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1

Earwigs  

E-print Network

Earwigs are abundant throughout Texas and can be a nuisance when they invade homes or damage plants. This publication explains the biology and habits of earwigs and offers three ways to control them: sanitation, mechanical means and chemical methods....

Mott, Dale; Jackman, John A.

2004-08-06

2

Controlling earwigs P.J. Pellitteri  

E-print Network

infestations. Earwigs eat an omnivorous diet of other insects and plants. This diet can be beneficial: earwigs be confused with injuries caused by slugs, cutworms, or even rabbits. Larger plants will tolerate the feeding

Balser, Teri C.

3

Kin selected siblicide and filial cannibalism in the European earwig  

E-print Network

Kin selected siblicide and filial cannibalism in the European earwig Ralph Dobler & Mathias can severely increase. Siblicide and cannibalism are then beneficial for the survivor by reducing in the evolution of siblicide and cannibalism4 . Predictions 1) victims of siblicidal acts live shorter than

Kölliker, Mathias

4

Transitional fossil earwigs - a missing link in Dermaptera evolution  

Microsoft Academic Search

BACKGROUND: The Dermaptera belongs to a group of winged insects of uncertain relationship within Polyneoptera, which has expanded anal region and adds numerous anal veins in the hind wing. Evolutional history and origin of Dermaptera have been in contention. RESULTS: In this paper, we report two new fossil earwigs in a new family of Bellodermatidae fam. nov. The fossils were

Jingxia Zhao; Yunyun Zhao; Chungkun Shih; Dong Ren; Yongjie Wang

2010-01-01

5

The chemical defense in larvae of the earwig Forficula auricularia.  

PubMed

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

Gasch, Tina; Vilcinskas, Andreas

2014-08-01

6

Artificial Intelligence 47 (1991) 161-184 161 Today the earwig,  

E-print Network

Artificial Intelligence 47 (1991) 161-184 161 Elsevier Today the earwig, man? tomorrow David Kirsh November 1987 Revised January 1988 Abstract Kirsh, D., Today the earwig, tomorrow man?, Artificial Intelligence 47 (1991) 161-184. A startling amount of intelligent activity can be controlled without reasoning

Kirsh, David

7

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

PubMed Central

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

Kocarek, Petr; John, Vaclav; Hulva, Pavel

2013-01-01

8

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

PubMed Central

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

Pichon, Samuel; Arbore, Roberto; Kuhn-Buhlmann, Simone; Kolliker, Mathias; Walser, Jean-Claude

2014-01-01

9

Right-handed penises of the earwigLabidura riparia (Insecta, Dermaptera, Labiduridae): Evolutionary relationships between structural and behavioral asymmetries  

Microsoft Academic Search

The number of penises vary in the insect suborder Forficulina (order Dermaptera; earwigs). Males of the families Diplatyidae, Pigidicranidae, Anisolabididae, Apachyidae, and Labiduridae have two penises (right and left), while those of the Spongipohridae, Chelisochidae, and Forficulidae have a single penis. The proposed phylo- genetic relationships among these families suggest that the single-penis families evolved from an ancestor possess- ing

Y. Kamimura

2006-01-01

10

Sagina maritima Don (Caryophyllaceae) and other halophytes in London  

Microsoft Academic Search

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

J. A. EDGINGTON

11

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

Microsoft Academic Search

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

L. Jerling

1988-01-01

12

Chromones and flavanones from artemisia campestris subsp. maritima  

Microsoft Academic Search

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

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

1998-01-01

13

Isoenzyme diversity and affinity between Dactylis glomerata and Puccinellia maritima (Poaceae)  

Microsoft Academic Search

Two Estonian populations of Dactylis glomerata and two of Puccinellia maritima were surveyed electrophoretically for eight enzymes to assess their diversity and affinity. Analysis of electrophoretic data indicated a significant amount of variability in the studied populations of D. glomerata and P. maritima as judged by the number of isoenzyme phenotypes and isoforms detected. Phenotypic affinity between D. glomerata and

Georgi B. Angelov

14

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

E-print Network

WORDS: Juniperus maritima, Puget Sound, J. scopulorum, J. virginiana, cryptic species, terpenoids, nr (Small) E. Murray (Adams, 2004). Juniperus scopulorum and J. virginiana are weedy junipers that occupyPhytologia (December 2007) 89(3) 263 JUNIPERUS MARITIMA, THE SEASIDE JUNIPER, A NEW SPECIES FROM

Adams, Robert P.

15

High-resolution structure of shikimate dehydrogenase from Thermotoga maritima reveals a tightly closed conformation.  

PubMed

Shikimate dehydrogenase (SDH), which catalyses the NADPH-dependent reduction of 3-dehydroshikimate to shikimate in the shikimate pathway, is an attractive target for the development of herbicides and antimicrobial agents. Structural analysis of a SDH from Thermotoga maritima encoded by the Tm0346 gene was performed to facilitate further structural comparisons between the various shikimate dehydrogenases. The crystal structure of SDH from T. maritima was determined at 1.45 SDH from T. maritima showed a monomeric architecture. The overall structure of SDH from T. maritima comprises the N-terminal ?/? sandwich domain for substrate binding and the C-terminal domain for NADP binding. When the T. maritima SDH structure was compared with those of the SDHs from other species, the SDH from T. maritima was in a tightly closed conformation, which should be open for catalysis. Notably, ?7 moves toward the active site (?5 Å), which forces the SDH of T. maritima in a more closed form. Four ammonium sulfate (AMS) ions were identified in the structure. They were located in the active site and appeared to mimic the role of the substrate in terms of the enzyme activity and stability. The new high resolution structural information reported in this study, including the AMS binding sites as a potent inhibitor binding site of SDHs, is expected to supplement the existing structural data and will be useful for structure-based antibacterial discovery against SDHs. PMID:22095087

Lee, Hyung Ho

2012-03-01

16

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

PubMed

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

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

2010-01-01

17

Volatile composition of oyster leaf (Mertensia maritima (L.) Gray).  

PubMed

Oyster leaf (Mertensia maritima), also called vegetarian oyster, has a surprising oyster-like aroma. Its volatile composition was investigated here for the first time. In total, 109 compounds were identified by gas chromatography-mass spectrometry (GC-MS) and quantified by GC-FID. The use of GC-olfactometry on both polar and nonpolar columns allowed the detection of the molecules having an oyster-like, marine odor. Four compounds were identified and confirmed by synthesis: (Z)-3-nonenal, (Z)-1,5-octadien-3-ol, (Z,Z)-3,6-nonadienal, and (Z)-1,5-octadien-3-one. After evaluation of freshly prepared reference samples, these compounds were confirmed to be reminiscent of the oyster-like marine notes perceived in the tasting of cut leaves. PMID:23140514

Delort, Estelle; Jaquier, Alain; Chapuis, Christian; Rubin, Mark; Starkenmann, Christian

2012-11-28

18

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

PubMed

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

Rouger, R; Jump, A S

2014-07-01

19

Loktanella maritima sp. nov. isolated from shallow marine sediments.  

PubMed

An aerobic, Gram-stain-negative, non-motile bacterium, KMM 9530(T), was isolated from a sediment sample collected from the Sea of Japan seashore. Comparative 16S rRNA gene sequence analysis positioned novel strain KMM 9530(T) in the genus Loktanella as a separate line adjacent to Loktanella sediminilitoris KCTC 32383(T), Loktanella tamlensis JCM 14020(T) and Loktanella maricola JCM 14564(T) with 98.5-98.2% sequence similarity. Strain KMM 9530(T) was characterized by its weak hydrolytic capacity and inability to assimilate most organic substrates. The major isoprenoid quinone was Q-10, polar lipids consisted of phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unknown phospholipid, an unknown aminolipid and unknown lipids, and the major fatty acid was C18 : 1?7c. On the basis of phylogenetic analysis, DNA-DNA hybridization and phenotypic characterization, it can be concluded that the novel strain KMM 9530(T) represents a novel species in the genus Loktanella, for which the name Loktanella maritima sp. nov. is proposed. The type strain of the species is KMM 9530(T) (?=?NRIC 0919(T)?=?JCM 19807(T)). PMID:24744019

Tanaka, Naoto; Romanenko, Lyudmila A; Kurilenko, Valeriya V; Svetashev, Vassilii I; Kalinovskaya, Natalia I; Mikhailov, Valery V

2014-07-01

20

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

PubMed

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

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

2008-12-01

21

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

PubMed Central

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

Perez, Eduardo; Stock, Ann M.

2013-01-01

22

Phytologia (April 2009) 91(1) 31 THE LEAF ESSENTIAL OIL OF JUNIPERUS MARITIMA R. P.  

E-print Network

in leaf terpenoids throughout the range of Juniperus scopulorum Sarg. and found that plants from the PugetPhytologia (April 2009) 91(1) 31 THE LEAF ESSENTIAL OIL OF JUNIPERUS MARITIMA R. P. ADAMS COMPARED WITH J. HORIZONTALIS, J. SCOPULORUM AND J. VIRGINIANA OILS Robert P. Adams Biology Department, Baylor

Adams, Robert P.

23

Salinity effects on germination, growth, and seed production of the halophyte Cakile maritima  

Microsoft Academic Search

Cakile maritima (Brassicaceae) is a halophyte that thrives on dunes along the Tunisian seashore. Besides its ecological interest for soil fixation, this plant produces seeds rich in lipids (40% on dry weight basis), making it a potential source of oil for industrial use. The purpose of the present work was to study the salt tolerance of this species at germination,

Ahmed Debez; Karim Ben Hamed; Claude Grignon; Chedly Abdelly

2004-01-01

24

Population structure and origins of Purple Sandpipers Calidris maritima in north Norway during winter  

Microsoft Academic Search

Wintering Purple Sandpipers Calidris maritima were captured at Varangerfjorden, Finnmark, in March 1992, and compared with samples from Troms county in November 1988 to describe the population structure in north Norway in terms of age and sex classes, and to determine the origins of these wintering birds. The overall percentage of first?year birds was 35% at Varangerfjorden, higher than that

Ron W. Summers; Rab Rae

2006-01-01

25

Physiology and ecologic relevance of salt secretion by the salt gland of Glaux maritima L  

Microsoft Academic Search

The effects of salinity in the root medium, time, and relative humidity on the salt secretion of Glaux maritima were investigated. Both in the greenhouse and in the field increasing salinity stimulated sodium and chloride secretion, whereas the essential elements potassium, calcium, and magnesium remained at low secretion levels, which might be interpreted as efficient mineral economy. The low secretion

Jelte Rozema; Ingrid Riphagen

1977-01-01

26

Clone dynamics, population dynamics and vegetation pattern of Glaux maritima on a Baltic sea shore meadow  

Microsoft Academic Search

The vegetative propagation ofGlaux maritima is correlated with growth habit which is inturn related to the light environment. Plant form and vegetative behaviour were recorded 1980–1984 and an attempt to correlate this to population dynamics and vegetation development was made.

L. Jerling

1988-01-01

27

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

SciTech Connect

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.

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

1994-12-31

28

Complete genome sequence of Hippea maritima type strain (MH2T)  

SciTech Connect

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.

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

2011-01-01

29

Xylanase Attachment to the Cell Wall of the Hyperthermophilic Bacterium Thermotoga maritima?  

PubMed Central

The cellular localization and processing of the endo-xylanases (1,4-?-d-xylan-xylanohydrolase; EC 3.2.1.8) of the hyperthermophile Thermotoga maritima were investigated, in particular with respect to the unusual outer membrane (“toga”) of this gram-negative bacterium. XynB (40 kDa) was detected in the periplasmic fraction of T. maritima cells and in the culture supernatant. XynA (120 kDa) was partially released to the surrounding medium, but most XynA remained cell associated. Immunogold labeling of thin sections revealed that cell-bound XynA was localized mainly in the outer membranes of T. maritima cells. Amino-terminal sequencing of purified membrane-bound XynA revealed processing of the signal peptide after the eighth residue, thereby leaving the hydrophobic core of the signal peptide attached to the enzyme. This mode of processing is reminiscent of type IV prepilin signal peptide cleavage. Removal of the entire XynA signal peptide was necessary for release from the cell because enzyme purified from the culture supernatant lacked 44 residues at the N terminus, including the hydrophobic part of the signal peptide. We conclude that toga association of XynA is mediated by residues 9 to 44 of the signal peptide. The biochemical and electron microscopic localization studies together with the amino-terminal processing data indicate that XynA is held at the cell surface of T. maritima via a hydrophobic peptide anchor, which is highly unusual for an outer membrane protein. PMID:18083821

Liebl, Wolfgang; Winterhalter, Christoph; Baumeister, Wolfgang; Armbrecht, Martin; Valdez, Michael

2008-01-01

30

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

Microsoft Academic Search

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

Robert P. Adams

31

Effects of elevated CO 2 on the vasculature and phenolic secondary metabolism of Plantago maritima  

Microsoft Academic Search

We have examined the effect of elevated CO2 on the vasculature and phenolic secondary metabolism on clones of the maritime plant Plantago maritima (L.). Plants were exposed to either ambient (360 ?mol CO2 mol?1) or elevated (600 ?mol CO2 mol?1) atmospheric CO2 within a Solardome facility and harvested after 12 months' growth. Histochemical analysis of the leaves identified increases in

Matthew P. Davey; David N. Bryant; Ian Cummins; Trevor W. Ashenden; Phillip Gates; Robert Baxter; Robert Edwards

2004-01-01

32

Characterization of a thermostable ?-glucosidase (BglB) from Thermotoga maritima showing transglycosylation activity  

Microsoft Academic Search

A ?-glucosidase gene (bglB) of an extremely thermophilic eubacterium, Thermotoga maritima was expressed in Esherichia coli to yield the active enzyme. The cloned enzyme was purified to homogeneity by heat treatment and ion exchange chromatographies. The purified enzyme gave a single band on SDS-PAGE with a molecular weight of 81kDa. The estimated Km and kcat values for p-nitrophenyl ?-d-glucopyranoside were

K Goyal; P Selvakumar; K Hayashi

2001-01-01

33

Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima  

Microsoft Academic Search

The 1,860,725-base-pair genome of Thermotoga maritima MSB8 contains 1,877 predicted coding regions, 1,014 (54%) of which have functional assignments and 863 (46%) of which are of unknown function. Genome analysis reveals numerous pathways involved in degradation of sugars and plant polysaccharides, and 108 genes that have orthologues only in the genomes of other thermophilic Eubacteria and Archaea. Of the Eubacteria

Karen E. Nelson; Rebecca A. Clayton; Steven R. Gill; Michelle L. Gwinn; Robert J. Dodson; Daniel H. Haft; Erin K. Hickey; Jeremy D. Peterson; William C. Nelson; Karen A. Ketchum; Lisa McDonald; Teresa R. Utterback; Joel A. Malek; Katja D. Linher; Mina M. Garrett; Ashley M. Stewart; Matthew D. Cotton; Matthew S. Pratt; Cheryl A. Phillips; Delwood Richardson; John Heidelberg; Granger G. Sutton; Robert D. Fleischmann; Jonathan A. Eisen; Owen White; Steven L. Salzberg; Hamilton O. Smith; J. Craig Venter; Claire M. Fraser

1999-01-01

34

Sequence, assembly and evolution of a primordial ferredoxin from Thermotoga maritima.  

PubMed Central

A gene coding for the ferredoxin of the primordial, strictly anaerobic and hyperthermophilic bacterium Thermotoga maritima was cloned, sequenced and expressed in Escherichia coli. The ferredoxin gene encodes a polypeptide of 60 amino acids that incorporates a single 4Fe-4S cluster. T. maritima ferredoxin expressed in E. coli is a heat-stable, monomeric protein, the spectroscopic properties of which show that its 4Fe-4S cluster is correctly assembled within the mesophilic host, and that it remains stable during purification under aerobic conditions. Removal of the iron-sulfur cluster results in an apo-ferredoxin that has no detectable secondary structure. This observation indicates that in vivo formation of the ferredoxin structure is coupled to the insertion of the iron-sulfur cluster into the polypeptide chain. Sequence comparison of T. maritima ferredoxin with other 4Fe-4S ferredoxins revealed high sequence identities (75% and 50% respectively) to the ferredoxins from the hyperthermophilic members of the Archaea, Thermococcus litoralis and Pyrococcus furiosus. The high sequence similarity supports a close relationship between these extreme thermophilic organisms from different phylogenetic domains and suggests that ferredoxins with a single 4Fe-4S cluster are the primordial representatives of the whole protein family. This observation suggests a new model for the evolution of ferredoxins. Images PMID:8168477

Darimont, B; Sterner, R

1994-01-01

35

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

SciTech Connect

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.

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

1995-12-31

36

Overexpression, crystallization, and preliminary X-ray crystallographic analysis of shikimate dehydrogenase from Thermotoga maritima.  

PubMed

Shikimate dehydrogenase (SDH), which catalyses the NADPH-dependent reduction of 3-dehydroshikimate to shikimate in the shikimate pathway, is an attractive target for the development of herbicides and antimicrobial agents. Previous structural studies showed that SDH exists in two conformations, an open form and a closed form, and it is believed that the conformational state is crucial to understanding a catalytic mechanism. To facilitate further structural comparisons among SDHs, structural analysis of an SDH from Thermotoga maritima encoded by the Tm0346 gene has been initiated. SDH from T. maritima has been overexpressed in Escherichia coli and crystallized at 296?K using ammonium sulfate as a precipitant. Crystals of T. maritima SDH diffracted to 1.45?Å resolution and belonged to orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a=54.21, b=62.45 and c=68.68?Å. The asymmetric unit contains a monomer, with a corresponding VM of 2.01?Å3?Da(-1) and a solvent content of 38.9% by volume. PMID:21795804

Lee, Hyung Ho

2011-07-01

37

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

SciTech Connect

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.

S Park; B Crane

2011-12-31

38

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

PubMed

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

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

39

Evaluation of the protective potential of Ambrosia maritima extract on acetaminophen-induced liver damage.  

PubMed

The hepatoprotective activity of the aqueous-methanolic extract of Ambrosia maritima was investigated against acetaminophen (paracetamol, 4-hydroxy acetanilide) induced hepatic damage. Acetaminophen at the dose of 640 mg/kg produced liver damage in rats as manifested by the significant (P < 0.001) rise in serum levels of glutamate oxaloacetate transaminase (AST), glutamate pyruvate transaminase (ALT) and alkaline phosphatase (ALP) to 1178.5 +/-118.05; 607.5 +/- 32.6 and 274.16 +/- 8.89 IU/l (n = 10), respectively, compared with respective control values of 97.83+/-3.23; 46.0 +/- 3.92 and 168.67 +/- 7.86 IU/l. Pretreatment of rats with the plant extract (100 and 200 mg/kg) lowered significantly (P < 0.001) the respective serum AST to 203.3+/-5.74 and 157.1 +/- 8.78 IU/l, ALT to 138.67 +/- 7.7 and 87.5 +/- 3.6 IU/l and ALP levels to 238.0 +/- 5.89 and 206.5 +/- 7.5 IU/l, respectively. Treatment of rats with acetaminophen led to a marked increase in lipid peroxidation as measured by malondialdehyde (MDA) (42%). This was associated with a significant reduction of the hepatic antioxidant system e.g. reduced glutathione (GSH) (65%), glutathione reductase (GSH-R) (35%), total glutathione peroxidase (GSH-Px) (32%) and glutathione-S-transferase (GST) (16%). These biochemical alterations resulting from acetaminophen administration were inhibited by pretreatment with A. maritima L. extract. These data suggest that the plant A. maritima L. may act as a hepatoprotective and antioxidant agent. PMID:11297846

Ahmed, M B; Khater, M R

2001-05-01

40

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

PubMed

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

Ciccarelli, Daniela; Noccioli, Cecilia; Pistelli, Luisa

2013-09-01

41

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

Microsoft Academic Search

Three acylated cyanidin 3-(3X-glucosylsambubioside)-5-glucosides (1–3) and one non-acylated cyanidin 3-(3X-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-(?-d-glucopyranosyl)-?-d-xylopyranosyl)-6-O-(trans-p-coumaroyl)-?-d-glucopyranoside]-5-O-[6-O-(malonyl)-(?-d-glucopyranoside) as a major pigment, and a

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

2008-01-01

42

Extracts from Alternanthera maritima as natural photosensitizers in photodynamic antimicrobial chemotherapy (PACT).  

PubMed

This study investigated the effect of photodynamic antimicrobial chemotherapy (PACT) using extracts from Alternanthera maritima on the viability of Candida dubliniensis. Human infections constitute a great health problem. Several antifungal drugs are currently available, but their uses are limited by a number of factors, such as low potency, poor solubility, microbial resistance, and drug toxicity. Therefore, the search for new and more effective antimicrobial agents and the development of alternative therapies, such as PACT, are necessary. Crude hexane and ethanol extracts of A. maritima were produced. The prepared extracts presented absorption at 650-700 nm. For bioassays, 50 microL of culture medium, 50 microL of extract (25 mg/mL) or control, and 5 microL of a suspension of the microorganism to be tested (C. dubliniensis ATCC 778157 or ATCC 777, 10(7)CFU/mL) were placed in a sterile 96-well microtiter plate (well cross section=0.38 cm(2)). The contents of each well were irradiated with a 685-nm diode laser with an output power of 35 mW, which was distributed through the well cross section yielding an energy dosage of 28 J/cm(2). In each assay (n=6), one plate was subjected to irradiation, and one was not. For each active sample, the number of colony-forming units per milliliter (CFU/mL) was obtained, and data were analyzed by the Tukey test. The chemical compositions of the extracts were determined by chromatographic and spectroscopic techniques. The results suggest inhibition of the growth of C. dubliniensis when irradiated with a diode laser in the presence of hexane and ethanol extracts from A. maritima as photosensitizers. Laser irradiation alone or crude extracts at 25mg/mL did not significantly reduce the number of CFU/mL. Steroids, triterpenes, and flavonoids were identified in the analyzed extracts. In conclusion, the photoactivation of crude hexane and ethanol extracts of A. maritima by red laser radiation at 685 nm promoted an antimicrobial effect, showing that these natural products can be used as photosensitizers in PACT. PMID:20172737

Gasparetto, Adriana; Lapinski, Tadia F; Zamuner, Stella R; Khouri, Sonia; Alves, Leandro P; Munin, Egberto; Salvador, Marcos J

2010-04-01

43

Galacto-oligosaccharide production by a thermostable recombinant ?-galactosidase from Thermotoga maritima  

Microsoft Academic Search

Summary A ?-galactosidase from Thermotoga maritima produced galacto-oligosaccharides (GOS) from lactose by transgalactosylation when expressed in Escherichia coli. The enzyme activity for GOS production was maximal at pH 6.0 and 90 °C. In thermal stability experiments, the enzyme followed first-order kinetics of pH and thermal inactivation, and half-lives at pH 5.0, pH 8.0, 80 °C, and 95 °C were 27 h, 82 h, 41 h, and

Eun-Su Ji; Nyun-Ho Park; Deok-Kun Oh

2005-01-01

44

The effect of calcium on the antioxidant systems in the halophyte Cakile maritima under salt stress  

Microsoft Academic Search

The purpose of the current investigation was to study the effect of Ca2+ (0, 3.5 and 20 mM concentrations) on the antioxidant systems in the halophyte Cakile maritima under NaCl stress (0, 100, 200 and 400 mM NaCl). Plants treated with both moderate calcium (3.5 mM) and salt levels (100 mM)\\u000a showed the maximum growth, and the addition of 20 mM calcium to the nutrient

Nader Ben Amor; Wided Megdiche; Ana Jiménez; Francisca Sevilla; Chedly Abdelly

2010-01-01

45

Metabolic Responses to Lead of Metallicolous and Nonmetallicolous Populations of Armeria maritima.  

PubMed

Metabolic responses to Pb(NO3)2 (Pb) ions of excised leaves of metallicolous (MPs) and nonmetallicolous populations (NMPs) of Armeria maritima, cultivated on normal soil, were examined. Detached leaves were exposure to Pb for 24 h, and metabolic parameters were investigated. Pb decreased the photosynthesis (Pn) rate and photosystem II (PSII) activity, whereas the photochemical efficiency of PSII remained unchanged. In both populations, Pb ions caused increase in O2 uptake of dark-treated leaves; however, respiration after Pn was not affected. Pb increased superoxide dismutase activity in MP leaves and malondialdehyde content in NMP leaves. Other metabolites after Pb treatment were increased (proline or H2O2) or decreased (malate). Ascorbate peroxidase activity and adenosine triphosphate content decreased more in MP than in NMP leaves. Our results indicate that A. maritima is well adapted to heavy metal-contaminated soils, and we discuss potential causes of the stimulation of respiration by Pb ions and possible reasons for the tolerance to oxidative stress of plants growing in a metal-rich habitat. PMID:25070267

Parys, Eugeniusz; Wasilewska, Wioleta; Siedlecka, Maria; Zienkiewicz, Maksymilian; Dro?ak, Anna; Romanowska, El?bieta

2014-11-01

46

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

PubMed Central

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

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

2013-01-01

47

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

NASA Astrophysics Data System (ADS)

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.

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

2013-09-01

48

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

PubMed

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

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

2014-04-01

49

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

E-print Network

Cytotoxic and Antimicrobial Constituents of the Bark of Diospyros maritima Collected in Two, Natural Products Laboratory, Research Triangle Institute, P.O. Box 12194, Research Triangle Park, North a new naphthoquinone derivative, (4S)-shinanolone (5), and a new natural product coumarin, 7,8-dimethoxy

Falkinham, Joseph

50

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

Microsoft Academic Search

The dune wintergreen (Pyrola rotundifolia ssp.maritima) is an evergreen perennial herb which has spread extensively in recent decades to, and on, various British dune systems including Braunton Burrows, N. Devon. Its multiplication is partly vegetative, by rhizomes bearing leaf rosettes. This study primarily concerns the relation between: (i) the growth of one particular invasive colony on Braunton Burrows, as shown

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

1985-01-01

51

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

Microsoft Academic Search

The dune wintergreen ( Pyrola rotundifolia ssp. maritima) is an evergreen perennial herb which has spread extensively in recent decades to, and on, various British dune systems including Braunton Burrows, N. Devon. Its multiplication is partly vegetative, by rhizomes bearing leaf rosettes. This study primarily concerns the relation between: (i) the growth of one particular invasive colony on Braunton Burrows,

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

1985-01-01

52

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

Microsoft Academic Search

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

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

2000-01-01

53

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

PubMed

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. PMID:17928016

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

2008-02-01

54

Overexpression and simple purification of the Thermotoga maritima 6-phosphogluconate dehydrogenase in Escherichia coli and its application for NADPH regeneration  

Microsoft Academic Search

BACKGROUND: Thermostable enzymes from thermophilic microorganisms are playing more and more important roles in molecular biology R&D and industrial applications. However, over-production of recombinant soluble proteins from thermophilic microorganisms in mesophilic hosts (e.g. E. coli) remains challenging sometimes. RESULTS: An open reading frame TM0438 from a hyperthermophilic bacterium Thermotoga maritima putatively encoding 6-phosphogluconate dehydrogenase (6PGDH) was cloned and expressed in

Yiran Wang; Y-H Percival Zhang

2009-01-01

55

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

Microsoft Academic Search

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

Gederts Ievinsh

2007-01-01

56

The effect of changes in salinity on the energy yielding processes of Chlorella vulgaris and Dunaliella maritima cells  

Microsoft Academic Search

The unicellular green halotolerant microalga Dunaliella maritima grown in medium containing 500mM NaCl and the freshwater microalga Chlorella vulgaris were used as model systems to study adaptation of energy yielding mechanisms of cells in culture to changes in salinity.A microcalorimetric method was used to study the alteration of the heat production rate of microalgae depending on the salt content in

A. Ju. Alyabyev; N. L. Loseva; L. Kh. Gordon; I. N. Andreyeva; G. G. Rachimova; V. I. Tribunskih; A. A. Ponomareva; R. B. Kemp

2007-01-01

57

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

SciTech Connect

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.

Tomanicek, Stephen J.; Hughes, Ronny C.; Ng, Joseph D.; Coates, Leighton (UAH); (ORNL)

2010-10-05

58

The structure of the flexible arm of Thermotoga maritima tRNase Z differs from those of homologous enzymes  

PubMed Central

tRNA 3?-processing endoribonuclease (tRNase Z) is one of the enzymes involved in the 3?-end processing of precursor tRNAs and is a member of the metallo-?-lactamase superfamily. tRNase Z crystal structures have revealed that the enzyme forms a dimer and has a characteristic domain, named a flexible arm or an exosite, which protrudes from the metallo-?-lactamase core and is involved in tRNA binding. The refined structure of Thermotoga maritima tRNase Z has been determined at 1.97?Å resolution, revealing the structure of the flexible arm and the zinc-bound active site. The structure of the flexible arm of T. maritima tRNase Z is distinct from those of the Bacillus subtilis and Escherichia coli tRNase Zs. A comparison of the three tRNase Z structures revealed differences in the dimer orientation, which may be related to the unique cleavage-site specificity of T. maritima tRNase Z. PMID:17671357

Ishii, Ryohei; Minagawa, Asako; Takaku, Hiroaki; Takagi, Masamichi; Nashimoto, Masayuki; Yokoyama, Shigeyuki

2007-01-01

59

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

NASA Astrophysics Data System (ADS)

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.

Behbehani, Manaf I.; Croker, Robert A.

1982-12-01

60

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

PubMed

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

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

2014-10-01

61

Crystal Structure of Thermotoga maritima 0065, a Member of the IclR Transcriptional Factor Family*  

PubMed Central

Members of the IclR family of transcription regulators modulate signal-dependent expression of genes involved in carbon metabolism in bacteria and archaea. The Thermotoga maritima TM0065 gene codes for a protein (TM-IclR) that is homologous to the IclR family. We have determined the crystal structure of TM-IclR at 2.2 Å resolution using MAD phasing and synchrotron radiation. The protein is composed of two domains: the N-terminal DNA-binding domain contains the winged helix-turn-helix motif, and the C-terminal presumed regulatory domain is involved in binding signal molecule. In a proposed signal-binding site, a bound Zn2+ ion was found. In the crystal, TM-IclR forms a dimer through interactions between DNA-binding domains. In the dimer, the DNA-binding domains are 2-fold related, but the dimer is asymmetric with respect to the orientation of signal-binding domains. Crystal packing analysis showed that TM-IclR dimers form a tetramer through interactions exclusively by signal-binding domains. A model is proposed for binding of IclR-like factors to DNA, and it suggests that signal-dependent transcription regulation is accomplished by affecting an oligomerization state of IclR and therefore its affinity for DNA target. PMID:11877432

Zhang, Rong-guang; Kim, Youngchang; Skarina, Tatiana; Beasley, Steven; Laskowski, Roman; Arrowsmith, Cheryl; Edwards, Aled; Joachimiak, Andrzej; Savchenko, Alexei

2009-01-01

62

Improvement of the efficiency of transglycosylation catalyzed by ?-galactosidase from Thermotoga maritima by protein engineering.  

PubMed

At high concentrations of p-nitrophenyl-?-D-galactopyranoside (pNPGal) as a substrate, its hydrolysis catalyzed by ?-galactosidase from Thermotoga maritima (TmGalA) is accompanied by transglycosylation resulting in production of a mixture of (?1,2)-, (?1,3)-, and (?1,6)-p-nitrophenyl (pNP)-digalactosides. Molecular modeling of the reaction stage preceding the formation of the pNP-digalactosides within the active site of the enzyme revealed amino acid residues which modification was expected to increase the efficiency of transglycosylation. Upon the site-directed mutagenesis to the predicted substitutions of the amino acid residues, genes encoding the wild type TmGalA and its mutants were expressed in E. coli, and the corresponding enzymes were isolated and tested for the presence of the transglycosylating activity in synthesis of different pNP-digalactosides. Three mutants, F328A, P402D, and G385L, were shown to markedly increase the total transglycosylation as compared to the wild type enzyme. Moreover, the F328A mutant displayed an ability to produce a regio-isomer with the (?1,2)-bond at yield 16-times higher than the wild type TmGalA. PMID:24237145

Bobrov, K S; Borisova, A S; Eneyskaya, E V; Ivanen, D R; Shabalin, K A; Kulminskaya, A A; Rychkov, G N

2013-10-01

63

Functional characterization of the glycosyltransferase domain of penicillin-binding protein 1a from Thermotoga maritima.  

