxic and mutagenic DNA double-strand breaks (DSBs). As x-ray structural information has only been available for the Pyrococcus furiosus enzyme (PfMre11), the conserved and variable features of this nuclease across the domains of life have not been experimentally defined. Our crystal structure and biochemical studies demonstrate that TM1635 from Thermotoga maritima, originally annotated as a putative nuclease, is the Mre11 endo/exonuclease from T. maritima (TmMre11) and the first such structure from eubacteria. TmMre11 and PfMre11 display similar overall structures, despite sequence identity in the twilight zone of only ∼20%. However, they differ substantially in their DNA specificity domains and in their dimeric organization. Residues in the nuclease domain are highly conserved, but those in the DNA specificity domain are not. The structural differences likely affect how Mre11s from different organisms recognize and interact with single-stranded DNA, double-stranded DNA and DNA hairpin structures during DNA repair. The TmMre11 nuclease active site has no bound metal ions, but is conserved in sequence and structure with exception of a histidine that is important in PfMre11 nuclease activity. Nevertheless, biochemical characterization confirms that TmMre11 possesses both endonuclease and exonuclease activities on ssDNA and dsDNA substrates, respectively. PMID:20122942

  7. Boosting dark fermentation with co-cultures of extreme thermophiles for biohythane production from garden waste.

    PubMed

    Abreu, Angela A; Tavares, Fábio; Alves, Maria Madalena; Pereira, Maria Alcina

    2016-11-01

    Proof of principle of biohythane and potential energy production from garden waste (GW) is demonstrated in this study in a two-step process coupling dark fermentation and anaerobic digestion. The synergistic effect of using co-cultures of extreme thermophiles to intensify biohydrogen dark fermentation is demonstrated using xylose, cellobiose and GW. Co-culture of Caldicellulosiruptor saccharolyticus and Thermotoga maritima showed higher hydrogen production yields from xylose (2.7±0.1molmol(-1) total sugar) and cellobiose (4.8±0.3molmol(-1) total sugar) compared to individual cultures. Co-culture of extreme thermophiles C. saccharolyticus and Caldicellulosiruptor bescii increased synergistically the hydrogen production yield from GW (98.3±6.9Lkg(-1) (VS)) compared to individual cultures and co-culture of T. maritima and C. saccharolyticus. The biochemical methane potential of the fermentation end-products was 322±10Lkg(-1) (CODt). Biohythane, a biogas enriched with 15% hydrogen could be obtained from GW, yielding a potential energy generation of 22.2MJkg(-1) (VS).

  8. On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales

    PubMed Central

    Zhaxybayeva, Olga; Swithers, Kristen S.; Lapierre, Pascal; Fournier, Gregory P.; Bickhart, Derek M.; DeBoy, Robert T.; Nelson, Karen E.; Nesbø, Camilla L.; Doolittle, W. Ford; Gogarten, J. Peter; Noll, Kenneth M.

    2009-01-01

    Since publication of the first Thermotogales genome, Thermotoga maritima strain MSB8, single- and multi-gene analyses have disagreed on the phylogenetic position of this order of Bacteria. Here we present the genome sequences of 4 additional members of the Thermotogales (Tt. petrophila, Tt. lettingae, Thermosipho melanesiensis, and Fervidobacterium nodosum) and a comprehensive comparative analysis including the original T. maritima genome. While ribosomal protein genes strongly place Thermotogales as a sister group to Aquificales, the majority of genes with sufficient phylogenetic signal show affinities to Archaea and Firmicutes, especially Clostridia. Indeed, on the basis of the majority of genes in their genomes (including genes that are also found in Aquificales), Thermotogales should be considered members of the Firmicutes. This result highlights the conflict between the taxonomic goal of assigning every species to a unique position in an inclusive Linnaean hierarchy and the evolutionary goal of understanding phylogenesis in the presence of pervasive horizontal gene transfer (HGT) within prokaryotes. Amino acid compositions of reconstructed ancestral sequences from 423 gene families suggest an origin of this gene pool even more thermophilic than extant members of this order, followed by adaptation to lower growth temperatures within the Thermotogales. PMID:19307556

  9. ‘Blue Carbon’ and Nutrient Stocks of Salt Marshes at a Temperate Coastal Lagoon (Ria de Aveiro, Portugal)

    NASA Astrophysics Data System (ADS)

    Sousa, Ana I.; Santos, Danielle B.; Silva, Eduardo Ferreira Da; Sousa, Lisa P.; Cleary, Daniel F. R.; Soares, Amadeu M. V. M.; Lillebø, Ana I.

    2017-01-01

    Ria de Aveiro is a mesotidal coastal lagoon with one of the largest continuous salt marshes in Europe. The objective of this work was to assess C, N and P stocks of Spartina maritima (low marsh pioneer halophyte) and Juncus maritimus (representative of mid-high marsh halophytes) combined with the contribution of Halimione portulacoides, Sarcocornia perennis, and Bolbochenous maritimus to the lagoon ≈4400 ha marsh area. A multivariate analysis (PCO), taking into account environmental variables and the annual biomass and nutrient dynamics, showed that there are no clear seasonal or spatial differences within low or mid-high marshes, but clearly separates J. maritimus and S. maritima marshes. Calculations of C, N and P stocks in the biomass of the five most representative halophytes plus the respective rhizosediment (25 cm depth), and taking into account their relative coverage, represents 252053 Mg C, 38100 Mg N and 7563 Mg P. Over 90% of the stocks are found within mid-high marshes. This work shows the importance of this lagoon’s salt marshes on climate and nutrients regulation, and defines the current condition concerning the ‘blue carbon’ and nutrient stocks, as a basis for prospective future scenarios of salt marsh degradation or loss, namely under SLR context.

  10. Evidence showing duplication and recombination of cel genes in tandem from hyperthermophilic Thermotoga sp.

    PubMed

    Kim, Min Keun; Kang, Tae Ho; Kim, Jungho; Kim, Hoon; Yun, Han Dae

    2012-12-01

    This study was conducted to assess the gene duplication and diversification of tandem cellulase genes in thermophilic bacteria. The tandem cellulase genes cel5C and cel5D were cloned from Thermotoga maritima MSB8, and a survey of the thermophilic bacterial genome for tandem cel genes from the databases was carried out. A clone having 2.3 kb fragment from T. maritima MSB8 showed cellulase activity, which had two open reading frames in tandem (cel5C and cel5D). The cel5C gene has 954 bp, which encodes a protein of 317 amino acid residues with a signal peptide of 23 amino acids, and the other gene cel5D consisting of 990 bp encoding a protein of 329 amino acid residues. These two proteins have similarity with the enzymes of glycosyl hydrolase family 5. From the enzyme assay, it was observed that Cel5C was extracellular and Cel5D was intracellular cellulase. Phylogenetic and homology matrix analyses of DNA and protein sequences revealed that family 12 cellulase enzymes Cel12A and Cel12B displayed higher homology (>50 %), but Cel5C and Cel5D enzymes belong to family 5 displayed lower homology (<30 %). In addition, repeated and mirror sequences in tandem genes are supposed to show the existence of gene duplication and recombination.

  11. Distribution and migration of seaside sparrows

    USGS Publications Warehouse

    Robbins, C.S.; Quay, Thomas; Funderberg, John B.=; Lee, David S.; Potter, Eloise F.; 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.

  12. 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.

  13. 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

  14. Remispora spitsbergenensis sp. nov., a marine lignicolous ascomycete from Svalbard, Norway.

    PubMed

    Pang, Ka-Lai; Chiang, Michael W L; Vrijmoed, Lilian L P

    2009-01-01

    Abstract: Remispora was established for R. maritima, a fungus with globose/subglobose, lightly colored and coriaceous ascomata; deliquescing asci; ellipsoidal ascospores; and bipolar, pleomorphic ascospore appendages. Seven species currently are included in Remispora: R crispa, R. galerita, R maritima, R. minuta, R. pilleata, R. quadriremis and R stellata. Variations on ascospore appendages can be observed in Remispora. In general the appendage is exosporic in nature and comprises an amorphous, electron-transparent matrix, and a fibrous, electron-dense component. An eighth Remispora species, R. spitsbergenensis sp. nov., is described here, discovered from washed-up wood collected at the shore of Longyearbyen, Svalbard, Norway. Ascospore appendages of R. spitsbergenensis appear as fibrous strands and amorphic material under the scanning electron microscope, which are characteristic of a Remispora species. Remispora spitsbergenensis resembles R. quadriremis and R. stellata because all possess four or more ascospore appendages at one end. Remispora spitsbergenensis possesses consistently four polar appendages at each end in contrast to six in R. stellata. Also ascospore appendages of R. spitsbergenensis are ribbon-like, compared with the obclavate, curved and attenuate appendages in R. quadriremis and R. stellata. A key for the identification of the eight Remispora species is provided.

  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

    2014-11-07

    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.

  16. Treating epilepsy: a review of Polish historical sources.

    PubMed

    Owczarek, Krzysztof

    2011-10-01

    The first surviving Polish publications on epilepsy were written in the 16th and 17th centuries. Many causes of epileptic seizures are quoted and they are divided into two categories: internal and external. Internal causes (causa interna) include imbalance in the basic bodily humors, that is, yellow bile, black bile, phlegm, and blood. According to medieval writers, the principal cause of epilepsy was vapor, a damp, cold volatile substance originating in the excessive production of one of the basic organismic liquids. Vapor allegedly stuck to the openings leading to the cerebral ventricles or blocked them entirely, resulting in convulsions. External causes (causa externa) include overeating and excessive drinking, teething, spoiled milk, poisons, badly treated spots and fever, cold air, moonlight, and wearing donkey hide. Medical treatments for epilepsy included surgical interventions (bloodletting) and pharmacological interventions. The latter included laxatives, sea onion (scilla maritima, urginea maritima), and ground human skull, all of which were supposed to protect the body from vapors. Medical practitioners of that time also advised that the factors and circumstances conducive to epileptic seizures be observed and identified so that patients could be isolated from these alleged causal factors and their seizures reduced or ended.

  17. ‘Blue Carbon’ and Nutrient Stocks of Salt Marshes at a Temperate Coastal Lagoon (Ria de Aveiro, Portugal)

    PubMed Central

    Sousa, Ana I.; Santos, Danielle B.; Silva, Eduardo Ferreira da; Sousa, Lisa P.; Cleary, Daniel F. R.; Soares, Amadeu M. V. M.; Lillebø, Ana I.

    2017-01-01

    Ria de Aveiro is a mesotidal coastal lagoon with one of the largest continuous salt marshes in Europe. The objective of this work was to assess C, N and P stocks of Spartina maritima (low marsh pioneer halophyte) and Juncus maritimus (representative of mid-high marsh halophytes) combined with the contribution of Halimione portulacoides, Sarcocornia perennis, and Bolbochenous maritimus to the lagoon ≈4400 ha marsh area. A multivariate analysis (PCO), taking into account environmental variables and the annual biomass and nutrient dynamics, showed that there are no clear seasonal or spatial differences within low or mid-high marshes, but clearly separates J. maritimus and S. maritima marshes. Calculations of C, N and P stocks in the biomass of the five most representative halophytes plus the respective rhizosediment (25 cm depth), and taking into account their relative coverage, represents 252053 Mg C, 38100 Mg N and 7563 Mg P. Over 90% of the stocks are found within mid-high marshes. This work shows the importance of this lagoon’s salt marshes on climate and nutrients regulation, and defines the current condition concerning the ‘blue carbon’ and nutrient stocks, as a basis for prospective future scenarios of salt marsh degradation or loss, namely under SLR context. PMID:28120885

  18. The functional exchangeability of pk- and k-turns in RNA structure

    PubMed Central

    Daldrop, Peter; Masquida, Benoît; Lilley, David M.J.

    2013-01-01

    Ribonuclease P RNA requires a sharply kinked RNA helix to make a loop-receptor interaction that creates the binding site for the substrate. In some forms of the ribozyme, this is accomplished by a k-turn, while others have a different element called the pk-turn. The structure of the pk-turn in RNase P of Thermotoga maritima is globally very similar to a k-turn, but lacks all the standard features of that structure, including long-range hydrogen bonds between the two helical arms. We show here that in an isolated RNA duplex, the pk-turn fails to adopt a tightly kinked structure, but rather is a flexible element. This suggests that the tertiary contacts of RNase P assist its folding into the required kinked structure. We find that we can replace the k-turn of the SAM-I riboswitch with the pk-turn, such that the resulting RNA retains its ability to bind SAM, although with lower affinity. We also find that we can replace the pk-turn of T. maritima RNase P with a standard k-turn (in either orientation) with retention of ribozyme activity. Thus, although the pk-turn cannot intrinsically fold into the kinked structure, it can be induced to fold correctly in context. And the pk-turn and k-turns can substitute functionally for one another. PMID:23364423

  19. Stable carbon isotope fractionation by acetotrophic sulfur-reducing bacteria.

    PubMed

    Goevert, Dennis; Conrad, Ralf

    2010-02-01

    Acetate is the most important intermediate in anaerobic degradation of organic matter. The carbon isotope effects associated with the oxidation of acetate (epsilon(ac)) were examined for four acetotrophic sulfur reducers, Desulfuromonas acetoxidans, Desulfuromonas thiophila, Desulfurella acetivorans, and Hippea maritima. During the consumption of acetate and sulfur, acetate was enriched in (13)C by 11.5 and 11.2 per thousand in Desulfuromonas acetoxidans and Desulfuromonas thiophila, respectively. By contrast, isotope fractionation in D. acetivorans and H. maritima resulted in isotope enrichment factors of epsilon(ac)=-6.3 per thousand and -8.4 per thousand, respectively. These sulfur-reducing bacteria all metabolize acetate via the tricarboxylic acid cycle, but have different mechanisms for the initial activation of acetate. In Desulfuromonas acetoxidans, acetyl-CoA is formed by succinyl-CoA : acetate-CoA-transferase, and in D. acetivorans by acetate kinase and phosphate acetyltransferase. Hence, values of epsilon(ac) seem to be characteristic for the type of activation of acetate to acetyl-CoA in acetotrophic sulfur reducers. Summarizing epsilon(ac)-values in anaerobic acetotrophic microorganisms, it appears that isotope fractionation depends on the mechanism of acetate activation to acetyl-CoA, on the key enzyme of the acetate dissimilation pathway, and on the bioavailability of acetate, which all have to be considered when using delta(13)C of acetate in environmental samples for diagnosis of the involved microbial populations.

  20. Mechanism for the definition of elongation and termination by the class II CCA-adding enzyme.

    PubMed

    Toh, Yukimatsu; Takeshita, Daijiro; Numata, Tomoyuki; Fukai, Shuya; Nureki, Osamu; Tomita, Kozo

    2009-11-04

    The CCA-adding enzyme synthesizes the CCA sequence at the 3' end of tRNA without a nucleic acid template. The crystal structures of class II Thermotoga maritima CCA-adding enzyme and its complexes with CTP or ATP were determined. The structure-based replacement of both the catalytic heads and nucleobase-interacting neck domains of the phylogenetically closely related Aquifex aeolicus A-adding enzyme by the corresponding domains of the T. maritima CCA-adding enzyme allowed the A-adding enzyme to add CCA in vivo and in vitro. However, the replacement of only the catalytic head domain did not allow the A-adding enzyme to add CCA, and the enzyme exhibited (A, C)-adding activity. We identified the region in the neck domain that prevents (A, C)-adding activity and defines the number of nucleotide incorporations and the specificity for correct CCA addition. We also identified the region in the head domain that defines the terminal A addition after CC addition. The results collectively suggest that, in the class II CCA-adding enzyme, the head and neck domains collaboratively and dynamically define the number of nucleotide additions and the specificity of nucleotide selection.

  1. More than one way to produce protein diversity: duplication and limited alternative splicing of an adhesion molecule gene in basal arthropods.

    PubMed

    Brites, Daniela; Brena, Carlo; Ebert, Dieter; Du Pasquier, Louis

    2013-10-01

    Exon duplication and alternative splicing evolved multiple times in metazoa and are of overall importance in shaping genomes and allowing organisms to produce many fold more proteins than there are genes in the genome. No other example is as striking as the one of the Down syndrome cell adhesion molecule (Dscam) of insects and crustaceans (pancrustaceans) involved in the nervous system differentiation and in the immune system. To elucidate the evolutionary history of this extraordinary gene, we investigated Dscam homologs in two basal arthropods, the myriapod Strigamia maritima and the chelicerate Ixodes scapularis. In both, Dscam diversified extensively by whole gene duplications resulting in multigene expansions. Within some of the S. maritima genes, exons coding for one of the immunoglobulin domains (Ig7) duplicated and are mutually exclusively alternatively spliced. Our results suggest that Dscam diversification was selected independently in chelicerates, myriapods, and pancrustaceans and that the usage of Dscam diversity by immune cells evolved for the first time in basal arthropods. We propose an evolutionary scenario for the appearance of the highly variable Dscam gene of pancrustaceans, adding to the understanding of how alternative splicing, exon, and gene duplication contribute to create molecular diversity associated with potentially new cellular functions.

  2. An Analysis of the Performance of the Fans of a Wind Tunnel at the Naval Postgraduate School.

    DTIC Science & Technology

    1985-12-01

    raduate School Monterey, alifornia 93943 5. Centro Tecnico Aeroespacial 1 Rua Paraibuna S/N 12225 Sao Jose dos Campos-SP Sao Paulo, BRAZIL 6. Centro...Tecnico Aeroespacial 2 Instituto de Atividades Espaciais Rua Paraibuna S/N 12225 Sao Jose dos Campos, SP Sao Paulo, BRAZIL 7. Centro Tecnico... Aeroespacial 2 Instituto de Atividades Espaciais Divisao de Sistemas Belicos Rua Paraibuna S/N 12225 Sao Jose dos Campos, SP Sao Paulo, BRAZIL 8. Lt.Col. Marcos

  3. 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

  4. 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.

  5. 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 Ompα) and the porin OmpB (or Ompβ). 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 β-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 β-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

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

    PubMed

    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 Ompα) and the porin OmpB (or Ompβ). 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 β-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 β-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.

  7. 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.

  8. 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.

  9. 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.

  10. Decline and disappearance of the Dusky Seaside Sparrow from Merritt Island, Florida

    USGS Publications Warehouse

    Sykes, P.W.

    1980-01-01

    The Dusky Seaside Sparrow, Ammospiza maritima nigrescens, was first discovered by Charles J. Maynard near Salt Lake on the St. Johns River west of Titusville, Brevard County, Florida, on March 17, 1872. Later that spring, Maynard found the sparrow to be quite common in the salt marsh on the Canaveral Peninsula in what is now the Merritt Island National Wildlife Refuge on the John F. Kennedy Space Center. The first Dusky nests were found 42 years later when Oscar E. Baynard and Henry Simpson located three on the peninsula along the edge of Indian River on May 21, 1914. The sparrow was abundant in the marsh on the east of the Indian River until the 1950s. By the early 1960s, the sparrow had disappeared from much of its former range and a decline occurred in an area under study on Merritt Island.

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

    USGS Publications Warehouse

    Euliss, N.H.; 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.

  12. Comparison of the role of two Spartina species in terms of phytostabilization and bioaccumulation of metals in the estuarine sediment.

    PubMed

    Cambrollé, J; Redondo-Gómez, S; Mateos-Naranjo, E; Figueroa, M E

    2008-12-01

    In the joint estuary of the Odiel and Tinto rivers (SW Spain), the invasive Spartina densiflora Brongn. and the native Spartina maritima (Curtis) Fernald are growing over sediments with extreme concentrations of heavy metals. The contents of As, Cu, Fe, Mn, Pb and Zn were determined in sediments, rhizosediments and different tissues of both species, from Odiel and Tinto marshes. S. densiflora showed a higher capability to retain metals around their roots and to control the uptake or transport of metals, mediated by a higher formation of plaques of Fe/Mn (hydro) oxides on the roots. At the Tinto marsh, there were no differences between the metal concentrations of the sediment and those of the rhizosediment, a fact that could be explained by the extremely high concentrations of metals which can pass over a threshold value, altering the properties of root cells and preventing roots from acting as a 'barrier' to the uptake or transport of metals.

  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. 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.

  15. D-Amino acid dipeptide production utilizing D-alanine-D-alanine ligases with novel substrate specificity.

    PubMed

    Sato, Masaru; Kirimura, Kohtaro; Kino, Kuniki

    2005-06-01

    D-Alanine-D-alanine ligase (Ddl) is an important enzyme in the synthesis of bacterial peptidoglycan. The genes encoding Ddls from Escherichia coli K12 (EcDdlB), Oceanobacillus iheyensis JCM 11309 (OiDdl), Synechocystis sp. PCC 6803 (SsDdl) and Thermotoga maritima ATCC 43589 (TmDdl), the genomic DNA sequences of which have been determined, were cloned and the substrate specificities of these recombinant Ddls were investigated. Although OiDdl had a high substrate specificity for D-alanine; EcDdlB, SsDdl and TmDdl showed broad substrate specificities for D-serine, D-threonine, D-cysteine and glycine, in addition to D-alanine. Four D-amino acid dipeptides were produced using EcDdlB, and D-amino acid homo-dipeptides were successfully produced at high yields except for D-threonyl-D-threonine.

  16. Biomolecular NMR using a microcoil NMR probe--new technique for the chemical shift assignment of aromatic side chains in proteins.

    PubMed

    Peti, Wolfgang; Norcross, James; Eldridge, Gary; O'Neil-Johnson, Mark

    2004-05-12

    A specially designed microcoil probe for use in biomolecular NMR spectroscopy is presented. The microcoil probe shows a mass-based sensitivity increase of a minimal factor of 7.5, allowing for the first time routine biomolecular NMR spectroscopy with microgram amounts of proteins. In addition, the exceptional radio frequency capabilities of this probe allowed us to record an aliphatic-aromatic HCCH-TOCSY spectrum for the first time. Using this spectrum, the side chains of aliphatic and aromatic amino acids can be completely assigned using only a single experiment. Using the conserved hypothetical protein TM0979 from Thermotoga maritima, we demonstrate the capabilities of this microcoil NMR probe to completely pursue the sequence specific backbone assignment with less than 500 microg of (13)C,(15)N labeled protein.

  17. Proteolysis in hyperthermophilic microorganisms

    DOE PAGES

    Ward, Donald E.; Shockley, Keith R.; Chang, Lara S.; ...

    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

  18. Crystal structures of TM0549 and NE1324—two orthologs of E. coli AHAS isozyme III small regulatory subunit

    PubMed Central

    Petkowski, Janusz J.; Chruszcz, Maksymilian; Zimmerman, Matthew D.; Zheng, Heping; Skarina, Tatiana; Onopriyenko, Olena; Cymborowski, Marcin T.; Koclega, Katarzyna D.; Savchenko, Alexei; Edwards, Aled; Minor, Wladek

    2007-01-01

    Crystal structures of two orthologs of the regulatory subunit of acetohydroxyacid synthase III (AHAS, EC 2.2.1.6) from Thermotoga maritima (TM0549) and Nitrosomonas europea (NE1324) were determined by single-wavelength anomalous diffraction methods with the use of selenomethionine derivatives at 2.3 Å and 2.5 Å, respectively. TM0549 and NE1324 share the same fold, and in both proteins the polypeptide chain contains two separate domains of a similar size. Each protein contains a C-terminal domain with ferredoxin-type fold and an N-terminal ACT domain, of which the latter is characteristic for several proteins involved in amino acid metabolism. The ferredoxin domain is stabilized by a calcium ion in the crystal structure of NE1324 and by a Mg(H2O)6 2+ ion in TM0549. Both TM0549 and NE1324 form dimeric assemblies in the crystal lattice. PMID:17586771

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

    PubMed

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

    2015-03-01

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

  20. 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.

  1. 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

  2. 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.

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

    PubMed

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

    2012-12-01

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

  4. Converting a Natural Protein Compartment into a Nanofactory for the Size-Constrained Synthesis of Antimicrobial Silver Nanoparticles.

    PubMed

    Giessen, Tobias W; Silver, Pamela A

    2016-12-16

    Engineered biological systems are used extensively for the production of high value and commodity organics. On the other hand, most inorganic nanomaterials are still synthesized via chemical routes. By engineering cellular compartments, functional nanoarchitectures can be produced under environmentally sustainable conditions. Encapsulins are a new class of microbial nanocompartments with promising applications in nanobiotechnology. Here, we engineer the Thermotoga maritima encapsulin EncTm to yield a designed compartment for the size-constrained synthesis of silver nanoparticles (Ag NPs). These Ag NPs exhibit uniform shape and size distributions as well as long-term stability. Ambient aqueous conditions can be used for Ag NP synthesis, while no reducing agents or solvents need to be added. The antimicrobial activity of the synthesized protein-coated or shell-free Ag NPs is superior to that of silver nitrate and citrate-capped Ag NPs. This study establishes encapsulins as an engineerable platform for the synthesis of biogenic functional nanomaterials.

  5. Food habits of mute swans in the Chesapeake Bay

    USGS Publications Warehouse

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

    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.

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

    PubMed

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

    2012-08-01

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

  7. The structure of RNA-free Rho termination factor indicates a dynamic mechanism of transcript capture.

    PubMed

    Canals, Albert; Usón, Isabel; Coll, Miquel

    2010-07-02

    The Rho factor is a ring-shaped ATP-dependent helicase that mediates transcription termination in most prokaryotic cells by disengaging the transcription elongation complex formed by the RNA polymerase, DNA, and the nascent RNA transcript. The crystal structures of key intermediates along the kinetic pathway of RNA binding to Rho unveiled an unprecedented mode of helicase loading and provided a model for the ATP turnover coupled to coordinated strand movement. Here we report the structure of the early RNA-free state of Rho, which had eluded crystallization for many years but now completes the series. The structure allows the characterization of the apo-form Rho from Thermotoga maritima to 2.3 A resolution, reveals an RNA-recruiting site that becomes hidden after occupancy of the adjacent specific primary RNA-binding site, and suggests an enriched model for mRNA capture that is consistent with previous data.

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

    PubMed

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

    2008-03-05

    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.

  9. 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.

  10. 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.

  11. 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

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

    PubMed Central

    Ołdziej, S.; Czaplewski, C.; Liwo, A.; Chinchio, M.; Nanias, M.; Vila, J. A.; Khalili, M.; Arnautova, Y. A.; Jagielska, A.; Makowski, M.; Schafroth, H. D.; Kaźmierkiewicz, 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 α and α+β proteins [60–70 residues with Cα rms deviation (rmsd) <6 Å]. However, for α+β proteins, significant topological errors occurred despite low rmsd values. In the second exercise, we predicted whole structures of five proteins (two α and three α+β, with sizes of 53–235 residues) with remarkably good accuracy. In particular, for the genomic target TM0487 (a 102-residue α+β protein from Thermotoga maritima), we predicted the complete, topologically correct structure with 7.3-Å Cα rmsd. So far this protein is the largest α+β 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 α-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 β-hairpin. These and other examples described in this work demonstrate significant progress in physics-based protein-structure prediction. PMID:15894609

  13. The effects of elevated CO2 and eutrophication on surface elevation gain in a European salt marsh.

    PubMed

    Reef, Ruth; Spencer, Tom; Mӧller, Iris; Lovelock, Catherine E; Christie, Elizabeth K; McIvor, Anna L; Evans, Ben R; Tempest, James A

    2017-02-01

    Salt marshes can play a vital role in mitigating the effects of global environmental change by dissipating incident storm wave energy and, through accretion, tracking increasing water depths consequent upon sea level rise. Atmospheric CO2 concentrations and nutrient availability are two key variables that can affect the biological processes that contribute to marsh surface elevation gain. We measured the effects of CO2 concentrations and nutrient availability on surface elevation change in intact mixed-species blocks of UK salt marsh using six open-top chambers receiving CO2 -enriched (800 ppm) or ambient (400 ppm) air. We found more rapid surface elevation gain in elevated CO2 conditions: an average increase of 3.4 mm over the growing season relative to ambient CO2 . Boosted regression analysis to determine the relative influence of different parameters on elevation change identified that a 10% reduction in microbial activity in elevated CO2 -grown blocks had a positive influence on elevation. The biomass of Puccinellia maritima also had a positive influence on elevation, while other salt marsh species (e.g. Suaeda maritima) had no influence or a negative impact on elevation. Reduced rates of water use by the vegetation in the high CO2 treatment could be contributing to elevation gain, either directly through reduced soil shrinkage or indirectly by decreasing microbial respiration rates due to lower redox levels in the soil. Eutrophication did not influence elevation change in either CO2 treatment despite doubling aboveground biomass. The role of belowground processes (transpiration, root growth and decomposition) in the vertical adjustment of European salt marshes, which are primarily minerogenic in composition, could increase as atmospheric CO2 concentrations rise and should be considered in future wetland models for the region. Elevated CO2 conditions could enhance resilience in vulnerable systems such as those with low mineral sediment supply or where

  14. Role of magnesium ions in the reaction mechanism at the interface between Tm1631 protein and its DNA ligand.

    PubMed

    Ogrizek, Mitja; Konc, Janez; Bren, Urban; Hodošček, Milan; Janežič, Dušanka

    2016-01-01

    A protein, Tm1631 from the hyperthermophilic organism Thermotoga maritima belongs to a domain of unknown function protein family. It was predicted that Tm1631 binds with the DNA and that the Tm1631-DNA complex is an endonuclease repair system with a DNA repair function (Konc et al. PLoS Comput Biol 9(11): e1003341, 2013). We observed that the severely bent, strained DNA binds to the protein for the entire 90 ns of classical molecular dynamics (MD) performed; we could observe no significant changes in the most distorted region of the DNA, where the cleavage of phosphodiester bond occurs. In this article, we modeled the reaction mechanism at the interface between Tm1631 and its proposed ligand, the DNA molecule, focusing on cleavage of the phosphodiester bond. After addition of two Mg(2+) ions to the reaction center and extension of classical MD by 50 ns (totaling 140 ns), the DNA ligand stayed bolted to the protein. Results from density functional theory quantum mechanics/molecular mechanics (QM/MM) calculations suggest that the reaction is analogous to known endonuclease mechanisms: an enzyme reaction mechanism with two Mg(2+) ions in the reaction center and a pentacovalent intermediate. The minimum energy pathway profile shows that the phosphodiester bond cleavage step of the reaction is kinetically controlled and not thermodynamically because of a lack of any energy barrier above the accuracy of the energy profile calculation. The role of ions is shown by comparing the results with the reaction mechanisms in the absence of the Mg(2+) ions where there is a significantly higher reaction barrier than in the presence of the Mg(2+) ions.Graphical abstractA protein, Tm1631 from the hyperthermophilic organism Thermotoga maritima belongs to a domain of unknown function protein family. We modeled the reaction mechanism at the interface between Tm1631 and its proposed ligand, the DNA molecule, focusing on cleavage of the phosphodiester bond.

  15. 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.

  16. 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.

  17. Non-complexed four cascade enzyme mixture: simple purification and synergetic co-stabilization.

    PubMed

    Myung, Suwan; Zhang, Y-H Percival

    2013-01-01

    Cell-free biosystems comprised of synthetic enzymatic pathways would be a promising biomanufacturing platform due to several advantages, such as high product yield, fast reaction rate, easy control and access, and so on. However, it was essential to produce (purified) enzymes at low costs and stabilize them for a long time so to decrease biocatalyst costs. We studied the stability of the four recombinant enzyme mixtures, all of which originated from thermophilic microorganisms: triosephosphate isomerase (TIM) from Thermus thermophiles, fructose bisphosphate aldolase (ALD) from Thermotoga maritima, fructose bisphosphatase (FBP) from T. maritima, and phosphoglucose isomerase (PGI) from Clostridium thermocellum. It was found that TIM and ALD were very stable at evaluated temperature so that they were purified by heat precipitation followed by gradient ammonia sulfate precipitation. In contrast, PGI was not stable enough for heat treatment. In addition, the stability of a low concentration PGI was enhanced by more than 25 times in the presence of 20 mg/L bovine serum albumin or the other three enzymes. At a practical enzyme loading of 1000 U/L for each enzyme, the half-life time of free PGI was prolong to 433 h in the presence of the other three enzymes, resulting in a great increase in the total turn-over number of PGI to 6.2×10(9) mole of product per mole of enzyme. This study clearly suggested that the presence of other proteins had a strong synergetic effect on the stabilization of the thermolabile enzyme PGI due to in vitro macromolecular crowding effect. Also, this result could be used to explain why not all enzymes isolated from thermophilic microorganisms are stable in vitro because of a lack of the macromolecular crowding environment.

  18. Adherence to a Physical Activity Program by Older Adults in Brazil

    ERIC Educational Resources Information Center

    de Souza, Doralice Lange; Vendruscolo, Rosecler

    2010-01-01

    This paper discusses the results of a qualitative research project in which we investigated adherence factors to a physical activity (PA) program for older adults in Brazil named "Sem Fronteiras: Atividades Corporais Para Adultos Maduros e Idosos", which translated into English means "Without Borders: Physical Activities for Mature…

  19. Qualitative analysis of the contributions of nutritionists to the development of an online instrument for monitoring the food intake of schoolchildren

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Consumo Alimentar e Atividade Fisica de Escolares (CAAFE) questionnaire is an online research tool that has been developed to enable the self-report of physical activity and diet by Brazilian schoolchildren aged 7–10 years. Formative research was conducted with nutritionists during the developme...

  20. Qualitative analysis of the contributions of nutritionists to the development of an online instrument for monitoring the food intake of schoolchildren

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Consumo Alimentar e Atividade Fisica de Escolares (CAAFE) questionnaire is an online research tool that has been developed to enable the self-report of physical activity and diet by Brazilian school children aged 7–10 years. Formative research was conducted with nutritionists during the developm...

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

    A set of laboratory experiments were conducted to study the effect of submerged aquatic vegetation in sediment resuspension under progressive waves. Three vegetation models (rigid, flexible and real plants of Ruppia maritima), six wave frequencies (in the range F=0.6-1.6 Hz) and four plant densities (Solid Plant Fractions, SPF in the range of 1-10%) were used. The sediment bed properties corresponded to a salt marsh wetland with a bimodal particle size distribution with two particle populations (population 1: particle diameters in the range of 2.5 to 6.0 μm, and population 2: particle diameters in the range of 6.0 to 100 μm). Within the canopy, wave velocities were attenuated for all the canopies studied and for all the frequencies analyzed. The change in the TKE (ΔTKE) compared with the case without plants was studied. For the rigid canopy model, in comparison to the unimpeded experiment, an increase in ΔTKE 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 ΔTKE 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 ΔTKE 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 ΔTKE was observed. The real case of a canopy of R. maritima behaved similarly to the flexible model canopy.

  2. 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

  3. 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(α1-2)Man(α1)OMe, Man(α1-3)Man(α1)OMe and Man(α1-4)Man(α1)OMe in two crystal forms [the complexes with Man(α1-3)Man(α1)OMe and Man(α1-4)Man(α1)OMe crystallized in space group P3{sub 2} and those with Man(α1-2)Man(α1)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(α1-2)Man(α1)OMe, Man(α1-3)Man(α1)OMe and Man(α1-4)Man(α1)OMe in two crystal forms [the complexes with Man(α1-3)Man(α1)OMe and Man(α1-4)Man(α1)OMe crystallized in space group P3{sub 2} and those with Man(α1-2)Man(α1)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(α1-4)Man(α1)OMe are reported here for the first time.

  4. 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

  5. Ensino e divulgação de astronomia no Planetário de Campinas

    NASA Astrophysics Data System (ADS)

    Faria, R. P.

    2003-08-01

    Projeto desenvolvido em 1981 por professores da Unicamp, sob a coordenação do Prof. Dr. Carlos Alfredo Argüello propunha a instalação de um Planetário em Campinas. Convênio firmado em 1982 entre a Unicamp, a Prefeitura de Campinas, a Funcamp e a Academia de Ciências do Estado de São Paulo, possibilitou a aquisição de um planetário Zeiss ZKP2, através do MEC, e em 28 de outubro de 1987 foi inaugurado o Planetário de Campinas. Desde então várias atividades de ensino e divulgação da Astronomia foram desenvolvidas regularmente. A verificação dos registros das atividades realizadas mostra um alto índice de atendimento, considerada a capacidade das instalações (sala de projeção para 60 pessoas, auditório com 45 poltronas e hall de exposições). As atividades dirigidas ao público, estudantes e professores, atenderam cerca de 400.000 participantes nos quase 16 anos de sua existência. Além de sessões públicas e escolares, com duração de 1 hora, são oferecidas às escolas vários outros tipos de atividades, com duração de 2,5 horas. Abordam diversos temas e são dirigidas a diferentes níveis de escolaridade. Cursos para o público e para professores, palestras, exposições e eventos especiais completam o quadro de atividades regulares. Mesmo enfrentando quase sempre dificuldades financeiras e administrativas verifica-se que o Planetário de Campinas realizou um trabalho quantitativamente e qualitativamente satisfatório, prestando bom serviços à comunidade de Campinas e de outras cidades de São Paulo e outros Estados. Isso é também atestado pela grande procura de reservas para suas atividades.

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

    PubMed Central

    Rambo, Robert P.; Tainer, John A.

    2010-01-01

    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 tRNAval, and yeast tRNAphe 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

  7. Salt-marsh plants as potential sources of Hg0 into the atmosphere

    NASA Astrophysics Data System (ADS)

    Canário, João; Poissant, Laurier; Pilote, Martin; Caetano, Miguel; Hintelmann, Holger; O'Driscoll, Nelson J.

    2017-03-01

    To assess the role of salt-marsh plants on the vegetation-atmospheric Hg0 fluxes, three salt marsh plant species, Halimione portulacoides, Sarcocornia fruticosa and Spartina maritima were selected from a moderately contaminated site in the Tagus estuary during May 2012. Total mercury in stems and leaves for each plant as well as total gaseous mercury and vegetation-air Hg0 fluxes were measured over two continuous days. Mercury fluxes were estimated with a dynamic flux Tedlar® bag coupled to a high-resolution automated mercury analyzer (Tekran 2537A). Other environmental parameters such as air temperature, relative humidity and net solar radiation were also measured aside. H. portulacoides showed the highest total mercury concentrations in stems and leaves and the highest average vegetation-air Hg0 flux (0.48 ± 0.40 ng Hg m-2 h-1). The continuous measurements converged to a daily pattern for all plants, with enhanced fluxes during daylight and lower flux during the night. It is noteworthy that throughout the measurements a negative flux (air-vegetation) was never observed, suggesting the absence of net Hg0 deposition. Based on the above fluxes and the total area occupied by each species we have estimated the total amount of Hg0 emitted from this salt-marsh plants. A daily emission of 1.19 mg Hg d-1 was predicted for the Alcochete marsh and 175 mg Hg d-1 for the entire salt marsh area of the Tagus estuary.

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

    PubMed Central

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

    2013-01-01

    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

  9. Spore dispersal of fetid Lysurus mokusin by feces of mycophagous insects.

    PubMed

    Chen, Gao; Zhang, Rui-Rui; Liu, Yang; Sun, Wei-Bang

    2014-08-01

    The ecological roles and biological mechanisms of zoochory in plants have long been foci in studies of co-evolutionary processes between plants and animals. However, the dispersal of fungal spores by animals has received comparatively little attention. In this study, the dispersal of spores of a selected fetid fungus, Lysurus mokusin, via feces of mycophagous insects was explored by: collecting volatiles emitted by the fungus using dynamic headspace extraction and analyzing them by GC-MS; testing the capacity of mycophagous insects to disperse its spores by counting spores in their feces; comparing the germinability of L. mokusin spores extracted from feces of nocturnal earwigs and natural gleba of the fungus; and assessing the ability of L. mokusin volatiles to attract insects in bioassays with synthetic scent mixtures. Numerous spores were detected in insects' feces, the bioassays indicated that L. mokusin odor (similar to that of decaying substances) attracts diverse generalist mycophagous insects, and passage through the gut of Anisolabis maritima earwigs significantly enhanced the germination rate of L. mokusin spores. Therefore, nocturnal earwigs and diurnal flies probably play important roles in dispersal of L. mokusin spores, and dispersal via feces may be an important common dispersal mechanism for fungal reproductive tissue.

  10. 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

  11. ASSESSING THE IMPACTS OF SALINITY AND NUTRIENT ...

    EPA Pesticide Factsheets

    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 northern shore once dominated by Zostera marina. This area is sandy, which may allow groundwater seepage. Ruppia is extremely salinity tolerant, and may also be more nutrient tolerant than Zostera. A six week microcosm experiment at two salinity (20 and 30 ppt) and 4 nutrient (0, 5, 10, and 30 µM inorganic N) levels to test their relative tolerance was conducted in 2014. Treatments were renewed daily to simulate tidal flushing and the exposure water was dosed with 15N for the first week of the experiment. At the end of the experiment, the plants were weighed and measured, and dried for later isotopic analysis. In the first experiment, Ruppia had significant structural responses to both nutrients and salinity; there was a slight decline in root weight and a decrease in the total number of shoots with increasing nutrients. Average Ruppia blade length decreased with increasing nutrients and this decrease was more evident at 30 ppt. In contrast, Zostera had no significant structural differences. For both species, there were no differences in shoot or root/rhizome weights in any treatment, nor were there differences in isotopic results due to salinity. However, δ15N in the tissue increase

  12. 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.

  13. 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.

  14. 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.

  15. Direct measurement of the kinetics of CBM9 fusion-tag bioprocessing using luminescence resonance energy transfer.

    PubMed

    Kavoosi, Mojgan; Creagh, A Louise; Turner, Robin F B; Kilburn, Douglas G; Haynes, Charles A

    2009-01-01

    The economics of affinity-tagging technologies, particularly at preparative scales, depends in part on the cost and efficiency of the bioprocessing step used to remove the affinity tag and obtain the final purified product (Lowe et al., J Biochem Biophys Methods. 2001;49:561-574). When CBM9, the family 9 cellulose binding module from Thermotoga maritima, serves as the affinity tag, the overall efficiency of tag removal is a function of the choice of processing enzyme and the local structure of the cleavage site, most notably the linker sequence flanking the bioprocessing recognition site on the tag side. A novel spectroscopic method is reported and used to rapidly and accurately measure CBM9 fusion-tag bioprocessing kinetics and their dependence on the choice of linker sequence. The assay monitors energy transfer between a lanthanide-based donor bound to the CBM9 tag and an acceptor fluorophore presented on the target protein or peptide. Enzyme-catalyzed cleavage of the fusion tag terminates this resonance energy transfer, resulting in a change in fluorescence intensity that can be monitored to quantify substrate concentration over time. The assay is simple, fast and accurate, providing k(cat)/K(M) values that contain standard errors of less than 3%. As a result, both substantial and subtle differences in bioprocessing kinetics can be measured and used to guide bioproduct design.

  16. Structural analysis of the diadenylate cyclase reaction of DNA-integrity scanning protein A (DisA) and its inhibition by 3'-dATP.

    PubMed

    Müller, Martina; Deimling, Tobias; Hopfner, Karl-Peter; Witte, Gregor

    2015-08-01

    The identification of the essential bacterial second messenger cyclic-di-AMP (c-di-AMP) synthesized by the DNA-integrity scanning protein A (DisA) has opened up a new and emerging field in bacterial signalling. To further analyse the diadenylate cyclase (DAC) reaction catalysed by the DAC domains of DisA, we crystallized Thermotoga maritima DisA in the presence of different ATP analogues and metal ions to identify the metal-binding site and trap the enzyme in pre- and post-reaction states. Through structural and biochemical assays we identified important residues essential for the reaction in the active site of the DAC domains. Our structures resolve the metal-binding site and thus explain the activation of ATP for the DAC reaction. Moreover, we were able to identify a potent inhibitor of the DAC domain. Based on the available structures and homology to annotated DAC domains we propose a common mechanism for c-di-AMP synthesis by DAC domains in c-di-AMP-producing species and a possible approach for its effective inhibition.

  17. Structural and functional studies of a metallo-β-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-β-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 αβ/βα fold, with the core β-strands having the β-sheet sandwich structure common to the metallo-β-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 β-lactamase and phosphodiesterase activities of Tm1162 have also been characterized.

  18. A new approach to assess and predict the functional roles of proteins across all known structures.

    PubMed

    Julfayev, Elchin S; McLaughlin, Ryan J; Tao, Yi-Ping; McLaughlin, William A

    2011-03-01

    The three dimensional atomic structures of proteins provide information regarding their function; and codified relationships between structure and function enable the assessment of function from structure. In the current study, a new data mining tool was implemented that checks current gene ontology (GO) annotations and predicts new ones across all the protein structures available in the Protein Data Bank (PDB). The tool overcomes some of the challenges of utilizing large amounts of protein annotation and measurement information to form correspondences between protein structure and function. Protein attributes were extracted from the Structural Biology Knowledgebase and open source biological databases. Based on the presence or absence of a given set of attributes, a given protein's functional annotations were inferred. The results show that attributes derived from the three dimensional structures of proteins enhanced predictions over that using attributes only derived from primary amino acid sequence. Some predictions reflected known but not completely documented GO annotations. For example, predictions for the GO term for copper ion binding reflected used information a copper ion was known to interact with the protein based on information in a ligand interaction database. Other predictions were novel and require further experimental validation. These include predictions for proteins labeled as unknown function in the PDB. Two examples are a role in the regulation of transcription for the protein AF1396 from Archaeoglobus fulgidus and a role in RNA metabolism for the protein psuG from Thermotoga maritima.

  19. Evidence for gene flow via seed dispersal from crop to wild relatives in Beta vulgaris (Chenopodiaceae): consequences for the release of genetically modified crop species with weedy lineages.

    PubMed Central

    Arnaud, J-F; Viard, F; Delescluse, M; Cuguen, J

    2003-01-01

    Gene flow and introgression from cultivated to wild plant populations have important evolutionary and ecological consequences and require detailed investigations for risk assessments of transgene escape into natural ecosystems. Sugar beets (Beta vulgaris ssp. vulgaris) are of particular concern because: (i) they are cross-compatible with their wild relatives (the sea beet, B. vulgaris ssp. maritima); (ii) crop-to-wild gene flow is likely to occur via weedy lineages resulting from hybridization events and locally infesting fields. Using a chloroplastic marker and a set of nuclear microsatellite loci, the occurrence of crop-to-wild gene flow was investigated in the French sugar beet production area within a 'contact-zone' in between coastal wild populations and sugar beet fields. The results did not reveal large pollen dispersal from weed to wild beets. However, several pieces of evidence clearly show an escape of weedy lineages from fields via seed flow. Since most studies involving the assessment of transgene escape from crops to wild outcrossing relatives generally focused only on pollen dispersal, this last result was unexpected: it points out the key role of a long-lived seed bank and highlights support for transgene escape via man-mediated long-distance dispersal events. PMID:12908976

  20. 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.

  1. [History of the Nippon Shinyaku Institute for Botanical Research].

    PubMed

    Yamaura, Takao

    2011-03-01

    Soon after its foundation in 1919, Nippon Shinyaku Co., Ltd began to develop the domestic production of Santonin, an anthelmintic agent, which, until then, had been totally imported from Russia. In 1927, Artemisia maritima ssp. monogyna was introduced from Europe and confirmed to contain Santonin. This European aster plant was named Mibu-yomogi after the place name of the headquarters of Nippon Shinyaku. In 1934, Yamashina Experimental Farm was founded to breed Mibu-yomogi cultivars of high quality as a plant material for Santonin production in Japan. In 1953, the Experimental Farm was reorganized into the Institute for Botanical Research for the continuous breeding of Santonin-containing aster plants and for the development of any new medicines from medicinal plants. Through the breeding of Santonin-containing aster plants, many cultivars including Yamashina No. 2 from Mibu-yomogi, Penta-yomogi and Hexa-yomogi which were crosssed with Mibu-yomogi and A. kurramensis, were bred. Furthermore, we still have four ethical drug products originated from medicinal plants. Since 1994, the Institute has become a botanical garden in order to maintain, develop and exhibit the plant collection and for the cultivation studies of rare plants.