PubMed

Class A penicillin-binding proteins (A-PBPs) are high-molecular weight membrane-bound bifunctional enzymes that catalyze the penicillin-sensitive transpeptidation and transglycosylation reaction steps involved in peptidoglycan assembling. We have over-expressed and characterized a soluble form of the glycosyltransferase domain of PBP1a (GT-PBP1a*) from the hyperthermophilic bacteria Thermotoga maritima. GT-PBP1a* efficiently catalyses peptidoglycan biosynthesis, as shown using an in vitro biosynthetized dansylated-lipid II substrate and a HPLC-coupled assay, and is specifically inhibited by moenomycin. GT-PBP1a* tends to spontaneously aggregate in detergent-free solution, a feature that supports existence of a secondary site for membrane association, distinct from the N-terminal transmembrane anchoring region. Overall, our preliminary data document the biochemical properties of GT-PBP1a* and should guide further studies aimed at deciphering the structural determinants involved into membrane binding by this class of enzymes. PMID:16725395

Offant, Julien; Michoux, François; Dermiaux, Annabelle; Biton, Jacques; Bourne, Yves

2006-06-01

64

Structure of a Diguanylate Cyclase from Thermotoga maritima: Insights into Activation, Feedback Inhibition and Thermostability  

PubMed Central

Large-scale production of bis-3?-5?-cyclic-di-GMP (c-di-GMP) would facilitate biological studies of numerous bacterial signaling pathways and phenotypes controlled by this second messenger molecule, such as virulence and biofilm formation. C-di-GMP constitutes also a potentially interesting molecule as a vaccine adjuvant. Even though chemical synthesis of c-di-GMP can be done, the yields are incompatible with mass-production. tDGC, a stand-alone diguanylate cyclase (DGC or GGDEF domain) from Thermotoga maritima, enables the robust enzymatic production of large quantities of c-di-GMP. To understand the structural correlates of tDGC thermostability, its catalytic mechanism and feedback inhibition, we determined structures of an active-like dimeric conformation with both active (A) sites facing each other and of an inactive dimeric conformation, locked by c-di-GMP bound at the inhibitory (I) site. We also report the structure of a single mutant of tDGC, with the R158A mutation at the I-site, abolishing product inhibition and unproductive dimerization. A comparison with structurally characterized DGC homologues from mesophiles reveals the presence of a higher number of salt bridges in the hyperthermophile enzyme tDGC. Denaturation experiments of mutants disrupting in turn each of the salt bridges unique to tDGC identified three salt-bridges critical to confer thermostability. PMID:25360685

Deepthi, Angeline; Liew, Chong Wai; Liang, Zhao-Xun; Swaminathan, Kunchithapadam; Lescar, Julien

2014-01-01

65

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

PubMed Central

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

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

2013-01-01

66

In the absence of thioredoxins, what are the reductants for peroxiredoxins in Thermotoga maritima?  

PubMed

Three peroxiredoxins (Prxs) were identified in Thermotoga maritima, which possesses neither glutathione nor typical thioredoxins: one of the Prx6 class; one 2-Cys PrxBCP; and a unique hybrid protein containing an N-terminal 1-Cys PrxBCP domain fused to a flavin mononucleotide-containing nitroreductase (Ntr) domain. No peroxidase activity was detected for Prx6, whereas both bacterioferritin comigratory proteins (BCPs) were regenerated by a NADH/thioredoxin reductase/glutaredoxin (Grx)-like system, constituting a unique peroxide removal system. Only two of the three Grx-like proteins were able to support peroxidase activity. The inability of TmGrx1 to regenerate oxidized 2-Cys PrxBCP probably results from the thermodynamically unfavorable difference in their disulfide/dithiol E(m) values, -150 and -315 mV, respectively. Mutagenesis of the Prx-Ntr fusion, combined with kinetic and structural analyses, indicated that electrons are not transferred between its two domains. However, their separate activities could function in a complementary manner, with peroxide originating from the chromate reductase activity of the Ntr domain reduced by the Prx domain. PMID:22866991

Couturier, Jérémy; Prosper, Pascalita; Winger, Alison M; Hecker, Arnaud; Hirasawa, Masakazu; Knaff, David B; Gans, Pierre; Jacquot, Jean-Pierre; Navaza, Alda; Haouz, Ahmed; Rouhier, Nicolas

2013-05-01

67

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

PubMed

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

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

2012-02-01

68

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

PubMed Central

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

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

2010-01-01

69

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

SciTech Connect

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.

Morar, Mariya; Anand, Ruchi; Hoskins, Aaron A.; Stubbe, JoAnne; Ealick, Steven E. (MIT); (Cornell)

2008-09-11

70

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

PubMed Central

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

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

2012-01-01

71

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

SciTech Connect

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.

Morar, Mariya; Hoskins, Aaron A.; Stubbe, JoAnne; Ealick, Steven E. (MIT); (Cornell)

2008-10-02

72

Ethanolic crude extract and flavonoids isolated from Alternanthera maritima: neutrophil chemiluminescence inhibition and free radical scavenging activity.  

PubMed

Extracts from Alternanthera maritima are used in Brazilian folk medicine for the treatment of infectious and inflammatory diseases. Bioassay-guided fractionation of A. maritima aerial parts yielded an ethanolic crude extract, its butanolic fraction and seven isolated flavonoids (two aglycones, two O-glycosides and three C-glycosides) with antioxidative activity. The ability of these samples to scavenge enzymatically generated free radicals (luminol-horseradish peroxidase-H2O2 reaction) and inhibit reactive oxygen species (ROS) production by opsonized zymosan-stimulated human neutrophils (PMNLs) was evaluated by chemiluminescence methods. In both assays, the butanolic fraction was significantly more active than the ethanolic crude extract, the flavonoid aglycones had high inhibitory activities and the C-glycosylated flavonoids had no significant effect even at the highest concentration tested (50 micromol/L). However, the O-glycosylated flavonoids inhibitory effects on chemiluminescence were strongly dependent on the chemical structure and assay type (cellular or cell-free system). Under the conditions tested, active samples were not toxic to human PMNLs. PMID:17708437

Souza, Joel G; Tomei, Rafael R; Kanashiro, Alexandre; Kabeya, Luciana M; Azzolini, Ana Elisa C S; Dias, Diones A; Salvador, Marcos J; Lucisano-Valim, Yara M

2007-01-01

73

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

PubMed

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. PMID:21702225

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

2011-06-01

74

Selenium Accumulation in Submerged Aquatic Macrophytes Potamogeton pectinatus L. and Ruppia maritima L. from Water with Elevated Chloride and Sulfate Salinity  

Microsoft Academic Search

Submerged aquatic macrophyte species Potamogeton crispus L. (curlyleaf pondweed) and Ruppia maritima L. (widegeongrass) were examined for selenium accumulation from agricultural drainage water in the field and under laboratory conditions. High concentrations of chloride and sulfate salts were found in the drainage water of the constructed wetland at Tulare Lake Drainage District, Corcorn, California. Samples of P. crispus and R.

Lin Wu; Xun Guo

2002-01-01

75

Selenium accumulation in submerged aquatic macrophytes Potamogeton pectinatus L. and Ruppia maritima L. from water with elevated chloride and sulfate salinity.  

PubMed

Submerged aquatic macrophyte species Potamogeton crispus L. (curlyleaf pondweed) and Ruppia maritima L. (widegeongrass) were examined for selenium accumulation from agricultural drainage water in the field and under laboratory conditions. High concentrations of chloride and sulfate salts were found in the drainage water of the constructed wetland at Tulare Lake Drainage District, Corcorn, California. Samples of P. crispus and R. maritima collected from the field, had similar plant-tissue Se concentrations, but the rhizomes accumulated significantly greater amounts of Se than the shoot tissues. When the plants were grown in culture solution supplemented with either chloride or sulfate salt, R. maritima was found to be more salt tolerant than P. crispus, and P. crispus accumulated more Se than R. maritima. Free seleno-amino acids were detected in the plant tissue, and organic Se was detected in the culture solution after 10 days of growth. The release of organic Se into the water by the plants may have a negative impact on the wetland environment. PMID:11800546

Wu, Lin; Guo, Xun

2002-01-01

76

THE [Fe-Fe]-HYDROGENASE MATURATION PROTEIN HydF FROM Thermotoga maritima IS A GTPase WITH AN IRON-SULFUR CLUSTER  

E-print Network

1 THE [Fe-Fe]-HYDROGENASE MATURATION PROTEIN HydF FROM Thermotoga maritima IS A GTPase WITH AN IRON-SULFUR-Fe]-hydrogenases (1), [Fe-Fe]-hydrogenases (2,3) and "Iron-Sulfur cluster- free" hydrogenase (4,5,6), which do for activity (10). Infrared spectroscopy studies have also demonstrated the presence of CO ligands in the "Iron-Sulfur

Paris-Sud XI, Université de

77

Properties and gene structure of the Thermotoga maritima alpha-amylase AmyA, a putative lipoprotein of a hyperthermophilic bacterium.  

PubMed Central

Thermotoga maritima MSB8 has a chromosomal alpha-amylase gene, designated amyA, that is predicted to code for a 553-amino-acid preprotein with significant amino acid sequence similarity to the 4-alpha-glucanotransferase of the same strain and to alpha-amylase primary structures of other organisms. Upstream of the amylase gene, a divergently oriented open reading frame which can be translated into a polypeptide with similarity to the maltose-binding protein MalE of Escherichia coli was found. The T. maritima alpha-amylase appears to be the first known example of a lipoprotein alpha-amylase. This is in agreement with observations pointing to the membrane localization of this enzyme in T. maritima. Following the signal peptide, a 25-residue putative linker sequence rich in serine and threonine was found. The amylase gene was expressed in E. coli, and the recombinant enzyme was purified and characterized. The molecular mass of the recombinant enzyme was estimated at 61 kDa by denaturing gel electrophoresis (63 kDa by gel permeation chromatography). In a 10-min assay at the optimum pH of 7.0, the optimum temperature of amylase activity was 85 to 90 degrees C. Like the alpha-amylases of many other organisms, the activity of the T. maritima alpha-amylase was dependent on Ca2+. The final products of hydrolysis of soluble starch and amylose were mainly glucose and maltose. The extraordinarily high specific activity of the T. maritima alpha-amylase (about 5.6 x 10(3) U/mg of protein at 80 degrees C, pH 7, with amylose as the substrate) together with its extreme thermal stability makes this enzyme an interesting candidate for biotechnological applications in the starch processing industry. PMID:9006052

Liebl, W; Stemplinger, I; Ruile, P

1997-01-01

78

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

NASA Astrophysics Data System (ADS)

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

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

1999-07-01

79

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

SciTech Connect

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

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

2004-01-01

80

Crystallization and preliminary X-ray diffraction analysis of the S-adenosylhomocysteine hydrolase (SAHH) from Thermotoga maritima.  

PubMed

S-Adenosylhomocysteine hydrolase (SAHH) catalyzes the reversible conversion of S-adenosylhomocysteine into adenosine and homocysteine. The SAHH from Thermotoga maritima (TmSAHH) was expressed in Escherichia coli and the recombinant protein was purified and crystallized. TmSAHH crystals belonging to space group C2, with unit-cell parameters a = 106.3, b = 112.0, c = 164.9?Å, ? = 103.5°, were obtained by the sitting-drop vapour-diffusion method and diffracted to 2.85?Å resolution. Initial phase determination by molecular replacement clearly indicated that the crystal contains one homotetramer per asymmetric unit. Further refinement of the crystal structure is in progress. PMID:25372832

He, Miao; Zheng, Yingying; Huang, Chun Hsiang; Qian, Guojun; Xiao, Xiansha; Ko, Tzu Ping; Shao, Weilan; Guo, Rey Ting

2014-11-01

81

Emergence of gynodioecy in wild beet (Beta vulgaris ssp. maritima L.): a genealogical approach using chloroplastic nucleotide sequences  

PubMed Central

Gynodioecy is a breeding system where both hermaphroditic and female individuals coexist within plant populations. This dimorphism is the result of a genomic interaction between maternally inherited cytoplasmic male sterility (CMS) genes and bi-parentally inherited nuclear male fertility restorers. As opposed to other gynodioecious species, where every cytoplasm seems to be associated with male sterility, wild beet Beta vulgaris ssp. maritima exhibits a minority of sterilizing cytoplasms among numerous non-sterilizing ones. Many studies on population genetics have explored the molecular diversity of different CMS cytoplasms, but questions remain concerning their evolutionary dynamics. In this paper we report one of the first investigations on phylogenetic relationships between CMS and non-CMS lineages. We investigated the phylogenetic relationships between 35 individuals exhibiting different mitochondrial haplotypes. Relying on the high linkage disequilibrium between chloroplastic and mitochondrial genomes, we chose to analyse the nucleotide sequence diversity of three chloroplastic fragments (trnK intron, trnD–trnT and trnL–trnF intergenic spacers). Nucleotide diversity appeared to be low, suggesting a recent bottleneck during the evolutionary history of B. vulgaris ssp. maritima. Statistical parsimony analyses revealed a star-like genealogy and showed that sterilizing haplotypes all belong to different lineages derived from an ancestral non-sterilizing cytoplasm. These results suggest a rapid evolution of male sterility in this taxon. The emergence of gynodioecy in wild beet is confronted with theoretical expectations, describing either gynodioecy dynamics as the maintenance of CMS factors through balancing selection or as a constant turnover of new CMSs. PMID:16777728

Fenart, Stephane; Touzet, Pascal; Arnaud, Jean-Francois; Cuguen, Joel

2006-01-01

82

The elucidation of the structure of Thermotoga maritima peptidoglycan reveals two novel types of cross-link.  

PubMed

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

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

2009-08-14

83

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

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

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

2013-06-01

84

Periplasmic Binding Proteins in Thermophiles: Characterization and Potential Application of an Arginine-Binding Protein from Thermotoga maritima: A Brief Thermo-Story  

PubMed Central

Arginine-binding protein from the extremophile Thermotoga maritima is a 27.7 kDa protein possessing the typical two-domain structure of the periplasmic binding proteins family. The protein is characterized by a very high specificity and affinity to bind to arginine, also at high temperatures. Due to its features, this protein could be taken into account as a potential candidate for the design of a biosensor for arginine. It is important to investigate the stability of proteins when they are used for biotechnological applications. In this article, we review the structural and functional features of an arginine-binding protein from the extremophile Thermotoga maritima with a particular eye on its potential biotechnological applications.

Ausili, Alessio; Staiano, Maria; Dattelbaum, Jonathan; Varriale, Antonio; Capo, Alessandro; D'Auria, Sabato

2013-01-01

85

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

Microsoft Academic Search

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

Jan Nadwodnik; Gertrud Lohaus

2008-01-01

86

Prevention of Selenite-Induced Cataractogenesis by an Ethanolic Extract of Cineraria maritima : An Experimental Evaluation of the Traditional Eye Medication  

Microsoft Academic Search

In the present study, the antioxidant potential of an ethanolic extract of Cineraria maritima and its efficacy in preventing selenite-induced cataractogenesis were assessed in vitro and in vivo. In the in vitro phase\\u000a of the study, lenses dissected out from the eyes of Wistar rats were incubated for 24 h at 37°C in Dulbecco’s modified Eagle\\u000a medium (DMEM) alone (group I),

Thirugnanasambandhar Sivasubramanian Anitha; Thangaraj Annadurai; Philip A. Thomas; Pitchairaj Geraldine

87

Transglycosylation reaction of xylanase B from the hyperthermophilic Thermotoga maritima with the ability of synthesis of tertiary alkyl ?- d-xylobiosides and xylosides  

Microsoft Academic Search

The recombinant xylanase B (XynB) of Thermotoga maritima MSB8 was characterized and was found to cleave p-nitrophenyl ?-d-xyloside via the transglycosylation reaction in the previous study. XynB was activated in the presence of alcohols, and XynB activity was increased by iso-propanol (2M) to 2.1-fold. This type of activation was investigated and was shown to be due to the transglycosylation activity

Zhengqiang Jiang; Yunping Zhu; Lite Li; Xiaohong Yu; Isao Kusakabe; Motomistu Kitaoka; Kiyoshi Hayashi

2004-01-01

88

Phylogenetic depth of Thermotoga maritima inferred from analysis of the fus gene: Amino acid sequence of elongation factor G and organization of the Thermotoga str operon  

Microsoft Academic Search

Summary The gene (fus) coding for elongation factor G (EF-G) of the extremely thermophilic eubacteriumThermotoga maritima was identified and sequenced. The EF-G coding sequence (2046 bp) was found to lie in an operon-like structure between the ribosomal protein S7 gene (rpsG) and the elongation factor Tu (EF-Tu) gene (tuf). TherpsG, fus, andtuf genes follow each other immediately in that order,

Orsola Tiboni; Rita Cantoni; Roberta Creti; Piero Cammarano; Anna Maria Sanangelantoni

1991-01-01

89

High-resolution X-ray structure of the DNA-binding protein HU from the hyper-thermophilic Thermotoga maritima and the determinants of its thermostability  

Microsoft Academic Search

The histone-like DNA-binding proteins (HU) are a convenient model for studying factors affecting thermostability because of their relatively simple, easily comparable structures, their common function, and their presence in organisms of widely differing thermostability. We report the determination of the high-resolution structure (1.53 Å) at 273 K and 100 K of the HU protein from the hyper-thermophilic eubacterium Thermotoga maritima

Evangelos Christodoulou; Wojciech R. Rypniewski; Constantinos E. Vorgias

2003-01-01

90

Nutritional and biological qualities of the ripened beans of Canavalia maritima from the coastal sand dunes of India.  

PubMed

Raw and pressure-cooked ripened beans of Canavalia maritima were assessed for nutritional quality. The beans possess high protein, carbohydrate, fiber and energy contents. Potassium, magnesium, zinc and manganese of the raw and cooked beans meet NRC/NAS recommended pattern for infants. The essential amino acids (threonine, valine, isoleucine, leucine, tyrosine/phenylalanine and lysine) in raw and cooked ripened beans fulfill the FAO/WHO/UNU recommended pattern for adults. Oleic acid in raw beans and linolenic acid in cooked beans were highest and linoleic and arachidonic acids were confined to raw beans. Cooking lowered the total phenolics, while tannins were negligible and devoid of orthodihydric phenols and trypsin inhibitors. Hemagglutinating activity decreased up to 50% in cooked beans. Rats fed with a pressure-cooked bean diet showed significant elevation of all growth and nitrogen balance parameters (P<0.05) than the rats which received the raw bean diet. The low protein quality of beans warrants appropriate thermal processing to eliminate antinutritional factors. PMID:19200923

Bhagya, B; Sridhar, K R; Raviraja, N S; Young, C-C; Arun, A B

2009-01-01

91

Structure of a D-tagatose 3-epimerase-related protein from the hyperthermophilic bacterium Thermotoga maritima.  

PubMed

The crystal structure of a D-tagatose 3-epimerase-related protein (TM0416p) encoded by the hypothetical open reading frame TM0416 in the genome of the hyperthermophilic bacterium Thermotoga maritima was determined at a resolution of 2.2 A. The asymmetric unit contained two homologous subunits and a dimer was generated by twofold symmetry. The main-chain coordinates of the enzyme monomer proved to be similar to those of D-tagatose 3-epimerase from Pseudomonas cichorii and D-psicose 3-epimerase from Agrobacterium tumefaciens; however, TM0416p exhibited a unique solvent-accessible substrate-binding pocket that reflected the absence of an alpha-helix that covers the active-site cleft in the two aforementioned ketohexose 3-epimerases. In addition, the residues responsible for creating a hydrophobic environment around the substrate in TM0416p differ entirely from those in the other two enzymes. Collectively, these findings suggest that the substrate specificity of TM0416p is likely to differ substantially from those of other D-tagatose 3-epimerase family enzymes. PMID:19255464

Sakuraba, Haruhiko; Yoneda, Kazunari; Satomura, Takenori; Kawakami, Ryushi; Ohshima, Toshihisa

2009-03-01

92

Structure of a d-tagatose 3-epimerase-related protein from the hyperthermophilic bacterium Thermotoga maritima  

PubMed Central

The crystal structure of a d-tagatose 3-epimerase-related protein (TM0416p) encoded by the hypothetical open reading frame TM0416 in the genome of the hyperthermophilic bacterium Thermotoga maritima was determined at a resolution of 2.2?Å. The asymmetric unit contained two homologous subunits and a dimer was generated by twofold symmetry. The main-chain coordinates of the enzyme monomer proved to be similar to those of d-tagatose 3-­epimerase from Pseudomonas cichorii and d-psicose 3-epimerase from Agrobacterium tumefaciens; however, TM0416p exhibited a unique solvent-accessible substrate-binding pocket that reflected the absence of an ?-helix that covers the active-site cleft in the two aforementioned ketohexose 3-epimerases. In addition, the residues responsible for creating a hydrophobic environment around the substrate in TM0416p differ entirely from those in the other two enzymes. Collectively, these findings suggest that the substrate specificity of TM0416p is likely to differ substantially from those of other d-tagatose 3-­epimerase family enzymes. PMID:19255464

Sakuraba, Haruhiko; Yoneda, Kazunari; Satomura, Takenori; Kawakami, Ryushi; Ohshima, Toshihisa

2009-01-01

93

The spatial structure of sexual and cytonuclear polymorphism in the gynodioecious Beta vulgaris ssp. maritima: I/ at a local scale.  

PubMed Central

We have analyzed the spatial distribution of the sex phenotypes and of mitochondrial, chloroplast, and nuclear markers within two gynodioecious populations of Beta vulgaris ssp. maritima. Within both populations, sexual phenotype variation is controlled mainly by the cytoplasmic genotype, although in one study population a joint polymorphism of cytonuclear factors is clearly involved. In spite of contrasts in the ecology (mainly due to different habitats), a clear common feature in both populations is the highly patchy distribution of cytoplasmic haplotypes, contrasting with the wide distribution of nuclear diversity. This high contrast between cytoplasmic vs. nuclear spatial structure may have important consequences for the maintenance of gynodioecy. It provides opportunities for differential selection since nuclear restorer alleles are expected to be selected for in the presence of their specific cytoplasmic male sterile (CMS) type, but to be neutral (or selected against if there is a cost of restoration) in the absence of their CMS type. Selective processes in such a cytonuclear landscape may explain the polymorphism we observed at restorer loci for two CMS types. PMID:11290724

Laporte, V; Viard, F; Bena, G; Valero, M; Cuguen, J

2001-01-01

94

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

PubMed Central

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

ISNARD, SANDRINE; ROWE, NICK; SPECK, THOMAS

2003-01-01

95

Stationary phase and nutrient levels trigger transcription of a genomic locus containing a novel peptide (TM1316) in the hyperthermophilic bacterium Thermotoga maritima.  

PubMed

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

Frock, Andrew D; Montero, Clemente I; Blumer-Schuette, Sara E; Kelly, Robert M

2013-11-01

96

Evaluation of the protective potential of Artemisia maritima extract on acetaminophen- and CCl4-induced liver damage.  

PubMed

The hepatoprotective activity of the aqueous-methanolic extract of Artemisia maritima was investigated against acetaminophen (paracetamol, 4-hydroxy acetanilide)- and carbon tetrachloride (CCl4)-induced hepatic damage. Acetaminophen produced 100% mortality at the dose of 1 g/kg in mice, while pretreatment of animals with the plant extract (500 mg/kg) reduced the death rate to 20%. Acetaminophen at the dose of 640 mg/kg produced liver damage in rats as manifested by the significant (P < 0.001) rise in serum levels of glutamate oxaloacetate transaminase (GOT) and glutamate pyruvate transaminase (GPT) to 1529 +/- 172 I.U./l and 904 +/- 116 I.U./l (n = 10), respectively, compared to respective control values of 87 +/- 12 I.U./l and 31 +/- 5 I.U./l. Pretreatment of rats with the plant extract (500 mg/kg) lowered significantly (P < 0.001) the respective serum GOT and GPT levels to 112 +/- 10 I.U./l and 47 +/- 11 I.U./l. Similarly, a hepatotoxic dose of CCl4 (1.5 ml/kg, orally) raised significantly (P < 0.01) the serum GOT and GPT levels to 463 +/- 122 I.U./l and 366 +/- 58 I.U./l (n = 10), respectively, compared to respective control values of 92 +/- 18 I.U./l and 35 +/- 9 I.U./l. The same dose of plant extract (500 mg/kg) was able to prevent significantly (P < 0.01) the CCl4-induced rise in serum transaminases and the estimated values of GOT and GPT were 105 +/- 29 I.U./l and 53 +/- 17 I.U./l, respectively. Moreover, it prevented CCl4-induced prolongation in pentobarbital sleeping time confirming hepatoprotectivity and validates the traditional use of this plant against liver damage. PMID:7564420

Janbaz, K H; Gilani, A H

1995-06-23

97

Characterization of Multi-Functional Properties and Conformational Analysis of MutS2 from Thermotoga maritima MSB8  

PubMed Central

The MutS2 homologues have received attention because of their unusual activities that differ from those of MutS. In this work, we report on the functional characteristics and conformational diversities of Thermotoga maritima MutS2 (TmMutS2). Various biochemical features of the protein were demonstrated via diverse techniques such as scanning probe microscopy (SPM), ATPase assays, analytical ultracentrifugation, DNA binding assays, size chromatography, and limited proteolytic analysis. Dimeric TmMutS2 showed the temperature-dependent ATPase activity. The non-specific nicking endonuclease activities of TmMutS2 were inactivated in the presence of nonhydrolytic ATP (ADPnP) and enhanced by the addition of TmMutL. In addition, TmMutS2 suppressed the TmRecA-mediated DNA strand exchange reaction in a TmMutL-dependent manner. We also demonstrated that small-angle X-ray scattering (SAXS) analysis of dimeric TmMutS2 exhibited nucleotide- and DNA-dependent conformational transitions. Particularly, TmMutS2-ADPnP showed the most compressed form rather than apo-TmMutS2 and the TmMutS2-ADP complex, in accordance with the results of biochemical assays. In the case of the DNA-binding complexes, the stretched conformation appeared in the TmMutS2-four-way junction (FWJ)-DNA complex. Convergences of biochemical- and SAXS analysis provided abundant information for TmMutS2 and clarified ambiguous experimental results. PMID:22545085

Ban, Changill

2012-01-01

98

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

NASA Astrophysics Data System (ADS)

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

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

1985-12-01

99

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

SciTech Connect

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.

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

2009-04-01

100

Characterization of exceptionally thermostable single-stranded DNA-binding proteins from Thermotoga maritima and Thermotoga neapolitana  

PubMed Central

Background In recent years, there has been an increasing interest in SSBs because they find numerous applications in diverse molecular biology and analytical methods. Results We report the characterization of single-stranded DNA binding proteins (SSBs) from the thermophilic bacteria Thermotoga maritima (TmaSSB) and Thermotoga neapolitana (TneSSB). They are the smallest known bacterial SSB proteins, consisting of 141 and 142 amino acid residues with a calculated molecular mass of 16.30 and 16.58 kDa, respectively. The similarity between amino acid sequences of these proteins is very high: 90% identity and 95% similarity. Surprisingly, both TmaSSB and TneSSB possess a quite low sequence similarity to Escherichia coli SSB (36 and 35% identity, 55 and 56% similarity, respectively). They are functional as homotetramers containing one single-stranded DNA binding domain (OB-fold) in each monomer. Agarose mobility assays indicated that the ssDNA-binding site for both proteins is salt independent, and fluorescence spectroscopy resulted in a size of 68 ± 2 nucleotides. The half-lives of TmaSSB and TneSSB were 10 h and 12 h at 100°C, respectively. When analysed by differential scanning microcalorimetry (DSC) the melting temperature (Tm) was 109.3°C and 112.5°C for TmaSSB and TneSSB, respectively. Conclusion The results showed that TmaSSB and TneSSB are the most thermostable SSB proteins identified to date, offering an attractive alternative to TaqSSB and TthSSB in molecular biology applications, especially with using high temperature e. g. polymerase chain reaction (PCR). PMID:20950419

2010-01-01

101

Historical biogeography in a linear system: genetic variation of sea rocket (Cakile maritima) and sea holly (Eryngium maritimum) along European coasts.  

PubMed

The exclusively coastal Cakile maritima and Eryngium maritimum represent a linear biogeographical system. Genetic variation among 25 individuals of C. maritima and 16 individuals of E. maritimum, from the coasts of Europe, North Africa and the Canary Islands, was analysed using random amplified polymorphic DNAs (RAPDs) and intersimple sequence repeats (ISSRs). Genetic distances (Dice) were calculated and used to investigate the correlation between genetic and geographical distances, to construct Neighbour Joining (NJ) trees, and to compare mean genetic distances between areas within and across species. Genetic distances and geographical distances measured along the coast are well correlated in Cakile and Eryngium. This implies that dispersal in both species is largely along the coast. The NJ analyses resulted in the recognition of Atlantic and Mediterranean clusters in both Cakile and Eryngium. The genetic distance between these two clusters is much larger in Eryngium (0. 285) than in Cakile (0.037). Mean genetic distances are substantially higher in the Mediterranean than in the Atlantic clusters in both species, and higher in Cakile than in Eryngium particularly in the Atlantic cluster. It is argued that all similarities and differences between the two species can be explained with the presumed distribution of the two species in the Würm glacial as reconstructed from their extant temperature requirements, the distribution of ice cover, permafrost, and sea surface temperatures in that period, and indirect fossil evidence. PMID:11091318

Clausing, G; Vickers, K; Kadereit, J W

2000-11-01

102

Understanding the population genetic structure of coastal species (Cakile maritima): seed dispersal and the role of sea currents in determining population structure.  

PubMed

The nature and extent of long-distance seed dispersal are currently poorly understood, largely due to the inherent difficulty in detecting such a phenomenon. Genetic methods provide one of the few general approaches that offer the potential to accurately address this issue. Phenotypic and allozymic approaches were applied to characterize inter-population seed dispersal of the sea rocket (Cakile maritima, Brassicaceae), a glabrous and succulent annual herb. Genetic variation was assessed on 360 individuals sampled from nine populations. Genetic diversity across populations was high, 37% of which was represented by Qst and 16% by Fst. When genetic distances were used to construct the UPGMA dendrogram, populations were clustered into three groups at the 90% similarity level. The pattern of clustering can be explained by examining the direction of sea currents around Tunisian coasts. We have shown in this study that C. maritima seeds can survive up to 4 months immersion in sea water and up to 1 year of floating in sea water; therefore, seed dispersal between populations is possible both in terms of seed survival and current patterns. PMID:18426620

Gandour, Mhemmed; Hessini, Kamel; Abdelly, Chedly

2008-04-01

103

A thermostable S-adenosylhomocysteine hydrolase from Thermotoga maritima: Properties and its application on S-adenosylhomocysteine production with enzymatic cofactor regeneration.  

PubMed

S-adenosylhomocysteine (SAH) is an effective sedative, a good sleep modulator, and a new anticonvulsant. SAH can be synthesized from adenosine and homocysteine by using microbial S-adenosylhomocysteine hydrolase (SAHase). The extremely thermostable SAHase and lactate dehydrogenase (LDH) from Thermotoga maritima were successfully overexpressed in Escherichia coli, and purified by heat treatments. The SAHase exhibited the highest activity at 85°C and pH 8.0 with a specific activity of 6.2U/mg when NAD concentration was 1mM. However, optimal SAHase reaction conditions shifted to 100°C and pH 11.2, and its specific activity increased to 36.8U/mg after NAD concentration was raised to 8mM. Biosynthesis of SAH at 85°C largely increased the adenosine solubility which was a limiting factor for improving the titer of product. At 85°C and pH 8.0, 24?mol of SAH was obtained when 0.5mg of SAHase was applied to a 10ml reaction mixture. The SAH production was further increased to 153?mol by adding LDH and pyruvate into the reaction mixture for NAD regeneration. Therefore, extremely thermostable enzymes SAHase and LDH from T. maritima form an efficient NAD consumption and regeneration system for SAH biosynthesis. This method has great potential for industrial-scale enzymatic production of SAH. PMID:25152414

Qian, Guojun; Chen, Caiping; Zhou, Rong; He, Yanbin; Shao, Weilan

2014-10-01

104

Salt tolerance in the halophyte Suaeda maritima L. Dum. : The maintenance of turgor pressure and water-potential gradients in plants growing at different salinities.  