  2. 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 α-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 α-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.

  3. 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.

  4. Effect of conductive polymers coated anode on the performance of microbial fuel cells (MFCs) and its biodiversity analysis.

    PubMed

    Li, Chao; Zhang, Libin; Ding, Lili; Ren, Hongqiang; Cui, Hao

    2011-06-15

    Conductive polymer, one of the most attractive electrode materials, has been applied to coat anode of MFC to improve its performance recently. In this paper, two conductive polymer materials, polyaniline (PANI) and poly(aniline-co-o-aminophenol) (PAOA) were used to modify carbon felt anode and physical and chemical properties of the modified anodes were studied. The power output and biodiversity of modified anodes, along with unmodified carbon anode were compared in two-chamber MFCs. Results showed that the maximum power density of PANI and PAOA MFC could reach 27.4 mW/m(2) and 23.8 mW/m(2), comparing with unmodified MFC, increased by 35% and 18% separately. Low temperature caused greatly decrease of the maximum voltage by 70% and reduced the sorts of bacteria on anodes in the three MFCs. Anode biofilm analysis showed different bacteria enrichment: a larger mount of bacteria and higher biodiversity were found on the two modified anodes than on the unmodified one. For PANI anode, the two predominant bacteria were phylogenetically closely related to Hippea maritima and an uncultured clone MEC_Bicarb_Ac-008; for PAOA, Clostridiales showed more enrichment. Compare PAOA with PANI, the former introduced phenolic hydroxyl group by copolymerization o-aminophenol with aniline, which led to a different microbial community and the mechanism of group effect was proposed.

  5. Cultivation of an immobilized (hyper)thermophilic marine microbial community in a bioreactor.

    PubMed

    Landreau, M; Duthoit, F; Roussel, E; Schönherr, S; Georges, Myriam; Godfroy, A; Le Blay, G

    2016-09-01

    Cultivation in a bioreactor of immobilized deep-sea hydrothermal microbial community was tested in order to assess the stability and reactivity of this new system. A community composed of eight hydrothermal strains was entrapped in a polymer matrix that was used to inoculate a continuous culture in a gas-lift bioreactor. The continuous culture was performed for 41 days at successively 60°C, 55°C, 60°C, 85°C and 60°C, at pH 6.5, in anaerobic condition and constant dilution rate. Oxic stress and pH variations were tested at the beginning of the incubation. Despite these detrimental conditions, three strains including two strict anaerobes were maintained in the bioreactor. High cell concentrations (3 × 10(8) cells mL(-1)) and high ATP contents were measured in both liquid fractions and beads. Cloning-sequencing and qPCR revealed that Bacillus sp. dominated at the early stage, and was later replaced by Thermotoga maritima and Thermococcus sp. Acetate, formate and propionate concentrations varied simultaneously in the liquid fractions. These results demonstrate that these immobilized cells were reactive to culture conditions. They were protected inside the beads during the stress period and released in the liquid fraction when conditions were more favorable. This confirms the advantage of immobilization that highlights the resilience capacity of certain hydrothermal microorganisms after a stress period.

  6. 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).

  7. Functional analyses for tRNase Z variants: an aspartate and a histidine in the active site are essential for the catalytic activity.

    PubMed

    Elbarbary, Reyad A; Takaku, Hiroaki; Nashimoto, Masayuki

    2008-12-01

    We performed functional analyses for various single amino-acid substitution variants of Escherichia coli, Bacillus subtilis, and human tRNase Zs. The well-conserved six histidine, His(I)-His(VI), and two aspartate, Asp(I) and Asp(II), residues together with metal ions are thought to form the active site of tRNase Z. The Mn(2+)-rescue analysis for Thermotoga maritima tRNase Z(S) has suggested that Asp(I) and His(V) directly contribute the proton transfer for the catalysis, and a catalytic mechanism has been proposed. However, experimental evidence supporting the proposed mechanism was limited. Here we intensively examined E. coli and B. subtilis tRNase Z(S) variants and human tRNase Z(L) variants for cleavage activities on pre-tRNAs in the presence of Mg(2+) or Mn(2+) ions. We observed that the Mn(2+) ions cannot rescue the activities of Asp(I)Ala and His(V)Ala variants from each species, which are lost in the presence of Mg(2+). This observation may support the proposed catalytic mechanism.

  8. 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 Quintín 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 m 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 Quintín Bay can be used in future change detection analyses to monitor the health of seagrasses in the bay.

  9. Plant cell calcium-rich environment enhances thermostability of recombinantly produced alpha-amylase from the hyperthermophilic bacterium Thermotoga maritime.

    PubMed

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

    2009-12-01

    In the industrial processing of starch for sugar syrup and ethanol production, a liquefaction step is involved where starch is initially solubilized at high temperature and partially hydrolyzed with a thermostable and thermoactive alpha-amylase. Most amylases require calcium as a cofactor for their activity and stability, therefore calcium, along with the thermostable enzyme, are typically added to the starch mixture during enzymatic liquefaction, thereby increasing process costs. An attractive alternative would be to produce the enzyme directly in the tissue to be treated. In a proof of concept study, tobacco cell cultures were used as model system to test in planta production of a hyperthermophilic alpha-amylase from Thermotoga maritima. While comparable biochemical properties to recombinant production in Escherichia coli were observed, thermostability of the plant-produced alpha-amylase benefited significantly from high intrinsic calcium levels in the tobacco cells. The plant-made enzyme retained 85% of its initial activity after 3 h incubation at 100 degrees C, whereas the E. coli-produced enzyme was completely inactivated after 30 min under the same conditions. The addition of Ca(2+) or plant cell extracts from tobacco and sweetpotato to the E. coli-produced enzyme resulted in a similar stabilization, demonstrating the importance of a calcium-rich environment for thermostability, as well as the advantage of producing this enzyme directly in plant cells where calcium is readily available.

  10. 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 β4α4 loop, shifted towards an active state upon mutation. Removal of β4α4 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

  11. 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.

  12. 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.

  13. 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.

  14. 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

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

    PubMed Central

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

    2015-01-01

    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. Arg187 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

  16. Hybridization can facilitate species invasions, even without enhancing local adaptation

    PubMed Central

    Mesgaran, Mohsen B.; Lewis, Mark A.; Ades, Peter K.; Donohue, Kathleen; Ohadi, Sara; Li, Chengjun

    2016-01-01

    The founding population in most new species introductions, or at the leading edge of an ongoing invasion, is likely to be small. Severe Allee effects—reductions in individual fitness at low population density—may then result in a failure of the species to colonize, even if the habitat could support a much larger population. Using a simulation model for plant populations that incorporates demography, mating systems, quantitative genetics, and pollinators, we show that Allee effects can potentially be overcome by transient hybridization with a resident species or an earlier colonizer. This mechanism does not require the invocation of adaptive changes usually attributed to invasions following hybridization. We verify our result in a case study of sequential invasions by two plant species where the outcrosser Cakile maritima has replaced an earlier, inbreeding, colonizer Cakile edentula (Brassicaceae). Observed historical rates of replacement are consistent with model predictions from hybrid-alleviated Allee effects in outcrossers, although other causes cannot be ruled out. PMID:27601582

  17. One-Pot Biosynthesis of High-Concentration α-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

    2016-03-02

    α-Glucose 1-phosphate (G1P) is synthesized from 5% (w/v) corn starch and 1 M phosphate mediated by α-glucan phosphorylase (αGP) 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 αGP 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.

  18. Plastisphere in action: evidence for an interaction between expanded polystyrene and dunal plants.

    PubMed

    Poeta, Gianluca; Fanelli, Giuliano; Pietrelli, Loris; Acosta, Alicia T R; Battisti, Corrado

    2017-03-29

    Among the many threats that can be recorded on sandy beaches, plastic litter represents a serious problem for these complex and endangered ecosystems. Expanded polystyrene (EPS) is increasingly abundant as a form of plastic litter in natural environments, particularly along shores and waterways. Nevertheless, despite the great number of scientific articles concerning the impact of litter on animal species, there are still no research focusing on the interaction between this type of beach litter and other biodiversity components. In this work, we reported the first evidence of interactions between EPS and living plants along a sandy beach of Tyrrhenian central Italy. We sampled 540 EPS items, mainly deriving from fishery activities (>75%). We obtained evidence for an interaction between EPS and plants: about 5% of items resulted perforated or have roots of three species (Phragmites australis, Spartina versicolor, Anthemis maritima). Apparently, we did not observed a relationship between plants and EPS items size. More research is needed to assess if the plant assemblage growing on EPS is random or if peculiar substrate exerts some sort of selection on the plant community.

  19. 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

  20. 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; Zając, A; Kałużny, 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.

  1. Solvent effects on catalysis by Escherichia coli dihydrofolate reductase.

    PubMed

    Loveridge, E Joel; Tey, Lai-Hock; Allemann, Rudolf K

    2010-01-27

    Hydride transfer catalyzed by dihydrofolate reductase (DHFR) has been described previously within an environmentally coupled model of hydrogen tunneling, where protein motions control binding of substrate and cofactor to generate a tunneling ready conformation and modulate the width of the activation barrier and hence the reaction rate. Changes to the composition of the reaction medium are known to perturb protein motions. We have measured kinetic parameters of the reaction catalyzed by DHFR from Escherichia coli in the presence of various cosolvents and cosolutes and show that the dielectric constant, but not the viscosity, of the reaction medium affects the rate of reaction. Neither the primary kinetic isotope effect on the reaction nor its temperature dependence were affected by changes to the bulk solvent properties. These results are in agreement with our previous report on the effect of solvent composition on catalysis by DHFR from the hyperthermophile Thermotoga maritima. However, the effect of solvent on the temperature dependence of the kinetic isotope effect on hydride transfer catalyzed by E. coli DHFR is difficult to explain within a model, in which long-range motions couple to the chemical step of the reaction, but may indicate the existence of a short-range promoting vibration or the presence of multiple nearly isoenergetic conformational substates of enzymes with similar but distinct catalytic properties.

  2. Mesohaline submerged aquatic vegetation survey along the U.S. gulf of Mexico coast, 2000: A stratified random approach

    USGS Publications Warehouse

    Carter, J.; Merino, J.H.; Merino, S.L.

    2009-01-01

    Estimates of submerged aquatic vegetative (SAV) along the U.S. Gulf of Mexico (Gulf) generally focus on seagrasses. In 2000, we attempted a synoptic survey of SAV in the mesohaline (5-20 ppt) zone of estuarine and nearshore areas of the northeastern Gulf. Areas with SAV were identified from existing aerial 1992 photography, and a literature review was used to select those areas that were likely to experience mesohaline conditions during the growing season. In 2000, a drought year, we visited 217 randomly selected SAV beds and collected data on species composition and environmental conditions. In general, sites were either clearly polyhaline (2: 20 ppt) or oligohaline (S 5 ppt), with only five sites measuring between 5 and 20 ppt. Ruppia maritima L. (13-35 ppt, n = 28) was the only species that occurred in mesohaline salinities. Halodule wrightii Asch. occurred in 73% of the beds. The nonindigenous Myriophyllum spicatum L. was present in four locations with salinities below 3 ppt. No nonindigenous macroalgae were identified, and no nonindigenous angiosperms occurred in salinities above 3 ppt. Selecting sample locations based on historical salinity data was not a successful strategy for surveying SAV in mesohaline systems, particularly during a drought year. Our ability to locate SAV beds within 50 m of their aerially located position 8 yr later demonstrates some SAV stability in the highly variable conditions of the study area. ?? 2009 by the Marine Environmental Silences Consortium of Alabama.

  3. DNA condensation by TmHU studied by optical tweezers, AFM and molecular dynamics simulations

    PubMed Central

    Olbrich, Carsten; Brutzer, Hergen; Salomo, Mathias; Kleinekathöfer, Ulrich; Keyser, Ulrich F.; Kremer, Friedrich

    2010-01-01

    The compaction of DNA by the HU protein from Thermotoga maritima (TmHU) is analysed on a single-molecule level by the usage of an optical tweezers-assisted force clamp. The condensation reaction is investigated at forces between 2 and 40 pN applied to the ends of the DNA as well as in dependence on the TmHU concentration. At 2 and 5 pN, the DNA compaction down to 30% of the initial end-to-end distance takes place in two regimes. Increasing the force changes the progression of the reaction until almost nothing is observed at 40 pN. Based on the results of steered molecular dynamics simulations, the first regime of the length reduction is assigned to a primary level of DNA compaction by TmHU. The second one is supposed to correspond to the formation of higher levels of structural organisation. These findings are supported by results obtained by atomic force microscopy. PMID:22210966

  4. Structure of the Rad50 DNA double-strand break repair protein in complex with DNA.

    PubMed

    Rojowska, Anna; Lammens, Katja; Seifert, Florian U; Direnberger, Carolin; Feldmann, Heidi; Hopfner, Karl-Peter

    2014-12-01

    The Mre11-Rad50 nuclease-ATPase is an evolutionarily conserved multifunctional DNA double-strand break (DSB) repair factor. Mre11-Rad50's mechanism in the processing, tethering, and signaling of DSBs is unclear, in part because we lack a structural framework for its interaction with DNA in different functional states. We determined the crystal structure of Thermotoga maritima Rad50(NBD) (nucleotide-binding domain) in complex with Mre11(HLH) (helix-loop-helix domain), AMPPNP, and double-stranded DNA. DNA binds between both coiled-coil domains of the Rad50 dimer with main interactions to a strand-loop-helix motif on the NBD. Our analysis suggests that this motif on Rad50 does not directly recognize DNA ends and binds internal sites on DNA. Functional studies reveal that DNA binding to Rad50 is not critical for DNA double-strand break repair but is important for telomere maintenance. In summary, we provide a structural framework for DNA binding to Rad50 in the ATP-bound state.

  5. Laūq: A Sustained-Release Dosage Form for Respiratory Disorders in Traditional Persian Medicine.

    PubMed

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

    2016-01-01

    Laūq 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 laūq 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 laūqs, 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 laūqs with newer drug delivery systems like lozenges.

  6. 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

  7. 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

  8. Exploring conformational equilibria of a heterodimeric ABC transporter

    PubMed Central

    Timachi, M Hadi; Hutter, Cedric AJ; Hohl, Michael; Assafa, Tufa; Böhm, Simon; Mittal, Anshumali; Seeger, Markus A; Bordignon, Enrica

    2017-01-01

    ABC exporters pump substrates across the membrane by coupling ATP-driven movements of nucleotide binding domains (NBDs) to the transmembrane domains (TMDs), which switch between inward- and outward-facing (IF, OF) orientations. DEER measurements on the heterodimeric ABC exporter TM287/288 from Thermotoga maritima, which contains a non-canonical ATP binding site, revealed that in the presence of nucleotides the transporter exists in an IF/OF equilibrium. While ATP binding was sufficient to partially populate the OF state, nucleotide trapping in the pre- or post-hydrolytic state was required for a pronounced conformational shift. At physiologically high temperatures and in the absence of nucleotides, the NBDs disengage asymmetrically while the conformation of the TMDs remains unchanged. Nucleotide binding at the degenerate ATP site prevents complete NBD separation, a molecular feature differentiating heterodimeric from homodimeric ABC exporters. Our data suggest hydrolysis-independent closure of the NBD dimer, which is further stabilized as the consensus site nucleotide is committed to hydrolysis. DOI: http://dx.doi.org/10.7554/eLife.20236.001 PMID:28051765

  9. 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.

  10. 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.

  11. 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.; 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.

  12. Antioxidant Potential of Bark Extracts from Boreal Forest Conifers

    PubMed Central

    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

  13. Structure of indole-3-glycerol phosphate synthase from Thermus thermophilus HB8: implications for thermal stability.

    PubMed

    Bagautdinov, Bagautdin; Yutani, Katsuhide

    2011-12-01

    The three-dimensional structure of indole-3-glycerol phosphate synthase (IGPS) from the thermophilic bacterium Thermus thermophilus HB8 (TtIGPS) has been determined at 1.8 Å resolution. The structure adopts a typical (β/α)(8)-barrel fold with an additional N-terminal extension of 46 residues. A detailed comparison of the crystal structure of TtIGPS with available structures of IGPS from the archaeon Sulfolobus solfataricus (SsIGPS) and the bacteria Thermotoga maritima (TmIGPS) and Escherichia coli (EcIGPS) has been performed. Although the overall folds of the proteins are the same, there are differences in amino-acid composition, structural rigidity, ionic features and stability clusters which may account for the high thermostability of the hyperthermophilic (SsIGPS and TmIGPS) and thermophilic (TtIGPS) proteins when compared with the mesophilic EcIGPS. The thermostability of IGPS seems to be established mainly by favourable interactions of charged residues, salt bridges and the spatial distribution of relatively rigid clusters of extensively interacting residues.

  14. [Impacts of Ochotona pallasi disturbance on alpine grassland community characteristics].

    PubMed

    Zhao, Guo-qin; Li, Guang-yong; Ma, Wen-hu; Zhao, Dian-zhi; Li, Xiao-yan

    2013-08-01

    Plateau pika is the main fossorial mammal in the alpine grassland in Qinghai Lake Watershed of Northwest China. Based on the field investigation data from 18 alpine grassland quadrats in the Watershed, and by using redundancy analysis (RDA) and the surface fitting offered by 'R-Vegan' , the disturbance intensity of plateau pika (Ochotona pallasi) was classified as four levels. In order to explore the impacts of plateau pika disturbance on the alpine grassland ecosystem and its grazing quality, the community characteristics under different disturbance intensities by plateau pika were analyzed, and a conceptual model about the alpine grassland community succession was proposed. The results showed that with the increase of the disturbance intensity, the dominant species changed from Juncus roemerianus to Poa pratensis and Laux maritima. When the disturbance was small, the community had high quantitative values of coverage, aboveground biomass, biodiversity, and species richness, but the proportion of weeds was also high. When the disturbance was large, the quantitative values were the lowest, while the proportion of weeds was the highest. When the disturbance was moderate, the community had relatively high quantitative values, and the proportion of grasses and sedges was the highest. It was concluded that the community' s characteristic values under low plateau pika disturbance intensity were high but the grazing quality was low, while high disturbance intensity resulted in the grassland degradation. Therefore, the disturbance intensity in the threshold could maintain the stability of alpine grassland ecosystem and improve its grazing quality.

  15. Mesohaline submerged aquatic vegetation survey along the U.S. gulf of Mexico coast, 2001 and 2002: A salinity gradient approach

    USGS Publications Warehouse

    Merino, J.H.; Carter, J.; Merino, S.L.

    2009-01-01

    Distribution of marine submerged aquatic vegetation (SAV; i.e., seagrass) in the northern Gulf of Mexico coast has been documented, but there are nonmarine submersed or SAV species occurring in estuarine salinities that have not been extensively reported. We sampled 276 SAV beds along the gulf coast in Florida, Alabama, Mississippi, Louisiana, and Texas in 2001 and 2002 in oligohaline to polyhaline (0 to 36 parts per thousand) waters to determine estuarine SAV species distribution and identify mesohaline SAV communities. A total of 20 SAV and algal species was identified and habitat characteristics such as salinity, water depth, pH, conductivity, turbidity, dissolved oxygen, and sediment composition were collected. Fourteen SAV species occurred two or more times in our samples. The most frequently occurring species was Ruppia maritima L. (n = 148), occurring in over half of SAV beds sampled. Eleocharis sp. (n = 47), characterized with an emergent rather than submerged growth form, was a common genus in the SAV beds sampled. A common marine species was Halodule wrightii Asch. (n = 36). Nonindigenous species Myriophyllum spicatum L. (n = 31) and Hydrilla verticillata (L. f.) Royle (n = 6) were present only in oligohaline water. Analyzing species occurrence and environmental characteristics using canonical correspondence and two-way indicator species analysis, we identify five species assemblages distinguished primarily by salinity and depth. Our survey increases awareness of nonmarine SAV as a natural resource in the gulf, and provides baseline data for future research. ?? 2009 by the Marine Environmental Sciences Consortium of Alabama.

  16. Insights into the mechanism of membrane pyrophosphatases by combining experiment and computer simulation

    PubMed Central

    Shah, Nita R.; Wilkinson, Craig; Harborne, Steven P. D.; Turku, Ainoleena; Li, Kun-Mou; Sun, Yuh-Ju; Harris, Sarah; Goldman, Adrian

    2017-01-01

    Membrane-integral pyrophosphatases (mPPases) couple the hydrolysis of pyrophosphate (PPi) to the pumping of Na+, H+, or both these ions across a membrane. Recently solved structures of the Na+-pumping Thermotoga maritima mPPase (TmPPase) and H+-pumping Vigna radiata mPPase revealed the basis of ion selectivity between these enzymes and provided evidence for the mechanisms of substrate hydrolysis and ion-pumping. Our atomistic molecular dynamics (MD) simulations of TmPPase demonstrate that loop 5–6 is mobile in the absence of the substrate or substrate-analogue bound to the active site, explaining the lack of electron density for this loop in resting state structures. Furthermore, creating an apo model of TmPPase by removing ligands from the TmPPase:IDP:Na structure in MD simulations resulted in increased dynamics in loop 5–6, which results in this loop moving to uncover the active site, suggesting that interactions between loop 5–6 and the imidodiphosphate and its associated Mg2+ are important for holding a loop-closed conformation. We also provide further evidence for the transport-before-hydrolysis mechanism by showing that the non-hydrolyzable substrate analogue, methylene diphosphonate, induces low levels of proton pumping by VrPPase. PMID:28345008

  17. Crystal structure of levansucrase from the Gram-negative bacterium Gluconacetobacter diazotrophicus

    PubMed Central

    2005-01-01

    The endophytic Gram-negative bacterium Gluconacetobacter diazotrophicus SRT4 secretes a constitutively expressed levansucrase (LsdA, EC 2.4.1.10), which converts sucrose into fructooligosaccharides and levan. The enzyme is included in GH (glycoside hydrolase) family 68 of the sequence-based classification of glycosidases. The three-dimensional structure of LsdA has been determined by X-ray crystallography at a resolution of 2.5 Å (1 Å=0.1 nm). The structure was solved by molecular replacement using the homologous Bacillus subtilis (Bs) levansucrase (Protein Data Bank accession code 1OYG) as a search model. LsdA displays a five-bladed β-propeller architecture, where the catalytic residues that are responsible for sucrose hydrolysis are perfectly superimposable with the equivalent residues of the Bs homologue. The comparison of both structures, the mutagenesis data and the analysis of GH68 family multiple sequences alignment show a strong conservation of the sucrose hydrolytic machinery among levansucrases and also a structural equivalence of the Bs levansucrase Ca2+-binding site to the LsdA Cys339–Cys395 disulphide bridge, suggesting similar fold-stabilizing roles. Despite the strong conservation of the sucrose-recognition site observed in LsdA, Bs levansucrase and GH32 family Thermotoga maritima invertase, structural differences appear around residues involved in the transfructosylation reaction. PMID:15869470

  18. Rational design of a fusion partner for membrane protein expression in E. coli

    PubMed Central

    Luo, Jianying; Choulet, Julie; Samuelson, James C

    2009-01-01

    We have designed a novel protein fusion partner (P8CBD) to utilize the co-translational SRP pathway in order to target heterologous proteins to the E. coli inner membrane. SRP-dependence was demonstrated by analyzing the membrane translocation of P8CBD-PhoA fusion proteins in wt and SRP-ffh77 mutant cells. We also demonstrate that the P8CBD N-terminal fusion partner promotes over-expression of a Thermotoga maritima polytopic membrane protein by replacement of the native signal anchor sequence. Furthermore, the yeast mitochondrial inner membrane protein Oxa1p was expressed as a P8CBD fusion and shown to function within the E. coli inner membrane. In this example, the mitochondrial targeting peptide was replaced by P8CBD. Several practical features were incorporated into the P8CBD expression system to aid in protein detection, purification, and optional in vitro processing by enterokinase. The basis of membrane protein over-expression toxicity is discussed and solutions to this problem are presented. We anticipate that this optimized expression system will aid in the isolation and study of various recombinant forms of membrane-associated protein. PMID:19530231

  19. 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.