PubMed

Osmotic potentials and individual epidermal cell turgor pressures were measured in the leaves of seedlings of Suaeda maritima growing over a range of salinities. Leaf osmotic potentials were lower (more negative) the higher the salt concentration of the solution and were lowest in the youngest leaves and stem apices, producing a gradient of osmotic potential towards the apex of the plant. Epidermal cell turgor pressures were of the order of 0.25 to 0.3 MPa in the youngest leaves measured, decreasing to under 0.05 MPa for the oldest leaves. This pattern of turgor pressure was largely unaffected by external salinity. Calculation of leaf water potential indicated that the gradient between young leaves and the external medium was not altered by salinity, but with older leaves, however, this gradient diminished from being the same as that for young leaves in the absence of NaCl, to under 30% of this value at 400 mM NaCl. These results are discussed in relation to the growth response of S. maritima. PMID:24241145

Clipson, N J; Tomos, A D; Flowers, T J; Jones, R G

1985-08-01

105

The characterization of Thermotoga maritima ferritin reveals an unusual subunit dissociation behavior and efficient DNA protection from iron-mediated oxidative stress.  

PubMed

Ferritin from the hyperthermophilic anaerobe Thermotoga maritima, a bacterium of ancient phylogenetic origin, is structurally similar to known bacterial and eukaryotic ferritins: 24 identical subunits assemble into a shell having octahedral symmetry and a Mr of about 460 kDa. T. maritima ferritin (TmFtn), purified to homogeneity as a recombinant protein, contains approximately 2-3 iron atoms and can incorporate efficiently up to 3,500 atoms in the form of a ferric oxy-hydroxide mineral at 80°C, the optimal growth temperature of the bacterium. The 24-mer unexpectedly dissociates reversibly into dimers at low ionic strengths. In turn, dimers re-associate into the native 24-mer assembly at high protein concentrations and upon incorporation of iron micelles containing at least 500 Fe(III). TmFtn uses O(2) as efficient iron oxidant. The reaction stoichiometry is 3-4 O(2):Fe(II) as in all bacterial ferritins. Accordingly no H(2)O(2) is released into solution, a feature reflected in the in vitro ability of TmFtn to reduce significantly iron-mediated oxidative damage to DNA at 80°C. A similar TmFtn-mediated ROS detoxifying role likely occurs in the bacterium which lacks the SOD/catalase defense systems of the aerobic world. PMID:21487935

Ceci, Pierpaolo; Forte, Elena; Di Cecca, Gisa; Fornara, Manuela; Chiancone, Emilia

2011-05-01

106

Enhanced catalytic efficiency in quercetin-4'-glucoside hydrolysis of Thermotoga maritima ?-glucosidase A by site-directed mutagenesis.  

PubMed

Te-BglA and Tm-BglA are glycoside hydrolase family 1 ?-glucosidases from Thermoanaerobacter ethanolicus JW200 and Thermotoga maritima, respectively, with 53% sequence identity. However, Te-BglA could more effectively hydrolyze isoflavone glucosides to their aglycones than could Tm-BglA, possibly due to the difference in amino acid residues around their glycone binding pockets. Site-directed mutagenesis was used to replace the amino acid residues of Tm-BglA with the corresponding residues of Te-BglA, generating three single mutants (F221L, N223L, and G224T), as well as the corresponding three double mutants (F221L/N223L, F221L/G224T, and N223L/G224T) and one triple mutant (F221L/N223L/G224T). The seven mutants have been purified, characterized, and compared to the wild-type Tm-BglA. The effects of the mutations on kinetics, enzyme activity, and substrate specificity were determined. All mutants showed pH-activity curves narrower on the basic side and wider on the acid side and had similar optimal pH and stability at pH 6.5-8.3. They were more stable up to 85 °C, but G224T displayed higher optimal temperature than Tm-BglA. Seven mutants indicated an obvious increase in catalytic efficiency toward p-nitrophenyl ?-D-glucopyranoside (pNPG) but an increase or not change in K(m). All mutants showed a decrease in catalytic efficiency of isoflavonoid glycosides and were not changed for F221L and lost for N223L in enzymatic hydrolysis on quercetin glucosides. Contrarily, G224T resulted in a dramatic increase conversion of Q4' (35.5%) and Q3,4' (28.6%) in accord with an increased turnover number (k(cat), 1.4×) and catalytic efficiency (k(cat)/K(m), 2.2×) as well as a decrease in K(m) (0.24) for Q4'. Modeling showed that G224T mutation at position 224 may enhance the interaction between G224T and 5-OH and 3-OH on the quercetin backbone of Q4'. PMID:24933681

Sun, Huihui; Xue, Yemin; Lin, Yufei

2014-07-16

107

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

PubMed Central

Adenosine triphosphate (ATP) binding cassette transporters (ABC transporters) are ATP hydrolysis-dependent transmembrane transporters. Here, the overproduction, purification and crystallization of the putative ABC transporter ATP-binding protein TM0222 from Thermotoga maritima are reported. The protein was crystallized in the hexagonal space group P6422, with unit-cell parameters a = b = 148.49, c = 106.96?Å, ? = 120.0°. Assuming the presence of two molecules in the asymmetric unit, the calculated V M is 2.84?Å3?Da?1, which corresponds to a solvent content of 56.6%. A three-wavelength MAD data set was collected to 2.3?Å resolution from SeMet-substituted TM0222 crystals. Data sets were collected on the BL38B1 beamline at SPring-8, Japan. PMID:18540059

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

2008-01-01

108

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

PubMed Central

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

Sahu, Binod B; Shaw, Birendra P

2009-01-01

109

Phylogenetic depth of Thermotoga maritima inferred from analysis of the fus gene: amino acid sequence of elongation factor G and organization of the Thermotoga str operon.  

PubMed

The gene (fus) coding for elongation factor G (EF-G) of the extremely thermophilic eubacterium Thermotoga maritima was identified and sequenced. The EF-G coding sequence (2046 bp) was found to lie in an operon-like structure between the ribosomal protein S7 gene (rpsG) and the elongation factor Tu (EF-Tu) gene (tuf). The rpsG, fus, and tuf genes follow each other immediately in that order, which corresponds to the order of the homologous genes in the str operon of Escherichia coli. The derived amino acid sequence of the EF-G protein (682 residues) was aligned with the homologous sequences of other eubacteria, eukaryotes (hamster), and archaebacteria (Methanococcus vannielii). Unrooted phylogenetic dendrograms, obtained both from the amino acid and the nucleotide sequence alignments, using a variety of methods, lend further support to the notion that the (present) root of the (eu)bacterial tree lies between Thermotoga and the other bacterial lineages. PMID:1920450

Tiboni, O; Cantoni, R; Creti, R; Cammarano, P; Sanangelantoni, A M

1991-08-01

110

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

PubMed

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

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

2008-01-01

111

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

PubMed Central

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

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

1992-01-01

112

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

PubMed

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. PMID:22490817

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

113

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

PubMed

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. PMID:25027721

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

2014-09-01

114

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

SciTech Connect

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.

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

2010-01-01

115

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

SciTech Connect

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.

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

2010-01-01

116

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

Federal Register 2010, 2011, 2012, 2013

...504), where it is considered an aggressive invasive weed of marshes and wetlands...1-11), and at least 4 particularly aggressive species have severely impacted the native...elevation range due to their particularly aggressive nature and large colony sizes...

2010-06-24

117

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

E-print Network

with corn, and used for both human and animal consumption (Mateo et al. 1981). Corn, Zea ~ma s L. , is the staple grain of Central America. It has been cultivated in Mesoamerica since 5000 B. C. , and provided the agricultural base for development... with corn, and used for both human and animal consumption (Mateo et al. 1981). Corn, Zea ~ma s L. , is the staple grain of Central America. It has been cultivated in Mesoamerica since 5000 B. C. , and provided the agricultural base for development...

Jones, Robert Wallace

2012-06-07

118

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

E-print Network

of this annual plant varied significantly between seasons as did the density of seeds in sediments. Seasonal/n, 41013 Sevilla, Spain (hector@ebd.csic.es). Submerged vascular plants have a vital role in non- marine aquatic ecosystems, influencing nutrient dy- namics and water chemistry, modulating the structure

Green, Andy J.

119

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

E-print Network

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 ...

Morar, Mariya

120

Crystal Structure of the Flagellar Rotor Protein Flin From Thermatoga Maritima  

Microsoft Academic Search

FliN is a component of the bacterial flagellum that is present at levels of more than 100 copies and forms the bulk of the C ring, a drum-shaped structure at the inner end of the basal body. FliN interacts with FliG and FliM to form the rotor-mounted switch complex that controls clockwise-counterclockwise switching of the motor. In addition to its

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

2005-01-01

121

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

E-print Network

. Brightness, contrast and colour balance of images were adjusted using Adobe Photoshop (version CS5). Antibody staining All steps were at room temperature, unless otherwise noted. Ovaries were rehydrated from methanol into PBX (1#1; PBS and 0.5% Triton X-100...

Green, Jack E.; Akam, Michael

2014-06-12

122

Effect of ingestion by five avian dispersers on the retention time, retrieval and germination of Ruppia maritima seeds  

Microsoft Academic Search

1. Vertebrates are important seed dispersers for many plants, particularly those inhabiting naturally fragmented habitats such as lakes and wetlands. Such dispersal often takes place through the transport of ingested seeds (endozoochory). 2. Endozoochorous passage of seeds is likely to vary among both disperser and dispersed species. We hypothesized that seed retention time and survival of gut passage varies among

I. Charalambidou; L. Santamaría; O. Langevoord

2003-01-01

123

Roosting and associated feeding behaviour of turnstones Arenaria Interpres and purple sandpipers Calidris maritima in north-east England.  

E-print Network

??Both individual Turnstones and Purple Sandpipers were largely site-faithful during winter; after the breeding season, however, fewer surviving Purple Sandpipers than Turnstones returned to the… (more)

Burton, Niall H.K.

1995-01-01

124

The embryoid development of Strigamia maritima and its bearing on post-embryonic segmentation of geophilomorph centipedes  

E-print Network

of Geophilomorpha. To try to better understand and define it, I carried out a detailed analysis of this phase of post- embryonic development, based on the improved techniques of culturing eggs and juveniles in mineral oil [22]. This analysis follows up published... remnant of anamorphic segmentation is still present. Results Embryoid stages in Strigamia The following description of stages is based on the best conditions under which live embryoid specimens can be observed, i.e. immersed, mostly in mineral oil...

Brena, Carlo

2014-01-01

125

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

E-print Network

 expansion  of  this  family.  The  search  for  IRs  led  to  the  annotation  of  69  genes,  15  of  which  belong  to  the  IGluR  subfamily,  which  is  not  involved  in  chemosensation,  but... ],  and  no  cryptochromes.   Thus,   none   of   the   known   arthropod   light   receptors   are   present.  Furthermore,   there   are   no   photolyases,   which   would   repair   UV   light   induced...

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

2014-01-01

126

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

Microsoft Academic Search

Decomposition of salt marsh plants results from physical, chemical and biological processes including abiotic and biotic fragmentation, microbial decay and chemical transformation. According to literature data, only a few species have the ability to feed directly on living plant material, so fungi and bacteria seem to be the principal competitors for the organic substrates. Nevertheless, by consuming bacteria, protists and

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

1999-01-01

127

2010 Virginia Polytechnic Institute and State University 3101-1527 Virginia Cooperative Extension programs and employment are open to all, regardless of race, color, national origin, sex, religion, age, disability, political beliefs, sexual orientation, o  

E-print Network

in this manner. LIFE CYCLE: Eggs are laid in small batches or clutches in a chamber two to three inches beneath debris that shelter earwigs may enhance the effectiveness of chemical treatment. Check to make sure seals and dries out quicker. If earwigs have gained entrance to a building, indoor treatment may be desirable

Liskiewicz, Maciej

128

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

E-print Network

.,  2011;  8   Garcia-­?Dominguez  et  al.,  2003).  With  on-­?going  condensation  of  the  head  field  9   these  col  positive  cells  form  a  dense  cluster  and  sink  under  the  surface  10...

Hunnekuhl, Vera S.; Akam, Michael

2014-01-01

129

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

Microsoft Academic Search

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

Jordi Figuerola; Andy J. Green

2004-01-01

130

Detection of intermediates in the oxidative half-reaction of the FAD-dependent thymidylate synthase from Thermotoga maritima: carbon transfer without covalent pyrimidine activation.  

PubMed

Thymidylate, a vital DNA precursor, is synthesized by thymidylate synthases (TSs). A second class of TSs, encoded by the thyX gene, is found in bacteria and a few other microbes and is especially widespread in anaerobes. TS encoded by thyX requires a flavin adenine dinucleotide prosthetic group for activity. In the oxidative half-reaction, the reduced flavin is oxidized by 2'-deoxyuridine 5'-monophosphate (dUMP) and (6R)-N5,N10-methylene-5,6,7,8-tetrahydrofolate (CH2THF), synthesizing 2'-deoxythymidine 5'-monophosphate (dTMP). dTMP synthesis is a complex process, requiring the enzyme to promote carbon transfer, probably by increasing the nucleophilicity of dUMP and the electrophilicity of CH2THF, and reduction of the transferred carbon. The mechanism of the oxidative half-reaction was investigated by transient kinetics. Two intermediates were detected, the first by a change in the flavin absorbance spectrum in stopped-flow experiments and the second by the transient disappearance of deoxynucleotide in acid quenching experiments. The effects of substrate analogues and the behavior of mutated enzymes on these reactions lead to the conclusion that activation of dUMP does not occur through a Michael-like addition, the mechanism for the activation analogous with that of the flavin-independent TS. Rather, we propose that the nucleophilicity of dUMP is enhanced by electrostatic polarization upon binding to the active site. This conclusion rationalizes many of our observations, for instance, the markedly slower reactions when two arginine residues that hydrogen bond with the uracil moiety of dUMP were mutated to alanine. The activation of dUMP by polarization is consistent with the majority of the published data on ThyX and provides a testable mechanistic hypothesis. PMID:25068636

Conrad, John A; Ortiz-Maldonado, Mariliz; Hoppe, Samuel W; Palfey, Bruce A

2014-08-19

131

TRENDS in Ecology & Evolution Vol.17 No.8 August 2002 http://tree.trends.com 0169-5347/02/$ see front matter 2002 Elsevier Science Ltd. All rights reserved.  

E-print Network

). The Neoptera comprise the Polyneoptera (e.g. grasshoppers, crickets, stick insects, earwigs, termites, mantids that there was an important shift in diversification at or after the origin of the Neoptera, and certainly before the origin

Mayhew, Peter

132

Major/Concen tration Advisor Grad  

E-print Network

as a Biospecimen for Breast Cancer Screening in Women Cell and Molec Dr. Leticia Marquez-Magana g David Newstrom g Julie S. Miller The relationship between maternal care and egg cannibalism in a colonial earwig

133

Mechanisms for turn alternation in four invertebrate species.  

PubMed

Free-choice behavior following one or more forced turns was observed in representatives of four invertebrate classes (earthworms, woodlice, millipedes, earwigs). While all animals alternated, species differences occurred in free turn angle and the effects of varied angle and number of forced turns. Overall, woodlice and millipedes turned at sharper angles and responded more to the forced turn conditions than earthworms and earwigs. From behavior observed following three forced turns in one direction and then one in the opposite, it was concluded that, in earlier experiments, earthworms alternated via tactile cues, woodlice mainly used kinesthetic but could also use tactile cues, millipedes mainly used tactile but could also use kinesthetic cues and earwigs may have relied on kinesthetic cues alone. Since phyletic differences did not seem appropriate, the results were discussed in terms of other characteristics such as body shape and life style. PMID:24896868

Hughes, R N

1987-02-01

134

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

E-print Network

in Brazoria County, Texas (Latitude 29' 03' 23. 80" Longitude 95' 13' 23. 08"). The site was formed as a goose eatout in which the elevation of an intermediate marsh (comprised primarily of Scirpus americanus) was lowered, allowing periodic tidal inundation... in Brazoria County, Texas (Latitude 29' 03' 23. 80" Longitude 95' 13' 23. 08"). The site was formed as a goose eatout in which the elevation of an intermediate marsh (comprised primarily of Scirpus americanus) was lowered, allowing periodic tidal inundation...

Schubert, William James

2012-06-07

135

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

Microsoft Academic Search

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

Jouke Prop; Charlotte Deerenberg

1991-01-01

136

Your sister is yummy, my brother too...  

E-print Network

1975; Mock&Parker 1997 at different life stages: prenatal, juvenile, adults Gilmore et al. 1993; Baur organism European earwig (Forficila auricularia) first instar larvae (nymphs) genetic diversity in family Disco Kin recognition Ralph Dobler Kin selected siblicide and cannibalism Fisher's exact test p = 0

Kölliker, Mathias

137

doi: 10.1098/rsbl.2012.0151 , 547-550 first published online 25 April 201282012Biol. Lett.  

E-print Network

;Animal behaviour When it is costly to have a caring mother: food limitation erases the benefits genetic conflicts and variation in relatedness among family members influence the costs/benefits ratio Meunier and Mathias Kölliker erases the benefits of parental care in earwigs When it is costly to have

Kölliker, Mathias

138

Phytologia (August 2013) 95(3)226 The following paper  

E-print Network

. 2012. Taxonomy of the multi-seeded, entire leaf taxa of the Juniperus, section Sabina: sequence, 2013). KEY WORDS: Juniperus, sect. sabina, correction. Figure 3 (revised). Minimum spanning network. jarkendensis J. semiglobosa ++ J. s. v. jarkendensis J. maritima J. scopulorum ++ J. maritima J. phoenicea J

Adams, Robert P.

139

The arbuscular mycorrhizal fungus Glomus geosporum in European saline, sodic and gypsum soils  

Microsoft Academic Search

Plants of saline and sodic soils of the Hungarian steppe and of gypsum rock in the German Harz mountains, thus soils of high ionic strength and electric conductivity, were examined for their colonization by arbuscular mycorrhizal fungi (AMF). Roots of several plants of the saline and sodic soils such as Artemisia maritima, Aster tripolium or Plantago maritima are strongly colonized

Melanie Landwehr; Ulrich Hildebrandt; Petra Wilde; Kerstin Nawrath; Tibor Tóth; Borbála Biró; Hermann Bothe

2002-01-01

140

Aquatic macrophytes in saline lakes of the Canadian prairies  

Microsoft Academic Search

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

U. Theodore Hammer; J. Michael Heseltine

1988-01-01

141

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

SciTech Connect

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.

K Cho; B Crane; S Park

2011-12-31

142

Radical scavenging, antioxidant and antimicrobial activities of halophytic species Laetitia Meot-Durosa*  

E-print Network

Radical scavenging, antioxidant and antimicrobial activities of halophytic species Laetitia Meot maritimum, Cakile maritima, Crithmum maritimum, antimicrobial, antioxidant, phenol content Abbreviations; BCC: Brittany Culture Collection; GAE: Gallic Acid Equivalents; TAC: Total Antioxidant Capacity. hal

Paris-Sud XI, Université de

143

Mechanistic Insights into the Diverged Enzymes of the Amidohydrolase Superfamily  

E-print Network

. maritima 1 Fe 7/9/02 1J6P SAH/TMA deaminase T. maritima 1 Ni 7/9/02 1J6O TatD-related deoxy- ribonuclease T. maritima None 7/2/02 1J5S uronate isomerase T. maritima None 9/18/07 2VC7 SsoPox lactonase, PTE S. solfataricus 1 Fe, 1Co, (4S)-4... DHO S. Aureus 1 Zn (?) 10 Table 1.1: Continued. 5/12/06 2GZX TatD deoxy- ribonuclease MW0446 S. aureus 2 Ni 8/1/06 2DVX 2,6-dihydroxy- benzoate decarboxylase Rhizobium sp. 1 Zn, 2,3- dihydroxybenzaldehyde 8...

Nguyen, Tinh T.

2011-02-22

144

ARTICLE IN PRESS Maltodextrin-binding proteins from diverse bacteria and archaea are  

E-print Network

, Thermococcus litoralis, Vibrio cholerae, Thermotoga 18 maritima, and Yersinia pestis) to promote the solubility varying degrees of amino 59acid sequence identity with Eco MBP (Yersinia pestis (Ype), 6085%; Vibrio

145

US Forest Service Species Assessments in Region 2 Complied 1/05/2007 by Steve J. Popovich, USFS, ARP SO, Fort Collins, Colorado  

E-print Network

/scp/evalrationale/index.shtmlUTH To date, all completed plant assessments include those below. Coming soon: Triteleia grandiflora, Liparis loeselii, Penstemon laricifolius ssp. exilifolius, and Armeria maritima ssp. siberica. Dicots: · HTUAletes

146

Date/Time: Friday 16 Sept: to // Saturday 17 Sept: to Number of search hours (total): hours (Fri) // hours (Sat)  

E-print Network

Plum Prunus maritima 6 Bird's Foot Trefoil/Lotus Lotus corniculatus 7 Black Cherry Prunus serotina 8 virginiana 41 Eastern White Pine Pinus strobus 42 Elodea Elodea canadensis 43 Grass Leaf Goldenrod Euthamia

Columbia University

147

Application of conditional sampling for measuring ecosystem-scale carbon dioxide exchange in coastal wetlands  

E-print Network

and Salt cornia virgi ni ca, with distinct patches of Batis mari ti ma, Lyci um carolinianum, Suadea linearis, Monathocloe littoralis, Distichlis spicata, and Limonium nashii spread throughout the delta region. Ruppia maritima is the dominant submergent... and Salt cornia virgi ni ca, with distinct patches of Batis mari ti ma, Lyci um carolinianum, Suadea linearis, Monathocloe littoralis, Distichlis spicata, and Limonium nashii spread throughout the delta region. Ruppia maritima is the dominant submergent...

Cobos, Douglas Russell

2012-06-07

148

Kulturverfahren zur Bestimmung der Salz- und Über-flutungsverträglichkeit von Puccinellia spp. (Gramineae)  

Microsoft Academic Search

In the ecology ofPuccinellia species (P. maritima, P. distans, P. retroflexa andP. limosa of the German flora described to date) two environmental factors seem to be very important: the salinity of the soil or of the tidal sea water and, especially in regard toP. maritima, the periodical inundation during the tidal cycle. The latter species forms an important community (Puccinellietum

K. von Weihe; G. Dreyling

1970-01-01

149

Unterschiedliche NaCl-Abhängigkeit des tagesperiodischen CO 2 -Gaswechsels bei einigen halisch wachsenden Küstenpflanzen  

Microsoft Academic Search

CO2-exchange, diurnal changes in malate- and ion concentrations of the halophytes Carpobrotus edulis, Crithmum maritimum, Mesembryanthemum nodiflorum, Salicornia fruticosa, Suaeda maritima, and Trifolium fragiferum were investigated after culture at different NaCl concentrations. In Carp. edulis and Mes. nodiflorum the diurnal rhythm of CO2-exchange is in accordance with that of crassulacean acid metabolism (CAM), in Sal. fruticosa, Crithm. maritimum, Suaeda maritima,

Siegfried Treichel; Peter Bauer

1974-01-01

150

Which insect species numerically respond to allochthonous inputs?  

PubMed

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

Sugiura, Shinji; Ikeda, Hiroshi

2013-08-01

151

Which insect species numerically respond to allochthonous inputs?  

NASA Astrophysics Data System (ADS)

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

Sugiura, Shinji; Ikeda, Hiroshi

2013-08-01

152

Were the original eubacteria thermophiles?  

NASA Technical Reports Server (NTRS)

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.

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

1987-01-01

153

Sugar Transport and Metabolism in Thermotoga  

SciTech Connect

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.

Noll, Kenneth M.; Romano, Antonio H.

2003-02-11

154

Cues of Maternal Condition Influence Offspring Selfishness  

PubMed Central

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

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

2014-01-01

155

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

PubMed

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

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

2014-01-01

156

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

SciTech Connect

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.

Swithers, Kristen S [University of Connecticut, Storrs; DiPippo, Jonathan L [University of Connecticut, Storrs; Bruce, David [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Pennacchio, Len [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Lykidis, A [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Stetter, Karl O [Universitat Regensburg, Regensburg, Germany; Nelson, Karen E [J. Craig Venter Institute; Gogarten, Peter [University of Connecticut, Storrs; Noll, Kenneth M [University of Connecticut, Storrs

2011-01-01

157

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

PubMed

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

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

2002-01-01

158

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

PubMed

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

Meunier, J; Kölliker, M

2013-10-01

159

Evolution of mal ABC transporter operons in the Thermococcales and Thermotogales  

Microsoft Academic Search

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

Kenneth M Noll; Pascal Lapierre; J Peter Gogarten; Dhaval M Nanavati

2008-01-01

160

Suitability of some farmscaping plants as nectar sources for the parasitoid wasp, Microplitis croceipes (Hymenoptera: Braconidae): Effects on longevity and body nutrients  

Microsoft Academic Search

In support of an ongoing study to evaluate potential farmscaping plants for utilization in organic vegetable production systems, we examined the effects of the nectar of three flowering plant species, sweet alyssum (Lobularia maritima), buckwheat (Fagopyrum sagittatum), and licorice mint (Agastache foeniculum), on the lifespan and body nutrient levels of the wasp, Microplitis croceipes (Cresson) (Hymenoptera: Braconidae), a key parasitoid

Timothy D. Nafziger; Henry Y. Fadamiro

2011-01-01

161

Experimental establishment of a declining dry-grassland flagship species in relation to seed origin and target environment  

Microsoft Academic Search

Supporting species persistence may involve (re)connecting suitable habitats. However, for many declining species habitat suitability and drivers of establishment are poorly known. We addressed this experimentally for a declining flagship species of dry grasslands in Germany, Armeria maritima subsp. elongata. In three regions, we sowed seeds from each of eight source populations back to their origin and to eight apparently

Birgit Seifert; Markus Fischer

2010-01-01

162

Distribution of aquatic plants and absorption of radionuclides by plants through the leaf surface in brackish Lake Obuchi, Japan, bordered by nuclear fuel cycle facilities  

Microsoft Academic Search

We investigated the distribution of aquatic plants and the absorption of radionuclides by them in the brackish Lake Obuchi, Japan, which is bordered by nuclear fuel cycle facilities. We studied 5 species of submerged plants: Zannichellia palustris, Ruppia maritima, Potamogeton pectinatus, Zostera japonica, and Z. marina. The plants contained many elements, including radionuclides. The concentrations of 238U, 137Cs, and 90Sr

K. Kondo; H. Kawabata; S. Ueda; H. Hasegawa; J. Inaba; O. Mitamura; Y. Seike; Y. Ohmomo

2003-01-01

163

Palaeoecology of Lake Zeribar, Iran, in the Pleniglacial, Lateglacial and Holocene, reconstructed from plant macrofossils  

Microsoft Academic Search

Changes in aquatic and marsh vegetation at Lake Zeribar in the Zagros Mountains, Iran, during the last 40 000 years were reconstructed on the basis of plant macrofossils. Several episodes of low water level and increased salinity were evidenced by peaks of Chenopodium rubrum seeds and the occurrence of obligate (Salicornia sp., Ruppia maritima and Suaeda sp.) and facultative (Zannichellia

Krystyna Wasylikowa

2005-01-01

164

Distributional range extension of the seagrass Halophila nipponica into coastal waters off the Korean peninsula  

Microsoft Academic Search

Eight temperate seagrass species (five in the genus Zostera, two in the genus Phyllospadix, and Ruppia maritima) have been previously reported in coastal waters off the Korean peninsula, which lies between 33°N and 43°N. Recently, a species of Halophila, a genus which occurs predominantly in tropical and subtropical areas, has been observed on the southern coast of Korea for the

Jeong Bae Kim; Jung-Im Park; Chang-Su Jung; Pil-Yong Lee; Kun-Seop Lee

2009-01-01

165

The vegetation of ultrabasic soils on the Isle of Rhum II. The causes of the debris  

Microsoft Academic Search

The relationship between the Rhum ultrabasic skeletal soils and their debris vegetation was investigated by plant analyses and field and laboratory experiments. Samples of Agrostis vinealis, Arenaria norvegica ssp norvegica, Calluna vulgaris, Festuca vivipara, Plantago maritima and Racomitrium lanuginosum from these soils usually had low concentrations of potassium and calcium, and high concentrations of sodium, magnesium (and high Mg\\/Ca quotients),

John Henry H. Looney; John Proctor

1989-01-01

166

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

E-print Network

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

Paris-Sud XI, Université de

167

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

Microsoft Academic Search

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

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

1996-01-01

168

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

E-print Network

98368 ABSTRACT Trees from two populations of Juniperus commonly identified as J. scopulorum growing that Juniperus trees identified as J. scopulorum Sarg. have been reported from the dry side (northeastPhytologia (April 2010) 92(1)68 DISCOVERY AND SNPS ANALYSES OF POPULATIONS OF JUNIPERUS MARITIMA

Adams, Robert P.

169

Genetic analysis of male fertility restoration in wild cytoplasmic male sterility G of beet  

Microsoft Academic Search

Cytoplasmic male sterility (CMS) has been used in the breeding of sugar beet for decades but is also more generally an important feature of the reproductive system in its wild relative, Beta vulgaris ssp. maritima. Among the several CMSs found in wild populations, the G CMS is a mitochondrial variant of the respiratory chain. The segregants derived from a cross

Pascal Touzet; Nathalie Hueber; Alexandra Bürkholz; Stephen Barnes; Joël Cuguen

2004-01-01

170

Gas exchange and water balance of a mistletoe species and its mangrove hosts  

Microsoft Academic Search

The gas exchange and water relations of the hemiparasite Pthirusa maritima and two its mangrove host species, Conocarpus erectus and Coccoloba uvifera, were studied in an intertidal zone of the Venezuelan coast. Carbon uptake and transpiration, leaf osmotic and total water potential, as well as nutrient content in the xylem sap and leaves of mistletoes and hosts were followed through

G. Goldstein; F. Rada; L. Sternberg; J. L. Burguera; M. Burguera; A. Orozco; M. Montilla; O. Zabala; A. Azocar; M. J. Canales; A. Celis

1989-01-01

171

The seed oils of some species of the family Cruciferae  

Microsoft Academic Search

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

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

1973-01-01

172

Forecast Technical Document Tree Species  

E-print Network

koreana Pine 4 14 SP PMO Western white pine Pinus monticola Pine 4 14 LP PTA Loblolly pine Pinus taeda pine Pinus nigra var nigra Pine 6 20 CP BIP Bishop pine Pinus muricata Pine 6 20 LP CP Corsican pine Pinus nigra var maritima Pine 6 20 CP LP Lodgepole pine Pinus contorta Pine 4 14 LP MAP Maritime pine

173

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

Microsoft Academic Search

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

Ole R. Therkildsen; Thomas Bregnballe

2006-01-01

174

Predatory bugs show higher abundance close to flower strips in pear orchards  

Microsoft Academic Search

Many beneficial insects depend on floral resources during their adult state. Flowering herbs can play an important role in providing these resources and thereby enhancing biological control. We implemented five flower species (Centaurea cyanus, Fagopyrum esculentum, Lobularia maritima, Thymus serphyllum, Sinapis alba), associated with the presence of predatory bugs, in a pear orchard in order to improve the biological control

Karin Winkler; Herman Helsen; Bishnu Hari Devkota

175

Nitrogen resorption from senescing leaves of three salt marsh plant species  

Microsoft Academic Search

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

P. Cartaxana; F. Catarino

2002-01-01

176

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

Microsoft Academic Search

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

Jordi Figuerola; Andy J. Green; L. Santamaría

2002-01-01

177

The status of Lecanora zosterae in the British Isles  

Microsoft Academic Search

Lecanora zosterae (Ach.) Nyl. is a distinct species belonging to the Lecanora dispersa group. In the British Isles it is confined to the coast where it grows mostly on the exposed turf above sea cliffs. Some 76% of the population occurs on decayed thrift Armeria maritima. The related Lecanora umbrina (Ach.) A. Massal. is lectotypified; it is the correct name

Jack Rodney Laundon

2003-01-01

178

Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics  

E-print Network

. maritima. The latter effect can be measured by contact order or solvent accessibility, and in addition concern such diverse industries as household cleaning, textile washing, paper bleaching, fruit juice the mesophilic and thermophilic groups is the difference in charged­polar amino- acids (the "CvP bias") 6; 7

Alvarez, Nadir

179

Seasonal patterns of CO 2 and water vapor exchange of three salt marsh succulents  

Microsoft Academic Search

Diurnal carbon dioxide exchange patterns of three salt marsh succulents, Borrichia frutescens, Batis maritima and Salicornia virginica, were determined on a seasonal basis in the marsh at Sapelo Island, Georgia. Year-round photosynthetic activity was observed in these species though winter rates of CO2 exchange were reduced. Net primary productivity, estimated using gas exchange techniques, agreed with previously reported harvest data.

Ann E. Antlfinger; E. L. Dunn

1979-01-01

180

Seed morphology and endosperm structure of selected species of Primulaceae, Myrsinaceae, and Theophrastaceae and their systematic importance  

Microsoft Academic Search

Seed size and shape, seed coat surface pattern, seed coat thickness, and endosperm structure were investigated in Androsace septentrionalis, Cortusa matthioli, Hottonia palustris, Primula elatior, Soldanella carpatica (Primulaceae), Anagallis arvensis, A. minima, Cyclamen purpurascens, Glaux maritima, Lysimachia nemorum, L. vulgaris, Trientalis europaea (Myrsinaceae), and Samolus valerandi (Theophrastaceae). Three seed size categories were distinguished on the basis of biometric measurements. Almost

Maria Morozowska; Aneta Czarna; Marcin Kujawa; Andrzej M. Jagodzinski

2011-01-01

181

The effect of cattle and sheep grazing on salt-marsh vegetation at Skallingen, Denmark  

Microsoft Academic Search

The aggregated effect of cattle and sheep grazing on Puccinellion maritimae and other salt-marsh vegetation has been studied together with changes in species composition, the percentage cover of each species, total cover and the percentage of bare ground, six years after grazing had been prevented by construction of experimental exclosures. The results of these experiments are discussed in relation to

A. Jensen

1985-01-01

182

Heavy metal uptake by marsh plants in hydroponic solution cultures  

Microsoft Academic Search

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

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

1981-01-01

183

Phytosociological survey of Northern California dunes  

Microsoft Academic Search

The vegetation of sandy coasts of California between Point Arena and Morro Bay, was investigated. Near the tide line, was annual vegetation of the Cakile maritima community. Dunal vegetation included the new Abronio latifoliae-Ambrosietea chamissonis class with the new Ambrosietalia chamissonis order and the new Ambrosion chamissonis alliance (proposed). Foredune vegetation included the two new Abronio latifoliae-Elymetum mollis and Atriplici

Simona Casavecchia; Edoardo Biondi

2001-01-01

184

Response of Salt Marsh Ponds to Eutropication Austin N. Ritter1,3  

E-print Network

and 30x ambient for 3 d during the study period. During the summer, when fertilization was occurring, we abundance of benthic micro-algae, and the numerical abundance of protists. Additionally we measured benthic algae biomass, floating algae mat percent cover, and R. maritima percent cover. During the fall

Vallino, Joseph J.

185

Response of primary producers to nutrient enrichment in a shallow estuary  

USGS Publications Warehouse

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.

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

1998-01-01

186

Acoustic detection of Oryctes rhinoceros (Coleoptera: Scarabaeidae: Dynastinae) and Nasutitermes luzonicus (Isoptera: Termitidae) in palm trees in urban Guam.  

PubMed

Adult and larval Oryctes rhinoceros (L.) (Coleoptera: Scarabaeidae: Dynastinae) were acoustically detected in live and dead palm trees and logs in recently invaded areas of Guam, along with Nasutitermes luzonicus Oshima (Isoptera: Termitidae), and other small, sound-producing invertebrates and invertebrates. The low-frequency, long-duration sound-impulse trains produced by large, active O. rhinoceros and the higher frequency, shorter impulse trains produced by feeding N. luzonicus had distinctive spectral and temporal patterns that facilitated their identification and discrimination from background noise, as well as from roaches, earwigs, and other small sound-producing organisms present in the trees and logs. The distinctiveness of the O. rhinoceros sounds enables current usage of acoustic detection as a tactic in Guam's ongoing O. rhinoceros eradication program. PMID:20857720

Mankin, R W; Moore, A

2010-08-01

187

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

PubMed

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. PMID:19632654

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

2009-08-01

188

Notes on Lichen Genus Buellia De Not. (lichenized Ascomycetes) from South Korea.  

PubMed

Based on a literature survey and assessment of the important features of lichen genus Buellia (spore shape and size, anatomy of the exciple as well as analysis of the lichen substances), the present paper describes four new records of B. maritima, B. polyspora, B. spuria and B. stellulata from South Korea. Among them, B. maritima and B. polyspora are firstly reported in East Asia including in China, the Korean Peninsula and Japan. Brief description of all the new records along with earlier described species placed under genus Amandinea and Hafellia are provided with their distribution and chemistry. A key to all the Buellia species reported so far from South Korea is also provided. PMID:23956628

Joshi, Yogesh; Wang, Xin Yu; Lökös, László; Koh, Young Jin; Hur, Jae-Seoun

2010-03-01

189

Notes on Lichen Genus Buellia De Not. (lichenized Ascomycetes) from South Korea  

PubMed Central

Based on a literature survey and assessment of the important features of lichen genus Buellia (spore shape and size, anatomy of the exciple as well as analysis of the lichen substances), the present paper describes four new records of B. maritima, B. polyspora, B. spuria and B. stellulata from South Korea. Among them, B. maritima and B. polyspora are firstly reported in East Asia including in China, the Korean Peninsula and Japan. Brief description of all the new records along with earlier described species placed under genus Amandinea and Hafellia are provided with their distribution and chemistry. A key to all the Buellia species reported so far from South Korea is also provided. PMID:23956628

Joshi, Yogesh; Wang, Xin Yu; Lokos, Laszlo; Koh, Young Jin

2010-01-01

190

The Late-Weichselian Flora of the Isle of Man.  

PubMed

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

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

1970-03-26

191

Large methyl halide emissions from south Texas salt marshes  

NASA Astrophysics Data System (ADS)

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

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

2014-06-01

192

Effect of habitat quality on diet flexibility in Barbary macaques.  

PubMed

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

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

2014-07-01

193

Wetland monitoring using classification trees and SPOT5 seasonal time series  

Microsoft Academic Search

Multiseason reflectance data from radiometrically and geometrically corrected multispectral SPOT-5 images of 10-m resolution were combined with thorough field campaigns and land cover digitizing using a binary classification tree algorithm to estimate the area of marshes covered with common reeds (Phragmites australis) and submerged macrophytes (Potamogeton pectinatus, P. pusillus, Myriophyllum spicatum, Ruppia maritima, Chara sp.) over an area of 145,000ha.

Aurélie Davranche; Gaëtan Lefebvre; Brigitte Poulin

2010-01-01

194

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

Microsoft Academic Search

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

Douglas A. Barnum; David S. Gilmer

1988-01-01

195

Abundance of submerged vascular vegetation in the Rhode River from 1966 to 1973  

Microsoft Academic Search

Surveys on the distribution and abundance of submerged vascular plants in the Rhode River showed that there was an irregular\\u000a decline in the amount of vegetation from 1966 to 1973, along with significant changes in species dominance. In 1966, redheadgrass\\u000a (Potamogeton perfoliatus) and Eurasian watermilfoil (Myriophyllum spicatum) were both very abundant with lesser amounts of widgeongrass (Ruppia maritima), horned pondweed

Charles H. Southwick; Frank W. Pine

1975-01-01

196

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

Microsoft Academic Search

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

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

2006-01-01

197

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

Microsoft Academic Search

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

Matthew C. Perry; Francis M. Uhler

1988-01-01

198

The crystal structure of spermidine synthase with a multisubstrate adduct inhibitor  

Microsoft Academic Search

Polyamines are essential in all branches of life. Spermidine synthase (putrescine aminopropyltransferase, PAPT) catalyzes the biosynthesis of spermidine, a ubiquitous polyamine. The crystal structure of the PAPT from Thermotoga maritima (TmPAPT) has been solved to 1.5 Angstroms resolution in the presence and absence of AdoDATO (S-adenosyl-1,8-diamino-3-thiooctane), a compound containing both substrate and product moieties. This, the first structure of an

Sergey Korolev; Yoshihiko Ikeguchi; Tatiana Skarina; Steven Beasley; Cheryl Arrowsmith; Alexei Savchenko; Aled Edwards; Andrzej Joachimiak; Anthony E. Pegg

2001-01-01

199

Enhancement of transglycosylation activity by construction of chimeras between mesophilic and thermophilic ?-glucosidase  

Microsoft Academic Search

The family 3 ?-glucosidase from Thermotoga maritima is a highly thermostable enzyme (85°C) that displays transglycosylation activity. In contrast, the ?-glucosidase from Cellvibrio gilvus is mesophilic (35°C) and displays no such transglycosylation activity. Both enzymes consist of two domains, an N-terminal and a C-terminal domain, and the amino acid identities between the two enzymes in these domains are 32.4 and

Kshamata Goyal; Bong Jo Kim; Jong-Deog Kim; Yeon-Kye Kim; Motomitsu Kitaoka; Kiyoshi Hayashi

2002-01-01

200

Use of drift substrates to characterize marine fungal communities from the west coast of Portugal.  

PubMed

This survey reports the occurrence, diversity and similarity of marine fungi associated with five categories of drift substrates (Arundo donax, Phragmites australis, Spartina maritima, "other stems" and driftwood) collected on four sandy beaches of the western coast of Portugal. "Other stems" and driftwood are composite samples with a variety of identified and unidentified pieces of non-woody and woody substrates respectively. Fifty-six taxa were identified, including 38 Ascomycota and 18 anamorphic fungi. Twenty-six taxa were generalists; however several cases of "substrate recurrence" were identified. The very frequent fungi differed among the categories of studied substrates, with the exception of Corollospora maritima, very frequent on four categories. Except for S. maritima, P. australis and driftwood, cases of multiple fungal colonization were rare. S. maritima was the single substrate with five different marine fungi on one sample, as well as with the highest number of very frequent fungi, highest percentage of colonization and average number of fungi per sample. Driftwood presented the highest value of fungal richness (37 taxa) and A. donax the lowest (22 taxa). ANOSIM analysis of similarity showed that all substrates supported different fungal communities with the exception of the pair P. australis/"other stems". The effect of sample size on estimated fungal richness was tested, and the results let us conclude that, although most of the sporadic fungi (<1% occurrence) will be detected only in a very large number of samples, 60 samples of A. donax and "other stems" and 70 samples of all the other substrates may suffice to assess their respective representative marine mycota. PMID:22241614

Azevedo, Egidia; Rebelo, Rui; Caeiro, Maria Filomena; Barata, Margarida

2012-01-01

201

Identification and molecular characterization of an endoglucanase gene, celS , from the extremely thermophilic archaeon Sulfolobus solfataricus  

Microsoft Academic Search

A genomic region upstream of the alcohol dehydrogenase (Ssadh) gene was cloned and sequenced from a library of Sulfolobus solfataricus MT4 strain. The isolated 4,040-bp DNA fragment revealed an open reading frame (celS), lying in the opposite direction to Ssadh, which showed significant similarity to endo-#-1,4-glucanases from Pyrococcus furiosus, Thermotoga maritima, and Thermotoga neapolitana. celS was shown to be a

Danila Limauro; Raffaele Cannio; Gabriella Fiorentino; Mosè Rossi; Simonetta Bartolucci

2001-01-01

202

Structure of CheA, a Signal-Transducing Histidine Kinase  

Microsoft Academic Search

Histidine kinases allow bacteria, plants, and fungi to sense and respond to their environment. The 2.6 Å resolution crystal structure of Thermotoga maritima CheA (290-671) histidine kinase reveals a dimer where the functions of dimerization, ATP binding, and regulation are segregated into domains. The kinase domain is unlike Ser\\/Thr\\/Tyr kinases but resembles two ATPases, Gyrase B and Hsp90. Structural analogies

Alexandrine M. Bilwes; Lisa A. Alex; Brian R. Crane; Melvin I. Simon

1999-01-01

203

Measurement of in situ phytoextraction of zinc by spontaneous metallophytes growing on a former smelter site.  

PubMed

This work was undertaken to measure the in situ phytoextraction of zinc using a former zinc-smelter site where metallophyte plants have been growing for 30 years. The site exhibited a gradient in the total metal concentration in the upper horizon (from 3230 to 8530 mg Zn kg(-1)). Soils were sampled from four different sectors (I-IV), and plant shoots were harvested, identified, their biomass weighed and analysed for zinc. The results showed that three plant species were dominant on the site, including Arabidopsis halleri (cress), Armeria maritima (seathrift), and Arrhenatherum elatius (fromental). A. maritima was the predominant species according to the biomass production on the most polluted sector 1. As the concentration of metals in soils decreased. A. maritima disappeared and A. halleri increased. The biomass of A. elatius was the highest on the less polluted soils. Concentrations in zinc in the aerial parts of plants varied from 73 (sector IV) to 6269 mg kg(-1) DM (sector 1). The concentration of Zn in A. halleri decreased with the decrease in concentration of zinc in soil. Phytoextraction was calculated from the biomass and its concentration of metal. It was at a maximum in sector III with a high contribution of A. halleri and A. elatius and reached 10 kg Zn ha(-1), a promising amount for phytoextraction considering the absence of any agricultural practices. In sector 1, phytoextraction was four times lower despite a 2.6 times higher concentration of Zn in the upper horizon. In conclusion, phytoextraction was strongly dependent on the concentration of the available metal in soils which may limit the growth of plants, and favour tolerant but low biomass plant species such as A. maritima. PMID:11712599

Schwartz, C; Gérard, E; Perronnet, K; Morel, J L

2001-11-12

204

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

Microsoft Academic Search

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

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

1998-01-01

205

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

Microsoft Academic Search

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

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

2009-01-01

206

Photochemical and biophysical feedbacks of C? and C? Mediterranean halophytes to atmospheric CO? enrichment confirmed by their stable isotope signatures.  

PubMed

According the latest predictions, an increase of about two times in atmospheric CO2 concentrations, is expected to occur by the end of this century. In order to understand the effects of this atmospheric composition changes on two abundant Mediterranean halophytes (Halimione portulacoides and Spartina maritima), mesocosmos trials were performed simulating two atmospheric CO2 environments (380 ppm and 760 ppm of CO2 respectively). The two chosen halophyte species present different metabolic characteristics: H. portulacoides, is a C3 specie while S. maritima is a C4 species. Distinct feedbacks were obtained for each of the studied species. Stable Isotope discrimination showed that both species showed an enhancement of the Rubisco carboxylation capacity and photosynthetic efficiency mostly due to an increase in intracellular [CO2]. In H. portulacoides CO2 fertilization induced an enhancement of ETR and a decrease in non-photochemical quenching and in dissipated energy fluxes. On the other hand the C4 grass S. maritima, already at full capacity, showed no photosynthetic enhancement. In fact this highly productive grass presented lower photosynthetic efficiencies accompanied by increases in dissipated energy fluxes mostly due to reductions in energy flux associated with the transport of reducing power throughout the quinone pool. The accumulation of reducing power led to oxidative stress, and thus the photosynthetic ability of this grass was greatly reduced. Both these feedbacks to realistic future CO2 concentrations are important consideration for in future primary productivity models, indicating a possible reduced abundance of the pioneer S. maritima and an increased biomass spreading of the sediment stabilizer H. portulacoides, inevitably affecting the morphology and function of the salt marshes imposed by these atmospheric changes, both in terms of ecosystem functioning and loss of biodiversity. PMID:24713121

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

2014-07-01

207

Molecular Phylogeny of Hybridizing Species from the Genus Spartina Schreb. (Poaceae)  

Microsoft Academic Search

Interspecific hybridization events have been reported in the genus Spartina Schreb. (Poaceae), involving the east American species Spartina alterniflora, and including either introgression (e.g., with the western American Spartina foliosa) or allopolyploid speciation (e.g., with the Euro–African Spartina maritima). Molecular phylogenetic analysis of the genus has been undertaken in order to understand phylogenetic relationships and genetic divergence among these hybridizing

A. Baumel; M. L. Ainouche; R. J. Bayer; A. K. Ainouche; M. T. Misset

2002-01-01

208

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

Microsoft Academic Search

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

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

1975-01-01

209

Allocation of nitrogen and carbon in an estuarine salt marsh in Portugal  

Microsoft Academic Search

Above and below-ground biomass and nitrogen and carbon composition ofSpartina maritima, Halimione portulacoides andArthrocnemum perenne, dominating species in plant communities of the lower, middle and higher salt marsh, respectively, were compared in an estuarine\\u000a salt marsh in Portugal. Plant and soil nitrogen and carbon pools were estimated. For all three species root biomass was significantly\\u000a higher (70–92% of total biomass)

F. Catarino

1997-01-01

210

Leaching requirement and salinity threshold for the yield and agronomic characteristics of halophytes under salt stress  

Microsoft Academic Search

An experiment was carried out at Nahshala Farm, north west of Al-Ain City, U.A.E. during the 1998–2000 growing seasons, using six halophytes (Batis maritima, Distichlis spicata, Juncus roemerianus, Paspalum vaginatum, Salicornia bigelovii and Spartina alterniflora) and two levels of leaching fraction (0·25 and 0·50) under three irrigation salinity levels (10, 20, and 40 gL?1) in a randomized complete block design

El-Sayed H. El-Haddad; Maher M. Noaman

2001-01-01

211

Strandline and sand dune vegetation of coasts of Greece and some other Aegean countries  

Microsoft Academic Search

The coastal strandline and sand-dune vegetation of Greece has been reviewed. All published relevés available were collected and classified using numerical methods (TWINSPAN). The communities studied belong to three classes, one for strandline vegetation (Cakiletea maritimae), and two for sand-dune vegetation (Ammophiletea and Cisto-Micromerietea). A hierarchical syntaxonomic overview is given. The following communities and associations were distinguished: Salsolo-Matthioletum tricuspidatae, Cakilo-Xanthietum

K. V. Sykora; D. Babalonas; E. S. Papastergiadou

2003-01-01

212

Raster based coastal marsh classification within the Galveston Bay ecosystem, Texas  

E-print Network

, creating errors in the final classification. This study will also attempt to accurately classify vegetation communities within these habitat types. Species such as smooth cordgrass (Spartina alterniflora),leafy three-square (Scirpus robustus... can be used to distinguish individual vegetation communities such as Spartina alterniflora, Scirpus robustus, 7 and Typha domingensis, which compose the low marsh Spartina patens, Batis maritima, Borrichia frutescens, Salicornia virginica...

Edwards, Aron Shaun

2009-05-15

213

Invasive alien plants in marine protected areas: the Spartina anglica affair in the European Wadden Sea  

Microsoft Academic Search

The common cord-grass Spartina anglica, a fertile hybrid of S. maritima and S. alterniflora, was planted in the European Wadden Sea extensively during the late 1920s and 1930s to promote sediment accretion. After\\u000a establishment, it colonised as a pioneer plant in the upper tidal zone, where it occurs frequently in coherent swards at the\\u000a seaward front of saltmarshes and in patches on

Stefan Nehring; Karl-Jürgen Hesse

2008-01-01

214

The Response of Fodderbeet to Salinity : Introduction of a non-conventional fodder crop (Fodderbeet) to salt affected lands of Pakistan  

Microsoft Academic Search

Summary In the experiments described in this thesis on fodderbeet Beta vulgaris subsp. vulgaris cv. Majoral and seabeet Beta vulgaris subsp. maritima grown under saline conditions the seed germination of four fodderbeet Beta vulgaris subsp. vulgaris cultivars was first studied in response to salinity (EC 4-20 dS m-1~ 40-200 mM NaCl) and three temperatures (20o, 25o and 30 oC). The

B. H. Niazi

2007-01-01

215

GTPase Activity, Structure, and Mechanical Properties of Filaments Assembled from Bacterial Cytoskeleton Protein MreB  

PubMed Central

MreB, a major component of the recently discovered bacterial cytoskeleton, displays a structure homologous to its eukaryotic counterpart actin. Here, we study the assembly and mechanical properties of Thermotoga maritima MreB in the presence of different nucleotides in vitro. We found that GTP, not ADP or GDP, can mediate MreB assembly into filamentous structures as effectively as ATP. Upon MreB assembly, both GTP and ATP release the gamma phosphate at similar rates. Therefore, MreB is an equally effective ATPase and GTPase. Electron microscopy and quantitative rheology suggest that the morphologies and micromechanical properties of filamentous ATP-MreB and GTP-MreB are similar. In contrast, mammalian actin assembly is favored in the presence of ATP over GTP. These results indicate that, despite high structural homology of their monomers, T. maritima MreB and actin filaments display different assembly, morphology, micromechanics, and nucleotide-binding specificity. Furthermore, the biophysical properties of T. maritima MreB filaments, including high rigidity and propensity to form bundles, suggest a mechanism by which MreB helical structure may be involved in imposing a cylindrical architecture on rod-shaped bacterial cells. PMID:16428401

Esue, Osigwe; Wirtz, Denis; Tseng, Yiider

2006-01-01

216

Homology Modeling of the CheW Coupling Protein of the Chemotaxis Signaling Complex  

PubMed Central

Homology models of the E. coli and T. maritima chemotaxis protein CheW were constructed to assess the quality of structural predictions and their applicability in chemotaxis research: i) a model of E. coli CheW was constructed using the T. maritima CheW NMR structure as a template, and ii) a model of T. maritima CheW was constructed using the E. coli CheW NMR structure as a template. The conformational space accessible to the homology models and to the NMR structures was investigated using molecular dynamics and Monte Carlo simulations. The results show that even though static homology models of CheW may be partially structurally different from their corresponding experimentally determined structures, the conformational space they can access through their dynamic variations can be similar, for specific regions of the protein, to that of the experimental NMR structures. When CheW homology models are allowed to explore their local accessible conformational space, modeling can provide a rational path to predicting CheW interactions with the MCP and CheA proteins of the chemotaxis complex. Homology models of CheW (and potentially, of other chemotaxis proteins) should be seen as snapshots of an otherwise larger ensemble of accessible conformational space. PMID:23950985

Cashman, Derek J.; Ortega, Davi R.; Zhulin, Igor B.; Baudry, Jerome

2013-01-01

217

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

PubMed

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

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

2014-01-01

218

Salt marsh community structure in the Tijuana Estuary, California  

NASA Astrophysics Data System (ADS)

Vegetation of the Tijuana Estuary salt marsh was investigated in relationship to measured environmental factors over a one-meter elevation gradient. Elevation was a good indicator of the changing environment, with lower elevations having higher salinity, more inundation, higher soil organic matter and more clay than upper elevations. Dominance of vascular plants changed gradually with elevation. Spartina foliosa dominated the lowest elevations, then Salicornia bigelovii and Batis maritima, Jaumea carnosa, Suaeda californica, Frankenia grandifolia, Monanthochloe littoralis, and Salicornia subterminalis, with Salicornia virginica common at all but the highest elevations studied. The vegetation could not be separated into realistic zones or associations on the basis of occurrence measured in 0·25 m 2 quadrats. The most discernible change in composition across the elevation gradient corresponds to the replacement of the tall Spartina foliosa with a mixture of low-growing succulents at 6-7 dm above Mean Sea Level. Species interactions of joint occurrence and cover were investigated to develop hypotheses concerning the role of competition in determining species distributions. It is hypothesized that Salicornia virginica, which has a bimodal distribution over the elevation gradient, is limited in the central part of its range by competition with Batis maritima or Salicornia bigelovii or both. And, because of their common co-occurrence and mutual abundance, it is hypothesized that Batis maritima and Salicornia bigelovii are not competitors.

Zedler, Joy B.

219

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

NASA Astrophysics Data System (ADS)

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

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

2009-07-01

220

Remote sensing of biomass of salt marsh vegetation in France  

NASA Technical Reports Server (NTRS)

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.

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

1988-01-01

221

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

PubMed

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. PMID:22504722

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

2008-10-01

222

Ability of salt marsh plants for TBT remediation in sediments  

Microsoft Academic Search

Introduction  The capability of Halimione portulacoides, Spartina maritima, and Sarcocornia fruticosa (halophytes very commonly found in salt marshes from Mediterranean areas) for enhancing remediation of tributyltin (TBT)\\u000a from estuarine sediments was investigated, using different experimental conditions.\\u000a \\u000a \\u000a \\u000a \\u000a Methods  The influence of H. portulacoides on degradation of the butyltin compounds was assessed in two different ways: (1) a 9-month ex situ study carried out

Pedro N. Carvalho; M. Clara P. Basto; Manuela F. G. M. Silva; Ana Machado; A. A. Bordalo; M. Teresa S. D. Vasconcelos

2010-01-01

223

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

SciTech Connect

Eight marsh plant species (Cyperus esculentus, Scirpus validus, Spartina patens, Scirpus robustus, Triglochin maritima, Distichlis spicata, Spartina alterniflora, and Spartina foliosa) were grown under greenhouse conditions in chemically controlled nutrient solutions. Heavy metals (zinc, cadmium, nickel, chromium, and lead) were added to the nutrient solutions at levels of 0, 0.5, and 1.0 mg/l. Plant parts (leaves, rhizomes, tubers, and roots) were harvested separately for each species and analyzed for heavy metal content. The concentration and plant uptake of heavy metals in each plant species will be discussed.

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

1975-01-01

224

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

NASA Astrophysics Data System (ADS)

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

Sanad Soliman, Mahmoud; El-Ansary, Afaf

225

Screening seeds of Scottish plants for antibacterial activity.  

PubMed

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

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

2002-11-01

226

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

PubMed Central

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

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

2009-01-01

227

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

NASA Astrophysics Data System (ADS)

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

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

2008-12-01

228

Diet of western Burrowing Owls wintering in southern Texas  

USGS Publications Warehouse

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

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

2007-01-01

229

Surveillance of Listeria monocytogenes in human and environmental specimens in Nova Scotia, 1974 to 1981.  

PubMed

We examined specimens for L. monocytogenes using the "cold enrichment" technique of Gray et al. (J. Bacteriol., 55: 471, 1948) and a nalidixic agar plate (Ann. Inst. Pasteur 111: 90, 1966). Between 1974 and May 1981, we isolated L. monocytogenes from four of 5,255 specimens (rectal, vaginal and placental swabs; blood; spinal fluid; semen; necropsy material) which came from eight human populations (neonates, children, adult men, and pregnant and nonpregnant women) and from 161 animals. Three of the isolated strains were type 1, and they came from a newborn born at 32 weeks' gestation, that child's mother, and another woman who had recently delivered. The fourth (type 4b) came from a newborn twin born at 36 1/2 weeks' gestation. In June through October 1981, in 529 specimens, we isolated L. monocytogenes type 1/2 from two of four larvae tested (four earwigs and five slugs were all negative) and from three of 27 samples of fresh chicken liver (however, 18 samples of coleslaw were negative). At the same time, we isolated L. monocytogenes (not yet typed) from a rectal swab from one of 112 dogs examined. Rectal swabs from 107 cats were negative, as were vaginal swabs from 144 women and urine samples from 108 newborns. PMID:6442655

Embil, J A; Ewan, E P; MacDonald, S W

1984-01-01

230

Conformational Flexibility and Peptide Interaction of the Translocation ATPase SecA  

SciTech Connect

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.

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

2010-09-21

231

Accumulation and soil-to-plant transfer of radionuclides in the Nile Delta coastal black sand habitats.  

PubMed

The radionuclide content was estimated in the soil of three black sand habitats in the Mediterranean coast of Egypt, namely, sand mounds and coastal sand planes and dunes. In addition, a total of 14 heavy minerals found in the soils were characterized. The soil to plant transfer of uranium and thorium was tested on three black sand species, namely, Cakile maritima Scop., Senecio glaucus L. and Rumex Pictus Forssk. The transfer of thorium and uranium radionuclides from the soil to plant is complex process that is subjected to many variables; among which are the organic matter and clay content of the soil, the type of radionuclides and plant species. The study revealed a strong negative relationship between uranium and thorium uptake by S. glaucus and R. pictus and the clay and organic matter content of soil. Concentration of thorium in the soil has a negative correlation with soil-to-plant transfer factor. The study results suggest the possibility of using black sand species for phytoremediation of soils contaminated with radioactive elements. The potentiality of S. glaucus as phytoremediator of radionuclides polluted soils is greater than R. pictus which in turn outweigh C. maritima. PMID:21598782

Hegazy, A K; Emam, M H

2011-02-01

232

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

NASA Astrophysics Data System (ADS)

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

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

2013-01-01

233

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

NASA Astrophysics Data System (ADS)

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. (

Kevrekidis, Theodoros

2004-09-01

234

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

PubMed

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

Jakobsson, Anna; Ågren, Jon

2014-05-01

235

Distribution and migration of seaside sparrows  

USGS Publications Warehouse

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.

Robbins, C.S.

1983-01-01

236

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

PubMed Central

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

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

237

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

NASA Astrophysics Data System (ADS)

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

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

2013-09-01

238

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

PubMed Central

The unifying structural characteristic of members of the bacterial order Thermotogales is their toga, an unusual cell envelope that includes a loose-fitting sheath around each cell. Only two toga-associated structural proteins have been purified and characterized in Thermotoga maritima: the anchor protein OmpA1 (or Omp?) and the porin OmpB (or Omp?). The gene encoding OmpA1 (ompA1) was cloned and sequenced and later assigned to TM0477 in the genome sequence, but because no peptide sequence was available for OmpB, its gene (ompB) was not annotated. We identified six porin candidates in the genome sequence of T. maritima. Of these candidates, only one, encoded by TM0476, has all the characteristics reported for OmpB and characteristics expected of a porin including predominant ?-sheet structure, a carboxy terminus porin anchoring motif, and a porin-specific amino acid composition. We highly enriched a toga fraction of cells for OmpB by sucrose gradient centrifugation and hydroxyapatite chromatography and analyzed it by LC/MS/MS. We found that the only porin candidate that it contained was the TM0476 product. This cell fraction also had ?-sheet character as determined by circular dichroism, consistent with its enrichment for OmpB. We conclude that TM0476 encodes OmpB. A phylogenetic analysis of OmpB found orthologs encoded in syntenic locations in the genomes of all but two Thermotogales species. Those without orthologs have putative isofunctional genes in their place. Phylogenetic analyses of OmpA1 revealed that each species of the Thermotogales has one or two OmpA homologs. T. maritima has two OmpA homologs, encoded by ompA1 (TM0477) and ompA2 (TM1729), both of which were found in the toga protein-enriched cell extracts. These annotations of the genes encoding toga structural proteins will guide future examinations of the structure and function of this unusual lineage-defining cell sheath. PMID:22768259

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

239

POLYPEPTIDE AND POLYSACCHARIDE PROCESSING IN HYPERTHERMOPHILIC MICROORGANISMS  

SciTech Connect

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.

KELLY, ROBERT M.

2008-12-22

240

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

USGS Publications Warehouse

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.

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

1988-01-01

241

X-ray diffraction structure of a plant glycosyl hydrolase family 32 protein: fructan 1-exohydrolase IIa of Cichorium intybus.  

PubMed

Fructan 1-exohydrolase, an enzyme involved in fructan degradation, belongs to the glycosyl hydrolase family 32. The structure of isoenzyme 1-FEH IIa from Cichorium intybus is described at a resolution of 2.35 A. The structure consists of an N-terminal fivefold beta-propeller domain connected to two C-terminal beta-sheets. The putative active site is located entirely in the beta-propeller domain and is formed by amino acids which are highly conserved within glycosyl hydrolase family 32. The fructan-binding site is thought to be in the cleft formed between the two domains. The 1-FEH IIa structure is compared with the structures of two homologous but functionally different enzymes: a levansucrase from Bacillus subtilis (glycosyl hydrolase family 68) and an invertase from Thermotoga maritima (glycosyl hydrolase family 32). PMID:15659099

Verhaest, Maureen; Van den Ende, Wim; Roy, Katrien Le; De Ranter, Camiel J; Laere, André Van; Rabijns, Anja

2005-02-01

242

Acylated cyanidin 3-sambubioside-5-glucosides in three garden plants of the Cruciferae.  

PubMed

Seven acylated cyanidin 3-sambubioside-5-glucosides were isolated from the flowers of three garden plants in the Cruciferae. Specifically, four pigments were isolated from Lobularia maritima (L.) Desv., together with a known pigment, as well as, three pigments from Lunaria annua L., and two known pigments from Cheiranthus cheiri L. These pigments were determined to be cyanidin 3-O-[2-O-((acyl-II)-(beta-d-xylopyranosyl))-6-O-(acyl-I)-beta-d-glucopyranoside]-5-O-[6-O-(acyl-III)-beta-d-glucopyranoside], in which the acyl-I group is represented by glucosyl-p-coumaric acid, p-coumaric acid and ferulic acid, acyl-II by caffeic acid and ferulic acid, and acyl-III by malonic acid, respectively. The distribution and biosynthesis of acylated cyanidin 3-sambubioside-5-glucosides are discussed according to the variations of acylation and glucosylation at their 3-sambubiose residues. PMID:16777160

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

2006-06-01

243

Feeding ecology of waterfowl wintering on evaporation ponds in California  

USGS Publications Warehouse

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.

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

1991-01-01

244

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

PubMed Central

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

Martinez-Hackert, Erik; Hendrickson, Wayne A.