  20. Cloning and Expression Analysis of a Gene Encoding for Ascorbate Peroxidase and Responsive to Salt Stress in Beet (Beta vulgaris).

    PubMed

    Dunajska-Ordak, Kamila; Skorupa-Kłaput, Monika; Kurnik, Katarzyna; Tretyn, Andrzej; Tyburski, Jarosław

    2014-01-01

    BvpAPX is a full-length cDNA-encoding peroxisomal ascorbate peroxidase isolated from leaves of salt-stressed beet (Beta vulgaris) plants. A high level of identity has been reported between the deduced amino acid sequence of BvpAPX and other known ascorbate peroxidases. The genomic sequence of BvpAPX revealed a gene composed of 5 exons and 4 introns. Several sequence motifs revealed in the 5'UTR region of the gene confer to BvpAPX a putative responsiveness to various abiotic stresses. We determined the effect of salt stress on BvpAPX expression in leaves of the cultivated beet varieties, Huzar and Janosik, and their wild salt-tolerant relative B. vulgaris ssp. maritima. Plants were subjected to salt stress during a 32-day culture period (long-term salt treatment). An alternative salinization protocol consisted of an 18-h incubation of detached beet leaves in media supplemented with toxic salt concentrations (short-term salt treatment). RT-Q-PCR analysis revealed that BvpAPX expression markedly increased in leaves of plants subjected to conditions of long-term treatment with salinity, whereas BvpAPX transcript levels remained unaffected in detached leaves during short-term salt treatment. In addition, several leaf redox system parameters, such as ascorbate peroxidase activity or ascorbic acid, hydrogen peroxide, and lipid hydroperoxide concentration, were determined in the leaves of beet plants subjected to salt stress conditions.

  1. Identification of amino acids of the beet necrotic yellow vein virus p25 protein required for induction of the resistance response in leaves of Beta vulgaris plants.

    PubMed

    Chiba, Soutaro; Miyanishi, Masaki; Andika, Ida Bagus; Kondo, Hideki; Tamada, Tetsuo

    2008-05-01

    The RNA3-encoded p25 protein of beet necrotic yellow vein virus (BNYVV) is responsible for the production of rhizomania symptoms of sugar beet roots (Beta vulgaris subsp. vulgaris). Here, it was found that the presence of the p25 protein is also associated with the resistance response in rub-inoculated leaves of sugar beet and wild beet (Beta vulgaris subsp. maritima) plants. The resistance phenotype displayed a range of symptoms from no visible lesions to necrotic or greyish lesions at the inoculation site, and only very low levels of virus and viral RNA accumulated. The susceptible phenotype showed large, bright yellow lesions and developed high levels of virus accumulation. In roots after Polymyxa betae vector inoculation, however, no drastic differences in virus and viral RNA accumulation levels were found between plants with susceptible and resistant phenotypes, except at an early stage of infection. There was a genotype-specific interaction between BNYVV strains and two selected wild beet lines (MR1 and MR2) and sugar beet cultivars. Sequence analysis of natural BNYVV isolates and site-directed mutagenesis of the p25 protein revealed that 3 aa residues at positions 68, 70 and 179 are important in determining the resistance phenotype, and that host-genotype specificity is controlled by single amino acid changes at position 68. The mechanism of the occurrence of resistance-breaking BNYVV strains is discussed.

  2. 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.

  3. Pycnogenol: a blend of procyanidins with multifaceted therapeutic applications?

    PubMed

    D'Andrea, Gabriele

    2010-10-01

    Great interest is currently centred on the biologic activities of pycnogenol a standardized plant extract obtained from the bark of the French maritime pine Pinus pinaster (formerly known as Pinus maritima), Aiton, subspecies Atlantica des Villar (Pycnogenol, Horphag Research Ltd., UK, Geneve, Switzerland), which grows in the coastal southwest France. The quality of this extract is specified in the United States Pharmacopeia (USP 28). Between 65% and 75% of Pycnogenol are procyanidins comprising of catechin and epicatechin subunits with varying chain lengths. Other constituents are polyphenolic monomers, phenolic or cinnamic acids and their glycosides. As many studies indicate, pycnogenol components are highly bioavailable. Uniquely, pycnogenol displays greater biologic effects as a mixture than its purified components do individually indicating that the components interact synergistically. Pycnogenol is now utilized throughout the world as a nutritional supplement and as a phytochemical remedy for various diseases ranging from chronic inflammation to circulatory dysfunction, including several impaired psycho-physiological functions. Owing to the basic chemical structure of its components, the most obvious feature of pycnogenol is its strong antioxidant activity. In fact, phenolic acids, polyphenols, and in particular flavonoids, are composed of one (or more) aromatic rings bearing one or more hydroxyl groups and are therefore potentially able to quench free radicals by forming resonance-stabilized phenoxyl radicals. In this review, emphasizing the molecular, cellular, and functional bases of therapy, data appearing in the peer-reviewed literature and focussing the main therapeutic applications of pycnogenol will be summarized and critically evaluated.

  4. Effect of pycnogenol on glucose transport in mature 3T3-L1 adipocytes.

    PubMed

    Lee, Hee-Hyun; Kim, Kui-Jin; Lee, Ok-Hwan; Lee, Boo-Yong

    2010-08-01

    Pycnogenol, a procyanidins-enriched extract of Pinus maritima bark, possesses antidiabetic properties, which improves the altered parameters of glucose metabolism that are associated with type 2 diabetes mellitus (T2DM). Since the insulin-stimulated antidiabetic activities of natural bioactive compounds are mediated by GLUT4 via the phosphatidylinositol-3-kinase (PI3K) and/or p38 mitogen activated protein kinase (p38-MAPK) pathway, the effects of pycnogenol were examined on the molecular mechanism of glucose uptake by the glucose transport system. 3T3-L1 adipocytes were treated with various concentrations of pycnogenol, and glucose uptake was examined using a non-radioisotope enzymatic assay and by molecular events associated with the glucose transport system using semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR). The results show that pycnogenol increased glucose uptake in fully differentiated 3T3-L1 adipocytes and increased the relative abundance of both GLUT4 and Akt mRNAs through the PI3K pathway in a dose dependent manner. Furthermore, pycnogenol restored the PI3K antagonist-induced inhibition of glucose uptake in the presence of wartmannin, an inhibitor of the PI3K. Overall, these results indicate that pycnogenol may stimulate glucose uptake via the PI3K dependent tyrosine kinase pathways involving Akt. Further the results suggest that pycnogenol might be useful in maintaining blood glucose control.

  5. 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.

  6. Diversity and Plant Growth Promoting Capacity of Endophytic Fungi Associated with Halophytic Plants from the West Coast of Korea.

    PubMed

    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; Yoon, Hyeokjun; Kim, Jong-Guk

    2015-12-01

    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.

  7. Direct Membrane Binding by Bacterial Actin MreB

    PubMed Central

    Salje, Jeanne; van den Ent, Fusinita; de Boer, Piet; Löwe, Jan

    2011-01-01

    Summary Bacterial actin MreB is one of the key components of the bacterial cytoskeleton. It assembles into short filaments that lie just underneath the membrane and organize the cell wall synthesis machinery. Here we show that MreB from both T. maritima and E. coli binds directly to cell membranes. This function is essential for cell shape determination in E. coli and is proposed to be a general property of many, if not all, MreBs. We demonstrate that membrane binding is mediated by a membrane insertion loop in TmMreB and by an N-terminal amphipathic helix in EcMreB and show that purified TmMreB assembles into double filaments on a membrane surface that can induce curvature. This, the first example of a membrane-binding actin filament, prompts a fundamental rethink of the structure and dynamics of MreB filaments within cells. PMID:21816350

  8. Construction and transformation of a Thermotoga-E. coli shuttle vector

    PubMed Central

    2012-01-01

    Background Thermotoga spp. are attractive candidates for producing biohydrogen, green chemicals, and thermostable enzymes. They may also serve as model systems for understanding life sustainability under hyperthermophilic conditions. A lack of genetic tools has hampered the investigation and application of these organisms. This study aims to develop a genetic transfer system for Thermotoga spp. Results Methods for preparing and handling Thermotoga solid cultures under aerobic conditions were optimized. A plating efficiency of ~50% was achieved when the bacterial cells were embedded in 0.3% Gelrite. A Thermotoga-E. coli shuttle vector pDH10 was constructed using pRQ7, a cryptic mini-plasmid found in T. sp. RQ7. Plasmid pDH10 was introduced to T. maritima and T. sp. RQ7 by electroporation and liposome-mediated transformation. Transformants were isolated, and the transformed kanamycin resistance gene (kan) was detected from the plasmid DNA extracts of the recombinant strains by PCR and was confirmed by restriction digestions. The transformed DNA was stably maintained in both Thermotoga and E. coli even without the selective pressure. Conclusions Thermotoga are transformable by multiple means. Recombinant Thermotoga strains have been isolated for the first time. A heterologous kan gene is functionally expressed and stably maintained in Thermotoga. PMID:22225774

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

    PubMed

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

    2010-12-09

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

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

    PubMed

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

    2005-09-22

    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 A 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.

  11. Response of some common annual bedding plants to three species of meloidogyne.

    PubMed

    McSorley, R; Frederick, J J

    1994-12-01

    Twelve ornamental bedding plant cultivars were grown in soil infested with isolates of Meloidogyne incognita race 1, M. javanica, or M. arenaria race 1 in a series of tests in containers in a growth room. Root galling (0-5 scale) and eggs/plant were evaluated 8-10 weeks after soil infestation and seedling transplantation. Snapdragon, Antirrhinum majus cv. First Ladies, was extensively galled and highly susceptible (mean gall rating >/=4.2 and >/=14,500 eggs/plant), and Celosia argentea cv. Century Mix and Coleus blumei cv. Rainbow were susceptible (>1,500 eggs/plant) to all three Meloidogyne isolates. Response of Petunia x hybrida varied with cultivar and nematode isolate. Little or no galling or egg production from any Meloidogyne isolate was observed on Ageratum houstonianum cv. Blue Mink, Lobularia maritima cv. Rosie O'Day, or Tagetes patula cv. Dwarf Primrose. Galling was slight (mean rating 4.0 and >/=7,900 eggs/plant) by M. javanica and M. arenaria but was nearly free of galling from M. incognita. Zinna elegans cv. Scarlet was nearly free of galling from M. incognita and M. arenaria but was susceptible (mean gall rating = 2.9; 3,400 eggs/plant) to M. javanica.

  12. Initial binding of ions to the interhelical loops of divalent ion transporter CorA: replica exchange molecular dynamics simulation study.

    PubMed

    Zhang, Tong; Mu, Yuguang

    2012-01-01

    Crystal structures of Thermotoga maritima magnesium transporter CorA, reported in 2006, revealed its homo-pentameric constructions. However, the structure of the highly conserved extracellular interhelical loops remains unsolved, due to its high flexibility. We have explored the configurations of the loops through extensive replica exchange molecular dynamics simulations in explicit solvent model with the presence of either Co(III) Hexamine ions or Mg(2+) ions. We found that there are multiple binding sites available on the interhelical loops in which the negatively charged residues, E316 and E320, are located notably close to the positively charged ions during the simulations. Our simulations resolved the distinct binding patterns of the two kinds of ions: Co(III) Hexamine ions were found to bind stronger with the loop than Mg(2+) ions with binding free energy -7.3 kJ/mol lower, which is nicely consistent with the previous data. Our study provides an atomic basis description of the initial binding process of Mg(2+) ions on the extracellular interhelical loops of CorA and the detailed inhibition mechanism of Co(III) Hexamine ions on CorA ions transportation.

  13. 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.

  14. Neurogenesis in myriapods and chelicerates and its importance for understanding arthropod relationships.

    PubMed

    Stollewerk, Angelika; Chipman, Ariel D

    2006-04-01

    Several alternative hypotheses on the relationships between the major arthropod groups are still being discussed. We reexamine here the chelicerate/myriapod relationship by comparing previously published morphological data on neurogenesis in the euarthropod groups and presenting data on an additional myriapod (Strigamia maritima). Although there are differences in the formation of neural precursors, most euarthropod species analyzed generate about 30 single neural precursors (insects/crustaceans) or precursor groups (chelicerates/myriapods) per hemisegment that are arranged in a regular pattern. The genetic network involved in recruitment and specification of neural precursors seems to be conserved among euarthropods. Furthermore, we show here that neural precursor identity seems to be achieved in a similar way. Besides these conserved features we found 2 characters that distinguish insects/crustaceans from myriapods/chelicerates. First, in insects and crustaceans the neuroectoderm gives rise to epidermal and neural cells, whereas in chelicerates and myriapods the central area of the neuroectoderm exclusively generates neural cells. Second, neural cells arise by stem-cell-like divisions of neuroblasts in insects and crustaceans, whereas groups of mainly postmitotic neural precursors are recruited for the neural fate in chelicerates and myriapods. We discuss whether these characteristics represent a sympleisiomorphy of myriapods and chelicerates that has been lost in the more derived Pancrustacea or whether these characteristics are a synapomorphy of myriapods and chelicerates, providing the first morphological support for the Myriochelata group.

  15. 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.

  16. 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.

  17. Interactions of Endoglucanases with Amorphous Cellulose Films Resolved by Neutron Reflectometry and Quartz Crystal Microbalance with Dissipation Monitoring

    SciTech Connect

    Cheng, Gang; Liu, Zelin; Kent, Michael S; Majewski, Jaroslaw; Michael, Jablin; Jaclyn, Murton K; Halbert, Candice E; Datta, Supratim; Chao, Wang; Brown, Page

    2012-01-01

    A study of the interaction of four endoglucanases with amorphous cellulose films by neutron reflectometry (NR) and quartz crystal microbalance with dissipation monitoring (QCM-D) is reported. The endoglucanases include a mesophilic fungal endoglucanase (Cel45A from H. insolens), a processive endoglucanase from a marine bacterium (Cel5H from S. degradans), and two from thermophilic bacteria (Cel9A from A. acidocaldarius and Cel5A from T. maritima). The use of amorphous cellulose is motivated by the promise of ionic liquid pretreatment as a second generation technology that disrupts the native crystalline structure of cellulose. The endoglucanases displayed highly diverse behavior. Cel45A and Cel5H, which possess carbohydrate-binding modules (CBMs), penetrated and digested within the bulk of the films to a far greater extent than Cel9A and Cel5A, which lack CBMs. While both Cel45A and Cel5H were active within the bulk of the films, striking differences were observed. With Cel45A, substantial film expansion and interfacial broadening were observed, whereas for Cel5H the film thickness decreased with little interfacial broadening. These results are consistent with Cel45A digesting within the interior of cellulose chains as a classic endoglucanase, and Cel5H digesting predominantly at chain ends consistent with its designation as a processive endoglucanase.

  18. The biological soil crusts of the San Nicolas Island: Enigmatic algae from a geographically isolated ecosystem

    USGS Publications Warehouse

    Flechtner, V.R.; Johansen, J.R.; Belnap, J.

    2008-01-01

    Composite soil samples from 7 sites on San Nicolas Island were evaluated quantitatively and qualitatively for the presence of cyanobacteria and eukaryotic microalgae. Combined data demonstrated a rich algal flora with 19 cyanobacterial and 19 eukaryotic microalgal genera being identified, for a total of 56 species. Nine new species were identified and described among the cyanobacteria and the eukaryotic microalgae that were isolated: Leibleinia edaphica, Aphanothece maritima, Chroococcidiopsis edaphica, Cyanosarcina atroveneta, Hassallia californica, Hassallia pseudoramosissima, Microchaete terrestre, Palmellopsis californiens, and Pseudotetracystis compactis. Distinct distributional patterns of algal taxa existed among sites on the island and among soil algal floras of western North America. Some algal taxa appeared to be widely distributed across many desert regions, including Microcoleus vaginatus, Nostoc punctiforme, Nostoc paludosum, and Tolypothrix distorta, Chlorella vulgaris, Diplosphaera cf. chodatii, Myrmecia astigmatica, Myrmecia biatorellae, Hantzschia amphioxys, and Luticola mutica. Some taxa share a distinctly southern distribution with soil algae from southern Arizona, southern California, and Baja California (e.g., Scenedesmus deserticola and Eustigmatos magnus). The data presented herein support the view that the cyanobacterial and microalgal floras of soil crusts possess significant biodiversity, much of it previously undescribed.

  19. Facile method for automated genotyping of single nucleotide polymorphisms by mass spectrometry

    PubMed Central

    Sauer, Sascha; Gelfand, David H.; Boussicault, Francis; Bauer, Keith; Reichert, Fred; Gut, Ivo G.

    2002-01-01

    In the future, analysis of single nucleotide polymorphisms (SNPs) should become a powerful tool for many genetic applications in areas such as association studies, pharmacogenetics and traceability in the agro-alimentary sector. A number of technologies have been developed for high-throughput genotyping of SNPs. Here we present the simplified GOOD assay for SNP genotyping by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI). The simplified GOOD assay is a single-tube, purification-free, three-step procedure consisting of PCR, primer extension and phosphodiesterase II digestion followed by mass spectrometric analysis. Due to the application of charge-tag technology, no sample purification is required prior to the otherwise very impurity-sensitive MALDI analysis. The use of methylphosphonate containing primers and ddNTPs or α-S-ddNTPs together with a novel DNA polymerase derived from Thermotoga maritima for primer extension allow the fluent preparation of negatively charge-tagged, allele-specific products. A key feature of this polymerase is its preference for ddNTPs and α-S-ddNTPs over dNTPs. The simplified GOOD assay was run with automatic liquid handling at the lowest manageable volumes, automatic data acquisition and interpretation. We applied this novel procedure to genotyping SNPs of candidate genes for hypertension and cardiovascular disease. PMID:11861927

  20. Rising from the sea: correlations between sulfated polysaccharides and salinity in plants.

    PubMed

    Aquino, Rafael S; Grativol, Clicia; Mourão, Paulo A S

    2011-04-28

    High salinity soils inhibit crop production worldwide and represent a serious agricultural problem. To meet our ever-increasing demand for food, it is essential to understand and engineer salt-resistant crops. In this study, we evaluated the occurrence and function of sulfated polysaccharides in plants. Although ubiquitously present in marine algae, the presence of sulfated polysaccharides among the species tested was restricted to halophytes, suggesting a possible correlation with salt stress or resistance. To test this hypothesis, sulfated polysaccharides from plants artificially and naturally exposed to different salinities were analyzed. Our results revealed that the sulfated polysaccharide concentration, as well as the degree to which these compounds were sulfated in halophytic species, were positively correlated with salinity. We found that sulfated polysaccharides produced by Ruppia maritima Loisel disappeared when the plant was cultivated in the absence of salt. However, subjecting the glycophyte Oryza sativa Linnaeus to salt stress did not induce the biosynthesis of sulfated polysaccharides but increased the concentration of the carboxylated polysaccharides; this finding suggests that negatively charged cell wall polysaccharides might play a role in coping with salt stress. These data suggest that the presence of sulfated polysaccharides in plants is an adaptation to high salt environments, which may have been conserved during plant evolution from marine green algae. Our results address a practical biological concept; additionally, we suggest future strategies that may be beneficial when engineering salt-resistant crops.

  1. Coenzyme Engineering of a Hyperthermophilic 6-Phosphogluconate Dehydrogenase from NADP+ to NAD+ with Its Application to Biobatteries

    PubMed Central

    Chen, Hui; Zhu, Zhiguang; Huang, Rui; Zhang, Yi-Heng Percival

    2016-01-01

    Engineering the coenzyme specificity of redox enzymes plays an important role in metabolic engineering, synthetic biology, and biocatalysis, but it has rarely been applied to bioelectrochemistry. Here we develop a rational design strategy to change the coenzyme specificity of 6-phosphogluconate dehydrogenase (6PGDH) from a hyperthermophilic bacterium Thermotoga maritima from its natural coenzyme NADP+ to NAD+. Through amino acid-sequence alignment of NADP+- and NAD+-preferred 6PGDH enzymes and computer-aided substrate-coenzyme docking, the key amino acid residues responsible for binding the phosphate group of NADP+ were identified. Four mutants were obtained via site-directed mutagenesis. The best mutant N32E/R33I/T34I exhibited a ~6.4 × 104-fold reversal of the coenzyme selectivity from NADP+ to NAD+. The maximum power density and current density of the biobattery catalyzed by the mutant were 0.135 mW cm−2 and 0.255 mA cm−2, ~25% higher than those obtained from the wide-type 6PGDH-based biobattery at the room temperature. By using this 6PGDH mutant, the optimal temperature of running the biobattery was as high as 65 °C, leading to a high power density of 1.75 mW cm−2. This study demonstrates coenzyme engineering of a hyperthermophilic 6PGDH and its application to high-temperature biobatteries. PMID:27805055

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

    DOE PAGES

    Deller, Marc C.; Johnson, Hope A.; Miller, Mitchell D.; ...

    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

  3. 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.

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

    PubMed

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

    2013-07-11

    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.

  5. 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

  6. 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.

  7. Status and threats on seagrass beds using GIS in Vietnam

    NASA Astrophysics Data System (ADS)

    Luong, Cao Van; Thao, Nguyen Van; Komatsu, Teruhisa; Ve, Nguyen Dac; Tien, Dam Duc

    2012-10-01

    Seagrasses, marine flowering plants, are widely distributed along temperate and tropical coastlines of the world. Seagrasses have key ecological roles in coastal ecosystems and can form extensive meadows supporting high biodiversity. Till now, fourteen seagrass species belonging to four families were found in Vietnam: Halophila beccarii, H. decipiens, H. ovalis, H. minor, Thalassia hemprichii, Enhalus acoroides, Ruppia maritima, Halodule pinifolia, H. uninervis, Syringodium isoetifolium, Cymadocea rotundata, C. serrulata and Thalassodendron ciliatum. A total area of seagrass beds in Vietnam is estimated to be approximately 17000 ha by satellite images and GIS technology. In recent years, the distribution areas and densities of seagrass beds in Vietnam have been serious decreased compared with those 10-15 years ago. The decline level depended on the impacts by the natural process, the economical activities and the conservation awareness of local people. Thus, it is different at each coastal area. Generally speaking, the distribution areas and densities of seagrass beds were decreased by more than 50%. Seagrasses on tidal flats in some areas such as Quang Ninh, Hai Phong, Phu Quoc seem to be nearly lost. The distribution areas of seagrass beds in 2009 at Tam Giang-Cau Hai lagoon and Cua Dai estuary was decreased by 50-70% of those in early 1990s.

  8. Fluorescence in insects

    NASA Astrophysics Data System (ADS)

    Welch, Victoria L.; Van Hooijdonk, Eloise; Intrater, Nurit; Vigneron, Jean-Pol

    2012-10-01

    Fluorescent molecules are much in demand for biosensors, solar cells, LEDs and VCSEL diodes, therefore, considerable efforts have been expended in designing and tailoring fluorescence to specific technical applications. However, naturally occurring fluorescence of diverse types has been reported from a wide array of living organisms: most famously, the jellyfish Aequorea victoria, but also in over 100 species of coral and in the cuticle of scorpions, where it is the rule, rather than the exception. Despite the plethora of known insect species, comparatively few quantitative studies have been made of insect fluorescence. Because of the potential applications of natural fluorescence, studies in this field have relevance to both physics and biology. Therefore, in this paper, we review the literature on insect fluorescence, before documenting its occurrence in the longhorn beetles Sternotomis virescens, Sternotomis variabilis var. semi rufescens, Anoplophora elegans and Stellognatha maculata, the tiger beetles Cicindela maritima and Cicindela germanica and the weevil Pachyrrhynchus gemmatus purpureus. Optical features of insect fluorescence, including emitted wavelength, molecular ageing and naturally occurring combinations of fluorescence with bioluminescence and colour-producing structures are discussed.