2009-01-01

245

Parnas Lecture PaL Structural studies of bacterial nucleotide excision repair pathway  

E-print Network

DNA damages are structural abnormalities which must be removed for the organism to survive. One of the primary mechanisms to achieve this is Nucleotide Excision Repair (NER) pathway. NER system can repair a wide spectrum of different DNA lesions. In bacteria location of the DNA lesion is detected by a dimeric ATPase called UvrA. In next step DNA is handed over to UvrB which verifies the presence of the damage. Fragment containing the lesion is excised by UvrC nuclease. In order to elucidate the mechanism of DNA damage detection, we solved a crystal structure of Thermotoga maritima UvrA protein in complex with a modified DNA [1]. In the structure, the DNA is bound in a cleft running across the UvrA dimer. The protein binds thse DNA duplex in its terminal regions on both sides of the modification site

Marcin Jaciuk; El?bieta Nowak; Anna Ta?ska; Marcin Nowotny

246

Feasibility of using hyperaccumulating plants to bioremediate metal-contaminated soil  

SciTech Connect

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.

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

1995-12-31

247

Structure determination of two new amino acid-containing derivatives of adenosine from tRNA of thermophilic bacteria and archaea.  

PubMed

Two new nucleosides have been identified in unfractionated transfer RNA of two thermophilic bacteria, Thermodesulfobacterium commune, and Thermotoga maritima, six hyperthermophilic archaea, including Pyrobaculum islandicum, Pyrococcus furiosus and Thermococcus sp. and two mesophilic archaea, Methanococcus vannielii and Methanolobus tindarius. Structures were determined primarily by mass spectrometry, as 3-hydroxy-N-[[(9-beta-D-ribofuranosyl-9H-purin-6- yl)amino]carbonyl]norvaline, (hn6A), structure 1, and 3-hydroxy-N-[[(9-beta-D-ribofuranosyl-9H-2-methylthiopurin-6- yl)amino]carbonyl]norvaline (ms2hn6A), 2. The amino acid side chain was characterized as 3-hydroxynorvaline (3) by gas chromatography-mass spectrometry of the trimethylsilyl derivative after cleavage from 1 and 2 by alkaline hydrolysis. Evidence for the amino acid-purine carbamoyl linkage was obtained from the collision-induced dissociation mass spectrum of trimethylsilylated 1, and the total structure was confirmed by chemical synthesis of 1. PMID:1280806

Reddy, D M; Crain, P F; Edmonds, C G; Gupta, R; Hashizume, T; Stetter, K O; Widdel, F; McCloskey, J A

1992-11-11

248

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

PubMed

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

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

2012-08-01

249

Direct Membrane Binding by Bacterial Actin MreB  

PubMed Central

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

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

2011-01-01

250

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

NASA Technical Reports Server (NTRS)

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.

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

1989-01-01

251

Food habits of mute swans in the Chesapeake Bay  

USGS Publications Warehouse

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.

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

2004-01-01

252

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

PubMed Central

Transcription and translation use raw materials and energy generated metabolically to create the macromolecular machinery responsible for all cellular functions, including metabolism. A biochemically accurate model of molecular biology and metabolism will facilitate comprehensive and quantitative computations of an organism's molecular constitution as a function of genetic and environmental parameters. Here we formulate a model of metabolism and macromolecular expression. Prototyping it using the simple microorganism Thermotoga maritima, we show our model accurately simulates variations in cellular composition and gene expression. Moreover, through in silico comparative transcriptomics, the model allows the discovery of new regulons and improving the genome and transcription unit annotations. Our method presents a framework for investigating molecular biology and cellular physiology in silico and may allow quantitative interpretation of multi-omics data sets in the context of an integrated biochemical description of an organism. PMID:22760628

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

2013-01-01

253

Emissions of biogenic sulphur compounds from several wetland soils in Florida  

NASA Astrophysics Data System (ADS)

Emission rates of the biogenic sulphur gases hydrogen sulphide, dimethyl sulphide, carbon disulphide and dimethyl disulphide have been measured from the exposed soils of five wetland plant communities in Florida. Dimethyl sulphide and hydrogen sulphide were the predominant species emitted. All the studied ecosystems showed diel variation in the emission rates of the biogenic sulphur gases with the highest emissions rates occurring early- to mid-afternoon, and the lowest emission rates occurring during the early morning. The relative magnitude of emissions from the individual ecosystems followed the trend Distichlis spicata > Avicennia germinans > Batis maritima ? Juncus roemerianus ? Cladium jamaicense. Only the emission rates from the peaty D. spicata site are comparable in magnitude to previous emission measurements in wetland ecosystems of Spartina alterniflora and associated mud flats.

Cooper, W. J.; Cooper, D. J.; Saltzman, E. S.; Mello, W. Z. de; Savoie, D. L.; Zika, R. G.; Prospero, J. M.

254

Temporal and spatial variation in the macrophyte distribution in coastal lagoon Lake Nakaumi and its neighboring waters  

NASA Astrophysics Data System (ADS)

During the period May-December 1996, macrophyte distribution and its abundance were investigated for 24 sites in coastal lagoon Lake Nakaumi and its neighboring waters, southwestern Honshu, Japan. More than 21 taxa, including two aquatic angiosperms, were found and the taxa with high frequency of occurrence were Enteromorpha spp. and Sargassum thunbergii. Ruppia maritima, one of the endangered aquatic macrophytes in Japan, was also found making dense meadows in Honjou, an area planned to be reclaimed. Four distinct distributional regions were recognized in the lake by principal component analysis (PCA) using the seasonal maximum cover of each species, and a significant relation was found between PCA axis 1 and electric conductivity. A long-term change in floristic composition is also discussed based on the present results and literature.

Kunii, Hidenobu; Minamoto, Kouichi

2000-10-01

255

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

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

Saarela, Jeffery M.

2012-01-01

256

Structure of dihydrodipicolinate synthase from Methanocaldococcus jannaschii  

PubMed Central

In bacteria and plants, dihydrodipicolinate synthase (DHDPS) plays a key role in the (S)-lysine biosynthesis pathway. DHDPS catalyzes the first step of the condensation of (S)-aspartate-?-semialdehyde and pyruvate to form an unstable compound, (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid. The activity of DHDPS is allosterically regulated by (S)-lysine, a feedback inhibitor. The crystal structure of DHDPS from Methanocaldococcus jannaschii (MjDHDPS) was solved by the molecular-replacement method and was refined to 2.2?Å resolution. The structure revealed that MjDHDPS forms a functional homo­tetramer, as also observed in Escherichia coli DHDPS, Thermotoga maritima DHDPS and Bacillus anthracis DHDPS. The binding-site region of MjDHDPS is essentially similar to those found in other known DHDPS structures. PMID:20054116

Padmanabhan, Balasundaram; Strange, Richard W.; Antonyuk, Svetlana V.; Ellis, Mark J.; Hasnain, S. Samar; Iino, Hitoshi; Agari, Yoshihiro; Bessho, Yoshitaka; Yokoyama, Shigeyuki

2009-01-01

257

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

PubMed

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

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

2010-11-01

258

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

PubMed

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

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

2014-12-01

259

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

PubMed

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. PMID:23585905

Myung, Suwan; Zhang, Y-H Percival

2013-01-01

260

Hyperthermostable acetyl xylan esterase  

PubMed Central

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

Drzewiecki, Katharina; Angelov, Angel; Ballschmiter, Meike; Tiefenbach, Klaus-Jurgen; Sterner, Reinhard; Liebl, Wolfgang

2010-01-01

261

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

PubMed Central

Background 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. Results 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. Conclusion Although the large-scale ligand-induced changes are mediated through similar regions, and are produced by similar backbone movements in tmRBP and ecRBP, the small-scale ligand-induced structural rearrangements differentiate the mesophile and thermophile. This suggests there are mechanistic differences in the manner by which these two proteins bind their ligands and are an example of how two structurally similar proteins utilize different mechanisms to form a ligand-bound state. PMID:19019243

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

2008-01-01

262

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

PubMed

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

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

2014-01-01

263

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

PubMed

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

De Maeyer, Luk; Geerinck, Rik

2009-01-01

264

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

NASA Astrophysics Data System (ADS)

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

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

265

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

SciTech Connect

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.

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

2012-01-01

266

Triad pattern algorithm for predicting strong promoter candidates in bacterial genomes  

PubMed Central

Background Bacterial promoters, which increase the efficiency of gene expression, differ from other promoters by several characteristics. This difference, not yet widely exploited in bioinformatics, looks promising for the development of relevant computational tools to search for strong promoters in bacterial genomes. Results We describe a new triad pattern algorithm that predicts strong promoter candidates in annotated bacterial genomes by matching specific patterns for the group I ?70 factors of Escherichia coli RNA polymerase. It detects promoter-specific motifs by consecutively matching three patterns, consisting of an UP-element, required for interaction with the ? subunit, and then optimally-separated patterns of -35 and -10 boxes, required for interaction with the ?70 subunit of RNA polymerase. Analysis of 43 bacterial genomes revealed that the frequency of candidate sequences depends on the A+T content of the DNA under examination. The accuracy of in silico prediction was experimentally validated for the genome of a hyperthermophilic bacterium, Thermotoga maritima, by applying a cell-free expression assay using the predicted strong promoters. In this organism, the strong promoters govern genes for translation, energy metabolism, transport, cell movement, and other as-yet unidentified functions. Conclusion The triad pattern algorithm developed for predicting strong bacterial promoters is well suited for analyzing bacterial genomes with an A+T content of less than 62%. This computational tool opens new prospects for investigating global gene expression, and individual strong promoters in bacteria of medical and/or economic significance. PMID:18471287

Dekhtyar, Michael; Morin, Amelie; Sakanyan, Vehary

2008-01-01

267

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

PubMed Central

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

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

2010-01-01

268

X-ray Crystallography and Isothermal Titration Calorimetry Studies of the Salmonella Zinc Transporter ZntB  

PubMed Central

SUMMARY The ZntB Zn2+ efflux system is important for maintenance of Zn2+ homeostasis in Enterobacteria. We report crystal structures of ZntB cytoplasmic domains from Salmonella enterica serovar Typhimurium (StZntB) in dimeric and physiologically relevant homopentameric forms at 2.3 Å and 3.1 Å resolutions, respectively. The funnel-like structure is similar to that of the homologous Thermotoga maritima CorA Mg2+ channel and a Vibrio parahaemolyticus ZntB (VpZntB) soluble domain structure. However, the central ?7 helix forming the inner wall of the StZntB funnel is oriented perpendicular to the membrane instead of the marked angle seen in CorA or VpZntB. Consequently, the StZntB funnel pore is cylindrical, not tapered, which may represent an “open” form of the ZntB soluble domain. Our crystal structures and isothermal titration calorimetry data indicate that there are three Zn2+ binding sites in the full-length ZntB, two of which could be involved in Zn2+ transport. PMID:21565704

Wan, Qun; Ahmad, Md Faiz; Fairman, James; Gorzelle, Bonnie; de la Fuente, María; Dealwis, Chris; Maguire, Michael E.

2011-01-01

269

Structure of the Cytoplasmic Segment of Histidine Kinase Receptor QseC, a Key Player in Bacterial Virulence†  

PubMed Central

QseC is a histidine kinase (HK) receptor involved in quorum sensing, a mechanism by which bacteria respond to fluctuations in cell population. We conducted a structural study of the cytoplasmic domain of QseC (QseC-CD) using X-ray crystallography. The 2.5 Å structure of the apo-enzyme revealed that the kinase domain of QseC retains the overall fold of the typical HK kinase domain. The construct that we used is inactive in the autokinase reaction and its inactivity is most likely caused by its atypical dimerization interface, as compared to that observed in the T.maritima HK cytoplasmic domain structure. Restoration of the activity may require that the entire dimerization domain be present in the protein construct. QseC, which plays an important role in bacterial pathogenesis, is a promising drug target and the structure of QseCCD provides a platform for developing more potent inhibitors of pathogen virulence. PMID:20594156

Xie, Wei; Dickson, Chris; Kwiatkowski, Witek; Choe, Senyon

2012-01-01

270

Persistent organochlorine levels in six prey species of the gyrfalcon Falco rusticolus in Iceland.  

PubMed

Our previous investigations have revealed very high levels of organochlorines (OCs) in the Icelandic gyrfalcon Falco rusticolus, a resident top predator. We now examine six potential prey species of birds, both resident and migratory, in order to elucidate the most likely route of the OCs to the gyrfalcon. The ptarmigan Lagopus mutus, the most important prey of the gyrfalcon, contained very low levels of OCs. Bioaccumulation of polychlorinated biphenyls (PCBs) and DDTs in mallards Anas platyrhynchos, tufted ducks Aythya fuligula, golden plovers Pluvialis apricaria, purple sandpipers Calidris maritima, and black guillemots Cepphus grylle reflected their position in the foodchain. The differences in OC-levels seem nevertheless too high just to reflect the different food-chain levels of these species in Iceland. The winter grounds of the migratory golden plovers and tufted ducks appear to be more contaminated than the Icelandic terrestrial habitat of ptarmigans or the freshwater habitat as reflected in mallards, both resident species. However, spending the winter on the coast in Iceland, results in high levels of contaminants in purple sandpipers and black guillemots. Our results indicate OC contamination of the marine ecosystem in Iceland while the terrestrial and freshwater ecosystems are little affected. It is postulated that gyrfalcons receive the major part of the observed contamination from prey other than ptarmigan, especially birds associated with the marine ecosystem and also from migratory birds. PMID:11234542

Olafsdóttir, K; Petersen, A E; Magnúsdóttir, E V; Björnsson, T; Jóhannesson, T

2001-01-01

271

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

SciTech Connect

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

Š e; #269; kut; #279; , Jolita; McCloskey, Diane E.; Thomas, H. Jeanette; Secrist III, John A.; Pegg, Anthony E.; Ealick, Steven E. (Cornell); (Southern Research); (UPENN-MED)

2011-11-17

272

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

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

273

Use of digital multispectral videography to assess seagrass distribution in San Quinti??n Bay, Baja California, Mexico [Uso de videografi??a multiespectral digital para evaluar la distributio??n del pasto marino en Bahi??a San Quinti??n, Baja California, Me??xico  

USGS Publications Warehouse

Apparent threats to the spatial distribution of seagrass in San Quinti??n Bay prompted us to make a detailed assessment of habitats in the bay. Six coastal habitats and three seagrass subclasses were delineated using airborne digital multispectral videography (DMSV), Eelgrass, Zostera marina, was the predominant seagrass and covered 40% (1949 ha) of the areal extent of the bay in 1999. Eelgrass grew over a wide range of tidal depths from about -3.0 in mean lower low water (MLLW) to about 1.0 m MLLW, but greatest spatial extent occurred in intertidal areas -0.6 m to 1.0 m MLLW. Exposed-continuous (i.e., high density) eelgrass was the most abundant habitat in the bay. Widgeongrass, Ruppia maritima, was the only other seagrass present and covered 3% (136 ha) of the areal extent of the entire bay. Widgeongrass grew in single species stands in the upper intertidal (??? 0.4 MLLW) and intermixed with eelgrass at lower tidal depths. Overall accuracy of the six habitat classes and three subclasses in the DMSV map was relatively high at 84%. Our detailed map of San Quintin Bay can be used in future change detection analyses to monitor the health of seagrasses in the bay.

Ward, D.H.; Tibbitts, T.L.; Morton, A.; Carrera-Gonzalez, E.; Kempka, R.

2004-01-01

274

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

PubMed

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 A (1 A=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 beta-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

Martínez-Fleites, Carlos; Ortíz-Lombardía, Miguel; Pons, Tirso; Tarbouriech, Nicolas; Taylor, Edward J; Arrieta, Juan G; Hernández, Lázaro; Davies, Gideon J

2005-08-15

275

Anaerobic high-throughput cultivation method for isolation of thermophiles using biomass-derived substrates.  

PubMed

Flow cytometry (FCM) techniques have been developed for sorting mesophilic organisms, but the difficulty increases if the target microbes are thermophilic anaerobes. We demonstrate a reliable, high-throughput method of screening thermophilic anaerobic organisms using FCM and 96-well plates for growth on biomass-relevant substrates. The method was tested using the cellulolytic thermophiles Clostridium thermocellum (T(opt) = 55 °C), Caldicellulosiruptor obsidiansis (T(opt) = 78 °C) and the fermentative hyperthermophiles, Pyrococcus furiosus (T(opt) = 100 °C) and Thermotoga maritima (T(opt) = 80 °C). Multi-well plates were incubated at various temperatures for approximately 72-120 h and then tested for growth. Positive growth resulting from single cells sorted into individual wells containing an anaerobic medium was verified by OD(600). Depending on the growth substrate, up to 80 % of the wells contained viable cultures, which could be transferred to fresh media. This method was used to isolate thermophilic microbes from Rabbit Creek, Yellowstone National Park (YNP), Wyoming. Substrates for enrichment cultures including crystalline cellulose (Avicel), xylan (from Birchwood), pretreated switchgrass and Populus were used to cultivate organisms that may be of interest to lignocellulosic biofuel production. PMID:22843398

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

2012-01-01

276

Fluorescence in insects  

NASA Astrophysics Data System (ADS)

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.

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

2012-10-01

277

Status and threats on seagrass beds using GIS in Vietnam  

NASA Astrophysics Data System (ADS)

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.

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

2012-10-01

278

Crystal structure of ribosomal protein L4 shows RNA-binding sites for ribosome incorporation and feedback control of the S10 operon  

PubMed Central

Ribosomal protein L4 resides near the peptidyl transferase center of the bacterial ribosome and may, together with rRNA and proteins L2 and L3, actively participate in the catalysis of peptide bond formation. Escherichia coli L4 is also an autogenous feedback regulator of transcription and translation of the 11 gene S10 operon. The crystal structure of L4 from Thermotoga maritima at 1.7 ? resolution shows the protein with an alternating ?/? fold and a large disordered loop region. Two separate binding sites for RNA are discernible. The N–terminal site, responsible for binding to rRNA, consists of the disordered loop with flanking ?–helices. The C–terminal site, a prime candidate for the interaction with the leader sequence of the S10 mRNA, involves two non-consecutive ?–helices. The structure also suggests a C–terminal protein-binding interface, through which L4 could be interacting with protein components of the transcriptional and/or translational machineries. PMID:10698923

Worbs, Michael; Huber, Robert; Wahl, Markus C.

2000-01-01

279

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

PubMed

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

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

2013-01-01

280

Flow synthesis of phenylserine using threonine aldolase immobilized on Eupergit support  

PubMed Central

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

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

2013-01-01

281

Crystal structure of the N-terminal domain of MinC dimerized via domain swapping  

PubMed Central

Proper cell division at the mid-site of gram-negative bacteria reflects critical regulation by the min system (MinC, MinD and MinE) of the cytokinetic Z ring, which is a polymer composed of FtsZ subunits. MinC and MinD act together to inhibit aberrantly positioned Z-ring formation. MinC consists of two domains: an N-terminal domain (MinCNTD), which interacts with FtsZ and inhibits FtsZ polymerization, and a C-terminal domain (MinCCTD), which interacts with MinD and inhibits the bundling of FtsZ filaments. These two domains reportedly function together, and both are essential for normal cell division. The full-length dimeric structure of MinC from Thermotoga maritima has been reported, and shows that MinC dimerization occurs via MinCCTD; MinCNTD is not involved in dimerization. Here the crystal structure of Escherichia coli MinCNTD (EcoMinCNTD) is reported. EcoMinCNTD forms a dimer via domain swapping between the first ? strands in each subunit. It is therefore suggested that the dimerization of full-length EcoMinC occurs via both MinCCTD and MinCNTD, and that the dimerized EcoMinCNTD likely plays an important role in inhibiting aberrant Z-ring localization. PMID:24121353

An, Jun Yop; Kim, Tae Gyun; Park, Kyoung Ryoung; Lee, Jung-Gyu; Youn, Hyung-Seop; Lee, Youngjin; Kang, Jung Youn; Kang, Gil Bu; Eom, Soo Hyun

2013-01-01

282

Crystal structure of the RNA component of bacterial ribonuclease P  

SciTech Connect

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

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

2010-03-08

283

The Periplasmic Loop Provides Stability to the Open State of the CorA Magnesium Channel*  

PubMed Central

Crystal structures of the CorA Mg2+ channel have suggested that metal binding in the cytoplasmic domain stabilizes the pentamer in a closed conformation. The open “metal free” state of the channel is, however, still structurally uncharacterized. Here, we have attempted to map conformational states of CorA from Thermotoga maritima by determining which residues support the pentameric structure in the presence or absence of Mg2+. We find that when Mg2+ is present, the pentamer is stabilized by the putative gating sites (M1/M2) in the cytoplasmic domain. Strikingly however, we find that the conserved and functionally important periplasmic loop is vital for the integrity of the pentamer when Mg2+ is absent from the M1/M2 sites. Thus, although the periplasmic loops were largely disordered in the x-ray structures of the closed channel, our data suggests a prominent role for the loops in stabilizing the open conformation of the CorA channels. PMID:22722933

Palombo, Isolde; Daley, Daniel O.; Rapp, Mikaela

2012-01-01

284

The Structural Basis of Sirtuin Substrate Affinity  

SciTech Connect

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.

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

2006-01-01

285

Syntrophic butyrate and propionate oxidation processes: from genomes to reaction mechanisms.  

PubMed

In anoxic environments such as swamps, rice fields and sludge digestors, syntrophic microbial communities are important for decomposition of organic matter to CO2 and CH4 . The most difficult step is the fermentative degradation of short-chain fatty acids such as propionate and butyrate. Conversion of these metabolites to acetate, CO2 , formate and hydrogen is endergonic under standard conditions and occurs only if methanogens keep the concentrations of these intermediate products low. Butyrate and propionate degradation pathways include oxidation steps of comparably high redox potential, i.e. oxidation of butyryl-CoA to crotonyl-CoA and of succinate to fumarate, respectively, that require investment of energy to release the electrons as hydrogen or formate. Although investigated for several decades, the biochemistry of these reactions is still not completely understood. Genome analysis of the butyrate-oxidizing Syntrophomonas wolfei and Syntrophus aciditrophicus and of the propionate-oxidizing Syntrophobacter fumaroxidans and Pelotomaculum thermopropionicum reveals the presence of energy-transforming protein complexes. Recent studies indicated that S. wolfei uses electron-transferring flavoproteins coupled to a menaquinone loop to drive butyryl-CoA oxidation, and that S. fumaroxidans uses a periplasmic formate dehydrogenase, cytochrome b:quinone oxidoreductases, a menaquinone loop and a cytoplasmic fumarate reductase to drive energy-dependent succinate oxidation. Furthermore, we propose that homologues of the Thermotoga maritima bifurcating [FeFe]-hydrogenase are involved in NADH oxidation by S. wolfei and S. fumaroxidans to form hydrogen. PMID:23766220

Müller, Nicolai; Worm, Petra; Schink, Bernhard; Stams, Alfons J M; Plugge, Caroline M

2010-08-01

286

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

PubMed Central

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

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

2012-01-01

287

1 Wetland monitoring using classification trees and SPOT-5 seasonal time series.  

E-print Network

Multi-season reflectance data from radiometrically and geometrically corrected multispectral SPOT-5 images of 10-m resolution were combined with thorough field campaigns and land cover digitizing using a binary classification tree algorithm to estimate the area of marshes covered with common reeds (Phragmites australis) and submerged macrophytes (Potamogeton pectinatus, P. pusillus, Myriophyllum spicatum, Ruppia maritima, Chara sp.) over an area of 145 000 ha. Accuracy of these models was estimated by cross-validation and by calculating the percentage of correctly classified pixels on the resulting maps. Robustness of this approach was assessed by applying these models to an independent set of images using independent field data for validation. Biophysical parameters of both habitat types were used to interpret the misclassifications. The resulting trees provided a cross-validation accuracy of 98.7% for common reed and 97.4 % for submerged macrophytes. Variables discriminating reed marshes from other land covers were the difference in the near-infrared band between March and June, the

Aurélie Davranche; Gaëtan Lefebvre; Brigitte Poulin

2012-01-01

288

FtsA forms actin-like protofilaments  

PubMed Central

FtsA is an early component of the Z-ring, the structure that divides most bacteria, formed by tubulin-like FtsZ. FtsA belongs to the actin family of proteins, showing an unusual subdomain architecture. Here we reconstitute the tethering of FtsZ to the membrane via FtsA's C-terminal amphipathic helix in vitro using Thermotoga maritima proteins. A crystal structure of the FtsA:FtsZ interaction reveals 16 amino acids of the FtsZ tail bound to subdomain 2B of FtsA. The same structure and a second crystal form of FtsA reveal that FtsA forms actin-like protofilaments with a repeat of 48?Å. The identical repeat is observed when FtsA is polymerized using a lipid monolayer surface and FtsAs from three organisms form polymers in cells when overexpressed, as observed by electron cryotomography. Mutants that disrupt polymerization also show an elongated cell division phenotype in a temperature-sensitive FtsA background, demonstrating the importance of filament formation for FtsA's function in the Z-ring. PMID:22473211

Szwedziak, Piotr; Wang, Qing; Freund, Stefan MV; Löwe, Jan

2012-01-01

289

Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA  

PubMed Central

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

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

2010-01-01

290

Cloning of the Gene Encoding a Novel Thermostable ?-Galactosidase from Thermus brockianus ITI360  

PubMed Central

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

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

1999-01-01

291

Simultaneous RP-HPLC-DAD separation, and determination of flavonoids and phenolic acids in Plantago L. species.  

PubMed

A rapid reversed-phase (RP) high-performance liquid chromatography method was developed and applied for simultaneous separation, and determination of flavonoids and phenolic acids in eight Plantago L. taxa (P. altissima L., P. argentea Chaix, P. coronopus L., P. holosteum Scop. ssp. depauperata Pilger, P. holosteum ssp. holosteum, P. holosteum ssp. scopulorum (Degen) Horvati?, P. lagopus L., and P. maritima L.) growing in Croatia. Chromatographic separation was carried out on Zorbax Eclipse XDB-C18 using gradient elution with a H2 O (pH?2.5, adjusted with CF3 COOH) and MeCN mixture at 30°. The contents of analyzed phenolic compounds (% of the dry weight of the leaves, dw) varied among examined species: rutin (max. 0.024%, P. argentea), hyperoside (max. 0.020%, P. lagopus), quercitrin (max. 0.013%, P. holosteum ssp. holosteum), quercetin (max. 0.028%, P. holosteum ssp. scopulorum), chlorogenic acid (max. 0.115%, P. lagopus), and caffeic acid (max. 0.046%, P. coronopus). Isoquercitrin was detected only in P. argentea (0.020%), while isochlorogenic acid content was below limit of quantification in all investigated species. Multivariate analyses (UPGMA and PCA) showed significant differences in contents of investigated polyphenolic compounds between different Plantago taxa. Accordingly, investigated substances might be employed as chemotaxonomic markers in the study of the complex genus Plantago. PMID:23847075

Juriši? Grubeši?, Renata; Sre?nik, Goran; Kremer, Dario; Vukovi? Rodríguez, Jadranka; Nikoli?, Toni; Vladimir-Kneževi?, Sanda

2013-07-01

292

A legacy of contrasting spatial genetic structure on either side of the Atlantic-Mediterranean transition zone in a marine protist.  

PubMed

The mechanisms that underpin the varied spatial genetic structures exhibited by free-living marine microorganisms remain controversial, with most studies emphasizing a high dispersal capability that should redistribute genetic diversity in contrast to most macroorganisms whose populations often retain a genetic signature of demographic response to historic climate fluctuations. We quantified the European phylogeographic structure of the marine flagellate Oxyrrhis marina and found a marked difference in spatial genetic structure, population demography, and genetic diversity between the northwest Atlantic and Mediterranean Sea that reflects the persistent separation of these regions as well as context-dependent population responses to contrasting environments. We found similar geographic variation in the level of genetic diversity in the sister species Oxyrrhis maritima. Because the capacity for wide dispersal is not always realized, historic genetic footprints of range expansion and contraction persist in contemporary populations of marine microbes, as they do in larger species. Indeed, the well-described genetic effects of climatic variation on macroorganisms provide clear, testable hypotheses about the processes that drive genetic divergence in marine microbes and thus about the response to future environmental change. PMID:23213247

Lowe, Chris D; Martin, Laura E; Montagnes, David J S; Watts, Phillip C

2012-12-18

293

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

SciTech Connect

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

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

2002-01-01

294

Structure-Based Function Prediction of Uncharacterized Protein Using Binding Sites Comparison  

PubMed Central

A challenge in structural genomics is prediction of the function of uncharacterized proteins. When proteins cannot be related to other proteins of known activity, identification of function based on sequence or structural homology is impossible and in such cases it would be useful to assess structurally conserved binding sites in connection with the protein's function. In this paper, we propose the function of a protein of unknown activity, the Tm1631 protein from Thermotoga maritima, by comparing its predicted binding site to a library containing thousands of candidate structures. The comparison revealed numerous similarities with nucleotide binding sites including specifically, a DNA-binding site of endonuclease IV. We constructed a model of this Tm1631 protein with a DNA-ligand from the newly found similar binding site using ProBiS, and validated this model by molecular dynamics. The interactions predicted by the Tm1631-DNA model corresponded to those known to be important in endonuclease IV-DNA complex model and the corresponding binding free energies, calculated from these models were in close agreement. We thus propose that Tm1631 is a DNA binding enzyme with endonuclease activity that recognizes DNA lesions in which at least two consecutive nucleotides are unpaired. Our approach is general, and can be applied to any protein of unknown function. It might also be useful to guide experimental determination of function of uncharacterized proteins. PMID:24244144

Konc, Janez; Hodoscek, Milan; Ogrizek, Mitja; Trykowska Konc, Joanna; Janezic, Dusanka

2013-01-01

295

Impact of fresh and composted solid olive husk and their water-soluble fractions on soil heavy metal fractionation; microbial biomass and plant uptake.  

PubMed

The use of waste materials as organic amendments in soil remediation can affect metal solubility; this interaction will vary with the characteristics of the organic matter that is added to the soil. A pot experiment was carried out in a calcareous, metal-polluted soil, using Beta maritima L. as an indicator species for the treatment effects on metal solubility. The treatments were: fresh solid olive husk, a mature compost, their respective water extracts (as the most reactive and biodegradable fraction) and an unamended, control soil. The compost reduced metal availability and plant uptake, while fresh olive husk favoured Mn bioavailability and produced phytotoxicity. The water-soluble extract from fresh solid olive husk also provoked elevated Mn solubility in soil, but did not increase Mn uptake by plants. The application of water-soluble organic matter obtained from compost did not affect heavy metal solubility significantly. Therefore, composted olive husk seems to be the most-appropriate material for the development of bioremediation strategies. PMID:21216095

de la Fuente, Carlos; Clemente, Rafael; Martínez-Alcalá, Isabel; Tortosa, Germán; Bernal, M Pilar

2011-02-28

296

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

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

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

2003-01-01

297

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

USGS Publications Warehouse

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

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

1995-01-01

298

Chemical and in vitro assessment of Alaskan coastal vegetation antioxidant capacity.  

PubMed

Alaska Native (AN) communities have utilized tidal plants and marine seaweeds as food and medicine for generations, yet the bioactive potential of these resources has not been widely examined. This study screened six species of Alaskan seaweed ( Fucus distichus , Saccharina latissima , Saccharina groenlandica , Alaria marginata , Pyropia fallax , and Ulva lactuca ) and one tidal plant ( Plantago maritima ) for antioxidant activity. Total polyphenolic content (TPC) was determined, and chemical antioxidant capacity was assessed by 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging, ferrous ion chelating, and nitric oxide (NO) inhibition assays. In vitro inhibition of radical oxygen species (ROS) generation and NO synthesis was evaluated in a RAW 264.7 macrophage culture. Greatest TPC (557.2 ?g phloroglucinol equivalents (PGE)/mg extract) was discovered in the ethyl acetate fraction of F. distichus, and highest DDPH scavenging activity was exhibited by F. distichus and S. groenlandica fractions (IC50 = 4.29-5.12 ?g/mL). These results support the potential of Alaskan coastal vegetation, especially the brown algae, as natural sources of antioxidants for preventing oxidative degeneration and maintaining human health. PMID:24147955

Kellogg, Joshua; Lila, Mary Ann

2013-11-20

299

Construction of a chimeric thermoacidophilic beta-endoglucanase  

PubMed Central

Background The archeaon Sulfolobus solfataricus P2 encodes a thermoacidophilic cellulase which shows an extreme acid and thermal stability with a pH optimum at 1.8 and a temperature optimum at 80°C. This extraordinary enzyme could be useful for biotechnological exploitation but the expression and purification in expression hosts like E. coli is unsatisfactory due to the high aggregation tendency of the recombinant enzyme. The thermophilic cellulase CelA from Thermotoga maritima belongs to the same glycoside hydrolase family (GH12) but has a neutral pH optimum. In contrast to SSO1949 this enzyme is expressed partially soluble in E. coli. Results We aimed to constructed a hybrid enzyme based on these two beta-endoglucanases which should successfully combine the advantageous properties of both cellulases, i.e. recombinant expression in E. coli, acidophily and thermophily. We constructed two hybrid proteins after bioinformatic analysis: both hybrids are expressed insoluble in E. coli, but one hybrid enzyme was successfully refolded from washed inclusion bodies. Conclusions The refolded active chimeric enzyme shows a temperature optimum of approximately 85°C and a pH optimum of approximately pH 3 thus retaining the advantageous properties of the Sulfolobus parent enzyme. This study suggests that the targeted construction of chimeric enzymes is an alternative to point mutational engineering efforts as long as parent enzymes with the wanted properties are available. PMID:23627611

2013-01-01

300

Functional Characterization of Two M42 Aminopeptidases Erroneously Annotated as Cellulases  

PubMed Central

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

Dutoit, Raphael; Brandt, Nathalie; Legrain, Christianne; Bauvois, Cedric

2012-01-01

301

Clusters of Branched Aliphatic Side Chains Serve As Cores of Stability in the Native State of the HisF TIM Barrel Protein  

PubMed Central

Imidazole-3-glycerol phosphate synthase is a heterodimeric allosteric enzyme that catalyzes consecutive reactions in imidazole biosynthesis through its HisF and HisH subunits. The unusually slow unfolding reaction of the isolated HisF TIM barrel domain from the thermophilic bacteria, Thermotoga maritima, enabled an NMR-based site-specific analysis of the main-chain hydrogen bonds that stabilize its native conformation. Very strong protection against exchange with solvent deuterium in the native state was found in a subset of buried positions in ?-helices and pervasively in the underlying ?-strands associated with a pair of large clusters of isoleucine, leucine and valine (ILV) side chains located in the ?7(??)8(??)1–2 and ?2(??)3–6?7 segments of the (??)8 barrel. The most densely packed region of the large cluster, ?3(??)4–6?7, correlates closely with the core of stability previously observed in computational, protein engineering and NMR dynamics studies, demonstrating a key role for this cluster in determining the thermodynamic and structural properties of the native state of HisF. When considered with the results of previous studies where ILV clusters were found to stabilize the hydrogen-bonded networks in folding intermediates for other TIM barrel proteins, it appears that clusters of branched aliphatic side chains can serve as cores of stability across the entire folding reaction coordinate of one of the most common motifs in biology. PMID:23333740

Gangadhara, Basavanapura N.; Laine, Jennifer M.; Kathuria, Sagar V.; Massi, Francesca; Matthews, C. Robert

2013-01-01

302

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

SciTech Connect

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.

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

2009-09-02

303

Cross-linked polymer nanofibers for hyperthermophilic enzyme immobilization: approaches to improve enzyme performance.  

PubMed

We report an enzyme immobilization method effective at elevated temperatures (up to 105 °C) and sufficiently robust for hyperthermophilic enzymes. Using a model hyperthermophilic enzyme, ?-galactosidase from Thermotoga maritima, immobilization within chemically cross-linked poly(vinyl alcohol) (PVA) nanofibers to provide high specific surface area is achieved by (1) electrospinning a blend of a PVA and enzyme and (2) chemically cross-linking the polymer to entrap the enzyme within a water insoluble PVA fiber. The resulting enzyme-loaded nanofibers are water-insoluble at elevated temperatures, and enzyme leaching is not observed, indicating that the cross-linking effectively immobilizes the enzyme within the fibers. Upon immobilization, the enzyme retains its hyperthermophilic nature and shows improved thermal stability indicated by a 5.5-fold increase in apparent half-life at 90 °C, but with a significant decrease in apparent activity. The loss in apparent activity is attributed to enzyme deactivation and mass transfer limitations. Improvements in the apparent activity can be achieved by incorporating a cryoprotectant during immobilization to prevent enzyme deactivation. For example, immobilization in the presence of trehalose improved the apparent activity by 10-fold. Minimizing the mat thickness to reduce interfiber diffusion was a simple and effective method to further improve the performance of the immobilized enzyme. PMID:25058141

Tang, Christina; Saquing, Carl D; Morton, Stephen W; Glatz, Brittany N; Kelly, Robert M; Khan, Saad A

2014-08-13

304

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

PubMed

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

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

2014-09-01

305

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

NASA Astrophysics Data System (ADS)

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.

Maher, Louis J.; Miller, Norton G.; Baker, Richard G.; Curry, B. Brandon; Mickelson, David M.

1998-03-01

306

Allosteric Inhibitors at the Heterodimer Interface of Imidazole Glycerol Phosphate Synthase  

NASA Astrophysics Data System (ADS)

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

Snoeberger, Ning-Shiuan Nicole

307

Ecology of mysid shrimps in the Bornholm Basin (central Baltic Sea)  

NASA Astrophysics Data System (ADS)

Mysid shrimps are an important trophic link in the food web of the Baltic Sea. In 2002 and 2003 we investigated species composition, distribution, life cycle and prey in the Bornholm Basin (central Baltic). Three species and one genus were identified: Mysis mixta, Neomysis integer, Mesopodopsis slabberi and Praunus sp . The dominant M. mixta and N. integer occurred in the whole study area but were more abundant in the peripheral, more shallow regions. Size frequency distribution indicated one generation for M. mixta and probably two for N. integer. Main prey of all size classes in both species was the cladoceran Bosmina coregoni maritima during summer and autumn. In spring and winter also copepods of the species Temora longicornis and Pseudocalanus acuspes were important prey items. Detritus and phytoplankton cells were of minor importance and many individuals had empty guts. Mysid shrimps in the deep basin might be advected from more shallow areas, as the abundance of all species was much lower than in coastal regions. The deep Bornholm Basin does not seem to be a favourable habitat, probably due to the inaccessibility of the oxygen deficient bottom layer. Under current hydrographic conditions mysids are probably not important predators of zooplankton and thus not competitors of planktivorous fish in the Bornholm Basin.

Barz, Kristina; Hirche, Hans-Jürgen

2009-12-01

308

Additions to the Mycosphaerella complex.  

PubMed

Species in the present study were compared based on their morphology, growth characteristics in culture, and DNA sequences of the nuclear ribosomal RNA gene operon (including ITS1, ITS2, 5.8S nrDNA and the first 900 bp of the 28S nrDNA) for all species and partial actin and translation elongation factor 1-alpha gene sequences for Cladosporium species. New species of Mycosphaerella (Mycosphaerellaceae) introduced in this study include M. cerastiicola (on Cerastium semidecandrum, The Netherlands), and M. etlingerae (on Etlingera elatior, Hawaii). Mycosphaerella holualoana is newly reported on Hedychium coronarium (Hawaii). Epitypes are also designated for Hendersonia persooniae, the basionym of Camarosporula persooniae, and for Sphaerella agapanthi, the basionym of Teratosphaeria agapanthi comb. nov. (Teratosphaeriaceae) on Agapathus umbellatus from South Africa. The latter pathogen is also newly recorded from A. umbellatus in Europe (Portugal). Furthermore, two sexual species of Cladosporium (Davidiellaceae) are described, namely C. grevilleae (on Grevillea sp., Australia), and C. silenes (on Silene maritima, UK). Finally, the phylogenetic position of two genera are newly confirmed, namely Camarosporula (based on C. persooniae, teleomorph Anthracostroma persooniae), which is a leaf pathogen of Persoonia spp. in Australia, belongs to the Teratosphaeriaceae, and Sphaerulina (based on S. myriadea), which occurs on leaves of Fagaceae (Carpinus, Castanopsis, Fagus, Quercus), and belongs to the Mycosphaerellaceae. PMID:22679588

Crous, Pedro W; Tanaka, Kazuaki; Summerell, Brett A; Groenewald, Johannes Z

2011-06-01

309

Effects of ammonium and aluminium on the development and nutrition of Pinus nigra in hydroculture.  

PubMed

Application of ammonium and aluminium to young Pinus nigra var. maritima (Ait.) Melville trees resulted in a variety of negative effects. Excess ammonium led to an increase in shoot/root ratio. The biomass of the fine roots declined, resulting in an increase of the coarse/fine root ratio. The degree of mycorrhizal infection of the roots decreased. The nitrogen content of the trees increased considerably, whereas particularly the levels of calcium magnesium, manganese and zinc decreased sharply. Excess aluminium resulted in a simultaneous reduction of root and shoot biomass, a decline of the fine root system, an increase in the coarse/fine root ratio and a decrease in the degree of mycorrhizal infection. Uptake of the divalent cations calcium, magnesium, iron, manganese and zinc was restricted substantially, The nitrogen and phosphorus contents of the trees were hardly affected, whilst the potassium content of the shoot increased and of the roots decreased. This implicates that a deteriorating fine root system has to supply water and nutrients to a more demanding shoot. In the long term, high ammonium inputs and aluminium dissolution in forest ecosystems will lead to substantial nutrient deficiencies, just as has been found in the field. PMID:15092085

Boxman, A W; Krabbendam, H; Bellemakers, M J; Roelofs, J G

1991-01-01

310

Different status of the gene for ribosomal protein S16 in the chloroplast genome during evolution of the genus Arabidopsis and closely related species.  

PubMed

The ribosomal protein S16 (RPS16), the product of the rps16, is generally encoded in the chloroplast genomes of flowering plants. However, it has been reported that chloroplast-encoded RPS16 in mono- and dicotyledonous plants has been substituted by the product of nuclear-encoded rps16, which was transferred from the mitochondria to the nucleus before the early divergence of angiosperms. Current databases show that the chloroplast-encoded rps16 has become a pseudogene in four species of the Brassicaceae (Aethionema grandiflorum, Arabis hirsuta, Draba nemorosa, and Lobularia maritima). Further analysis of Arabidopsis thaliana and its close relatives has shown that pseudogenization has also occurred via the loss of its splicing capacity (Arabidopsis thaliana and Olimarabidopsis pumila). In contrast, the spliced product of chloroplast-encoded rps16 is observed in close relatives of Arabidopsis thaliana (Arabidopsis arenosa, Arabidopsis lyrata, and Crucihimalaya lasiocarpa). In this study, we identified the different functional status of rps16 in several chloroplast genomes in the genus Arabidopsis and its close relatives. Our results strongly suggest that nuclear- and chloroplast-encoded rps16 genes coexisted for at least 126 million years. We raise the possibility of the widespread pseudogenization of rps16 in the angiosperm chloroplast genomes via the loss of its splicing capacity, even when the rps16 encoded in the chloroplast genome is transcriptionally active. PMID:21317544

Roy, Shradha; Ueda, Minoru; Kadowaki, Koh-ichi; Tsutsumi, Nobuhiro

2010-01-01

311

The Root-Knot Nematode Producing Galls on Spartina alterniflora Belongs to the Genus Meloidogyne: Rejection of Hypsoperine and Spartonema spp.  

PubMed Central

Root-knot nematodes are a major group of plant-parasitic nematodes, but their sister group within the Tylenchida remains to be identified. To find the sister group and for any investigation of the evolutionary biology of the genus Meloidogyne, it would be useful to identify the most basal species within Meloidogyninae. Meloidogyne spartinae, a root-knot nematode parasitic on cordgrass (Spartina spp.), constitutes a potentially interesting early diverging (or at least highly divergent) root-knot nematode because it was originally described in a different genus, Hypsoperine (and later Spartonema), due to its unique anatomy and biology (although it was later put in synonymy by some, but not all, taxonomists). We have sequenced the whole 18S rDNA of this species and compared it to other sequences of this region that are available in GenBank for numerous Meloidogyne species. Phylogenetic analysis unambiguously locates the branch corresponding to M. spartinae as a lately diverging species, more closely related to M. maritima, M. duytsi or the M. ardenensis-hapla group. Thus, the distinction of a separate genus (Hypsoperine or Spartonema) for this species is not justified. PMID:19259481

Plantard, Olivier; Valette, Sylvie; Gross, Michael F.

2007-01-01

312

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

PubMed Central

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

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

2013-01-01

313

A possible degree of motional freedom in bacterial chemoreceptor cytoplasmic domains and its potential role in signal transduction  

PubMed Central

We describe an array of gaps in an antiparallel four-helix bundle structure, the cytoplasmic domains of bacterial chemoreceptors. For a given helix, the side chain interactions that define a helix’s position are analyzed in terms of residue interfaces, the most important of which are a-a, g-g, d-d, g-d, and a-d. It was found that the interdigitation of the side groups does not entirely fill the space along the long axis of the structure, which results in a rather regular array of gaps. A simulated piston motion of helix CD1 along the helical axis direction by 1.2Å shows that 85% of the side chain interactions still satisfy Van der Waals criteria, while the remaining clashes could be avoided by small rotations of side chains. Therefore, two states could exist in the structure, related by a piston motion. Analysis of the crystal structure of a small four-helix bundle, the P1short domain of CheA in Thermotoga Maritima, reveals that the two coexisting states related by a 1.3-1.7Å piston motion are defined by the same mechanism. This two-state model is a plausible candidate mechanism for the long distance signal transduction in bacterial chemoreceptors and is qualitatively consistent with literature chemoreceptor mutagenesis results. Such a mechanism could exist in many other structures with interdigitating ?-helices. PMID:21968904

Hu, Weiguo

2011-01-01

314

Ritual plants of Muslim graveyards in northern Israel  

PubMed Central

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

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

2006-01-01

315

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

PubMed

Plateau pika is the main fossorial mammal in the alpine grassland in Qinghai Lake Watershed of Northwest China. Based on the field investigation data from 18 alpine grassland quadrats in the Watershed, and by using redundancy analysis (RDA) and the surface fitting offered by 'R-Vegan' , the disturbance intensity of plateau pika (Ochotona pallasi) was classified as four levels. In order to explore the impacts of plateau pika disturbance on the alpine grassland ecosystem and its grazing quality, the community characteristics under different disturbance intensities by plateau pika were analyzed, and a conceptual model about the alpine grassland community succession was proposed. The results showed that with the increase of the disturbance intensity, the dominant species changed from Juncus roemerianus to Poa pratensis and Laux maritima. When the disturbance was small, the community had high quantitative values of coverage, aboveground biomass, biodiversity, and species richness, but the proportion of weeds was also high. When the disturbance was large, the quantitative values were the lowest, while the proportion of weeds was the highest. When the disturbance was moderate, the community had relatively high quantitative values, and the proportion of grasses and sedges was the highest. It was concluded that the community' s characteristic values under low plateau pika disturbance intensity were high but the grazing quality was low, while high disturbance intensity resulted in the grassland degradation. Therefore, the disturbance intensity in the threshold could maintain the stability of alpine grassland ecosystem and improve its grazing quality. PMID:24380328

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

2013-08-01

316

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

PubMed Central

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

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

2010-01-01

317

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

NASA Astrophysics Data System (ADS)

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

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

1994-11-01

318

Air pollution effects on the ultrastructure of Phlomis fruticosa mesophyll cells  

SciTech Connect

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.

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

1987-04-01

319

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

PubMed

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

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

2011-01-01

320

Crystal structure of a 4-thiouridine synthetase-RNA complex reveals specificity of tRNA U8 modification  

PubMed Central

In prokaryotes and archaea transfer ribonucleic acid (tRNA) stability as well as cellular UV protection relies on the post-transcriptional modification of uracil at position 8 (U8) of tRNAs by the 4-thiouridine synthetase ThiI. Here, we report three crystal structures of ThiI from Thermotoga maritima in complex with a truncated tRNA. The RNA is mainly bound by the N-terminal ferredoxin-like domain (NFLD) and the THUMP domain of one subunit within the ThiI homo-dimer thereby positioning the U8 close to the catalytic center in the pyrophosphatase domain of the other subunit. The recognition of the 3’-CCA end by the THUMP domain yields a molecular ruler defining the specificity for U8 thiolation. This first structure of a THUMP/NFLD-RNA complex might serve as paradigm for the RNA recognition by THUMP domains of other proteins. The ternary ThiI–RNA–ATP complex shows no significant structural changes due to adenosine triphosphate (ATP) binding, but two different states of active site loops are observed independent of the nucleotide loading state. Thereby conformational changes of the active site are coupled with conformational changes of the bound RNA. The ThiI–RNA complex structures indicate that full-length tRNA has to adopt a non-canonical conformation upon binding to ThiI. PMID:24705700

Neumann, Piotr; Naumann, Peter-Thomas; Erwin, Whitney M.; Lauhon, Charles T.; Ficner, Ralf

2014-01-01

321

Structure and characterization of the 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Aeropyrum pernix  

PubMed Central

The first enzyme in the shikimic acid biosynthetic pathway, 3-deoxy-D-arabinoheptulosonate 7-phosphate synthase (DAH7PS), varies significantly in size and complexity in the bacteria and plants that express it. The DAH7PS from the archaebacterium Aeropyrum pernix (DAH7PSAp) is among the smallest and least complex of the DAH7PS enzymes, leading to the hypothesis that DAH7PSAp would not be subject to feedback regulation by shikimic acid pathway products. We overexpressed DAH7PSAp in Escherichia coli, purified it, and characterized its enzymatic activity. We then solved its X-ray crystal structure with a divalent manganese ion and phosphoenolpyruvate bound (PDBID: 1VS1). DAH7PSAp is a homodimeric metalloenzyme in solution. Its enzymatic activity increases dramatically above 60°C, with optimum activity at 95°C. Its pH optimum at 60°C is 5.7. DAH7PSAp follows Michaelis-Menten kinetics at 60° C, with a KM for erythrose 4-phosphate of 280 ?M, a KM for phosphoenolpyruvate of 891 ?M, and a kcat of 1.0 s-1. None of the downstream products of the shikimate biosynthetic pathway we tested inhibited the activity of DAH7PSAp. The structure of DAH7PSAp is similar to the structures of DAH7PS from Thermatoga maritima (PDB ID: 3PG8) and Pyrococcus furiosus (PDB ID: 1ZCO), and is consistent with its designation as an unregulated DAH7PS. PMID:22035970

Zhou, Lily; Wu, Jing; Janakiraman, Vijayalakshmi; Shumilin, Igor A.; Bauerle, Ronald; Kretsinger, Robert H.

2011-01-01

322

Ex-527 inhibits Sirtuins by exploiting their unique NAD+-dependent deacetylation mechanism  

PubMed Central

Sirtuins are protein deacetylases regulating metabolism and stress responses. The seven human Sirtuins (Sirt1–7) are attractive drug targets, but Sirtuin inhibition mechanisms are mostly unidentified. We report the molecular mechanism of Sirtuin inhibition by 6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide (Ex-527). Inhibitor binding to potently inhibited Sirt1 and Thermotoga maritima Sir2 and to moderately inhibited Sirt3 requires NAD+, alone or together with acetylpeptide. Crystal structures of several Sirtuin inhibitor complexes show that Ex-527 occupies the nicotinamide site and a neighboring pocket and contacts the ribose of NAD+ or of the coproduct 2’-O-acetyl-ADP ribose. Complex structures with native alkylimidate and thio-analog support its catalytic relevance and show, together with biochemical assays, that only the coproduct complex is relevant for inhibition by Ex-527, which stabilizes the closed enzyme conformation preventing product release. Ex-527 inhibition thus exploits Sirtuin catalysis, and kinetic isoform differences explain its selectivity. Our results provide insights in Sirtuin catalysis and inhibition with important implications for drug development. PMID:23840057

Gertz, Melanie; Fischer, Frank; Nguyen, Giang Thi Tuyet; Lakshminarasimhan, Mahadevan; Schutkowski, Mike; Weyand, Michael; Steegborn, Clemens

2013-01-01

323

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

USGS Publications Warehouse

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 betterment of all resources.

Perry, M.C.

2002-01-01

324

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

USGS Publications Warehouse

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.

Lohnes, E.J.R.

2004-01-01

325

Thermophilic anaerobic oxidation of methane by marine microbial consortia  

PubMed Central

The anaerobic oxidation of methane (AOM) with sulfate controls the emission of the greenhouse gas methane from the ocean floor. AOM is performed by microbial consortia of archaea (ANME) associated with partners related to sulfate-reducing bacteria. In vitro enrichments of AOM were so far only successful at temperatures ?25?°C; however, energy gain for growth by AOM with sulfate is in principle also possible at higher temperatures. Sequences of 16S rRNA genes and core lipids characteristic for ANME as well as hints of in situ AOM activity were indeed reported for geothermally heated marine environments, yet no direct evidence for thermophilic growth of marine ANME consortia was obtained to date. To study possible thermophilic AOM, we investigated hydrothermally influenced sediment from the Guaymas Basin. In vitro incubations showed activity of sulfate-dependent methane oxidation between 5 and 70?°C with an apparent optimum between 45 and 60?°C. AOM was absent at temperatures ?75?°C. Long-term enrichment of AOM was fastest at 50?°C, yielding a 13-fold increase of methane-dependent sulfate reduction within 250 days, equivalent to an apparent doubling time of 68 days. The enrichments were dominated by novel ANME-1 consortia, mostly associated with bacterial partners of the deltaproteobacterial HotSeep-1 cluster, a deeply branching phylogenetic group previously found in a butane-amended 60?°C-enrichment culture of Guaymas sediments. The closest relatives (Desulfurella spp.; Hippea maritima) are moderately thermophilic sulfur reducers. Results indicate that AOM and ANME archaea could be of biogeochemical relevance not only in cold to moderate but also in hot marine habitats. PMID:21697963

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

2011-01-01

326

Laboratory Directed Research & Development program. Annual report to the Department of Energy  

SciTech Connect

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.

Ogeka, G.J.; Romano, A.J.

1995-12-01

327

Ancestral Chromosomal Blocks Are Triplicated in Brassiceae Species with Varying Chromosome Number and Genome Size1  

PubMed Central

The paleopolyploid character of genomes of the economically important genus Brassica and closely related species (tribe Brassiceae) is still fairly controversial. Here, we report on the comparative painting analysis of block F of the crucifer Ancestral Karyotype (AK; n = 8), consisting of 24 conserved genomic blocks, in 10 species traditionally treated as members of the tribe Brassiceae. Three homeologous copies of block F were identified per haploid chromosome complement in Brassiceae species with 2n = 14, 18, 20, 32, and 36. In high-polyploid (n ? 30) species Crambe maritima (2n = 60), Crambe cordifolia (2n = 120), and Vella pseudocytisus (2n = 68), six, 12, and six copies of the analyzed block have been revealed, respectively. Homeologous regions resembled the ancestral structure of block F within the AK or were altered by inversions and/or translocations. In two species of the subtribe Zillineae, two of the three homeologous regions were combined via a reciprocal translocation onto one chromosome. Altogether, these findings provide compelling evidence of an ancient hexaploidization event and corresponding whole-genome triplication shared by the tribe Brassiceae. No direct relationship between chromosome number and genome size variation (1.2–2.5 pg/2C) has been found in Brassiceae species with 2n = 14 to 36. Only two homeologous copies of block F suggest a whole-genome duplication but not the triplication event in Orychophragmus violaceus (2n = 24), and confirm a phylogenetic position of this species outside the tribe Brassiceae. Chromosome duplication detected in Orychophragmus as well as chromosome rearrangements shared by Zillineae species demonstrate the usefulness of comparative cytogenetics for elucidation of phylogenetic relationships. PMID:17720758

Lysak, Martin A.; Cheung, Kwok; Kitschke, Michaela; Bures, Petr

2007-01-01

328

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

PubMed

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. PMID:24283966

You, Chun; Zhang, Y-H Percival

2014-06-20

329

A diferrous-dinitrosyl intermediate in the N2O-generating pathway of a deflavinated flavo-diiron protein.  

PubMed

Flavo-diiron proteins (FDPs) function as anaerobic nitric oxide scavengers in some microorganisms, catalyzing reduction of nitric to nitrous oxide. The FDP from Thermotoga maritima can be prepared in a deflavinated form with an intact diferric site (deflavo-FDP). Hayashi et al. [(2010) Biochemistry 49, 7040-7049] reported that reaction of NO with reduced deflavo-FDP produced substoichiometric N2O. Here we report a multispectroscopic approach to identify the iron species in the reactions of deflavo-FDP with NO. Mössbauer spectroscopy identified two distinct ferrous species after reduction of the antiferromagnetically coupled diferric site. Approximately 60% of the total ferrous iron was assigned to a diferrous species associated with the N2O-generating pathway. This pathway proceeds through successive diferrous-mononitrosyl (S = (1)/2 Fe(II){FeNO}(7)) and diferrous-dinitrosyl (S = 0 [{FeNO}(7)]2) species that form within ?100 ms of mixing of the reduced protein with NO. The diferrous-dinitrosyl intermediate converted to an antiferromagnetically coupled diferric species that was spectroscopically indistinguishable from that in the starting deflavinated protein. These diiron species closely resembled those reported for the flavinated FDP [Caranto et al. (2014) J. Am. Chem. Soc. 136, 7981-7992], and the time scales of their formation and decay were consistent with the steady state turnover of the flavinated protein. The remaining ?40% of ferrous iron was inactive in N2O generation but reversibly bound NO to give an S = (3)/2 {FeNO}(7) species. The results demonstrate that N2O formation in FDPs can occur via conversion of S = 0 [{FeNO}(7)]2 to a diferric form without participation of the flavin cofactor. PMID:25144650

Caranto, Jonathan D; Weitz, Andrew; Giri, Nitai; Hendrich, Michael P; Kurtz, Donald M

2014-09-01

330

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

PubMed

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

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

2007-06-01

331

Ultrafast real-time visualization of active site flexibility of flavoenzyme thymidylate synthase ThyX  

PubMed Central

In many bacteria the flavoenzyme thymidylate synthase ThyX produces the DNA nucleotide deoxythymidine monophosphate from dUMP, using methylenetetrahydrofolate as carbon donor and NADPH as hydride donor. Because all three substrates bind in close proximity to the catalytic flavin adenine dinucleotide group, substantial flexibility of the ThyX active site has been hypothesized. Using femtosecond time-resolved fluorescence spectroscopy, we have studied the conformational heterogeneity and the conformational interconversion dynamics in real time in ThyX from the hyperthermophilic bacterium Thermotoga maritima. The dynamics of electron transfer to excited flavin adenine dinucleotide from a neighboring tyrosine residue are used as a sensitive probe of the functional dynamics of the active site. The fluorescence decay spanned a full three orders of magnitude, demonstrating a very wide range of conformations. In particular, at physiological temperatures, multiple angstrom cofactor-residue displacements occur on the picoseconds timescale. These experimental findings are supported by molecular dynamics simulations. Binding of the dUMP substrate abolishes this flexibility and stabilizes the active site in a configuration where dUMP closely interacts with the flavin cofactor and very efficiently quenches fluorescence itself. Our results indicate a dynamic selected-fit mechanism where binding of the first substrate dUMP at high temperature stabilizes the enzyme in a configuration favorable for interaction with the second substrate NADPH, and more generally have important implications for the role of active site flexibility in enzymes interacting with multiple poly-atom substrates and products. Moreover, our data provide the basis for exploring the effect of inhibitor molecules on the active site dynamics of ThyX and other multisubstrate flavoenzymes. PMID:23671075

Laptenok, Sergey P.; Bouzhir-Sima, Latifa; Lambry, Jean-Christophe; Myllykallio, Hannu; Liebl, Ursula; Vos, Marten H.

2013-01-01

332

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

PubMed

The aquatic insect fauna of salt marshes is poorly characterized, with the possible exception of biting Diptera. Aquatic insects play a vital role in salt marsh ecology, and have great potential importance as biological indicators for assessing marsh health. In addition, they may be impacted by measures to control mosquitoes such as changes to the marsh habitat, altered hydrology, or the application of pesticides. Given these concerns, the goals of this study were to conduct the first taxonomic survey of salt marsh aquatic insects on Long Island, New York, USA and to evaluate their utility for non-target pesticide impacts and environmental biomonitoring. A total of 18 species from 11 families and five orders were collected repeatedly during the five month study period. Diptera was the most diverse order with nine species from four families, followed by Coleoptera with four species from two families, Heteroptera with three species from three families, then Odonata and the hexapod Collembola with one species each. Water boatmen, Trichocorixa verticalis Fieber (Heteroptera: Corixidae) and a shore fly, Ephydra subopaca Loew (Diptera: Ephydridae), were the two most commonly encountered species. An additional six species; Anurida maritima Guérin-Méneville (Collembola: Neanuridae), Mesovelia mulsanti White (Heteroptera: Mesovelidae), Enochrus hamiltoni Horn (Coleoptera: Hydrophilidae), Tropisternus quadristriatus Horn (Coleoptera: Hydrophilidae), Dasyhelea pseudocincta Waugh and Wirth (Diptera: Ceratopogonidae), and Brachydeutera argentata Walker (Diptera: Ephydridae), were found regularly. Together with the less common Erythrodiplax berenice Drury (Odonata: Libellulidae), these nine species were identified as the most suitable candidates for pesticide and environmental impact monitoring due to abundance, position in the food chain, and extended seasonal occurrence. This study represents a first step towards developing an insect-based index of biological integrity for salt marsh health assessment. PMID:22957707

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

2011-01-01

333

Ancestral patterning of tergite formation in a centipede suggests derived mode of trunk segmentation in trilobites.  

PubMed

Trilobites have a rich and abundant fossil record, but little is known about the intrinsic mechanisms that orchestrate their body organization. To date, there is disagreement regarding the correspondence, or lack thereof, of the segmental units that constitute the trilobite trunk and their associated exoskeletal elements. The phylogenetic position of trilobites within total-group Euarthropoda, however, allows inferences about the underlying organization in these extinct taxa to be made, as some of the fundamental genetic processes for constructing the trunk segments are remarkably conserved among living arthropods. One example is the expression of the segment polarity gene engrailed, which at embryonic and early postembryonic stages is expressed in extant panarthropods (i.e. tardigrades, onychophorans, euarthropods) as transverse stripes that define the posteriormost region of each trunk segment. Due to its conservative morphology and allegedly primitive trunk tagmosis, we have utilized the centipede Strigamia maritima to study the correspondence between the expression of engrailed during late embryonic to postembryonic stages, and the development of the dorsal exoskeletal plates (i.e. tergites). The results corroborate the close correlation between the formation of the tergite borders and the dorsal expression of engrailed, and suggest that this association represents a symplesiomorphy within Euarthropoda. This correspondence between the genetic and phenetic levels enables making accurate inferences about the dorsoventral expression domains of engrailed in the trunk of exceptionally preserved trilobites and their close relatives, and is suggestive of the widespread occurrence of a distinct type of genetic segmental mismatch in these extinct arthropods. The metameric organization of the digestive tract in trilobites provides further support to this new interpretation. The wider evolutionary implications of these findings suggest the presence of a derived morphogenetic patterning mechanism responsible for the reiterated occurrence of different types of trunk dorsoventral segmental mismatch in several phylogenetically distant, extinct and extant, arthropod groups. PMID:23285116

Ortega-Hernández, Javier; Brena, Carlo

2012-01-01

334

Toward a molecular understanding of metal transport by P(1B)-type ATPases.  