  9. Coenzyme Engineering of a Hyperthermophilic 6-Phosphogluconate Dehydrogenase from NADP+ to NAD+ with Its Application to Biobatteries

    NASA Astrophysics Data System (ADS)

    Chen, Hui; Zhu, Zhiguang; Huang, Rui; Zhang, Yi-Heng Percival

    2016-11-01

    Engineering the coenzyme specificity of redox enzymes plays an important role in metabolic engineering, synthetic biology, and biocatalysis, but it has rarely been applied to bioelectrochemistry. Here we develop a rational design strategy to change the coenzyme specificity of 6-phosphogluconate dehydrogenase (6PGDH) from a hyperthermophilic bacterium Thermotoga maritima from its natural coenzyme NADP+ to NAD+. Through amino acid-sequence alignment of NADP+- and NAD+-preferred 6PGDH enzymes and computer-aided substrate-coenzyme docking, the key amino acid residues responsible for binding the phosphate group of NADP+ were identified. Four mutants were obtained via site-directed mutagenesis. The best mutant N32E/R33I/T34I exhibited a ~6.4 × 104-fold reversal of the coenzyme selectivity from NADP+ to NAD+. The maximum power density and current density of the biobattery catalyzed by the mutant were 0.135 mW cm‑2 and 0.255 mA cm‑2, ~25% higher than those obtained from the wide-type 6PGDH-based biobattery at the room temperature. By using this 6PGDH mutant, the optimal temperature of running the biobattery was as high as 65 °C, leading to a high power density of 1.75 mW cm‑2. This study demonstrates coenzyme engineering of a hyperthermophilic 6PGDH and its application to high-temperature biobatteries.

  10. Assessing the impacts of salinity and nutrient stress to Ruppia ...

    EPA Pesticide Factsheets

    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 northern shore historically dominated by Zostera marina. Ruppia is extremely salinity tolerant, and may also be more nutrient tolerant than Zostera. To test this hypothesis 6-week microcosm experiments were conducted in the summers of 2014 and 2015. Microcosms were renewed daily to simulate tidal flushing and the water column was dosed with a 15N tracer for the first week of the experiments. In the 2014 microcosm experiment two salinity (20, 30 ppt) and four nutrient (0, 5, 10, 30 µM inorganic N) levels were used to test the species’ relative tolerance. This experiment yielded structurally significant results for Ruppia but no significant differences were detected for Zostera. In 2015 this experiment was performed for a second time with lower salinity (5, 30 ppt) and higher nutrients (0, 30, 100, 300, 1000 µM inorganic N) in order to determine Zostera’s tolerance to nutrient and salinity stress and confirm the previously observed Ruppia results. Both species had significant structural responses to the nutrient and salinity variables. Isotopic analysis run on above-ground tissue indicated that with increasing nutrient levels δ15N in the seagrass shoots increased, suggesting that nutrients

  11. Tidal saline wetland regeneration of sentinel vegetation types in the Northern Gulf of Mexico: An overview

    USGS Publications Warehouse

    Jones, Scott F; Stagg, Camille L.; Krauss, Ken W.; Hester, Mark W.

    2016-01-01

    Tidal saline wetlands in the Northern Gulf of Mexico (NGoM) are dynamic and frequently disturbed systems that provide myriad ecosystem services. For these services to be sustained, dominant macrophytes must continuously recolonize and establish after disturbance. Macrophytes accomplish this regeneration through combinations of vegetative propagation and sexual reproduction, the relative importance of which varies by species. Concurrently, tidal saline wetland systems experience both anthropogenic and natural hydrologic alterations, such as levee construction, sea-level rise, storm impacts, and restoration activities. These hydrologic alterations can affect the success of plant regeneration, leading to large-scale, variable changes in ecosystem structure and function. This review describes the specific regeneration requirements of four dominant coastal wetland macrophytes along the NGoM (Spartina alterniflora, Avicennia germinans, Juncus roemerianus, and Batis maritima) and compares them with current hydrologic alterations to provide insights into potential future changes in dominant ecosystem structure and function and to highlight knowledge gaps in the current literature that need to be addressed.

  12. 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.

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

    USGS Publications Warehouse

    Maher, L.J.; 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.

  14. Mechanism of 3'-Matured tRNA Discrimination from 3'-Immature tRNA by Class-II CCA-Adding Enzyme.

    PubMed

    Yamashita, Seisuke; Tomita, Kozo

    2016-06-07

    CCA-adding enzyme adds the 3'-CCA of tRNA, using CTP and ATP as substrates, and terminates RNA synthesis after completion of CCA addition, without using a nucleic acid template. The complex structure of class-II Thermotoga maritima CCA-adding enzyme and mature tRNA with 3'-CCA revealed the mechanisms by which the enzyme terminates RNA synthesis after completion of 3'-CCA addition, and discriminates 3'-mature tRNA from 3'-immature tRNA. After completion of 3'-CCA addition at the catalytic site, the 3'-CCA refolds and relocates to the release site, which is discrete from the catalytic site. The 3'-CCA forms a continuously stacked, stable conformation together with the enzyme. Consequently, the 3'-mature tRNA rotates relative to the surface of the enzyme, and only the 3'-mature tRNA is ready for release. The 3'-regions of immature tRNAs cannot form the stable stacking conformation in the release site; thus, the 3' end is relocated in the catalytic site, and the 3'-CCA is reconstructed.

  15. 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

  16. Assemblage and diversity of fungi on wood and seaweed litter of seven northwest portuguese beaches.

    PubMed

    Sridhar, K R; Karamchand, K S; Pascoal, C; Cássio, F

    2012-01-01

    Three hundred and fifty woody litter and one hundred and forty seaweed litter sampled from seven beaches of Northwest Portugal were assessed for the filamentous fungal assemblage and diversity. The woody litter was screened for fungi up to 42 months using damp chamber incubation. They consisted of 36 taxa (ascomycetes, 21; basidiomycetes, 3; anamorphic taxa, 12) comprising 10 core group taxa (≥10%) (ascomycetes, 8; basidiomycete, 1; anamorphic taxa, 1). The total fungal isolates ranged between 150 and 243, while the number of fungal taxa per wood ranged between 3 and 4.9. The seaweed litter was screened up to four months in damp chamber incubation. They encompassed 29 taxa (ascomycetes, 16; basidiomycetes, 2; anamorphic taxa, 11) comprising 15 core group taxa (ascomycetes, 9; basidiomycete, 1; anamorphic taxa, 5). Total fungal isolates ranged between 56 and 120, while the number of fungal taxa per seaweed segment ranged between 4.8 and 6.3. Fifteen taxa of ascomycetes, two of basidiomycetes, and four anamorphic taxa were common to wood and seaweed litter. On both the substrates, two arenicolous fungi Arenariomyces trifurcates and Corollospora maritima were the predominant fungi (72.6-85.9%). The species abundance curves showed higher frequency of occurrence of fungal taxa in seaweed than woody litter. Our study revealed rich assemblage and diversity of marine fungi on wood and seaweed litter of Northwest Portugal beaches. The fungal composition and diversity of this survey have been compared with earlier investigations on marine fungi of Portugal coast.

  17. 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

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

    PubMed Central

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

    2013-01-01

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

  19. 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.

  20. 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.

  1. Tidal saline wetland regeneration of sentinel vegetation types in the Northern Gulf of Mexico: An overview

    NASA Astrophysics Data System (ADS)

    Jones, Scott F.; Stagg, Camille L.; Krauss, Ken W.; Hester, Mark W.

    2016-06-01

    Tidal saline wetlands in the Northern Gulf of Mexico (NGoM) are dynamic and frequently disturbed systems that provide myriad ecosystem services. For these services to be sustained, dominant macrophytes must continuously recolonize and establish after disturbance. Macrophytes accomplish this regeneration through combinations of vegetative propagation and sexual reproduction, the relative importance of which varies by species. Concurrently, tidal saline wetland systems experience both anthropogenic and natural hydrologic alterations, such as levee construction, sea-level rise, storm impacts, and restoration activities. These hydrologic alterations can affect the success of plant regeneration, leading to large-scale, variable changes in ecosystem structure and function. This review describes the specific regeneration requirements of four dominant coastal wetland macrophytes along the NGoM (Spartina alterniflora, Avicennia germinans, Juncus roemerianus, and Batis maritima) and compares them with current hydrologic alterations to provide insights into potential future changes in dominant ecosystem structure and function and to highlight knowledge gaps in the current literature that need to be addressed.

  2. 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

  3. 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.

  4. Postglacial vegetation history of Orcas Island, northwestern Washington

    NASA Astrophysics Data System (ADS)

    Leopold, Estella B.; Dunwiddie, Peter W.; Whitlock, Cathy; Nickmann, Rudy; Watts, William A.

    2016-05-01

    The revegetation of islands following retreat of Pleistocene glaciers is of great biogeographical interest. The San Juan Islands, Washington, feature regionally distinctive xerophytic plant communities, yet their vegetation history, as it relates to past climate and sea level, is poorly known. We describe a 13,700-year-old pollen record from Killebrew Lake Fen and compare the vegetation reconstruction with others from the region. The data suggest that the narrow channels surrounding Orcas Island were not a barrier to early postglacial immigration of plants. Between 13,700 and 12,000 cal yr BP, Pinus, Tsuga, Picea, Alnus viridis, and possibly Juniperus maritima were present in a mosaic that supported Bison antiquus and Megalonyx. The rise of Alnus rubra-type pollen and Pteridium spores at ca. 12,000 cal yr BP suggests a warming trend and probably more fires. Temperate conifer taxa, including Cupressaceae, Pseudotsuga, Tsuga heterophylla, and Abies, increased after 11,000 cal yr BP and especially in the last 7000 cal yr BP. After 6000 cal yr BP, Pseudotsuga and Cupressaceae dominated the vegetation. The last 1500 yr were the wettest period of the record. Due to its rain shadow location, Orcas Island experienced drier conditions than on the mainland during most of the postglacial period.

  5. Diet of the Antillean manatee (Trichechus manatus manatus) in Belize, Central America

    USGS Publications Warehouse

    Allen, Aarin Conrad; Beck, Cathy A.; Bonde, Robert K.; Powell, James A.; Gomez, Nicole Auil

    2017-01-01

    Belize contains important habitat for Antillean manatees (Trichechus manatus manatus) and provides refuge for the highest known population density of this subspecies. As these animals face impending threats, knowledge of their dietary habits can be used to interpret resource utilization. The contents of 13 mouth, 6 digestive tract (stomach, duodenum and colon), and 124 fecal samples were microscopically examined using a modified point technique detection protocol to identify key plant species consumed by manatees at two important aggregation sites in Belize: Southern Lagoon and the Drowned Cayes. Overall, 15 different items were identified in samples from manatees in Belize. Five species of seagrasses (Halodule wrightii, Thalassia testudinum, Ruppia maritima, Syringodium filiforme, and Halophila sp.) made up the highest percentage of items. The red mangrove (Rhizophora mangle), was also identified as an important food item. Algae (Ulva sp., Chara sp., Lyngbya sp.) and invertebrates (sponges and diatoms) were also consumed. Variation in the percentage of seagrasses, other vascular plants, and algae consumption was analyzed as a 4-factor analysis of variance (ANOVA) with main effects and interactions for locality, sex, size classification, and season. While sex and season did not influence diet composition, differences for locality and size classification were observed. These results suggest that analysis of diet composition of Antillean manatees may help to determine critical habitat and use of associated food resources which, in turn can be used to aid conservation efforts in Belize.

  6. 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.

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

    PubMed

    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.

  8. Chromosome elimination and sex determination in springtails (Insecta, Collembola).

    PubMed

    Dallai, R; Fanciulli, P P; Frati, F

    1999-10-15

    A post-zygotic mechanism of sex determination is described in the two symphypleonans Dicyrtomina ornata (Nicolet) and Ptenothrix italica Dallai. The process consists of the loss of two sex chromosomes from the male embryo. At the end of the first meiotic division of spermatogenesis, a second chromosome elimination occurs, allowing half the secondary spermatocytes, later transformed into spermatids, to receive a complete haploid set of chromosomes. The secondary spermatocytes, which receive an incomplete set of chromosomes, degenerate. Males of the two collembolan species, therefore, produce a reduced number (50%) of spermatozoa. Females of D. ornata have 2n = 12 and males 2n = 10 chromosomes; females of P. italica have 2n = 14 and males 2n = 12 chromosomes. In both species, oogenesis proceeds normally and chromosomes pair and form chiasmata in meiotic prophase. The adaptive significance of this post-zygotic mechanism of sex determination is discussed. The mechanism seems to be a characteristic feature of the suborder Symphypleona. The neanurid Arthropleona Anurida maritima (Guérin), which was studied for comparative analysis, has 2n = 8 chromosomes and normal spermatogenesis producing haploid nuclei with four chromosomes. J. Exp. Zool. (Mol. Dev. Evol.) 285:215-225, 1999.

  9. The Use of Seaplanes as an Advanced Weapon Systemxc

    DTIC Science & Technology

    1988-09-01

    Kreniski 1 Centro Tecnico Aeroespacial -IAE-ESB 12 225 - Sao Jose dos Campos - SP, Brasil 10. Director do Centro Tecnico Aeroespacial 1 Centro Tecnico... Aeroespacial 12 225 - Sao Jose dos Campos - SP, Brasil 11. Director do Instituto de Atividades Espaciais 1 Centro Tecnico Aeroespacial - IAE 12 225 - Sao...Jose dos Campos - SP, Brasil 98 12. Chefe da Divisao de Sistemas Belicos Centro Tecnico Aeroespacial 12 225 - Sao Jose dos Campos - SP, Brasil 13

  10. Projeto observatórios virtuais: educação através de telescópios robóticos

    NASA Astrophysics Data System (ADS)

    Santana, P. H. S.; Shida, R. Y.

    2003-08-01

    O principal objetivo do projeto Observatórios Virtuais é o ensino na área de ciências através de atividades práticas desenvolvidas em colaboração entre instituições de pesquisa em astronomia e escolas de ensino médio e fundamental. Este ano deverá ser concluída a implantação do programa piloto de estudos, pesquisas e observação astronômica direta, com utilização em tempo real de telescópios robóticos, que assim funcionarão como "observatórios virtuais". O objetivo pedagógico das atividades práticas baseadas nas imagens atronômicas é desenvolver as habilidades e competências dos alunos no uso do método científico. Para isso, serão realizados projetos interdisciplinares, a partir de observações astronômicas, já que a astronomia é uma área interdisciplinar por excelência. Essas atividades terão níveis diferenciados de complexidade, que podem ser adequados aos vários graus do ensino e realidades regionais. Será dada ênfase ao desenvolvimento e aplicação em São Paulo, onde atua a equipe do IAG/USP. Como resultados apresentados no presente trabalho, temos a criação de um software em português para o processamento de imagens obtidas através de CCDs e a elaboração de material para as atividades educacionais relacionadas.

  11. Validity and reliability of the Dietary Sodium Restriction Questionnaire (DSRQ).

    PubMed

    d'Almeida, Karina S M; Souza, Gabriela C; Rabelo-Silva, Eneida Rejane

    2013-01-01

    Introducción: El Dietary Sodium Restriction Questionnaire (DSRQ) evalúa actitudes y comportamientos de pacientes con insuficiencia cardiaca (IC) relacionados con el cumplimiento de la restricción de sodio. Recientemente, ha sido traducido y adaptado culturalmente para uso en Brasil. No obstante, una validación adicional del instrumento se requiere para que pueda ser utilizado en el manejo de pacientes con IC en Brasil. Objetivo: Probar la fiabilidad y validez de la versión brasileña del DSRQ. Métodos: Validez aparente y de contenido fueron evaluados por un grupo de especialistas. Validez de constructo se evaluó mediante análisis factorial exploratoria y confirmatoria. La fiabilidad y consistencia interna del cuestionario fue evaluada mediante el coeficiente alfa de Cronbach. Resultados: Un total de 206 pacientes ambulatorios con IC fueron evaluados (edad media, 60,4 ± 11,9 años). Los resultados de la validez aparente y de contenido demostró la equivalencia entre la versión brasileña y de la versión original. En el análisis factorial exploratorio, el análisis de componentes principales (PCA) se obtuvieron cuatro factores con valores superiores a 1. Tres modelos fueron probados en el análisis factorial confirmatoria, y el modelo de tres factores resultantes del PCA mostró el mejor ajuste, representando 49% de la varianza. El alfa obtenido para las escalas de actitud/norma subjetiva, control de la conducta percibido y comportamiento dependiente fueron 0,71, 0,67 y 0,79, respectivamente. Conclusiones: Nuestros resultados sugieren que la versión brasileña del DSRQ es un instrumento válido y fiable para medir las actitudes y comportamientos relacionados con una dieta baja en sodio en pacientes brasileños con IC.

  12. Astronomia para/com crianças carentes em Limeira

    NASA Astrophysics Data System (ADS)

    Bretones, P. S.; Oliveira, V. C.

    2003-08-01

    Em 2001, o Instituto Superior de Ciências Aplicadas (ISCA Faculdades de Limeira) iniciou um projeto pelo qual o Observatório do Morro Azul empreendeu uma parceria com o Centro de Promoção Social Municipal (CEPROSOM), instituição mantida pela Prefeitura Municipal de Limeira para atender crianças e adolescentes carentes. O CEPROSOM contava com dois projetos: Projeto Centro de Convivência Infantil (CCI) e Programa Criança e Adolescente (PCA), que atendiam crianças e adolescentes em Centros Comunitários de diversas áreas da cidade. Esses projetos têm como prioridades estabelecer atividades prazerosas para as crianças no sentido de retirá-las das ruas. Assim sendo, as crianças passaram a ter mais um tipo de atividade - as visitas ao observatório. Este painel descreve as várias fases do projeto, que envolveu: reuniões de planejamento, curso de Astronomia para as orientadoras dos CCIs e PCAs, atividades relacionadas a visitas das crianças ao Observatório, proposta de construção de gnômons e relógios de Sol nos diversos Centros Comunitários de Limeira e divulgação do projeto na imprensa. O painel inclui discussões sobre a aprendizagem de crianças carentes, relatos que mostram a postura das orientadoras sobre a pertinência do ensino de Astronomia, relatos do monitor que fez o atendimento no Observatório e o que o número de crianças atendidas representou para as atividades da instituição desde o início de suas atividades e, em particular, em 2001. Os resultados são baseados na análise de relatos das orientadoras e do monitor do Observatório, registros de visitas e matérias da imprensa local. Conclui com uma avaliação do que tal projeto representou para as Instituições participantes. Para o Observatório, em particular, foi feita uma análise com relação às outras modalidades de atendimentos que envolvem alunos de escolas e público em geral. Também é abordada a questão do compromisso social do Observatório na educação do

  13. 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

    ). 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.

  14. Seasonal occurrence and distribution of submerged aquatic macrophytes in the tidal Potomac River

    USGS Publications Warehouse

    Haramis, G.M.; Carter, V.; Gammon, P.; Hupp, C.

    1979-01-01

    A systematic survey was conducted in the Tidal Potomac River in 1978 to determine the presence, abundance, and phenology of submersed aquatic macrophytes. The survey covered 81.5 km of main river and 59.3 km of tributary on the Maryland shore. Four regions were selected for the study: (1) Piscataway - Mattawoman Creek region (fresh-tidal river), (2) Nanjemoy Creek-Port Tobacco River region (transition zone), (3) Wicomico River region (estuary), and (4) St. Marys River region (estuary). The Wicomico River region was subdivided into fresh tidal river, transition zone and estuary for purposes of date analysis. Data were gathered by sampling each 15 m along transects running perpendicular to shore for a maximum distance of 300 m. Modified oyster tongs were used to sample both plants and benthic soils from an outboard boat. A total of 131 transects were established with a total of approximately 3500 grabs being taken per sampling period. Sampling was initiated in the spring and repeated in the summer and fall. Highest plant diversity and productivity were measured in the transition zone extending from Lower Cedar Point to beyond Maryland Point, a distance of approximately 30 km, and in the transition zone of the Wicomico River above Chaptico Bay. Fresh tidal areas were devoid of plants. The estuary had a sparse growth of horned pondweed (Zannichellia palustris) and widgeon grass (Ruppia maritima) in the spring: horned pondweed was not found in summer or fall. Redhead grass (Potomageton perfoliatus) was the most abundant pondweed; it matured in early summer and died back in mid-to-late summer. Wild celery (Vallisneria americana) and widgeon grass matured in early-to-late fall and were the most abundant plants during that period. Data analysis is being finalized and a publication is in preparation. This research will be continued over the next several seasons as part of the long term USGS effort on the Potomac

  15. Aquatic insects of New York salt marsh associated with mosquito larval habitat and their potential utility as bioindicators.

    PubMed

    Rochlin, Ilia; Dempsey, Mary E; Iwanejko, Tom; Ninivaggi, Dominick V

    2011-01-01

    The aquatic insect fauna of salt marshes is poorly characterized, with the possible exception of biting Diptera. Aquatic insects play a vital role in salt marsh ecology, and have great potential importance as biological indicators for assessing marsh health. In addition, they may be impacted by measures to control mosquitoes such as changes to the marsh habitat, altered hydrology, or the application of pesticides. Given these concerns, the goals of this study were to conduct the first taxonomic survey of salt marsh aquatic insects on Long Island, New York, USA and to evaluate their utility for non-target pesticide impacts and environmental biomonitoring. A total of 18 species from 11 families and five orders were collected repeatedly during the five month study period. Diptera was the most diverse order with nine species from four families, followed by Coleoptera with four species from two families, Heteroptera with three species from three families, then Odonata and the hexapod Collembola with one species each. Water boatmen, Trichocorixa verticalis Fieber (Heteroptera: Corixidae) and a shore fly, Ephydra subopaca Loew (Diptera: Ephydridae), were the two most commonly encountered species. An additional six species; Anurida maritima Guérin-Méneville (Collembola: Neanuridae), Mesovelia mulsanti White (Heteroptera: Mesovelidae), Enochrus hamiltoni Horn (Coleoptera: Hydrophilidae), Tropisternus quadristriatus Horn (Coleoptera: Hydrophilidae), Dasyhelea pseudocincta Waugh and Wirth (Diptera: Ceratopogonidae), and Brachydeutera argentata Walker (Diptera: Ephydridae), were found regularly. Together with the less common Erythrodiplax berenice Drury (Odonata: Libellulidae), these nine species were identified as the most suitable candidates for pesticide and environmental impact monitoring due to abundance, position in the food chain, and extended seasonal occurrence. This study represents a first step towards developing an insect-based index of biological integrity for

  16. 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.

  17. Highly Diverse Protein Library Based on the Ubiquitous (β/α)8 Enzyme Fold Yields Well-Structured Proteins Through In Vitro Folding Selection

    PubMed Central

    Golynskiy, Misha V.; Haugner, John C.

    2013-01-01

    Proper protein folding is a prerequisite for protein stability and enzymatic activity. While directed evolution can be a powerful tool to investigate enzymatic function and to isolate novel activities, well-designed libraries of folded proteins are essential. In vitro selection methods are particularly capable of searching for enzymatic activities in libraries of trillions of protein variants, yet high-quality libraries of well-folded enzymes with such high diversity are lacking. We describe the construction and detailed characterization of a folding-enriched protein library based on the ubiquitous (β/α)8 barrel fold found in five of the six enzyme classes. We introduced seven randomized loops on the catalytic face of the monomeric, thermostable (β/α)8 barrel of glycerophosphodiester phosphodiesterase (GDPD) from Thermotoga maritima. We employed an in vitro folding selection based on protease digestion to enrich intermediate libraries containing three to four randomized loops for folded variants and then combined them to assemble the final library (1014 DNA sequences). The resulting library was analyzed using the in vitro protease assay and an in vivo GFP-folding assay and contains ~1012 soluble monomeric protein variants. We isolated six library members and demonstrated that these proteins are soluble, monomeric and show (β/α)8 barrel fold-like secondary and tertiary structure. The quality of the folding-enriched library improved up to 50-fold compared to a control library that was assembled without the folding selection. To the best of our knowledge, this work is the first example of combining the ultra-high throughput method mRNA display with a selection for folding. The resulting (β/α)8 barrel libraries provide a valuable starting point to study the unique catalytic capabilities of the (β/α)8 fold, and to isolate novel enzymes. PMID:23956201

  18. 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.