PubMed

The P(1B) family of P-type ATPases couples the transport of cytoplasmic transition metals across biological membranes to the hydrolysis of ATP. These ubiquitous transporters function in maintaining cytoplasmic metal quotas and in the assembly of metalloproteins, and have been classified into subfamilies (P(1B-1)-P(1B-5)) on the basis of their transported substrates (Cu(+), Zn(2+), Cu(2+), and Co(2+)) and signature sequences in their transmembrane segments. In addition, each subgroup presents a characteristic membrane topology and specific regulatory cytoplasmic metal-binding domains. In recent years, significant major aspects of their transport mechanism have been described, including the stoichiometry of transport and the delivery of substrates to transport sites by metallochaperones. Toward understanding their structure, the metal coordination by transport sites has been characterized for Cu(+) and Zn(2+)-ATPases. In addition, atomic resolution structures have been determined, providing key insight into the elements that enable transition metal transport. Because the Cu(+)-transporting ATPases are found in humans and are linked to disease, this subfamily has been the focus of intense study. As a result, significant progress has been made toward understanding Cu(+)-ATPase function on the molecular level, using both the human proteins and the bacterial homologs, most notably the CopA proteins from Archaeoglobus fulgidus, Bacillus subtilis, and Thermotoga maritima. This chapter thus focuses on the mechanistic and structural information obtained by studying these latter Cu(+)-ATPases, with some consideration of how these aspects might differ for the other subfamilies of P(1B)-ATPases. PMID:23046649

Rosenzweig, Amy C; Argüello, José M

2012-01-01

335

Toward a Molecular Understanding of Metal Transport by P1B-Type ATPases  

PubMed Central

The P1B family of P-type ATPases couples the transport of cytoplasmic transition metals across biological membranes to the hydrolysis of ATP. These ubiquitous transporters function in maintaining cytoplasmic metal quotas and in the assembly of metalloproteins, and have been classified into subfamilies (P1B-1–P1B-5) on the basis of their transported substrates (Cu+, Zn2+, Cu2+, and Co2+) and signature sequences in their transmembrane segments. In addition, each subgroup presents a characteristic membrane topology and specific regulatory cytoplasmic metal-binding domains. In recent years, significant major aspects of their transport mechanism have been described, including the stoichiometry of transport and the delivery of substrates to transport sites by metallochaperones. Toward understanding their structure, the metal coordination by transport sites has been characterized for Cu+ and Zn2+-ATPases. In addition, atomic resolution structures have been determined, providing key insight into the elements that enable transition metal transport. Because the Cu+-transporting ATPases are found in humans and are linked to disease, this subfamily has been the focus of intense study. As a result, significant progress has been made toward understanding Cu+-ATPase function on the molecular level, using both the human proteins and the bacterial homologs, most notably the CopA proteins from Archaeoglobus fulgidus, Bacillus subtilis, and Thermotoga maritima. This chapter thus focuses on the mechanistic and structural information obtained by studying these latter Cu+-ATPases, with some consideration of how these aspects might differ for the other subfamilies of P1B-ATPases. PMID:23046649

Rosenzweig, Amy C.; Argüello, José M.

2012-01-01

336

Differentiation of the DnaA-oriC Subcomplex for DNA Unwinding in a Replication Initiation Complex*  

PubMed Central

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. PMID:22942281

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

2012-01-01

337

Developing genetically engineered encapsulin protein cage nanoparticles as a targeted delivery nanoplatform.  

PubMed

Protein cage nanoparticles are excellent candidates for use as multifunctional delivery nanoplatforms because they are built from biomaterials and have a well-defined structure. A novel protein cage nanoparticle, encapsulin, isolated from thermophilic bacteria Thermotoga maritima, is prepared and developed as a versatile template for targeted delivery nanoplatforms through both chemical and genetic engineering. It is pivotal for multifunctional delivery nanoplatforms to have functional plasticity and versatility to acquire targeting ligands, diagnostic probes, and drugs simultaneously. Encapsulin is genetically engineered to have unusual heat stability and to acquire multiple functionalities in a precisely controlled manner. Hepatocellular carcinoma (HCC) cell binding peptide (SP94-peptide, SFSIIHTPILPL) is chosen as a targeting ligand and displayed on the surface of engineered encapsulin (Encap_loophis42C123) through either chemical conjugation or genetic insertion. The effective and selective targeted delivery of SP94-peptide displaying encapsulin (SP94-Encap_loophis42C123) to HepG2 cells is confirmed by fluorescent microscopy imaging. Aldoxorubicin (AlDox), an anticancer prodrug, is chemically loaded to SP94-Encap_loophis42C123 via thiol-maleimide Michael-type addition, and the efficacy of the delivered drugs is evaluated with a cell viability assay. SP94-Encap_loophis42C123-AlDox shows comparable killing efficacy with that of free drugs without the platform's own cytotoxicity. Functional plasticity and versatility of the engineered encapsulin allow us to introduce targeting ligands, diagnostic probes, and therapeutic reagents simultaneously, providing opportunities to develop multifunctional delivery nanoplatforms. PMID:25180761

Moon, Hyojin; Lee, Jisu; Min, Junseon; Kang, Sebyung

2014-10-13

338

Molecular cloning and biochemical characterization of a heat-stable type I pullulanase from Thermotoga neapolitana.  

PubMed

The gene encoding a type I pullulanase from the hyperthermophilic anaerobic bacterium Thermotoga neapolitana (pulA) was cloned in Escherichia coli and sequenced. The pulA gene from T. neapolitana showed 91.5% pairwise amino acid identity with pulA from Thermotoga maritima and contained the four regions conserved in all amylolytic enzymes. pulA encodes a protein of 843 amino acids with a 19-residue signal peptide. The pulA gene was subcloned and overexpressed in E. coli under the control of the T7 promoter. The purified recombinant enzyme (rPulA) produced a 93-kDa protein with pullulanase activity. rPulA was optimally active at pH 5-7 and 80°C and had a half-life of 88 min at 80°C. rPulA hydrolyzed pullulan, producing maltotriose, and hydrolytic activities were also detected with amylopectin, starch, and glycogen, but not with amylose. This substrate specificity is typical of a type I pullulanase. Thin layer chromatography of the reaction products in the reaction with pullulan and aesculin showed that the enzyme had transglycosylation activity. Analysis of the transfer product using NMR and isoamylase treatment revealed it to be ?-maltotriosyl-(1,6)-aesculin, suggesting that the enzyme transferred the maltotriosyl residue of pullulan to aesculin by forming ?-1,6-glucosidic linkages. Our findings suggest that the pullulanase from T. neapolitana is the first thermostable type I pullulanase which has ?-1,6-transferring activity. PMID:22112909

Kang, Jinho; Park, Kyung-Min; Choi, Kyoung-Hwa; Park, Cheon-Seok; Kim, Go-Eun; Kim, Doman; Cha, Jaeho

2011-03-01

339

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

SciTech Connect

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.

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

2006-01-01

340

Impacts of summer ozone exposure on the growth and overwintering of UK upland vegetation  

NASA Astrophysics Data System (ADS)

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.

Hayes, Felicity; Mills, Gina; Williams, Philip; Harmens, Harry; Büker, Patrick

341

Breeding productivity of Smith Island black ducks  

USGS Publications Warehouse

We investigated the breeding performance of American black ducks (Anas rubripes) on Smith Island, Chesapeake Bay, to improve our understanding of island black duck breeding ecology and to make management recommendations to enhance productivity. During 1995-96, we implanted 56 female black ducks with 20-g radio transmitters and tracked 35 of the individuals through the breeding season to locate nests, determine nest fate, and identify brood habitat. We also increased preseason banding efforts and compared capture characteristics over 12 years with those from the Deal Island Wildlife Management Area, a banding site on the mainland of Tangier Sound. A low rate of nesting (37%), lack of renesting, and poor hatching success (31%) indicated that island salt marsh habitats present a harsh environment for breeding black ducks. Black ducks located 11 of 13 nests (85%) in black needlerush (Juncus roemerianus) marsh where they were vulnerable to flooding from extreme tides and to egg predators. No nests were found on forested tree hammocks, a feature that distinguishes Smith Island from nearby South Marsh and Bloodsworth Islands. Nest predators included red foxes (Vulpes vulpes), herring gulls (Larus argentams), fish crows (Corvus ossifragus), and, potentially, Norway rats (Rattus norvegicus). Unlike mainland red foxes, foxes radio tracked on Smith Island were found to be capable swimmers and effective low marsh predators. We found shoreline meadows of widgeon grass (Ruppia maritima) to be important foraging sites for black ducks and suspected that the virtual absence of fresh water in this high salinity environment (1217+ ppt) to incur some cost in terms of growth and survival of ducklings. Preseason bandings revealed a high proportion of banded adults and a strong positive correlation in age ratios with the Deal Island banding site. This latter finding strongly suggests a negative universal effect of storm tides on nest success for Tangier Sound black ducks. Management to reduce nest predators, especially gulls and foxes, likely will have the greatest immediate benefit for island breeding black ducks.

Haramis, G.M.; Jorde, D.G.; Olsen, G.H.; Stotts, D.B.; Harrison, M.K.

2002-01-01

342

Aquatic Insects of New York Salt Marsh Associated with Mosquito Larval Habitat and their Potential Utility as Bioindicators  

PubMed Central

The aquatic insect fauna of salt marshes is poorly characterized, with the possible exception of biting Diptera. Aquatic insects play a vital role in salt marsh ecology, and have great potential importance as biological indicators for assessing marsh health. In addition, they may be impacted by measures to control mosquitoes such as changes to the marsh habitat, altered hydrology, or the application of pesticides. Given these concerns, the goals of this study were to conduct the first taxonomic survey of salt marsh aquatic insects on Long Island, New York, USA and to evaluate their utility for non-target pesticide impacts and environmental biomonitoring. A total of 18 species from 11 families and five orders were collected repeatedly during the five month study period. Diptera was the most diverse order with nine species from four families, followed by Coleoptera with four species from two families, Heteroptera with three species from three families, then Odonata and the hexapod Collembola with one species each. Water boatmen, Trichocorixa verticalis Fieber (Heteroptera: Corixidae) and a shore fly, Ephydra subopaca Loew (Diptera: Ephydridae), were the two most commonly encountered species. An additional six species; Anurida maritima Guérin-Méneville (Collembola: Neanuridae), Mesovelia mulsanti White (Heteroptera: Mesovelidae), Enochrus hamiltoni Horn (Coleoptera: Hydrophilidae), Tropisternus quadristriatus Horn (Coleoptera: Hydrophilidae), Dasyhelea pseudocincta Waugh and Wirth (Diptera: Ceratopogonidae), and Brachydeutera argentata Walker (Diptera: Ephydridae), were found regularly. Together with the less common Erythrodiplax berenice Drury (Odonata: Libellulidae), these nine species were identified as the most suitable candidates for pesticide and environmental impact monitoring due to abundance, position in the food chain, and extended seasonal occurrence. This study represents a first step towards developing an insectbased index of biological integrity for salt marsh health assessment. PMID:22957707

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

2011-01-01

343

Tyrosine Latching of a Regulatory Gate Affords Allosteric Control of Aromatic Amino Acid Biosynthesis*  

PubMed Central

The first step of the shikimate pathway for aromatic amino acid biosynthesis is catalyzed by 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS). Thermotoga maritima DAH7PS (TmaDAH7PS) is tetrameric, with monomer units comprised of a core catalytic (?/?)8 barrel and an N-terminal domain. This enzyme is inhibited strongly by tyrosine and to a lesser extent by the presence of phenylalanine. A truncated mutant of TmaDAH7PS lacking the N-terminal domain was catalytically more active and completely insensitive to tyrosine and phenylalanine, consistent with a role for this domain in allosteric inhibition. The structure of this protein was determined to 2.0 ?. In contrast to the wild-type enzyme, this enzyme is dimeric. Wild-type TmaDAH7PS was co-crystallized with tyrosine, and the structure of this complex was determined to a resolution of 2.35 ?. Tyrosine was found to bind at the interface between two regulatory N-terminal domains, formed from diagonally located monomers of the tetramer, revealing a major reorganization of the regulatory domain with respect to the barrel relative to unliganded enzyme. This significant conformational rearrangement observed in the crystal structures was also clearly evident from small angle X-ray scattering measurements recorded in the presence and absence of tyrosine. The closed conformation adopted by the protein on tyrosine binding impedes substrate entry into the neighboring barrel, revealing an unusual tyrosine-controlled gating mechanism for allosteric control of this enzyme. PMID:21282100

Cross, Penelope J.; Dobson, Renwick C. J.; Patchett, Mark L.; Parker, Emily J.

2011-01-01

344

Ocean Acidification and the Loss of Phenolic Substances in Marine Plants  

PubMed Central

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

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

2012-01-01

345

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)

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 ?13C and ?15N 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.

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

2008-01-01

346

Starch biosynthetic genes and enzymes are expressed and active in the absence of starch accumulation in sugar beet tap-root  

PubMed Central

Background Starch is the predominant storage compound in underground plant tissues like roots and tubers. An exception is sugar beet tap-root (Beta vulgaris ssp altissima) which exclusively stores sucrose. The underlying mechanism behind this divergent storage accumulation in sugar beet is currently not fully known. From the general presence of starch in roots and tubers it could be speculated that the lack in sugar beet tap-roots would originate from deficiency in pathways leading to starch. Therefore with emphasis on starch accumulation, we studied tap-roots of sugar beet using parsnip (Pastinaca sativa) as a comparator. Results Metabolic and structural analyses of sugar beet tap-root confirmed sucrose as the exclusive storage component. No starch granules could be detected in tap-roots of sugar beet or the wild ancestor sea beet (Beta vulgaris ssp. maritima). Analyses of parsnip showed that the main storage component was starch but tap-root tissue was also found to contain significant levels of sugars. Surprisingly, activities of four main starch biosynthetic enzymes, phosphoglucomutase, ADP-glucose pyrophosphorylase, starch synthase and starch branching enzyme, were similar in sugar beet and parsnip tap-roots. Transcriptional analysis confirmed expression of corresponding genes. Additionally, expression of genes involved in starch accumulation such as for plastidial hexose transportation and starch tuning functions could be determined in tap-roots of both plant species. Conclusion Considering underground storage organs, sugar beet tap-root upholds a unique property in exclusively storing sucrose. Lack of starch also in the ancestor sea beet indicates an evolved trait of biological importance. Our findings in this study show that gene expression and enzymatic activity of main starch biosynthetic functions are present in sugar beet tap-root during storage accumulation. In view of this, the complete lack of starch in sugar beet tap-roots is enigmatic. PMID:24758347

2014-01-01

347

Potassium Acts as a GTPase-Activating Element on Each Nucleotide-Binding Domain of the Essential Bacillus subtilis EngA  

PubMed Central

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

Foucher, Anne-Emmanuelle; Reiser, Jean-Baptiste; Ebel, Christine; Housset, Dominique; Jault, Jean-Michel

2012-01-01

348

Seed dormancy distribution: explanatory ecological factors  

PubMed Central

Background and Aims Knowledge of those traits that vary with latitude should be helpful in predicting how they may evolve locally under climate change. In the sea beet Beta vulgaris ssp. maritima, seed dormancy largely controls the timing of germination, is highly heritable and varies geographically; it is therefore thought to be selected by climate. The aim here was to characterize the variation in seed dormancy among sea beet populations across the French distribution area, as well as the ecological factors in situ that are correlated with and that could therefore select for seed dormancy. The relative importance of genetic inheritance vs. non-genetic variation is also evaluated. Methods The proportions of dormant seeds from 85 natural populations encompassing different climates over the whole French distribution area were measured under controlled conditions. Germination phenology was observed in a common garden experiment. Dormancy variation of seeds collected in situ was compared with that of seeds collected on plants grown in the greenhouse. Key Results The proportions of dormant seeds in the greenhouse were highly variable, covering almost the entire range from 0 to 1, and followed a geographical pattern from lower dormancy at high latitudes to high dormancy at low latitudes. The distribution of dormancy was positively correlated with yearly temperatures, especially summer temperatures. Minimum temperatures in winter did not significantly explain the trait variation. The genetic component of the total variation was significant and is probably completed by an important adjustment to the local conditions brought about by maternal adaptive phenotypic plasticity. Conclusions Dormancy in sea beet could be interpreted as a way to limit summer germination and spread germination over the first autumn and spring or following autumns. This highly heritable trait has the potential to evolve in the relatively near future because of climate change. PMID:22952378

Wagmann, Kristen; Hautekèete, Nina-Coralie; Piquot, Yves; Meunier, Cécile; Schmitt, S. Eric; Van Dijk, Henk

2012-01-01

349

Structure, diversity and evolution of myriapod hemocyanins.  

PubMed

Oxygen transport in the hemolymph of many arthropods is mediated by hemocyanins, large copper-containing proteins that are well-studied in Chelicerata and Crustacea, but had long been considered unnecessary in the subphylum of Myriapoda. Only recently has it become evident that hemocyanins are present in Scutigeromorpha (Chilopoda) and Spirostreptida (Diplopoda). Here we present evidence for a more widespread occurrence of hemocyanin in the myriapods. By means of RT-PCR, western blotting and database searches, hemocyanins were identified in the symphylans Hanseniella audax and Symphylella vulgaris, the chilopod Scolopendra subspinipes dehaani and the diplopod Polydesmus angustus. No hemocyanins were found in the diplopods Polyxenus lagurus, Cylindroiulus punctatus, Glomeris marginata, Glomeris pustulata and Arthrosphaera brandtii, or the chilopods Lithobius forficatus, Geophilus flavus and Strigamia maritima. This suggests multiple independent losses in myriapod taxa. Two independent hemocyanin subunits were found that were already present in the myriapod stem line. We specifically investigated the structure of the hemocyanin of P. angustus, which consists of three distinct subunits that occur in an approximately equimolar ratio. As deduced by 3D electron microscopy, the quaternary structure is a 3 × 6-mer that resembles the half structure of the 6 × 6-mer hemocyanin from Scutigera coleoptrata. It was analyzed more closely by homology modeling of 1 × 6-mers and their rigid-body fitting to the electron density map of the 3 × 6-mer. In addition, we obtained the cDNA sequence of a putative myriapod phenoloxidase. Phenoloxidases are related to the arthropod hemocyanins, but diverged before radiation of the arthropod subphyla. PMID:24520955

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

2014-04-01

350

Frankia populations in soil and root nodules of sympatrically grown Alnus taxa.  

PubMed

The genetic diversity of Frankia populations in soil and in root nodules of sympatrically grown Alnus taxa was evaluated by rep-polymerase chain reaction (PCR) and nifH gene sequence analyses. Rep-PCR analyses of uncultured Frankia populations in root nodules of 12 Alnus taxa (n=10 nodules each) growing sympatrically in the Morton Arboretum near Chicago revealed identical patterns for nodules from each Alnus taxon, including replicate trees of the same host taxon, and low diversity overall with only three profiles retrieved. One profile was retrieved from all nodules of nine taxa (Alnus incana subsp. incana, Alnus japonica, Alnus glutinosa, Alnus incana subsp. tenuifolia, Alnus incana subsp. rugosa, Alnus rhombifolia, Alnus mandshurica, Alnus maritima, and Alnus serrulata), the second was found in all nodules of two plant taxa (A. incana subsp. hirsuta and A. glutinosa var. pyramidalis), and the third was unique for all Frankia populations in nodules of A. incana subsp. rugosa var. americana. Comparative sequence analyses of nifH gene fragments in nodules representing these three profiles assigned these frankiae to different subgroups within the Alnus host infection group. None of these sequences, however, represented frankiae detectable in soil as determined by sequence analysis of 73 clones from a Frankia-specific nifH gene clone library. Additional analyses of nodule populations from selected alders growing on different soils demonstrated the presence of different Frankia populations in nodules for each soil, with populations showing identical sequences in nodules from the same soil, but differences between plant taxa. These results suggest that soil environmental conditions and host plant genotype both have a role in the selection of Frankia strains by a host plant for root nodule formation, and that this selection is not merely a function of the abundance of a Frankia strain in soil. PMID:20838787

Pokharel, Anita; Mirza, Babur S; Dawson, Jeffrey O; Hahn, Dittmar

2011-01-01

351

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

NASA Astrophysics Data System (ADS)

Ingestion, enzymatic digestion and absorption of particulate detrital matter derived from six different vegetal sources by the common cockle Cerastoderma edule was analyzed in a series of seasonal experiments performed in March, May and October 2005. Two green macroalgae: Ulva lactuca and Enteromorpha sp; two vascular plants: Spartina maritima and Juncus maritimus, the red macroalgae Gracilaria gracilis; and the microalgae Isochrysis galbana were used in experiments. Detrital matter was elaborated by freeze-drying, grinding and sieving (< 63 ?m) vegetal tissues. Mono-specific detrital diets of similar organic content (? 60-70%) were elaborated by mixing detritus with ashed silt. We measured i) the biochemical composition of different detritus, ii) physiological components of the absorptive balance (i.e. clearance, ingestion, rejection and absorption rate and absorption efficiency), iii) the capability of the digestive gland to hydrolyze carbohydrates from different detritus (digestibility), as well as iv) glandular cellulase and xylanase activities. Detritus type, season and the interaction detritus-season exerted significant effects upon all the physiological components of absorptive balance. Effects were light at the pre-absorptive level, however, huge variations associated to absorption efficiency promoted large significant differences in absorption rates (AR) of different kind of detritus: irrespective of season, highest values corresponded to cockles fed the green macroalgae ( Ulva and Enteromorpha) and lowest to those fed the vascular plant Juncus maritimus. Recorded significant differences in enzymatic digestibility among detritus were found to explain ? 40% of differences recorded in AR, and the following regression could be fitted: AR = 0.232 (± 0.032) * Digestibility + 0,072 (± 0.015); r 2 = 0.415; F = 51.036; p < 0.001. Digestibility of Ulva and Enteromorpha was found to be significantly correlated with cellulase activity in the digestive gland, whereas digestibility of Juncus, Spartina and Gracilaria was correlated with xylanase activity. Obtained correlations are discussed in the frame of contrasting conclusions in the literature regarding the importance of detritus as a food source for bivalves.

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

2010-10-01

352

Histidine ligand variants of a flavo-diiron protein: Effects on structure and activities  

PubMed Central

Flavo-diiron proteins (FDPs) contain non-heme diiron and proximal flavin mononucleotide (FMN) active sites and function as terminal components of a nitric oxide reductase (NOR) and/or a four-electron dioxygen reductase (O2R). Despite conservation of most structural, spectroscopic and redox properties, O2R and NOR activities vary significantly among FDPs. A potential source of this variability is the iron ligation status of a conserved His residue, which provides an iron ligand in all but one known FDP structure, where this His residue is rotated away from iron and replaced by a solvent ligand. In order to test the effect of this His ligation status, we changed this ligating His residue (H90) in Thermotoga maritima (Tm) FDP to either Asn or Ala. The wild type Tm FDP shows significantly higher O2R than NOR activity. Single crystal X-ray crystallography revealed a remarkably conserved diiron site structure in the H90N and -A variants, differing mainly by either Asn or solvent coordination, respectively, in place of H90. The steady state activities were minimally affected by the H90 substitutions, remaining significantly higher for O2R vs NOR. The pre-steady state kinetics of the fully reduced FDP with O2 were also minimally affected by the H90 substitutions. The results indicate that the coordination status of this His ligand does not significantly modulate the O2R or NOR activities, and that FDPs can retain these activities when the individual iron centers are differentiated by His ligand substitution. This differentiation may have implications for the O2R and NOR mechanisms of FDPs. PMID:22990880

Fang, Han; Caranto, Jonathan D.; Mendoza, Rosalinda; Taylor, Alexander B.; Hart, P. John

2012-01-01

353

On the distribution and evaluation of Na, Mg and Cl in leaves of selected halophytes  

NASA Astrophysics Data System (ADS)

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.

Pongrac, Paula; Vogel-Mikuš, Katarina; Regvar, Marjana; Kaligari?, Mitja; Vavpeti?, Primož; Kelemen, Mitja; Grlj, Nataša; Shelef, Oren; Golan-Goldhirsh, Avi; Rachmilevitch, Shimon; Pelicon, Primož

2013-07-01

354

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

PubMed Central

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

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

2007-01-01

355

Identification of a novel NADH-specific aldo-keto reductase using sequence and structural homologies  

PubMed Central

The AKRs (aldo-keto reductases) are a superfamily of enzymes which mainly rely on NADPH to reversibly reduce various carbonyl-containing compounds to the corresponding alcohols. A small number have been found with dual NADPH/NADH specificity, usually preferring NADPH, but none are exclusive for NADH. Crystal structures of the dual-specificity enzyme xylose reductase (AKR2B5) indicate that NAD+ is bound via a key interaction with a glutamate that is able to change conformations to accommodate the 2?-phosphate of NADP+. Sequence comparisons suggest that analogous glutamate or aspartate residues may function in other AKRs to allow NADH utilization. Based on this, nine putative enzymes with potential NADH specificity were identified and seven genes were successfully expressed and purified from Drosophila melanogaster, Escherichia coli, Schizosaccharomyces pombe, Sulfolobus solfataricus, Sinorhizobium meliloti and Thermotoga maritima. Each was assayed for co-substrate dependence with conventional AKR substrates. Three were exclusive for NADPH (AKR2E3, AKR3F2 and AKR3F3), two were dual-specific (AKR3C2 and AKR3F1) and one was specific for NADH (AKR11B2), the first such activity in an AKR. Fluorescence measurements of the seventh protein indicated that it bound both NADPH and NADH but had no activity. Mutation of the aspartate into an alanine residue or a more mobile glutamate in the NADH-specific E. coli protein converted it into an enzyme with dual specificity. These results show that the presence of this carboxylate is an indication of NADH dependence. This should allow improved prediction of co-substrate specificity and provide a basis for engineering enzymes with altered co-substrate utilization for this class of enzymes. PMID:16813561

Di Luccio, Eric; Elling, Robert A.; Wilson, David K.

2006-01-01

356

Comparative analysis of 16S rRNA signature sequences of the genus Idiomarina and Idiomarina woesei sp. nov., a novel marine bacterium isolated from the Andaman Sea.  

PubMed

A Gram-negative, short rod, aerobic bacterium, designated W11(T), was isolated from seawater. Heterotrophic growth was observed at 10-45 °C and pH 6-10. Optimal growth was observed at 30-37 °C and pH 7-9. It can grow in the presence of 0.5-12% NaCl (w/v), and the optimal NaCl required for growth was 5-6%. 16S rRNA gene sequence similarity revealed that strain W11(T) clustered within the radiation of the genus Idiomarina and showed 99.24% similarity with Idiomarina donghaiensis JCM 15533(T), 97.64% with Idiomarina marina JCM 15083(T), 97.37% with Idiomarina tainanensis JCM 15084(T) and 97.16% with Idiomarina maritima JCM 15534(T). DNA-DNA similarities between strains W11(T) with other closely related strains were below 70%. Polar lipids included a phosphatidylgylycerol, a diphosphatidylglycerol, a phosphatidylethanolamine, an unidentified phosopholipid, two unidentified aminolipids and two unidentified lipids. DNA G + C content was 41.2 ± 0.1 mol%. Major fatty acids were iso-C15:0, iso-C17:0, iso-C17:1?9c, C16:0, iso-C11:0 3OH and C16:1?7c/C16:1?7c. The isoprenoid ubiquinone was Q8. On the basis of the present polyphasic taxonomic study, strain W11(T) is considered to represent a novel species of the genus Idiomarina, for which the name Idiomarina woesei sp. nov. is proposed. The type strain is W11(T) (= DSM 27808(T) = JCM 19499(T) = LMG 27903(T)). PMID:25078320

Poddar, Abhijit; Lepcha, Rinchen T; Mukherjee, Debasish; Bhattacharyya, Dhananjay; Das, Subrata K

2014-09-01

357

Structural Insights Into Amino Acid Binding and Gene Control by a Lysine Riboswitch  

SciTech Connect

In bacteria, the intracellular concentration of several amino acids is controlled by riboswitches1, 2, 3, 4. One of the important regulatory circuits involves lysine-specific riboswitches, which direct the biosynthesis and transport of lysine and precursors common for lysine and other amino acids. To understand the molecular basis of amino acid recognition by riboswitches, here we present the crystal structure of the 174-nucleotide sensing domain of the Thermotoga maritima lysine riboswitch in the lysine-bound (1.9 A) and free (3.1 A) states. The riboswitch features an unusual and intricate architecture, involving three-helical and two-helical bundles connected by a compact five-helical junction and stabilized by various long-range tertiary interactions. Lysine interacts with the junctional core of the riboswitch and is specifically recognized through shape-complementarity within the elongated binding pocket and through several direct and K+-mediated hydrogen bonds to its charged ends. Our structural and biochemical studies indicate preformation of the riboswitch scaffold and identify conformational changes associated with the formation of a stable lysine-bound state, which prevents alternative folding of the riboswitch and facilitates formation of downstream regulatory elements. We have also determined several structures of the riboswitch bound to different lysine analogues5, including antibiotics, in an effort to understand the ligand-binding capabilities of the lysine riboswitch and understand the nature of antibiotic resistance. Our results provide insights into a mechanism of lysine-riboswitch-dependent gene control at the molecular level, thereby contributing to continuing efforts at exploration of the pharmaceutical and biotechnological potential of riboswitches.

Serganov, A.; Huang, L; Patel, D

2008-01-01

358

Vegetation change on a northeast tidal marsh: Interaction of sea-level rise and marsh accretion  

SciTech Connect

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.

Warren, R.S.; Niering, W.A. (Connecticut College, New London (United States))

1993-01-01

359

Cobalamin-Independent Methionine Synthase (MetE): A Face-to-Face Double Barrel That Evolved by Gene Duplication  

PubMed Central

Cobalamin-independent methionine synthase (MetE) catalyzes the transfer of a methyl group from methyltetrahydrofolate to L-homocysteine (Hcy) without using an intermediate methyl carrier. Although MetE displays no detectable sequence homology with cobalamin-dependent methionine synthase (MetH), both enzymes require zinc for activation and binding of Hcy. Crystallographic analyses of MetE from T. maritima reveal an unusual dual-barrel structure in which the active site lies between the tops of the two (??)8 barrels. The fold of the N-terminal barrel confirms that it has evolved from the C-terminal polypeptide by gene duplication; comparisons of the barrels provide an intriguing example of homologous domain evolution in which binding sites are obliterated. The C-terminal barrel incorporates the zinc ion that binds and activates Hcy. The zinc-binding site in MetE is distinguished from the (Cys)3Zn site in the related enzymes, MetH and betaine–homocysteine methyltransferase, by its position in the barrel and by the metal ligands, which are histidine, cysteine, glutamate, and cysteine in the resting form of MetE. Hcy associates at the face of the metal opposite glutamate, which moves away from the zinc in the binary E·Hcy complex. The folate substrate is not intimately associated with the N-terminal barrel; instead, elements from both barrels contribute binding determinants in a binary complex in which the folate substrate is incorrectly oriented for methyl transfer. Atypical locations of the Hcy and folate sites in the C-terminal barrel presumably permit direct interaction of the substrates in a ternary complex. Structures of the binary substrate complexes imply that rearrangement of folate, perhaps accompanied by domain rearrangement, must occur before formation of a ternary complex that is competent for methyl transfer. PMID:15630480

2005-01-01

360

Insertion of endocellulase catalytic domains into thermostable consensus ankyrin scaffolds: effects on stability and cellulolytic activity.  

PubMed

Degradation of cellulose for biofuels production holds promise in solving important environmental and economic problems. However, the low activities (and thus high enzyme-to-substrate ratios needed) of hydrolytic cellulase enzymes, which convert cellulose into simple sugars, remain a major barrier. As a potential strategy to stabilize cellulases and enhance their activities, we have embedded cellulases of extremophiles into hyperstable ?-helical consensus ankyrin domain scaffolds. We found the catalytic domains CelA (CA, GH8; Clostridium thermocellum) and Cel12A (C12A, GH12; Thermotoga maritima) to be stable in the context of the ankyrin scaffold and to be active against both soluble and insoluble substrates. The ankyrin repeats in each fusion are folded, although it appears that for the C12A catalytic domain (CD; where the N and C termini are distant in the crystal structure), the two flanking ankyrin domains are independent, whereas for CA (where termini are close), the flanking ankyrin domains stabilize each other. Although the activity of CA is unchanged in the context of the ankyrin scaffold, the activity of C12A is increased between 2- and 6-fold (for regenerated amorphous cellulose and carboxymethyl cellulose substrates) at high temperatures. For C12A, activity increases with the number of flanking ankyrin repeats. These results showed ankyrin arrays to be a promising scaffold for constructing designer cellulosomes, preserving or enhancing enzymatic activity and retaining thermostability. This modular architecture will make it possible to arrange multiple cellulase domains at a precise spacing within a single polypeptide, allowing us to search for spacings that may optimize reactivity toward the repetitive cellulose lattice. PMID:23974146

Cunha, Eva S; Hatem, Christine L; Barrick, Doug

2013-11-01

361

Ethnopharmacological survey of wild medicinal plants in Showbak, Jordan.  

PubMed

Two main research questions are framing this investigation: (1) the main taxa of the medicinal importance value altered the Showbak forest stand and species composition? (2) The most safe species and what are the toxic ones (unsafe). These two research questions are the vital ones to draw a clear image about the wild medicinal plants of this investigated area of Showbak region in Jordan. 79 wild medicinal plant species were investigated in this study which are used in traditional medication for the treatment of various diseases. Most of the locals interviewed dealt with well-known safe medicinal plants such as Aaronsohnia factorovskyi Warb. et Eig., Achillea santolina L., Adiantum capillus-veneris L., Artemisia herba-alba L., Ceratonia siliqua L., Clematis recta L., Herniaria hirsuta L., Malva neglecta Wallr., Rosmarinus officinalis L., Ruta chalepensis L., Salvia triloba L., Sarcopoterium spinosa (L.) Spach., Thymbra capitata (L.) Hof, and Urginea maritima Barker. Many of the wild medicinal plants investigated were toxic and needed to be practiced by practitioners and herbalists rather than the local healers. These plants include Calotropis procera Willd R.Br., Citrullus colocynthis (L.) Sch., Datura stramonium L., Digitalis purpurea L., Ecballium elaterium (L.) A.Rich., Euphorbia helioscopia L., Euphorbia tinctoria Boiss., Glaucium corniculatum (L.) Curt., Hyoscyamus aureus L., Mandragora officinarum L., Nerium oleander L., Ricinus communis L., Solanum nigrum L., Withania somnifera (L.) Dunel. The conservation of medicinal plants and natural resources is becoming increasingly important, so this research is trying to collect information from local population concerning the use of medicinal plants in Showbak; identify the most important specie; determine the relative importance value of the species and calculate the informant consensus factor (ICF) for the medicinal plants. Obtaining results is relied on the interviewee's personal information and the medicinal use of specific plants. PMID:19429338

Al-Qura'n, S

2009-05-01

362

Comparison of NMR and crystal structures highlights conformational isomerism in protein active sites.  