  19. Differentiation of the DnaA-oriC subcomplex for DNA unwinding in a replication initiation complex.

    PubMed

    Ozaki, Shogo; Noguchi, Yasunori; Hayashi, Yasuhisa; Miyazaki, Erika; Katayama, Tsutomu

    2012-10-26

    In Escherichia coli, ATP-DnaA multimers formed on the replication origin oriC promote duplex unwinding, which leads to helicase loading. Based on a detailed functional analysis of the oriC sequence motifs, we previously proposed that the left half of oriC forms an ATP-DnaA subcomplex competent for oriC unwinding, whereas the right half of oriC forms a distinct ATP-DnaA subcomplex that facilitates helicase loading. However, the molecular basis for the functional difference between these ATP-DnaA subcomplexes remains unclear. By analyzing a series of novel DnaA mutants, we found that structurally distinct DnaA multimers form on each half of oriC. DnaA AAA+ domain residues Arg-227 and Leu-290 are specifically required for oriC unwinding. Notably, these residues are required for the ATP-DnaA-specific structure of DnaA multimers in complex with the left half of oriC but not for that with the right half. These results support the idea that the ATP-DnaA multimers formed on oriC are not uniform and that they can adopt different conformations. Based on a structural model, we propose that Arg-227 and Leu-290 play a crucial role in inter-ATP-DnaA interaction and are a prerequisite for the formation of unwinding-competent DnaA subcomplexes on the left half of oriC. These residues are not required for the interaction with DnaB, nucleotide binding, or regulatory DnaA-ATP hydrolysis, which further supports their important role in inter-DnaA interaction. The corresponding residues are evolutionarily conserved and are required for unwinding in the initial complexes of Thermotoga maritima, an ancient hyperthermophile. Therefore, our findings suggest a novel and common mechanism for ATP-DnaA-dependent activation of initial complexes.

  20. Nursery fidelity, food web interactions and primary sources of nutrition of the juveniles of Solea solea and S. senegalensis in the Tagus estuary (Portugal): A stable isotope approach

    NASA Astrophysics Data System (ADS)

    Vinagre, C.; Salgado, J.; Costa, M. J.; Cabral, H. N.

    2008-01-01

    Stable carbon and nitrogen isotopes were used to assess site fidelity of Solea solea and Solea senegalensis juveniles, to investigate food web interactions and to determine the dominant nutrient pathways in two nursery areas in the Tagus estuary, Portugal. Samples of water from the main sources and from the nursery areas and respective saltmarsh creeks were collected for isotope analysis, as well as sediment, benthic microalgae, saltmarsh halophytes, S. solea, S. senegalensis and its main prey, Nereis diversicolor, Scrobicularia plana and Corophium spp. While site fidelity was high in 0-group juveniles, it was lower for 1-group juveniles, possibly due to an increase in mobility and energy demands with increasing size. Analysis of the food web revealed a complex net of relations. Particulate organic matter from the freshwater sources, from each nursery's waters and saltmarsh creeks presented similar isotopic composition. Sediment isotopic composition and saltmarsh halophytes also did not differentiate the two areas. All components of the food web from the benthic microalgae upwards were isotopically different between the nursery areas. These components were always more enriched in δ13C and δ15N at the lower nursery area than at the nursery located upstream, appearing as if there were two parallel trophic chains with little trophic interaction between each other. A mixture of carbon and nitrogen sources is probably being incorporated into the food web. The lower nursery area is more dependent upon an isotopically enriched energy pathway, composed of marine particulate organic matter, marine benthic microalgae and detritus of the C 4 saltmarsh halophyte Spartina maritima. The two nursery areas present a different level of dependence upon the freshwater and marine energy pathways, due to hydrological features, which should be taken into account for S. solea and S. senegalensis fisheries and habitat management.

  1. Investigation of the catalytic mechanism of Sir2 enzyme with QM/MM approach: SN1 vs SN2?

    PubMed

    Liang, Zhongjie; Shi, Ting; Ouyang, Sisheng; Li, Honglin; Yu, Kunqian; Zhu, Weiliang; Luo, Cheng; Jiang, Hualiang

    2010-09-16

    Sir2, the histone deacetylase III family, has been subjected to a wide range of studies because of their crucial roles in DNA repair, longevity, transcriptional silencing, genome stability, apoptosis, and fat mobilization. The enzyme binds NAD(+) and acetyllysine as substrates and generates lysine, 2'-O-acetyl-ADP-ribose, and nicotinamide as products. However, the mechanism of the first step in Sir2 deacetylation reaction from various studies is controversial. To characterize this catalytic mechanism of acetyllysine deacetylation by Sir2, we employed a combined computational approach to carry out molecular modeling, molecular dynamics (MD) simulations, quantum mechanics/molecular mechanics (QM/MM) calculations on catalysis by both yeast Hst2 (homologue of SIR two 2) and bacterial Sir2TM (Sir2 homologue from Thermatoga maritima). Our three-dimensional (3D) model of the complex is composed of Sir2 protein, NAD(+), and acetyllysine (ALY) substrate. A 15-ns MD simulation of the complex revealed that Gln115 and His135 play a determining role in deacetylation. These two residues can act as bases to facilitate the deprotonation of 2'-OH from N-ribose. The result is in great agreement with previous mutagenesis analysis data. QM/MM calculations were further performed to study the mechanism of the first step in deacetylation in the two systems. The predicted potential energy barriers for yHst2 and Sir2TM are 12.0 and 15.7 kcal/mol, respectively. The characteristics of the potential energy surface indicated this reaction belongs to a SN2-like mechanism. These results provide insights into the Sir2 mechanism of nicotinamide inhibition and have important implications for the discovery of effectors against Sir2 enzymes.

  2. Ecology of beach wrack in northern New England with special reference to Orchestia platensis*1

    NASA Astrophysics Data System (ADS)

    Behbehani, Manaf I.; Croker, Robert A.

    1982-12-01

    The northern New England beach wrack community with special reference to the cosmopolitan amphipod crustacean, Orchestia platensis, was examined at estuarine and open coastal habitats. Beach wrack was dominated by the plant genera Ascophyllum, Zostera, Spartina and Chondrus, and was most abundant during spring and late summer. Animal community numbers, biomass and frequency in fresh to moderately decomposed wrack were dominated by O. platensis throughout the year at all habitats; oligochaetes and Collembola were also important. The abundance of O. platensis showed high spatial and temporal variability, with low abundance generally associated with decreased amounts of wrack during colder months. An exception was the winter presence of the species at one estuarine habitat, in patchy aggregations within gravel-cobble refuges. The abundance of O. platensis averaged 1280 (0.04 m 2) -1, with a maximum of 7040 (0.04 m 2) -1. The life cycle of O. platensis is bivoltine, with summer-hatched young reaching maturity within 1 month. Laboratory studies indicate females with up to 4 broods (30 days) -1, averaging 18 eggs brood -1. Orchestia platensis is omnivorous, eating fresh plant tissue, live oligochaetes, Limulus eggs and diatom 'fuzz'. The rate of laboratory consumption of algae and Zostera was 0.05 mg plant mg -1 wet body weight day -1. Presumptive predators of O. platensis are juvenile green crab, Carcinus maenus, and the earwig. Anisolabis maritima. The mobility, aggregation and aggressiveness of O. platensis assist the species in establishing and maintaining populations in the rigorous wrack habitat. The general competitive superiority of O. platensis over its congener, O. gammarella, and the co-occurrence of these species on both eastern and western Atlantic shores is discussed.

  3. 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.

  4. The response of primary producers to nutrient enrichment in a shallow estuary

    USGS Publications Warehouse

    Kinney, E.H.; Roman, C.T.

    1998-01-01

    Shallow coastal systems worldwide are exhibiting increased algal growth in response to nutrient enrichment. This study evaluates primary production patterns in an estuarine system (Bass Harbor Marsh, Maine) receiving low levels of anthropogenic nitrogen. Biomass, areal coverage and in situ oxygen production of green macroalgae, Ruppia maritima, and phytoplankton were measured over a growing season to determine net ecosystem production. Macroalgae and Ruppia exhibited strong seasonal biomass curves with early summer peaks; however, peak biomass of macroalgae (150 g dwt m-2) was substantially greater than Ruppia (33 g dwt m-2). Phytoplankton biomass, measured as chlorophyll a, was low (<1 ug l-1) early in the season and peaked (11 ug l-1) following a mid-summer decline in macroalgal biomass, suggesting a competitive interaction with macroalgae. Instantaneous net production rates varied over the growing season for all three primary producers. Ruppia net production ranged from near zero to 3.7 mg C g dwt-1 h-1, with higher rates during summer and much of the seasonal variability explained by temperature. Macroalgal (0.88 - 5.0 mg C g dwt-1 h-1) and phytoplankton (0 - 28 mg C m-3 h-1) net production did not exhibit any clear seasonal signal. Net primary production calculated on an areal basis demonstrated macroalgae's dominance in the lower basin of Bass Harbor Marsh, with peak summer rates (400 mg C m-2 h-1) greatly exceeding maximum rates for both Ruppia (70 mg C m-2 h-1) and phytoplankton (12 mg C m-2 h-1). When compared to other New England estuarine sites with short residence times, nutrient loading and peak green macroalgal biomass in Bass Harbor Marsh is relatively low; however, the strong dominance of opportunistic green macroalgae is a pattern that is characteristic of shallow coastal systems undergoing eutrophication.

  5. Stocks and sources of carbon buried in the salt marshes and seagrass beds of Patos Lagoon Estuary, Southern Brazil

    NASA Astrophysics Data System (ADS)

    Patterson, Elizabeth; Johnson, Beverly; Dostie, Philip; Copertino, Margareth

    2016-04-01

    This project investigates carbon stocks in salt marshes and seagrass beds in the Patos Lagoon estuary, the largest choked lagoon in the world, located in Southern Brazil. The study was conducted in the mesohaline region, at three shallow shoals. At each shoal, three sediment cores (50 cm deep) and plant biomass samples (above and belowground) were collected along a transect line, spanning from the marsh to seagrass beds (total = 9 sediment cores). The 50cm cores were subsampled and analyzed for organic carbon (C) and nitrogen (N) content, C/N ratios, and the isotope ratios of 13C/12C, and 15N/14N. The organic carbon content of these sediments ranged between 10% (in surface sediments) and 1% (deeper in the core), suggesting that both the salt marshes and seagrass beds in this region are sequestering carbon. Early results indicate that cores taken in marsh dominated by C3 plants (Scirpus maritimus) tended to be the most depleted in 13C with δ13C values around -25‰. Cores taken in marsh dominated by C4 plants (Spartina alterniflora, Spartina densiflora), seagrass beds (Ruppia maritima) , and non vegetated areas were generally isotopically heavier with δ13C values ranging -20‰ to -15‰, indicating a mix of organic sources in the sediments. The δ15N values and C/N ratios both varied with most values falling in a range of 2-8‰ and 7-20 respectively. Analysis of the δ 34S isotope composition of the sediments is currently underway and may provide better information on the relative contributions of macro and micro algae in the sediments. The present data will reveal the carbon stock size, as well as the types and history of organic matter deposition in Patos Lagoon estuary.

  6. 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

  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. Seagrass distribution and abundance in Eastern Gulf of Mexico coastal waters

    NASA Astrophysics Data System (ADS)

    Iverson, Richard L.; Bittaker, Henry F.

    1986-05-01

    The marine angiosperms Thalassia testudinum, Syringodium filiforme, and Halodule wrightii form two of the largest reported seagrass beds along the northwest and southern coasts of Florida where they cover about 3000 square km in the Big Bend area and about 5500 square km in Florida Bay, respectively. Most of the leaf biomass in the Big Bend area and outer Florida Bay was composed of Thalassia testudinum and Syringodium filiforme which were distributed throughout the beds but which were more abundant in shallow depths. A short-leaved form of Halodule wrightii grew in monotypic stands in shallow water near the inner edges of the beds, while Halophila decipiens and a longer-leaved variety of H. wrightii grew scattered throughout the beds, in monotypic stands near the outer edges of the beds, and in deeper water outside the beds. Halophila engelmanni was observed scattered at various depths throughout the seagrass beds and in monospecific patches in deep water outside the northern bed. Ruppia maritima grew primarily in brackish water around river mouths. The cross-shelf limits of the two major seagrass beds are controlled nearshore by increased water turbidity and lower salinity around river mouths and off-shore by light penetration to depths which receive 10% or more of sea surface photosynthetically active radiation. Seagrasses form large beds only along low energy reaches of the coast. The Florida Bay seagrass bed contained about twice the short-shoot density of both Thalassia testudinum and Syringodium filiforme, for data averaged over all depths, and about four times the average short-shoot density of both species in shallow water compared with the Big Bend seagrass bed. The differences in average seagrass abundance between Florida Bay and the Big Bend area may be a consequence of the effects of greater seasonal solar radiation and water temperature fluctuations experienced by plants in the northern bed, which lies at the northern distribution limit for American

  9. Conformational Transitions that Enable Histidine Kinase Autophosphorylation and Receptor Array Integration

    PubMed Central

    Greenswag, Anna R.; Muok, Alise; Li, Xiaoxiao; Crane, Brian R.

    2015-01-01

    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 find 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 nor 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 inter-subunit (trans) versus intra-subunit (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 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

  10. 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

  11. 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

  12. 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.

  13. Diurnal Fluxes of Carbonyl Sulfide (COS) in a Subtropical Salt Marsh

    NASA Astrophysics Data System (ADS)

    Whelan, M.; Min, D. H.; Rhew, R. C.; Liu, Y.

    2009-12-01

    The atmospheric sulfur budget has been greatly perturbed, with anthropogenic contributions exceeding natural emissions. Carbonyl sulfide (COS) is the most abundant, longest-lived reduced sulfur compound in the atmosphere, and COS concentration changes could have a significant effect on the global climate and the natural biogeochemical sulfur cycle. Measuring fluxes of COS presents a methodological challenge, and in situ measurements from terrestrial ecosystems are sparse. Terrestrial plants are considered to be the largest sink for COS in the troposphere, although specific species have been reported to act as sources. Here we describe production rates of COS from salt marsh plants on a Texas Gulf coast subtropical barrier island (27.8 °N, 97.1°W). In July 2009, static flux chamber measurements were performed on three sites over the course of 24 hours to capture the temporal and spatial variation of fluxes. Two of the sites were dominated by B. maritima, a common salt marsh plant, while one was a control plot with only marsh soil and no vegetation. Fluxes from the two sites were measured within an hour of each other and showed a very similar pattern with time, indicating that the COS emissions responded to the same environmental factors. Of the environmental parameters measured, fluxes correlated best with soil temperatures at 5 cm depth. The site with the drier of the two soils consistently yielded a 20-30% larger flux. The control plot produced an order of magnitude less COS, but still exhibited a positive flux. These results are part of an ongoing study on how subtropical salt marshes contribute to the global atmospheric sulfur budget.

  14. Structure of FliM Provides Insight into Assembly of the Switch Complex in the Bacterial Flagella Motor

    SciTech Connect

    Park,S.; Lowder, B.; Bilwes, A.; Blair, D.; Crane, B.

    2006-01-01

    Bacteria switch the direction their flagella rotate to control movement. FliM, along with FliN and FliG, compose a complex in the motor that, upon binding phosphorylated CheY, reverses the sense of flagellar rotation. The 2.0- Angstroms resolution structure of the FliM middle domain (FliMM) from Thermotoga maritima reveals a pseudo-2-fold symmetric topology similar to the CheY phosphatases CheC and CheX. A variable structural element, which, in CheC, mediates binding to CheD ({alpha}2') and, in CheX, mediates dimerization ({beta}x), has a truncated structure unique to FliM ({alpha}2'). An exposed helix of FliMM ({alpha}1) does not contain the catalytic residues of CheC and CheX but does include positions conserved in FliM sequences. Cross-linking experiments with site-directed cysteine mutants show that FliM self-associates through residues on {alpha}1 and {alpha}2'. CheY activated by BeF3- binds to FliM with {approx}40-fold higher affinity than CheY (Kd = 0.04 {micro}M vs. 2 {micro}M). Mapping residue conservation, suppressor mutation sites, binding data, and deletion analysis onto the FliMM surface defines regions important for contacts with the stator-interacting protein FliG and for either counterclockwise or clockwise rotation. Association of 33-35 FliM subunits would generate a 44- to 45-nm-diameter disk, consistent with the known dimensions of the C-ring. The localization of counterclockwise- and clockwise-biasing mutations to distinct surfaces suggests that the binding of phosphorylated CheY cooperatively realigns FliM around the ring.

  15. Radionuclides transfer into halophytes growing in tidal salt marshes from the Southwest of Spain.

    PubMed

    Luque, Carlos J; Vaca, Federico; García-Trapote, Ana; Hierro, Almudena; Bolívar, Juan P; Castellanos, Eloy M

    2015-12-01

    Estuaries are sinks of materials and substances which are released directly into them or transported from rivers that drain the basin. It is usual to find high organic matter loads and fine particles in the sediments. We analyzed radionuclide concentrations ((210)Po, (230)Th, (232)Th, (234)U, (238)U, (226)Ra, (228)Th, (228)Ra, (40)K) in sediments and three different organs (roots, stems and leaves) of three species of halophytes plants (Spartina maritima, Spartina densiflora and Sarcocornia perennis). The study was carried out in two tidal salt marshes, one polluted by U-series radionuclides and another nearby that was unpolluted and was used as a control (or reference) area. The Tinto River salt marsh shows high levels of U-series radionuclides coming from mining and industrial discharges. On the contrary, the unperturbed Piedras River salt marsh is located about 25 km from the Tinto marsh, and shows little presence of contaminants and radionuclides. The results of this work have shown that natural radionuclide concentrations (specially the U-isotopes) in the Tinto salt marsh sediments are one order of magnitude higher than those in the Piedras marsh. These radionuclide enhancements are reflected in the different organs of the plants, which have similar concentration increases as the sediments where they have grown. Finally, the transfer factor (TF) of the most polluted radionuclides (U-isotopes and (210)Po) in the Tinto area are one order of magnitude higher than in the Piedras area, indicating that the fraction of each radionuclide in the sediment originating from the pollution is more available for the plants than the indigenous fraction. This means that the plants of the salt marshes are unhelpful as bioindicators or for the phytoremediation of radionuclides.

  16. 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 are both buried, and access to the methyl group would presumably require structural rearrangement. These TM0872 crystal structures offer the first structural glimpses at this phylogenetically conserved sequence family.

  17. A New Root-Knot Nematode Parasitizing Sea Rocket from Spanish Mediterranean Coastal Dunes: Meloidogyne dunensis n. sp. (Nematoda: Meloidogynidae)

    PubMed Central

    Palomares Rius, J. E.; Vovlas, N.; Troccoli, A.; Liébanas, G.; Landa, B. B.; Castillo, P.

    2007-01-01

    High infection rates of European sea rocket feeder roots by an unknown root-knot nematode were found in a coastal dune soil at Cullera (Valencia) in central eastern Spain. Morphometry, esterase and malate dehydrogenase electrophoretic phenotypes and phylogenetic trees demonstrated that this nematode species differs clearly from other previously described root-knot nematodes. Studies of host-parasite relationships showed a typical susceptible reaction in naturally infected European sea rocket plants and in artificially inoculated tomato (cv. Roma) and chickpea (cv. UC 27) plants. The species is herein described and illustrated and named as Meloidogyne dunensis n. sp. The new root-knot nematode can be distinguished from other Meloidogyne spp. by: (i) perineal pattern rounded-oval, formed of numerous fine dorsal and ventral cuticle striae and ridges, lateral fields clearly visible; (ii) female excretory pore at the level of stylet knobs, EP/ST ratio 1.6; (iii) second-stage juveniles with hemizonid located 1 to 2 annuli anteriorly to excretory pore and long, narrow, tapering tail; and (iv) males with lateral fields composed of four incisures anteriorly and posteriorly, while six distinct incisures are observed for large part at mid-body. Phylogenetic trees derived from distance and maximum parsimony analyses based on 18S, ITS1–5.8S-ITS2 and D2-D3 of 28S rDNA showed that M. dunensis n. sp. can be differentiated from all described root-knot nematode species, and it is clearly separated from other species with resemblance in morphology, such as M. duytsi, M. maritima, M. mayaguensis and M. minor. PMID:19259488

  18. Thermophilic anaerobic oxidation of methane by marine microbial consortia.

    PubMed

    Holler, Thomas; Widdel, Friedrich; Knittel, Katrin; Amann, Rudolf; Kellermann, Matthias Y; Hinrichs, Kai-Uwe; Teske, Andreas; Boetius, Antje; Wegener, Gunter

    2011-12-01

    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.

  19. Domain-swapping of mesophilic xylanase with hyper-thermophilic glucanase

    PubMed Central

    2012-01-01

    Background Domain fusion is limited at enzyme one terminus. The issue was explored by swapping a mesophilic Aspergillus niger GH11 xylanase (Xyn) with a hyper-thermophilic Thermotoga maritima glucanase (Glu) to construct two chimeras, Xyn-Glu and Glu-Xyn, with an intention to create thermostable xylanase containing glucanase activity. Results When expressed in E. coli BL21(DE3), the two chimeras exhibited bi-functional activities of xylanase and glucanase. The Xyn-Glu Xyn moiety had optimal reaction temperature (Topt) at 50 °C and thermal in-activation half-life (t1/2) at 50 °C for 47.6 min, compared to 47 °C and 17.6 min for the Xyn. The Glu-Xyn Xyn moiety had equivalent Topt to and shorter t1/2 (5.2 min) than the Xyn. Both chimera Glu moieties were more thermostable than the Glu, and the three enzyme Topt values were higher than 96 °C. The Glu-Xyn Glu moiety optimal pH was 5.8, compared to 3.8 for the Xyn-Glu Glu moiety and the Glu. Both chimera two moieties cooperated with each other in degrading substrates. Conclusions Domain-swapping created different effects on each moiety properties. Fusing the Glu domain at C-terminus increased the xylanase thermostability, but fusing the Glu domain at N-terminus decreased the xylanase thermostability. Fusing the Xyn domain at either terminus increased the glucanase thermostability, and fusing the Xyn domain at C-terminus shifted the glucanase pH property 2 units higher towards alkaline environments. Fusing a domain at C-terminus contributes more to enzyme catalytic activity; whereas, fusing a bigger domain at N-terminus disturbs enzyme substrate binding affinity. PMID:22676349

  20. Phylogenetic analysis of sequences from diverse bacteria with homology to the Escherichia coli rho gene.

    PubMed Central

    Opperman, T; Richardson, J P

    1994-01-01

    Genes from Pseudomonas fluorescens, Chromatium vinosum, Micrococcus luteus, Deinococcus radiodurans, and Thermotoga maritima with homology to the Escherichia coli rho gene were cloned and sequenced, and their sequences were compared with other available sequences. The species for all of the compared sequences are members of five bacterial phyla, including Thermotogales, the most deeply diverged phylum. This suggests that a rho-like gene is ubiquitous in the Bacteria and was present in their common ancestor. The comparative analysis revealed that the Rho homologs are highly conserved, exhibiting a minimum identity of 50% of their amino acid residues in pairwise comparisons. The ATP-binding domain had a particularly high degree of conservation, consisting of some blocks with sequences of residues that are very similar to segments of the alpha and beta subunits of F1-ATPase and of other blocks with sequences that are unique to Rho. The RNA-binding domain is more diverged than the ATP-binding domain. However, one of its most highly conserved segments includes a RNP1-like sequence, which is known to be involved in RNA binding. Overall, the degree of similarity is lowest in the first 50 residues (the first half of the RNA-binding domain), in the putative connector region between the RNA-binding and the ATP-binding domains, and in the last 50 residues of the polypeptide. Since functionally defective mutants for E. coli Rho exist in all three of these segments, they represent important parts of Rho that have undergone adaptive evolution. PMID:8051015

  1. Structure of fructans from excised leaves of New Zealand flax.

    PubMed

    Sims, I M; Cairns, A J; Furneaux, R H

    2001-07-01

    The accumulation of total water-soluble carbohydrate, and specifically sucrose and fructan, by excised leaves of Phormium tenax and P. cookianum (family Phormiaceae J. G. Agardh, order Asparagales) was investigated. Total water-soluble carbohydrate content of excised leaves of P. tenax and P. cookianum increased during 48 h of continuous illumination at an average rate of 1.3 and 0.9 mg g(-1) fresh weight leaf per hour, respectively. The sucrose content of excised leaves increased throughout the experimental period. The fructan content of excised leaves of P. tenax increased slightly throughout the experimental period, whilst that of P. cookianum was variable and showed no overall change. Chemical and spectroscopic analysis of the fructans obtained from the two Phormium species showed that they were similar to each other and contained mostly 1-linked and terminal fructofuranosyl (Fruf) residues, together with smaller amounts of 6-linked Fruf, 1,6-branched Fruf, terminal and 6-linked glucopyranosyl residues. Separation of the fructans by thin-layer and high-performance anion-exchange chromatography revealed the presence of a complex mixture of fructo-oligosaccharides and higher molecular weight fructan. The branched structure of the fructans isolated from excised leaves of Phormium resembles that of fructans and fructo-oligosaccharides isolated from some related species within the order Asparagales (Agave vera cruz, Cordyline australis and Urginea maritima), but is distinct from the linear structure of fructans from others (Allium cepa and Asparagus officinalis). The structural heterogeniety of fructans within both the order Asparagales and superorder Liliiflorae may be a useful chemotaxonomic aid.

  2. 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.

  3. The enzymology of alanine aminotransferase (AlaAT) isoforms from Hordeum vulgare and other organisms, and the HvAlaAT crystal structure.

    PubMed

    Duff, Stephen M G; Rydel, Timothy J; McClerren, Amanda L; Zhang, Wenlan; Li, Jimmy Y; Sturman, Eric J; Halls, Coralie; Chen, Songyang; Zeng, Jiamin; Peng, Jiexin; Kretzler, Crystal N; Evdokimov, Artem

    2012-12-01

    In this paper we describe the expression, purification, kinetics and biophysical characterization of alanine aminotransferase (AlaAT) from the barley plant (Hordeum vulgare). This dimeric PLP-dependent enzyme is a pivotal element of several key metabolic pathways from nitrogen assimilation to carbon metabolism, and its introduction into transgenic plants results in increased yield. The enzyme exhibits a bi-bi ping-pong reaction mechanism with a K(m) for alanine, 2-oxoglutarate, glutamate and pyruvate of 3.8, 0.3, 0.8 and 0.2 mM, respectively. Barley AlaAT catalyzes the forward (alanine-forming) reaction with a k(cat) of 25.6 s(-1), the reverse (glutamate-forming) reaction with k(cat) of 12.1 s(-1) and an equilibrium constant of ~0.5. The enzyme is also able to utilize aspartate and oxaloacetate with ~10% efficiency as compared to the native substrates, which makes it much more specific than related bacterial/archaeal enzymes (that also have lower K(m) values). We have crystallized barley AlaAT in complex with PLP and l-cycloserine and solved the structure of this complex at 2.7 Å resolution. This is the first example of a plant AlaAT structure, and it reveals a canonical aminotransferase fold similar to structures of the Thermotoga maritima, Pyrococcus furiosus, and human enzymes. This structure bridges our structural understanding of AlaAT mechanism between three kingdoms of life and allows us to shed some light on the specifics of the catalysis performed by these proteins.

  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.

  5. Distribution and Segregation of Two Sympatric Brevoortia Species (Teleostei: Clupeidae)

    NASA Astrophysics Data System (ADS)

    Castillo-Rivera, M.; Kobelkowsky, A.

    2000-05-01

    The authors described and analysed the temporal and spatial distribution and segregation patterns ofBrevoortia patronus and B. gunteri, in a coastal lagoon of Veracruz, Mexico. A total of 394 individuals of B. gunteri (mean SL of 61·7 mm) and 378 of B. patronus (mean SL of 128·0) were collected, in 189 monthly and 48 diel (24-h cycles) samples. Both species showed two catchability peaks-one during March-May (dry season) and the second in July-October (rainy season)-and these peaks were related with the two primary production pulses in the system. These patterns were slightly different for each species, the first peak being more important for B. gunteri (68·6%), and the second for B. patronus (78·2%). Brevoortia patronus number was correlated with rainfall (P<0·01), and the relative abundance of both species was correlated with salinity (P<0·05). In 24-h cycle analysis, the two species were more abundant around midday (10:00 to 14:00 h), with few individuals captured during the night, and this behaviour was probably related to light intensity and their trophic activities. Moreover, no diel separation between species was observed. Spatially, B. gunteri was principally captured (67·4%) in sites with higher salinities and with no submerged vegetation, and B. patronus was mainly captured (70·9%) in sites with low salinity and with dense beds of Ruppia maritima. Thus, the authors consider salinity as an important factor in the seasonal and spatial segregation of Brevoortia species, with B. gunteri common in periods and zones with higher salinity and B. patronus in periods and areas of low salinity. The results presented here suggest that these segregation patterns permit resource partitioning between these species and facilitate their local co-existence.

  6. Assembly states of FliM and FliG within the flagellar switch complex.

    PubMed

    Sircar, Ria; Borbat, Peter P; Lynch, Michael J; Bhatnagar, Jaya; Beyersdorf, Matthew S; Halkides, Christopher J; Freed, Jack H; Crane, Brian R

    2015-02-27

    At the base of the bacterial flagella, a cytoplasmic rotor (the C-ring) generates torque and reverses rotation sense in response to stimuli. The bulk of the C-ring forms from many copies of the proteins FliG, FliM, and FliN, which together constitute the switch complex. To help resolve outstanding issues regarding C-ring architecture, we have investigated interactions between FliM and FliG from Thermotoga maritima with X-ray crystallography and pulsed dipolar ESR spectroscopy (PDS). A new crystal structure of an 11-unit FliG:FliM complex produces a large arc with a curvature consistent with the dimensions of the C-ring. Previously determined structures along with this new structure provided a basis to test switch complex assembly models. PDS combined with mutational studies and targeted cross-linking reveal that FliM and FliG interact through their middle domains to form both parallel and antiparallel arrangements in solution. Residue substitutions at predicted interfaces disrupt higher-order complexes that are primarily mediated by contacts between the C-terminal domain of FliG and the middle domain of a neighboring FliG molecule. Spin separations among multi-labeled components fit a self-consistent model that agree well with electron microscopy images of the C-ring. An activated form of the response regulator CheY destabilizes the parallel arrangement of FliM molecules to perturb FliG alignment in a process that may reflect the onset of rotation switching. These data suggest a model of C-ring assembly in which intermolecular contacts among FliG domains provide a template for FliM assembly and cooperative transitions.

  7. The mute swan, its status, behavior, and history in the U. K

    USGS Publications Warehouse

    Lohnes, E.J.R.; Perry, Matthew C.

    2004-01-01

    For many years the mute swan has been considered a royal bird. It is a prominent resident throughout the United Kingdom (U.K.), often found on the inland waterways. Some people consider it to be a nonmigratory native bird because it doesn't tend to move large distances and doesn't often venture far from freshwater. A mute swan may often live out its life cycle in the same river valley in which it hatched. Over the last 30-40 years, a large amount of research has been carried out on their life cycle, behavior, and mortality caused by such factors as lead poisoning from fishing weights. Throughout the U.K., there are a number of areas where mute swans may be found in large numbers, including (1) the River Thames (which passes through London), (2) Slimbridge Wetlands Center, (3) Berwick-upon- Tweed (the second largest mute swan colony in Britain), and (4) Abbotsbury Swannery (the worlds only managed swan colony). This last site is a truly unique area, and each year it often has over 150 nesting pairs producing between 2-12 eggs per nest. The management is minimal, and the site is ideal for their requirements because it is close to a number of freshwater sources, and has good nesting sites and large quantities of eelgrass Zostera marina and widgeon grass Ruppia maritima, their preferred food sources. The Swannery is located on the south coast of England at the western end of the Fleet Lagoon, a micro-tidal estuary, which borders the English Channel.

  8. Identification of a gene sequence encoding a putative pyruvate oxidoreductase in Serpulina pilosicoli.

    PubMed

    Rayment, S J; Lee, B J; Hampson, D J; Livesley, M A

    1998-09-01

    Serpulina pilosicoli is a recently described species of intestinal spirochaete which can be identified using a species-specific monoclonal antibody BJL/AC1 reactive with a 29-kDa protein located in the cell envelope. A genomic library of the type strain of S. pilosicoli P43/6/78T was created in lambda zap express and screened using BJL/AC1. Single positive clones were isolated and excised into the phagemid vector pBK-CMV. Phagemid DNA was purified and a single clone was selected for sequencing. The size of spirochaetal DNA insert was determined by digestion with restriction endonucleases EcoRI and PstI as being approximately 2.6 kb. The nucleotide sequence of the gene encoding the protein with which the antibody reacted was determined by cycle sequencing. The insert contained an open reading frame of 285 nucleotides. Translation of the nucleotide sequence into amino acid (aa) residues showed a sequence of 275 aa. Comparison of this sequence with databases revealed homology to pyruvate oxidoreductases from various organisms found in the gastroinestinal tract. These included the pyruvate ferredoxin oxidoreductase (POR) alpha submit of Helicobacter pylori (38.8% identity in 250 aa), pyruvate-flavodoxin oxidoreductase of Escherichia coli (28.7% identify in 258 aa) and Giardia intestinalis (25.1% identity in 251 aa). A significant level of homology was also observed with hyperthermophilic bacteria such as the POR of Thermatoga maritima (38.6% in 254 aa) and the 2-ketovalerate-ferredoxin oxidoreductase of Pyrococcus furiosus (34% in 262 aa).

  9. The N-terminal half-domain of the long form of tRNase Z is required for the RNase 65 activity

    PubMed Central

    Takaku, Hiroaki; Minagawa, Asako; Takagi, Masamichi; Nashimoto, Masayuki

    2004-01-01

    Transfer RNA (tRNA) 3′ processing endoribonuclease (tRNase Z) is an enzyme responsible for the removal of a 3′ trailer from pre-tRNA. There exists two types of tRNase Z: one is a short form (tRNase ZS) that consists of 300–400 amino acids, and the other is a long form (tRNase ZL) that contains 800–900 amino acids. Here we investigated whether the short and long forms have different preferences for various RNA substrates. We examined three recombinant tRNase ZSs from human, Escherichia coli and Thermotoga maritima, two recombinant tRNase ZLs from human and Saccharomyces cerevisiae, one tRNase ZL from pig liver, and the N- and C-terminal half regions of human tRNase ZL for cleavage of human micro-pre-tRNAArg and the RNase 65 activity. All tRNase ZLs cleaved the micro-pre-tRNA and showed the RNase 65 activity, while all tRNase ZSs and both half regions of human tRNase ZL failed to do so with the exception of the C-terminal half, which barely cleaved the micro-pre-tRNA. We also show that only the long forms of tRNase Z can specifically cleave a target RNA under the direction of a new type of small guide RNA, hook RNA. These results indicate that indeed tRNase ZL and tRNase ZS have different substrate specificities and that the differences are attributed to the N-terminal half-domain of tRNase ZL. Furthermore, the optimal concentrations of NaCl, MgCl2 and MnCl2 differed between tRNase ZSs and tRNase ZLs, and the Km values implied that tRNase ZLs interact with pre-tRNA substrates more strongly than tRNase ZSs. PMID:15317868

  10. 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.

  11. 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

  12. Contribution to the knowledge of the veterinary science and of the ethnobotany in Calabria region (Southern Italy)

    PubMed Central

    Passalacqua, Nicodemo G; De Fine, Giuseppe; Guarrera, Paolo Maria

    2006-01-01

    Background A series of preliminary research projects on plants used in Calabria (Southern Italy) in veterinary science and in other ethno-botanical fields (minor nourishment, domestic and handicraft sector) was carried out in the last twenty years. From the ethno-botanical point of view, Calabria is one of the most interesting region, since in the ancient times it was subject to the dominant cultures of several people (Greeks, Romans, Byzantines, Arabs, Normans etc.). Until some decades ago the road network was poorly developed and villages were isolated, so that the culture of the "subsistence" and some archaic customs were kept. Methods Data were collected by means of "open" interviews to farmers, shepherds and housewives in the last twenty years. More than 100 informants were interviewed, mostly over 50 years old. Plants were identified by local informants through gathering in the area or through examination of the fresh plants collected by the researchers. The collected data were compared with pharmacobotanical papers mainly of southern Italy and with other studies, in order to highlight novelties or concordances of uses. Results The use of 62 taxa distributed into 34 families are described. Among these, 8 are or were employed in veterinary science, 8 as anti-parasitic agents, 19 in minor nourishment, 5 as seasoning, 38 for other uses. Some toxic species for cattle are also mentioned. Conclusion Among the major findings: the use of Helleborus bocconei for bronchitis of bovines and of Scrophularia canina for lameness in veterinary science; Nerium oleander and Urginea maritima as anti-parasitic agents; Epilobium angustifolium, Centaurea napifolia L. and C. sphaerocephala L. in minor nourishment. PMID:17156472

  13. 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

  14. 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

  15. Single-minded and the evolution of the ventral midline in arthropods.

    PubMed

    Linne, Viktoria; Eriksson, Bo Joakim; Stollewerk, Angelika

    2012-04-01

    In insects and crustaceans, ventral midline cells are present that subdivide the CNS into bilateral symmetric halves. In both arthropod groups unpaired midline neurons and glial cells have been identified that contribute to the embryonic patterning mechanisms. In the fruitfly Drosophila melanogaster, for example, the midline cells are involved in neural cell fate specification along the dorso-ventral axis but also in axonal pathfinding and organisation of the axonal scaffold. Both in insects and malacostracan crustaceans, the bHLH-PAS transcription factor single-minded is the master regulator of ventral midline development and homology has been suggested for individual midline precursors in these groups. The conserved arrangement of the axonal scaffold as well as the regular pattern of neural precursors in all euarthropod groups raises the question whether the ventral midline system is conserved in this phylum. In the remaining euarthropod groups, the chelicerates and myriapods, a single-minded homologue has been identified in the spider Achaearanea tepidariorum (chelicerate), however, the gene is not expressed in the ventral midline but in the median area of the ventral neuroectoderm. Here we show that At-sim is not required for ventral midline development. Furthermore, we identify sim homologues in representatives of arthropods that have not yet been analysed: the myriapod Strigamia maritima and a representative of an outgroup to the euarthropods, the onychophoran Euperipatoides kanangrensis. We compare the expression patterns to the A. tepidariorum sim homologue expression and furthermore analyse the nature of the arthropod midline cells. Our data suggest that in arthropods unpaired midline precursors evolved from the bilateral median domain of the ventral neuroectoderm in the last common ancestor of Mandibulata (insects, crustaceans, myriapods). We hypothesize that sim was expressed in this domain and recruited to ventral midline development. Subsequently, sim

  16. Structure, diversity and evolution of myriapod hemocyanins.

    PubMed

    Pick, Christian; Scherbaum, Samantha; Hegedüs, Elöd; Meyer, Andreas; Saur, Michael; Neumann, Ruben; Markl, Jürgen; Burmester, Thorsten

    2014-04-01

    Oxygen transport in the hemolymph of many arthropods is mediated by hemocyanins, large copper-containing proteins that are well-studied in Chelicerata and Crustacea, but had long been considered unnecessary in the subphylum of Myriapoda. Only recently has it become evident that hemocyanins are present in Scutigeromorpha (Chilopoda) and Spirostreptida (Diplopoda). Here we present evidence for a more widespread occurrence of hemocyanin in the myriapods. By means of RT-PCR, western blotting and database searches, hemocyanins were identified in the symphylans Hanseniella audax and Symphylella vulgaris, the chilopod Scolopendra subspinipes dehaani and the diplopod Polydesmus angustus. No hemocyanins were found in the diplopods Polyxenus lagurus, Cylindroiulus punctatus, Glomeris marginata, Glomeris pustulata and Arthrosphaera brandtii, or the chilopods Lithobius forficatus, Geophilus flavus and Strigamia maritima. This suggests multiple independent losses in myriapod taxa. Two independent hemocyanin subunits were found that were already present in the myriapod stem line. We specifically investigated the structure of the hemocyanin of P. angustus, which consists of three distinct subunits that occur in an approximately equimolar ratio. As deduced by 3D electron microscopy, the quaternary structure is a 3 × 6-mer that resembles the half structure of the 6 × 6-mer hemocyanin from Scutigera coleoptrata. It was analyzed more closely by homology modeling of 1 × 6-mers and their rigid-body fitting to the electron density map of the 3 × 6-mer. In addition, we obtained the cDNA sequence of a putative myriapod phenoloxidase. Phenoloxidases are related to the arthropod hemocyanins, but diverged before radiation of the arthropod subphyla.

  17. Mechanism of Thermal Adaptation in the Lactate Dehydrogenases.

    PubMed

    Peng, Huo-Lei; Egawa, Tsuyoshi; Chang, Eric; Deng, Hua; Callender, Robert

    2015-12-10

    The mechanism of thermal adaptation of enzyme function at the molecular level is poorly understood but is thought to lie within the structure of the protein or its dynamics. Our previous work on pig heart lactate dehydrogenase (phLDH) has determined very high resolution structures of the active site, via isotope edited IR studies, and has characterized its dynamical nature, via laser-induced temperature jump (T-jump) relaxation spectroscopy on the Michaelis complex. These particular probes are quite powerful at getting at the interplay between structure and dynamics in adaptation. Hence, we extend these studies to the psychrophilic protein cgLDH (Champsocephalus gunnari; 0 °C) and the extreme thermophile tmLDH (Thermotoga maritima LDH; 80 °C) for comparison to the mesophile phLDH (38-39 °C). Instead of the native substrate pyruvate, we utilize oxamate as a nonreactive substrate mimic for experimental reasons. Using isotope edited IR spectroscopy, we find small differences in the substate composition that arise from the detailed bonding patterns of oxamate within the active site of the three proteins; however, we find these differences insufficient to explain the mechanism of thermal adaptation. On the other hand, T-jump studies of reduced β-nicotinamide adenine dinucleotide (NADH) emission reveal that the most important parameter affecting thermal adaptation appears to be enzyme control of the specific kinetics and dynamics of protein motions that lie along the catalytic pathway. The relaxation rate of the motions scale as cgLDH > phLDH > tmLDH in a way that faithfully matches kcat of the three isozymes.

  18. 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

  19. 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.

  20. 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.; Perry, M.C.

    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

  1. Structural Analysis of N-acetylglucosamine-6-phosphate Deacetylase Apoenzyme from Escherichia coli

    SciTech Connect

    Ferreira,F.; Mendoza-Hernandez, G.; Castaneda-Bueno, M.; Aparicio, R.; Fischer, H.; Calcagno, M.; Oliva, G.

    2006-01-01

    We report the crystal structure of the apoenzyme of N-acetylglucosamine-6-phosphate (GlcNAc6P) deacetylase from Escherichia coli (EcNAGPase) and the spectrometric evidence of the presence of Zn{sup 2+} in the native protein. The GlcNAc6P deacetylase is an enzyme of the amino sugar catabolic pathway that catalyzes the conversion of the GlcNAc6P into glucosamine 6-phosphate (GlcN6P). The crystal structure was phased by the single isomorphous replacement with anomalous scattering (SIRAS) method using low-resolution (2.9 Angstroms) iodine anomalous scattering and it was refined against a native dataset up to 2.0 Angstroms resolution. The structure is similar to two other NAGPases whose structures are known from Thermotoga maritima (TmNAGPase) and Bacillus subtilis (BsNAGPase); however, it shows a phosphate ion bound at the metal-binding site. Compared to these previous structures, the apoenzyme shows extensive conformational changes in two loops adjacent to the active site. The E. coli enzyme is a tetramer and its dimer-dimer interface was analyzed. The tetrameric structure was confirmed in solution by small-angle X-ray scattering data. Although no metal ions were detected in the present structure, experiments of photon-induced X-ray emission (PIXE) spectra and of inductively coupled plasma emission spectroscopy (ICP-AES) with enzyme that was neither exposed to chelating agents nor metal ions during purification, revealed the presence of 1.4 atoms of Zn per polypeptide chain. Enzyme inactivation by metal-sequestering agents and subsequent reactivation by the addition of several divalent cations, demonstrate the role of metal ions in EcNAGPase structure and catalysis.

  2. Ocean acidification and the loss of phenolic substances in marine plants.

    PubMed

    Arnold, Thomas; Mealey, Christopher; Leahey, Hannah; Miller, A Whitman; Hall-Spencer, Jason M; Milazzo, Marco; Maers, Kelly

    2012-01-01

    Rising atmospheric CO(2) 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. CO(2) availability is also increasing in the oceans, where anthropogenic emissions cause ocean acidification, decreasing seawater pH and shifting the carbonate system towards further CO(2) enrichment. Such conditions tend to increase seagrass productivity but may also increase rates of grazing on these marine plants. Here we show that high CO(2) / 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 CO(2) vent on the Island of Vulcano, Italy, where pH values decreased from 8.1 to 7.3 and pCO(2) 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 CO(2) 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 CO(2) world.

  3. 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

  4. Expression of myriapod pair rule gene orthologs

    PubMed Central

    2011-01-01

    Background Segmentation is a hallmark of the arthropods; most knowledge about the molecular basis of arthropod segmentation comes from work on the fly Drosophila melanogaster. In this species a hierarchic cascade of segmentation genes subdivides the blastoderm stepwise into single segment wide regions. However, segmentation in the fly is a derived feature since all segments form virtually simultaneously. Conversely, in the vast majority of arthropods the posterior segments form one at a time from a posterior pre-segmental zone. The pair rule genes (PRGs) comprise an important level of the Drosophila segmentation gene cascade and are indeed the first genes that are expressed in typical transverse stripes in the early embryo. Information on expression and function of PRGs outside the insects, however, is scarce. Results Here we present the expression of the pair rule gene orthologs in the pill millipede Glomeris marginata (Myriapoda: Diplopoda). We find evidence that these genes are involved in segmentation and that components of the hierarchic interaction of the gene network as found in insects may be conserved. We further provide evidence that segments are formed in a single-segment periodicity rather than in pairs of two like in another myriapod, the centipede Strigamia maritima. Finally we show that decoupling of dorsal and ventral segmentation in Glomeris appears already at the level of the PRGs. Conclusions Although the pair rule gene network is partially conserved among insects and myriapods, some aspects of PRG interaction are, as suggested by expression pattern analysis, convergent, even within the Myriapoda. Conserved expression patterns of PRGs in insects and myriapods, however, may represent ancestral features involved in segmenting the arthropod ancestor. PMID:21352542

  5. 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.

  6. Niche expansion, body size, and survival in Galápagos marine iguanas.

    PubMed

    Wikelski, M; Wrege, Peter H

    2000-07-01

    Foraging theory predicts that dietary niche breadth should expand as resource availability decreases. However, Galápagos marine iguanas often die during algae shortages (El Niños) although land plants abound where they rest and reproduce. On Seymour Norte island, a subpopulation of iguanas exhibited unique foraging behavior: they consistently included the succulent beach plant B. maritima in their diet. We investigated the consequences of land-plant feeding for body size and survival. Batis-eaters supplemented their algae diet both before and after intertidal zone foraging, and more Batis was eaten during tides unfavorable for intertidal zone foraging (dawn and dusk). Larger, energy-constrained iguanas fed more on land than did smaller animals. Compared to intertidal zone algae, Batis was 39% lower in caloric content (1.6 vs. 2.6 kcal g(-1) dry mass), 56% lower in protein (8.3 vs. 18.9% dry mass) and 57% lower in nitrogen (1.3 vs. 3.0% dry mass). In spite of its lower nutrient value, iguanas that supplemented their diet with this plant were able to attain nearly twice the body size of other iguanas on the island. Age estimates indicate that many Batis-eaters survived repeated El Niño episodes during which animals of their relative size-class experienced high mortality on other islands. The larger animals were, however, completely dependent upon this supplementary source of food to maintain condition, and all perished in the 1997-1998 El Niño when high tides inundated and killed Batis on Seymour Norte Island. We hypothesize that Batis feeding developed as a local foraging tradition, and that dietary conservatism and strong foraging site fidelity explain why the inclusion of land plants in the diet has been observed in only a single population. Ultimately, a unique algae-adapted hindgut morphology and physiology may limit a switch from marine to terrestrial diet.

  7. 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

  8. The exotic mute swan (Cygnus olor) in Chesapeake Bay, USA

    USGS Publications Warehouse

    Perry, M.C.; Perry, M.C.

    2002-01-01

    The exotic mute swan (Cygnus olor) has increased its population size in Chesapeake Bay (Maryland and Virginia) to approximately 4,500 since 1962 when five swans were released in the Bay. The Bay population of mute swans now represents 30% of the total Atlantic Flyway population (12,600) and has had a phenomenal increase of 1,200% from 1986 to 1999. Unlike the tundra swans (Cygnus columbianus) that migrate to the Bay for the winter, the mute swan is a year-long resident, and, therefore, reports of conflicts with nesting native waterbirds and the consumption of submerged aquatic vegetation (SAV) have raised concerns among resource managers. Populations of black skimmers (Rynchops niger) and least terns (Sterna antillarum) nesting on beaches and oyster shell bars have been eliminated by molting mute swans. 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. Widgeon grass (Ruppia maritima) constituted 56% and eel grass (Zostera marina) constituted 43% of the gullet food of mute swans. Other SAV and invertebrates (including bryozoans, shrimp, and amphipods) formed a much smaller amount of the food percentage (1%). Invertebrates are believed to have been selected accidently within the vegetation eaten by the swans. Corn (Zea mays) fed to swans by Bay residents during the winter probably supplement limited vegetative food resources in late winter. A program to control swan numbers by the addling of eggs and the killing of adult swans has been a contentious issue with some residents of the Bay area. A management plan is being prepared by a diverse group of citizens appointed by the Governor to advise the Maryland Department of Natural Resources on viable and optimum options to manage mute swans in the Maryland portion of Chesapeake Bay. Hopefully, the implementation of the plan will alleviate the existing conflicts to the

  9. 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

  10. 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.

  11. Structural Basis for Substrate Binding and the Catalytic Mechanism of Type III Pantothenate Kinase

    SciTech Connect

    Yang, Kun; Strauss, Erick; Huerta, Carlos; Zhang, Hong

    2008-07-15

    Pantothenate kinase (PanK) catalyzes the first step of the universal five-step coenzyme A (CoA) biosynthetic pathway. The recently characterized type III PanK (PanK-III, encoded by the coaX gene) is distinct in sequence, structure and enzymatic properties from both the long-known bacterial type I PanK (PanK-I, exemplified by the Escherichia coli CoaA protein) and the predominantly eukaryotic type II PanK (PanK-II). PanK-III enzymes have an unusually high K{sub m} for ATP, are resistant to feedback inhibition by CoA, and are unable to utilize the N-alkylpantothenamide family of pantothenate analogues as alternative substrates, thus making type III PanK ineffective in generating CoA analogues as antimetabolites in vivo. Previously, we reported the crystal structure of the PanK-III from Thermotoga maritima and identified it as a member of the 'acetate and sugar kinase/heat shock protein 70/actin' (ASKHA) superfamily. Here we report the crystal structures of the same PanK-III in complex with one of its substrates (pantothenate), its product (phosphopantothenate) as well as a ternary complex structure of PanK-III with pantothenate and ADP. These results are combined with isothermal titration calorimetry experiments to present a detailed structural and thermodynamic characterization of the interactions between PanK-III and its substrates ATP and pantothenate. Comparison of substrate binding and catalytic sites of PanK-III with that of eukaryotic PanK-II revealed drastic differences in the binding modes for both ATP and pantothenate substrates, and suggests that these differences may be exploited in the development of new inhibitors specifically targeting PanK-III.

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

    PubMed Central

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

    2015-01-01

    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

  13. Annexation of a high-activity enzyme in a synthetic three-enzyme complex greatly decreases the degree of substrate channeling.

    PubMed

    You, Chun; Zhang, Y-H Percival

    2014-06-20

    The self-assembled three-enzyme complex containing triosephosphate isomerase (TIM), aldolase (ALD), and fructose 1,6-biphosphatase (FBP) was constructed via a mini-scaffoldin containing three different cohesins and the three dockerin-containing enzymes. This enzyme complex exhibited 1 order of magnitude higher initial reaction rates than the mixture of noncomplexed three enzymes. In this enzyme cascade reactions, the reaction mediated by ALD was the rate-limiting step. To understand the in-depth role of the rate-limiting enzyme ALD in influencing the substrate channeling effect of synthetic enzyme complexes, low-activity ALD from Thermotoga maritima was replaced with a similar-size ALD isolated from Thermus thermophilus, where the latter had more than 5 times specific activity of the former. The synthetic three-enzyme complexes annexed with either low-activity or high-activity ALDs exhibited higher initial reaction rates than the mixtures of the two-enzyme complex (TIM-FBP) and the nonbound low-activity or high activity ALD at the same enzyme concentration. It was also found that the annexation of more high-activity ALD in the synthetic enzyme complexes drastically decreased the degree of substrate channeling from 7.5 to 1.5. These results suggested that the degree of substrate channeling in synthetic enzyme complexes depended on the enzyme choice. This study implied that the construction of synthetic enzyme enzymes in synthetic cascade pathways could be a very important tool to accrelerate rate-limiting steps controlled by low-activity enzymes.

  14. Identification of an intermediate methyl carrier in the radical S-adenosylmethionine methylthiotransferases RimO and MiaB.

    PubMed

    Landgraf, Bradley J; Arcinas, Arthur J; Lee, Kyung-Hoon; Booker, Squire J

    2013-10-16

    RimO and MiaB are radical S-adenosylmethionine (SAM) enzymes that catalyze the attachment of methylthio (-SCH3) groups to macromolecular substrates. RimO attaches a methylthio group at C3 of aspartate 89 of protein S12, a component of the 30S subunit of the bacterial ribosome. MiaB attaches a methylthio group at C2 of N(6)-(isopentenyl)adenosine, found at nucleotide 37 in several prokaryotic tRNAs. These two enzymes are prototypical members of a subclass of radical SAM enzymes called methylthiotransferases (MTTases). It had been assumed that the sequence of steps in MTTase reactions involves initial sulfur insertion into the organic substrate followed by capping of the inserted sulfur atom with a SAM-derived methyl group. In this work, however, we show that both RimO and MiaB from Thermotoga maritima catalyze methyl transfer from SAM to an acid/base labile acceptor on the protein in the absence of their respective macromolecular substrates. Consistent with the assignment of the acceptor as an iron-sulfur cluster, denaturation of the SAM-treated protein with acid results in production of methanethiol. When RimO or MiaB is first incubated with SAM in the absence of substrate and reductant and then incubated with excess S-adenosyl-l-[methyl-d3]methionine in the presence of substrate and reductant, production of the unlabeled product precedes production of the deuterated product, showing that the methylated species is chemically and kinetically competent to be an intermediate.

  15. Cation selectivity by the CorA Mg2+ channel requires a fully hydrated cation.

    PubMed

    Moomaw, Andrea S; Maguire, Michael E

    2010-07-27

    The CorA Mg(2+) channel is the primary uptake system in about half of all bacteria and archaea. However, the basis for its Mg(2+) selectivity is unknown. Previous data suggested that CorA binds a fully hydrated Mg(2+) ion, unlike other ion channels. The crystal structure of Thermotoga maritima CorA shows a homopentamer with two transmembrane segments per monomer connected by a short periplasmic loop. This highly conserved loop, (281)EFMPELKWS(289) in Salmonella enterica serovar Typhimurium CorA, is the only portion of the channel outside of the cell, suggesting a role in cation selectivity. Mutation of charged residues in the loop, E281 and K287, to any of several amino acids had little effect, demonstrating that despite conservation electrostatic interactions with these residues are not essential. While mutation of the universally conserved E285 gave a minimally functional channel, E285A and E285K mutants were the most functional, again indicating that the negative charge at this position is not a determining factor. Several mutations at K287 and W288 behaved anomalously in a transport assay. Analysis indicated that mutation of K287 and W288 disrupts cooperative interactions between distinct Mg(2+) binding sites. Overall, these results are not compatible with electrostatic interaction of the Mg(2+) ion with the periplasmic loop. Instead, the loop appears to form an initial binding site for hydrated Mg(2+), not for the dehydrated cation. The loop residues may function to accelerate dehydration of the before entry of Mg(2+) into the pore of the channel.

  16. 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

  17. Cloning and sequencing of the gene encoding glutamine synthetase I from the archaeum Pyrococcus woesei: anomalous phylogenies inferred from analysis of archaeal and bacterial glutamine synthetase I sequences.

    PubMed Central

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

    1993-01-01

    The gene glnA encoding glutamine synthetase I (GSI) from the archaeum Pyrococcus woesei was cloned and sequenced with the Sulfolobus solfataricus glnA gene as the probe. An operon reading frame of 448 amino acids was identified within a DNA segment of 1,528 bp. The encoded protein was 49% identical with the GSI of Methanococcus voltae and exhibited conserved regions characteristic of the GSI family. The P. woesei GSI was aligned with available homologs from other archaea (S. solfataricus, M. voltae) and with representative sequences from cyanobacteria, proteobacteria, and gram-positive bacteria. Phylogenetic trees were constructed from both the amino acid and the nucleotide sequence alignments. In accordance with the sequence similarities, archaeal and bacterial sequences did not segregate on a phylogeny. On the basis of sequence signatures, the GSI trees could be subdivided into two ensembles. One encompassed the GSI of cyanobacteria and proteobacteria, but also that of the high-G + C gram-positive bacterium Streptomyces coelicolor (all of which are regulated by the reversible adenylylation of the enzyme subunits); the other embraced the GSI of the three archaea as well as that of the low-G + C gram-positive bacteria (Clostridium acetobutilycum, Bacillus subtilis) and Thermotoga maritima (none of which are regulated by subunit adenylylation). The GSIs of the Thermotoga and the Bacillus-Clostridium lineages shared a direct common ancestor with that of P. woesei and the methanogens and were unrelated to their homologs from cyanobacteria, proteobacteria, and S. coelicolor. The possibility is presented that the GSI gene arose among the archaea and was then laterally transferred from some early methanogen to a Thermotoga-like organism. However, the relationship of the cyanobacterial-proteobacterial GSIs to the Thermotoga GSI and the GSI of low-G+C gram-positive bacteria remains unexplained. PMID:8098326

  18. 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

  19. Modelo de atmosfera solar ajustado às observações do raio solar em 17GHz

    NASA Astrophysics Data System (ADS)

    Selhorst, C. L.; Silva, A. V. R.; Costa, J. E. R.

    2003-08-01

    O estudo das variações do raio solar durante o ciclo de atividades do Sol e das diferenças em relação à sua distribuição angular nos fornece informações importantes sobre as mudanças na estrutura da atmosfera solar. Neste trabalho foram analisados mais de 3600 mapas do Sol em 17 GHz obtidos pelo Rádio Heliógrafo de Nobeyama (NoRH), durante 1 ciclo de atividade solar (1992-2003). O raio solar foi definido no ponto onde a temperatura de brilho do mapa era equivalente à metade da temperatura do Sol calmo (temperatura mais comum no mapa).Em relação à sua variação ao longo do ciclo solar, o estudo foi dividido em duas partes: a) ajuste de uma circunferência a pontos distribuídos ao redor do Sol todo. Este estudo mostrou uma variação correlacionada com o ciclo de atividade do Sol. b) ajuste da circunferência a pontos situados somente nas regiões polares. Neste caso os resultados mostraram que o raio polar sofre pouca variação durante o ciclo, com tendência à anticorrelação com este. Além disto, a média do raio polar, durante o período analisado, foi 1" menor que o raio medido no Sol todo. Para estudar a distribuição angular do raio solar, comparamos a média da distribuição de 10 mapas no período de mínima atividade solar com a média de 10 mapas no período de máximo, este estudo mostrou um grande aumento do raio na região equatorial no período de máxima atividade solar. As medidas do raio foram usadas como um dos parâmetros para a criação de um modelo atmosférico (além da temperatura de brilho do Sol e do abrilhantamento do limbo observado), onde mostramos que um modelo atmosférico com a região de transição situada a 3500 km fornece um raio 5" menor que as medidas observacionais. Esta incompatibilidade do modelo com os dados observacionais foi contornada com a inclusão de espículas, estas fazem com que o raio solar aumente proporcionalmente à altura que estas atingem na atmosfera solar. A anticorrelação do raio

  20. Optimal Digital Control of a Bank-to-Turn Missile.

    DTIC Science & Technology

    1984-03-01

    California 93943 6. Office of The Air Attache 3 Brazilian Embassy 3006 [’assachus sets Av NW Washington DC 20008 7. Centro Tqcnico Aeroespacial 1%Rua...Parabuna SIN imo".� Sao Jose ds Campos - S? Sao Paulo, BRAZIL 8. Centro Tecnico Aeroespacial 2 Institut? de Atividades Espaciais Rua Parai-buna S/N...12200 Sao Jose dos Campos - SP Sao Paulo, BRAZIL 9. Centro Tacnico Aeroespacial 2 I;stituto de Atividales Espaciais Divisao le Si4stemas Belicog Rua

  1. [Study of the Sociodemographic Factors and Risky Behaviours Associated with the Acquisition of Sexual Transmitted Infections by Foreign Exchange Students in Portugal].

    PubMed

    Gravata, Andreia; Castro, Rita; Borges-Costa, João

    2016-06-01

    Introdução: As infeções sexualmente transmissíveis são um problema de saúde pública, sendo mais frequentes em jovens. Este estudo teve como principal objetivo avaliar os fatores sociodemográficos e comportamentos associados à aquisição de infeções sexualmente transmissíveis e o conhecimento sobre infeção por Chlamydia trachomatis em estudantes estrangeiros em intercâmbio universitário em Portugal. Material e Métodos: Os fatores sociodemográficos e comportamentos de risco foram estudados por aplicação de um questionário a estudantes em intercâmbio universitário em Portugal, inscritos nos anos letivos de 2012/2013, 2013/2014 e 2014/2015. Resultados: Avaliaram-se 338 questionários: 58,3% participantes do sexo feminino e 40,8% do sexo masculino (17 aos 30 anos). A idade média apontada para o início da vida sexual foi de 17,5 anos e a média de parceiros sexuais de 6,9. Relativamente às questões inquiridas foi referido: 9,5% negaram atividade sexual oral; 29% com atividade sexual anal; 11,8% com atividade sexual com parceiros do mesmo género; 82,1% refere consumo de álcool/estupefacientes; 42,3% desconhecimento sobre a infeção por Chlamydia trachomatis e 21% sobre o risco de transmissão de infeção por via oral. Discussão: Apesar das infeções sexualmente transmissíveis poderem afetar indivíduos de todas as idades, raças e orientações sexuais, vários fatores demográficos, sociais e comportamentais têm revelado influência nas taxas de prevalência deste tipo de infeções.Conclusões: Nesta população os fatores de risco associados a uma maior prevalência de infeções sexualmente transmissíveis continuam a existir, nomeadamente início precoce da atividade sexual, parceiros sexuais múltiplos e ausência de medidas de proteção durante as relações sexuais.

  2. A atuação do Observatório Nacional registrada nos relatórios ministeriais 1889 a 1930

    NASA Astrophysics Data System (ADS)

    Rodrigues, T.

    2003-08-01

    O período republicano até 1930 foi marcante na história do Observatório Nacional. Diversas reformas levaram a instituição a três ministérios diferentes e mudaram a ênfase do seu trabalho. A tão aguardada mudança para uma nova sede, em São Cristóvão, em 1920, não foi suficiente para que a instituição acompanhasse o ritmo tomado pela astronomia no mundo e se firmasse como ambiente de pesquisa. Uma análise simplificada poderia caracterizar um período de produção científica insignificante, dado o distanciamento da instituição dos novos rumos da astrofísica e da rápida inovação dos instrumentos, além do pequeno volume de publicações. Era uma época em que ainda não existiam os mecanismos formais de apoio e avaliação da atividade científica. Esse trabalho procura identificar a real atividade do Observatório no conteúdo dos Relatórios Ministeriais que, ao final de cada ano, apresentava as atividades, sucessos e problemas enfrentados pela instituição. Questões como instrumental e recursos humanos necessários; entraves burocráticos e financeiros; e articulações com outros observatórios se complementaram entre si ao longo desses anos para definir o perfil institucional e alguns aspectos fundamentais para a construção da astronomia no país. É possível concluir que a ênfase em serviços geográficos e de meteorologia, ao lado da inadequação dos instrumentos e do local, quase fizeram desaparecer a pesquisa em astronomia. Porém, vale destacar a sobrevivência de alguns trabalhos, como, por exemplo, variação de latitude e observação de estrelas duplas que mantiveram importante intercâmbio com outros grupos de pesquisa, demonstrando o constante esforço dos astrônomos e das diretorias em defesa da atividade científica.

  3. [What factors determine the levels of physical activity after cardiac rehabilitation program?].

    PubMed

    Soares, Diogo; Viamonte, Sofia; Magalhães, Sandra; Ribeiro, Maria Miguel; Barreira, Ana; Fernandes, Preza; Torres, Severo

    2013-01-01

    Introdução: Os Programas de Reabilitação Cardíaca ganharam enorme relevância na prevenção de doenças cardiovasculares constituindo um desafio assegurar a prática de exercício físico regular durante e após o fim do programa supervisionado. O objetivo deste trabalho foi determinar os fatores que influenciam os hábitos de atividade física 12 meses após um Programa de Reabilitação Cardíaca.Material e Métodos: Estudo prospetivo abrangendo 580 doentes com cardiopatia isquémica consecutivamente orientados para Programas de Reabilitação Cardíaca na Unidade de Reabilitação Cardiovascular do Centro Hospitalar do Porto, entre Janeiro de 2008 e Junho de 2011. Avaliaram-se os níveis de atividade física através do International Physical Activity Questionnaire realizado no início do programa, aos 3 e 12 meses depois. Foram testados como potenciais determinantes dos hábitos de atividade física a longo prazo: idade; sexo; fatores de risco modificáveis; capacidade funcional (alcançada em prova de esforço); análises laboratoriais (HbA1c, perfil lipídico, Proteína C Reativa e Peptideo Natriurético Cerebral). Realizou-se análise de regressão linear para identificar os preditores significativos e encontrar o melhor ajuste do modelo.Resultados: A idade avançada, género feminino, a capacidade funcional, níveis de atividade física baixos previamente ao Programa de Reabilitação Cardíaca e uma fraca evolução do International Physical Activity Questionnaire durante o programa foram os melhores preditores univariáveis de uma evolução menos favorável do International Physical Activity Questionnaire nos 12 meses de follow-up. A análise de regressão linear multivariável concluiu que o melhor modelo explicativo incluía: idade, género, evolução do IPAQ no programa (R2 ajust = 0,318; f = 60,62; p < 0,001).Conclusão: A identificação de subgrupos de doentes com menor tendência à prática de atividade física permite desenvolver estrat

  4. Influence of soil properties on trace element availability and plant accumulation in a Mediterranean salt marsh polluted by mining wastes: implications for phytomanagement.

    PubMed

    Conesa, H M; María-Cervantes, A; Alvarez-Rogel, J; González-Alcaraz, M N

    2011-09-15

    The aims of this study were to determine the factors which control metal and As phytoavailability in the different microenvironments (Sand Dunes, Salt Flat, Dry River and Shrubs) present at a Mediterranean salt marsh polluted by mining wastes. We performed a field study following a plot sampling survey. The analyses of soil parameters (pH, electrical conductivity (EC), organic carbon contents, etc.), total metal and As concentrations and their phytoavailability assessed with EDTA were related to each microenvironment and the corresponding plant species uptake. The averages of pH and EC were slightly alkaline (pH ≈ 7.5) and saline (≈ 2.2 to 17.1 dS m(-1)) respectively. The soil samples from the Salt Flat subzone showed the highest metal concentrations (e.g. 51 mg kg(-1) Cd, 11,600 mg kg(-1) Pb) while for As, the highest concentrations occurred in the Dry River (380 mg kg(-1) As). The total metal and EDTA-extractable concentrations occurred as it follows: Salt Flat>Dry River>Degraded Dunes>Shrubs. In relation to plant metal and As accumulation, the highest root concentrations were obtained in the species from the Salt Flat subzone: ~17 mg kg(-1) As, ~620 mg kg(-1) Pb, for both, Juncus maritimus and Arthrocnemum macrostachyum. However the highest metal and As shoot concentrations occurred in species from the Sand Dunes: ~23 mg kg(-1) As ~270 mg kg(-1) Pb for Dittrichia viscosa; ~23 mg kg(-1) As, ~390 mg kg(-1) Zn for Crucianella maritima. The occurrence of edaphic gradients including salinity and texture determined the vegetation distribution. However, it cannot be concluded that there was a disturbance due to metal(loid)s soil concentrations in terms of vegetation composition except in the Degraded Dunes and Dry River. The higher EDTA-extractable concentrations were coincidental with the most saline soils but this did not result in higher metal(loid)s plant accumulation.

  5. Molecular signatures for the phylum (class) Thermotogae and a proposal for its division into three orders (Thermotogales, Kosmotogales ord. nov. and Petrotogales ord. nov.) containing four families (Thermotogaceae, Fervidobacteriaceae fam. nov., Kosmotogaceae fam. nov. and Petrotogaceae fam. nov.) and a new genus Pseudothermotoga gen. nov. with five new combinations.

    PubMed

    Bhandari, Vaibhav; Gupta, Radhey S

    2014-01-01

    fam. nov., Kosmotogaceae fam. nov. and Petrotogaceae fam. nov.). Additionally, the results of our phylogenetic/compatibility studies along with the species distribution patterns of 22 identified CSIs, provide compelling evidence that the current genus Thermotoga is comprised of two evolutionary distinct groups and that it should be divided into two genera. It is proposed that the emended genus Thermotoga should retain only the species Thermotoga maritima, Tt. neapolitana, Tt. petrophila, Tt. naphthophila, Thermotoga sp. EMP, Thermotoga sp. A7A and Thermotoga sp. RQ2 while the other Thermotoga species (viz. Tt. lettingae, Tt. thermarum, Tt. elfii, Tt. subterranean and Tt. hypogea) be transferred to a new genus, Pseudothermotoga gen. nov.

  6. Environmental implications of gene flow from sugar beet to wild beet--current status and future research needs.

    PubMed

    Bartsch, Detlef; Cuguen, Joel; Biancardi, Enrico; Sweet, Jeremy

    2003-01-01

    Gene flow via seed or pollen is a basic biological process in plant evolution. The ecological and genetic consequences of gene flow depend on the amount and direction of gene flow as well as on the fitness of hybrids. The assessment of potential risks of transgenic plants should take into account the fact that conventional crops can often cross with wild plants. The precautionary approach in risk management of genetically modified plants (GMPs) may make it necessary to monitor significant wild and weed populations that might be affected by transgene escape. Gene flow is hard to control in wind-pollinated plants like beet (Beta vulgaris). In addition, wild beet populations potentially can undergo evolutionary changes which might expand their geographical distribution. Unintended products of cultivated beets pollinated by wild beets are weed beets that bolt and flower during their first year of planting. Weed beets cause yield losses and can delay harvest. Wild beets are important plant genetic resources and the preservation of wild beet diversity in Europe has been considered in biosafety research. We present here the methodology and res