PubMed

The JCSG has recently developed a protocol for systematic comparisons of high-quality crystal and NMR structures of proteins. In this paper, the extent to which this approach can provide function-related information on the two functionally annotated proteins TM1081, a Thermotoga maritima anti-? factor antagonist, and A2LD1 (gi:13879369), a mouse ?-glutamylamine cyclotransferase, is explored. The NMR structures of the two proteins have been determined in solution at 313 and 298?K, respectively, using the current JCSG protocol based on the software package UNIO for extensive automation. The corresponding crystal structures were solved by the JCSG at 100?K and 1.6?Å resolution and at 100?K and 1.9?Å resolution, respectively. The NMR and crystal structures of the two proteins share the same overall molecular architectures. However, the precision of the structure determination along the amino-acid sequence varies over a significantly wider range in the NMR structures than in the crystal structures. Thereby, in each of the two NMR structures about 65% of the residues have displacements below the average and in both proteins the less well ordered residues include large parts of the active sites, in addition to some highly solvent-exposed surface areas. Whereas the latter show increased disorder in the crystal and in solution, the active-site regions display increased displacements only in the NMR structures, where they undergo local conformational exchange on the millisecond time scale that appears to be frozen in the crystals. These observations suggest that a search for molecular regions showing increased structural disorder and slow dynamic processes in solution while being well ordered in the corresponding crystal structure might be a valid initial step in the challenge of identifying putative active sites in functionally unannotated proteins with known three-dimensional structure. PMID:20944236

Serrano, Pedro; Pedrini, Bill; Geralt, Michael; Jaudzems, Kristaps; Mohanty, Biswaranjan; Horst, Reto; Herrmann, Torsten; Elsliger, Marc André; Wilson, Ian A; Wüthrich, Kurt

2010-10-01

363

Mobile dunes and eroding salt marshes  

NASA Astrophysics Data System (ADS)

The paper deals with general outlines of salt marsh and dune vegetation in the Ellenbogen and Listland area on Sylt (Schleswig-Holstein, FRG). The composition of current salt marsh vegetation is considered to be mainly the result of a long-lasting process of tidal inundation, grazing, and a permanent influence of groundwater seepage from the surrounding dunes. The lower salt marsh communities have shown constancy for 67 years, due to the effect of heavy grazing. The mid-upper salt marsh communities demonstrated a succession from a Puccinellia maritima-dominated community of the lower marsh to a Juncus gerardii-dominated community of the mid-upper salt marsh, which may be due to the transport of sand — over a short time — on the surface of the marsh. The area covered by plant communities of annuals below Mean High Water (MHW) seemed to diminish. Salt marsh soils, especially of the mid-upper marsh, indicate sandy layers resulting from sand drift of the dunes. Dry and wet successional series of the dunes in the Listland/Ellenbogen area both show grassy stages shifting to dwarf shrubs as final stages. White primary dunes can only be found on the accreting shoreline of the Ellenbogen, which is also grazed by sheep; vegetation cover therefore remains dominated by grasses, mosses and lichens. Three mobile dunes (as the most prominent features of this landscape) have been left unaffected by seeding and planting by local authorities. Grazing is considered to be an inadequate tool in nature conservation as long as natural processes are to prevail in the landscape as major determinants.

Neuhaus, R.

1994-06-01

364

[Cardiac glycosides: From ancient history through Withering's foxglove to endogeneous cardiac glycosides].  

PubMed

For centuries, drugs that increase the power of contraction of the failing heart have been used for the treatment of congestive heart failure (dropsy). The cardiac effect is due to the content of cardiac glycosides. Squill or sea onion, Urginea (Scilla) maritima, a seashore plant, was known by the ancient Romans and Syrians and possibly also by the ancient Egyptians. Squills were used erratically, but some prescriptions indicate that they may have been used for the treatment of oedematous states. The toxic effect of strophanthus species was known from poisoned arrows used by the natives in Africa. Digitalis, derived form the foxglove plant, Digitalis purpurea, is mentioned in writings as early as 1250; a Welsh family, known as the Physicians of Myddvai, collected different herbs and digitalis was included in their prescriptions. However, the druge was used erratically until the 18th century, when William Withering, an English physician and botanist, published a monograph describing the clinical effects of an extract of the foxglove plant. Later, in 1785, the indication and the toxicity of digitalis were reported in his book, "An account of the Foxglove and some of its medical uses with practical remarks on dropsy, and other diseases". In Denmark, the leaves of Digitalis purpurea or Digitalis lanata were tested for cardiac glycoside activity. The standardized digitalis powder was used in tinctures, infusions, and tablets. The preparations were included in successive editions of the Danish pharmacopoeia, some of the tinctures already in 1828, i.e. before the standardization of the drug. Isolation of cardiac glycosides from digitalis, strophanthus and squill and determination of their chemical structures initiated biochemical and pharmacological studies. The scientific advances led to an understanding of cardiac muscle contractility and the Na,K pump as the cellular receptor for the inotropic action of digitalis. Examination of putative endogenous ligands to the receptor revealed some endogenous cardiac glycosides of similar or identical structures as those found in digitalis, strophanthus and squill. Increased concentrations of these glycosides are found in patients with heart failure. Further investigations are needed to determine whether the secretion of glycosides might be a physiologic response to a diminished cardiac output. PMID:15685783

Norn, Svend; Kruse, Poul R

2004-01-01

365

Microfluidic mixing for non-equilibrium single-molecule optical spectroscopy  

NASA Astrophysics Data System (ADS)

We describe a series of experiments made possible by the combination of single-molecule fluorescence spectroscopy and microfluidic mixing. To perform these measurements, a microfluidic sample handling system was developed and characterized. This system allows observation at times as early as 2.4 ms after a reaction is triggered, which is an more than an order of magnitude earlier than previous microfabricated devices. Dilutions as high as 1:19 (v/v) are achieved, allowing measurements of molecular refolding in native conditions. The interconversion of subpopulations, masked by averaging in ensemble measurements, is observed. This technology also facilitates ultra-sensitive chemiluminescence measurements, using only microliters of sample. Microfluidics are designed and fabricated to extend single-molecule measurements to samples out of equilibrium. The system is optimized for sensitive optical detection and experimental convenience. Channels are replica-molded in poly-dimethyl-siloxane (PDMS) elastomer and sealed to coverglass. The resulting devices are compatible with a broad range of chemicals, and exhibit low background fluorescence. The combination of continuous flow, which decouples reaction progress from measurement duration, with low background enables single molecules to be probed at well defined times after a reaction is triggered. Fluid delivery and pressure connections are made using an interface optimized for rapid assembly, rapid sample exchange, and modular device replacement, while providing access for high numerical aperture optics. The kinetics of Csp, the cold shock protein from Thermotoga maritima, are studied with the mixer. An order of magnitude decrease in deadtime puts a new upper limit of 4.6 ms on the time required for collapse after mixing. This result is in agreement with indirect measurements of chain reconfiguration time, which suggest collapse happens on the timescale of 10--100 ns. Measurements of the kinetics of a DNA sequence that binds cocaine put a lower bound on its folding rate of 100 s-1. Single-Molecule measurements at equilibrium, in conjunction with ensemble measurements, demonstrate that this system can be described thermodynamically with a two-state model. In addition, standard free energy changes for folding, in the presence and absence of 1 mM cocaine, are obtained. Ensemble chemiluminescence experiments demonstrate the broad applicability of themixing system. The luciferase-luciferin system from Photinus pyralis, the North American firefly, is studied. Kinetically resolved chemiluminescence measurements are performed using only 50 femtomoles of target, and microliters of sample. This compares favorably to stopped-flow, which requires milliliters of sample and picomoles of target.

Pfeil, Shawn H.

366

Elongation Factor-Tu (EF-Tu) proteins structural stability and bioinformatics in ancestral gene reconstruction  

NASA Astrophysics Data System (ADS)

A paleo-experimental evolution report on elongation factor EF-Tu structural stability results has provided an opportunity to rewind the tape of life using the ancestral protein sequence reconstruction modeling approach; consistent with the book of life dogma in current biology and being an important component in the astrobiology community. Fractal dimension via the Higuchi fractal method and Shannon entropy of the DNA sequence classification could be used in a diagram that serves as a simple summary. Results from biomedical gene research provide examples on the diagram methodology. Comparisons between biomedical genes such as EEF2 (elongation factor 2 human, mouse, etc), WDR85 in epigenetics, HAR1 in human specificity, DLG1 in cognitive skill, and HLA-C in mosquito bite immunology with EF Tu DNA sequences have accounted for the reported circular dichroism thermo-stability data systematically; the results also infer a relatively less volatility geologic time period from 2 to 3 Gyr from adaptation viewpoint. Comparison to Thermotoga maritima MSB8 and Psychrobacter shows that Thermus thermophilus HB8 EF-Tu calibration sequence could be an outlier, consistent with free energy calculation by NUPACK. Diagram methodology allows computer simulation studies and HAR1 shows about 0.5% probability from chimp to human in terms of diagram location, and SNP simulation results such as amoebic meningoencephalitis NAF1 suggest correlation. Extensions to the studies of the translation and transcription elongation factor sequences in Megavirus Chiliensis, Megavirus Lba and Pandoravirus show that the studied Pandoravirus sequence could be an outlier with the highest fractal dimension and lowest entropy, as compared to chicken as a deviant in the DNMT3A DNA methylation gene sequences from zebrafish to human and to the less than one percent probability in computer simulation using the HAR1 0.5% probability as reference. The diagram methodology would be useful in ancestral gene reconstruction studies in astrobiology and also be applicable to the study of point mutation in conformational thermostabilization research with Synchrotron based X-ray data for drug applications such as Parkinson's disease.

Dehipawala, Sunil; Nguyen, A.; Tremberger, G.; Cheung, E.; Schneider, P.; Lieberman, D.; Holden, T.; Cheung, T.

2013-09-01

367

Neutron Reflectometry and QCM-D Study of the Interaction of Cellulase Enzymes with Films of Amorphous Cellulose  

SciTech Connect

Improving the efficiency of enzymatic hydrolysis of cellulose is one of the key technological hurdles to reduce the cost of producing ethanol and other transportation fuels from lignocellulosic material. A better understanding of how soluble enzymes interact with insoluble cellulose will aid in the design of more efficient enzyme systems. We report a study involving neutron reflectometry (NR) and quartz crystal microbalance with dissipation (QCM-D) of the interaction of a commercial fungal enzyme extract (T. viride), two purified endoglucanses from thermophilic bacteria (Cel9A from A. acidocaldarius and Cel5A from T. maritima), and a mesophilic fungal endoglucanase (Cel45A from H. insolens) with amorphous cellulose films. The use of amorphous cellulose is motivated by the promise of ionic liquid pretreatment as a second generation technology that disrupts the native crystalline structure of cellulose. NR reveals the profile of water through the film at nm resolution, while QCM-D provides changes in mass and film stiffness. At 20 oC and 0.3 mg/ml, the T. viride cocktail rapidly digested the entire film, beginning from the surface followed by activity throughout the bulk of the film. For similar conditions, Cel9A and Cel5A were active for only a short period of time and only at the surface of the film, with Cel9A releasing 40 from the ~ 700 film and Cel5A resulting in only a slight roughening/swelling effect at the surface. Subsequent elevation of the temperature to the Topt in each case resulted in a very limited increase in activity, corresponding to the loss of an additional 60 from the film for Cel9A and 20 from the film for Cel5A, and very weak penetration into and digestion within the bulk of the film, before the activity again ceased. The results for Cel9A and Cel5A contrast sharply with results for Cel45A where very rapid and extensive penetration and digestion within the bulk of the film was observed at 20 C. We speculate that the large differences are due to the use of the thermophilic enzymes far below their optimal temperatures and also the presence of a cellulose binding module (CBM) on Cel45A while the thermophilic enzymes lack a CBM.

Halbert, Candice E [ORNL; Ankner, John Francis [ORNL; Kent, Michael S [Sandia National Laboratories (SNL); Jaclyn, Murton K [Sandia National Laboratories (SNL); Browning, Jim [ORNL; Cheng, Gang [Joint Bioenergy Institute; Liu, Zelin [Virginia Polytechnic Institute and State University (Virginia Tech); Majewski, Jaroslaw [Los Alamos National Laboratory (LANL); Supratim, Datta [Joint Bioenergy Institute; Michael, Jablin [Los Alamos National Laboratory (LANL); Bulent, Akgun [NIST Center for Neutron Research (NCRN), Gaithersburg, MD; Alan, Esker [Virginia Polytechnic Institute and State University (Virginia Tech); Simmons, Blake [Sandia National Laboratories (SNL)

2011-01-01

368

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

All species from the phylum Thermotogae, class Thermotogae, are currently part of a single family, Thermotogaceae. Using genomic data from 17 Thermotogae species, detailed phylogenetic and comparative genomic analyses were carried out to understand their evolutionary relationships and identify molecular markers that are indicative of species relationships within the phylum. In the 16S rRNA gene tree and phylogenetic trees based upon two different large sets of proteins, members of the phylum Thermotogae formed a number of well-resolved clades. Character compatibility analysis on the protein sequence data also recovered a single largest clique that exhibited similar topology to the protein trees and where all nodes were supported by multiple compatible characters. Comparative genomic analyses have identified 85 molecular markers, in the form of conserved signature indels (CSIs), which are specific for different observed clades of Thermotogae at multiple phylogenetic depths. Eleven of these CSIs were specific for the phylum Thermotogae whereas nine others supported a clade comprising of the genera Thermotoga, Thermosipho and Fervidobacterium. Ten other CSIs provided evidence that the genera Thermosipho and Fervidobacterium shared a common ancestor exclusive of the other Thermotogae and four and eight CSIs in other proteins were specific for the genera Thermosipho and Fervidobacterium, respectively. Two other deep branching clades, one consisting of the genera Kosmotoga and Mesotoga and the other comprising of the genera Petrotoga and Marinitoga, were also supported by multiple CSIs. Based upon the consistent branching of the Thermotogae species using different phylogenetic approaches, and numerous identified CSIs supporting the distinctness of different clades, it is proposed that the class Thermotogae should be divided 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.). 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. PMID:24166034

Bhandari, Vaibhav; Gupta, Radhey S

2014-01-01

369

Construction of an in vitro bypassed pyruvate decarboxylation pathway using thermostable enzyme modules and its application to N-acetylglutamate production  

PubMed Central

Background Metabolic engineering has emerged as a practical alternative to conventional chemical conversion particularly in biocommodity production processes. However, this approach is often hampered by as yet unidentified inherent mechanisms of natural metabolism. One of the possible solutions for the elimination of the negative effects of natural regulatory mechanisms on artificially engineered metabolic pathway is to construct an in vitro pathway using a limited number of enzymes. Employment of thermostable enzymes as biocatalytic modules for pathway construction enables the one-step preparation of catalytic units with excellent selectivity and operational stability. Acetyl-CoA is a central precursor involved in the biosynthesis of various metabolites. In this study, an in vitro pathway to convert pyruvate to acetyl-CoA was constructed and applied to N-acetylglutamate production. Results A bypassed pyruvate decarboxylation pathway, through which pyruvate can be converted to acetyl-CoA, was constructed by using a coupled enzyme system consisting of pyruvate decarboxylase from Acetobacter pasteurianus and the CoA-acylating aldehyde dehydrogenase from Thermus thermophilus. To demonstrate the applicability of the bypassed pathway for chemical production, a cofactor-balanced and CoA-recycling synthetic pathway for N-acetylglutamate production was designed by coupling the bypassed pathway with the glutamate dehydrogenase from T. thermophilus and N-acetylglutamate synthase from Thermotoga maritima. N-Acetylglutamate could be produced from an equimolar mixture of pyruvate and ?-ketoglutarate with a molar yield of 55% through the synthetic pathway consisting of a mixture of four recombinant E. coli strains having either one of the thermostable enzymes. The overall recycling number of CoA was calculated to be 27. Conclusions Assembly of thermostable enzymes enables the flexible design and construction of an in vitro metabolic pathway specialized for chemical manufacture. We herein report the in vitro construction of a bypassed pathway capable of an almost stoichiometric conversion of pyruvate to acetyl-CoA. This pathway is potentially applicable not only to N-acetylglutamate production but also to the production of a wide range of acetyl-CoA-derived metabolites. PMID:24099461

2013-01-01

370

Interaction between submerged aquatic vegetation and turbulence generated by the wind: an experimental study  

NASA Astrophysics Data System (ADS)

In wetlands wind-induced turbulence significantly affects the bottom boundary, and the interaction between turbulence and plant canopies is therefore particularly important. The aim of this study is to advance understanding of the impact of this interaction in submerged aquatic vegetation (SAV) on vertical mixing in a fluid dominated by turbulence. Wind-generated turbulence was simulated in the laboratory using an oscillating grid. We quantify the vertical distribution of turbulent kinetic energy (TKE) above and within different types of vegetation, measured by an acoustic Doppler velocimeter. Experimental conditions are analysed in two canopy models (rigid and semi-rigid) with seven solid plant fractions (SPFs), three stem diameters (d), three oscillation grid frequencies (f) and four natural SAVs (Cladium mariscus, Potamogeton nodosus, Myriophyllum verticillatum and Ruppia maritima). Our observations suggest that the TKE above the constructed canopies was higher than that found without plants. The vertical profile varied according to the diameters of the individual stems and the SPF. Within the canopies, two zones could be distinguished. The 'transition zone', situated a few centimetres below the top of the canopy, was characterised by a reduction in the TKE. Below the transition zone, the TKE progressively decayed as the stems dissipated the turbulence, creating a zone where the TKE was lower than in the zone without stems. This is a well-known effect of SAV on turbulence, called sheltering or dampening. This phenomenon was enhanced by a decrease in the stem diameter and an increase in the SPF of the canopies, due to the reduction of the plant-to-plant distance. We have, therefore, not only observed a sheltering, but quantified it. The development of the sheltering slowed as the frequency increased, because the vegetation could not prevent the penetration of the turbulence. In the semi-rigid model, no transition zone was found inside the canopies, while sheltering was found from the very top of the plants and was intensified inside the canopies. Finally, sheltering for SAVs was similar to sheltering produced by semi-rigid plants with widespread sheltering inside the canopy.

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

2010-05-01

371

Effect of submerged aquatic vegetation on turbulence induced by an oscillating grid  

NASA Astrophysics Data System (ADS)

In wetlands wind-induced turbulence significantly affects the bottom boundary, and the interaction between turbulence and plant canopies is therefore particularly important. The aim of this study is to advance understanding of the impact of this interaction in submerged aquatic vegetation (SAV) on vertical mixing in a fluid dominated by turbulence. Wind-generated turbulence was simulated in the laboratory using an oscillating grid. We quantify the vertical distribution of turbulent kinetic energy (TKE) above and within different types of vegetation, measured by an acoustic Doppler velocimeter. Experimental conditions are analysed in two canopy models (rigid and semi-rigid) with seven solid plant fractions (SPFs) , three stem diameters (d) and three oscillation grid frequencies (f) and four natural SAVs ( Cladium mariscus, Potamogeton nodosus, Myriophyllum verticillatum and Ruppia maritima). Our observations suggest that the TKE above the constructed canopies was higher than that found without plants. The vertical profile varied according to the diameters of the individual stems and the SPF. Within the canopies, two zones could be distinguished. The 'transition zone', situated a few centimetres below the top of the canopy, was characterised by a reduction in the TKE. Below the transition zone, the TKE progressively decayed as the stems dissipated the turbulence, creating a zone where the TKE was lower than in the zone without stems. This is a well-known effect of SAV on turbulence, called sheltering or dampening. This phenomenon was enhanced by a decrease in the stem diameter and an increase in the SPF of the canopies, due to the reduction of the plant-to-plant distance. We have, therefore, not only observed a sheltering, but quantified it. The development of the sheltering slowed as the frequency increased, because the vegetation could not prevent the penetration of the turbulence. In the semi-rigid model, no transition zone was found inside the canopies, while sheltering was found from the very top of the plants and was intensified inside the canopies. Finally, sheltering for SAVs was similar to sheltering produced by semi-rigid plants with widespread sheltering inside the canopy. f: oscillation grid frequency.

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

2010-05-01

372

Genetic and Biochemical Dissection of a HisKA Domain Identifies Residues Required Exclusively for Kinase and Phosphatase Activities  

PubMed Central

Two-component signal transduction systems, composed of histidine kinases (HK) and response regulators (RR), allow bacteria to respond to diverse environmental stimuli. The HK can control both phosphorylation and subsequent dephosphorylation of its cognate RR. The majority of HKs utilize the HisKA subfamily of dimerization and histidine phosphotransfer (DHp) domains, which contain the phospho-accepting histidine and directly contact the RR. Extensive genetics, biochemistry, and structural biology on several prototypical TCS systems including NtrB-NtrC and EnvZ-OmpR have provided a solid basis for understanding the function of HK–RR signaling. Recently, work on NarX, a HisKA_3 subfamily protein, indicated that two residues in the highly conserved region of the DHp domain are responsible for phosphatase activity. In this study we have carried out both genetic and biochemical analyses on Myxococcus xanthus CrdS, a member of the HisKA subfamily of bacterial HKs. CrdS is required for the regulation of spore formation in response to environmental stress. Following alanine-scanning mutagenesis of the ?1 helix of the DHp domain of CrdS, we determined the role for each mutant protein for both kinase and phosphatase activity. Our results indicate that the conserved acidic residue (E372) immediately adjacent to the site of autophosphorylation (H371) is specifically required for kinase activity but not for phosphatase activity. Conversely, we found that the conserved Thr/Asn residue (N375) was required for phosphatase activity but not for kinase activity. We extended our biochemical analyses to two CrdS homologs from M. xanthus, HK1190 and HK4262, as well as Thermotoga maritima HK853. The results were similar for each HisKA family protein where the conserved acidic residue is required for kinase activity while the conserved Thr/Asn residue is required for phosphatase activity. These data are consistent with conserved mechanisms for kinase and phosphatase activities in the broadly occurring HisKA family of sensor kinases in bacteria. PMID:23226719

Willett, Jonathan W.; Kirby, John R.

2012-01-01

373

Vibrational Analysis of Mononitrosyl Complexes in Hemerythrin and Flavodiiron Proteins: Relevance to Detoxifying NO Reductase  

PubMed Central

Flavodiiron proteins (FDPs) play important roles in the microbial nitrosative stress response in low-oxygen environments by reductively scavenging nitric oxide (NO). Recently, we showed that FMN-free diferrous FDP from Thermotoga maritima exposed to 1 equiv NO forms a stable diiron-mononitrosyl complex (deflavo-FDP(NO)) that can react further with NO to form N2O [Hayashi, T.; Caranto, J. D.; Wampler, D. A.; Kurtz, D. M., Jr.; Moënne-Loccoz, P. Biochemistry 2010, 49, 7040–7049]. Here we report resonance Raman and low-temperature photolysis FTIR data that better define the structure of this diiron-mononitrosyl complex. We first validate this approach using the stable diiron-mononitrosyl complex of hemerythrin, Hr(NO), for which we observe a ?(NO) at 1658 cm?1, the lowest ?(NO) ever reported for a nonheme {FeNO}7 species. Both deflavo-FDP(NO) and the mononitrosyl adduct of the flavinated FPD (FDP(NO)) show ?(NO) at 1681 cm?1, which is also unusually low. These results indicate that, in Hr(NO) and FDP(NO), the coordinated NO is exceptionally electron rich, more closely approaching the Fe(III)(NO?) resonance structure. In the case of Hr(NO), this polarization may be promoted by steric enforcement of an unusually small FeNO angle, while in FDP(NO), the Fe(III)(NO?) structure may be due to a semi-bridging electrostatic interaction with the second Fe(II) ion. In Hr(NO), accessibility and steric constraints prevent further reaction of the diiron-mononitrosyl complex with NO, whereas in FDP(NO) the increased nucleophilicity of the nitrosyl group may promote attack by a second NO to produce N2O. This latter scenario is supported by theoretical modeling [Blomberg, L. M.; Blomberg, M. R.; Siegbahn, P. E. J. Biol. Inorg. Chem. 2007, 12, 79–89]. Published vibrational data on bioengineered models of denitrifying heme-nonheme NO reductases[Hayashi, T.; Miner, K. D.; Yeung, N.; Lin, Y.-W.; Lu, Y.; Moënne-Loccoz, P. Biochemistry 2011, 50, 5939–5947] support a similar mode of activation of a heme {FeNO}7 species by the nearby nonheme Fe(II). PMID:22449095

Hayashi, Takahiro; Caranto, Jonathan D.; Matsumura, Hirotoshi; Kurtz, Donald M.; Moenne-Loccoz, Pierre

2012-01-01

374

Topsoil morphology indicates bio-effective redox conditions in Venice salt marshes  

NASA Astrophysics Data System (ADS)

Visual traces of iron reduction and oxidation are linked to the redox status of soils and have been used to characterise the quality of agricultural soils. We tested whether this feature could also be used to explain the spatial pattern of the natural vegetation of tidal habitats. If so, an easy assessment of the effect of rising sea level on tidal ecosystems would be possible. Our study was conducted at the salt marshes of the northern lagoon of Venice, which are strongly threatened by erosion and rising sea level and are part of the world heritage "Venice and its lagoon". We analysed the abundance of plant species at 255 sampling points along a land-sea gradient. In addition, we surveyed the redox morphology (presence/absence of red iron oxide mottles in the greyish topsoil horizons) of the soils and the presence of disturbances. We used indicator species analysis, correlation trees and multivariate regression trees to analyse relations between soil properties and plant species distribution. Plant species with known sensitivity to anaerobic conditions (e.g. Halimione portulacoides) were identified as indicators for oxic soils (showing iron oxide mottles within a greyish soil matrix). Plant species that tolerate a low redox potential (e.g. Spartina maritima) were identified as indicators for anoxic soils (greyish matrix without oxide mottles). Correlation trees and multivariate regression trees indicate the dominant role of the redox morphology of the soils in plant species distribution. In addition, the distance from the mainland and the presence of disturbances were identified as tree-splitting variables. The small-scale variation of oxygen availability plays a key role for the biodiversity of salt marsh ecosystems. Our results suggest that the redox morphology of salt marsh soils indicates the plant availability of oxygen. Thus, the consideration of this indicator may enable an understanding of the heterogeneity of biological processes in oxygen-limited systems and may be a sensitive and easy-to-use tool to assess human impacts on salt marsh ecosystems.

Lang, Friederike; von der Lippe, Moritz; Schimpel, Susanne; Scozzafava-Jaeger, Tiberio; Straub, Wolfgang

2010-03-01

375

A survey of green plant tRNA 3'-end processing enzyme tRNase Zs, homologs of the candidate prostate cancer susceptibility protein ELAC2  

PubMed Central

Background tRNase Z removes the 3'-trailer sequences from precursor tRNAs, which is an essential step preceding the addition of the CCA sequence. tRNase Z exists in the short (tRNase ZS) and long (tRNase ZL) forms. Based on the sequence characteristics, they can be divided into two major types: bacterial-type tRNase ZS and eukaryotic-type tRNase ZL, and one minor type, Thermotoga maritima (TM)-type tRNase ZS. The number of tRNase Zs is highly variable, with the largest number being identified experimentally in the flowering plant Arabidopsis thaliana. It is unknown whether multiple tRNase Zs found in A. thaliana is common to the plant kingdom. Also unknown is the extent of sequence and structural conservation among tRNase Zs from the plant kingdom. Results We report the identification and analysis of candidate tRNase Zs in 27 fully sequenced genomes of green plants, the great majority of which are flowering plants. It appears that green plants contain multiple distinct tRNase Zs predicted to reside in different subcellular compartments. Furthermore, while the bacterial-type tRNase ZSs are present only in basal land plants and green algae, the TM-type tRNase ZSs are widespread in green plants. The protein sequences of the TM-type tRNase ZSs identified in green plants are similar to those of the bacterial-type tRNase ZSs but have distinct features, including the TM-type flexible arm, the variant catalytic HEAT and HST motifs, and a lack of the PxKxRN motif involved in CCA anti-determination (inhibition of tRNase Z activity by CCA), which prevents tRNase Z cleavage of mature tRNAs. Examination of flowering plant chloroplast tRNA genes reveals that many of these genes encode partial CCA sequences. Based on our results and previous studies, we predict that the plant TM-type tRNase ZSs may not recognize the CCA sequence as an anti-determinant. Conclusions Our findings substantially expand the current repertoire of the TM-type tRNase ZSs and hint at the possibility that these proteins may have been selected for their ability to process chloroplast pre-tRNAs with whole or partial CCA sequences. Our results also support the coevolution of tRNase Zs and tRNA 3'-trailer sequences in plants. PMID:21781332

2011-01-01

376

Where on Earth...? MISR Mystery Image Quiz #6  

NASA Technical Reports Server (NTRS)

Here's another chance to play geographical detective! This Multi-angle Imaging SpectroRadiometer (MISR) image covers an area of about 298 kilometers x 358 kilometers, and was captured by the instrument's vertical-viewing (nadir) camera on December 27, 2001. Use any reference materials you like and answer the following five questions: The large lagoon in the image is named for a particular type of bird. Name the bird. Note the sediment plume emanating from the southern end of the lagoon. Sailors in the 16th century imagined this outlet to be the mouth of a large river. What did they call the river? A series of wave-like points and curls form 'cusps' on the inner shores of the lagoon. Which ONE of the following is most responsible for the formation of these cusps? Violent storm impacts on erosion and accretion Wind and tide-driven sediment transport and circulation Tectonic folding associated with nearby mountain ridges Bathymetric effects of dredging operations True or false: Changes in regional precipitation associated with large scale atmospheric circulation patterns have no effect on the salinity of the lagoon's water. Which one of these is NOT distributed within the area covered by this image? Ruppia maritima Chelonia mydas Tapirus bairdii Microcystis aeruginosa E-mail your answers, name (initials are acceptable if you prefer), and your hometown by Tuesday, February 19, 2002 to suggestions@mail-misr.jpl.nasa.gov. Answers will be published on the MISR web site in conjunction with the next weekly image release. The names and home towns of respondents who answer all questions correctly by the deadline will also be published in the order responses were received. The first 3 people on this list who are not affiliated with NASA, JPL, or MISR and who did not win a prize in the last quiz will be sent a print of the image. A new 'Where on Earth...?' mystery appears as the MISR 'image of the week' approximately once per month. A new image of the week is released every Wednesday at noon Pacific time on the MISR home page http://www-misr.jpl.nasa.gov. The image also appears on the Atmospheric Sciences Data Center home page, http://eosweb.larc.nasa.gov, though usually with a several-hour delay. Image courtesy NASA/GSFC/LaRC/JPL, MISR Team.

2002-01-01

377

Indolepyruvate ferredoxin oxidoreductase from the hyperthermophilic archaeon Pyrococcus furiosus. A new enzyme involved in peptide fermentation.  

PubMed

Pyrococcus furiosus is a strictly anaerobic archaeon that grows optimally at 100 degrees C by a fermentative-type metabolism in which complex peptide mixtures such as yeast extract and Tryptone, and also certain sugars, are oxidized to organic acids, H2 and CO2. Enzymes involved in the utilization of peptides such as proteases, aromatic amino transferases, and glutamate dehydrogenase have been previously purified from this organism. It is shown here that P. furiosus also contains significant cytoplasmic concentrations of a new enzyme termed indolepyruvate ferredoxin oxidoreductase (IOR). This catalyzes the oxidative decarboxylation of aryl pyruvates, which are generated by the transamination of aromatic amino acids, to the corresponding aryl acetyl-CoA. IOR is a tetramer (alpha 2 beta 2) of two identical subunits (66,000 and 23,000 Da) with a molecular weight of 180,000. The enzyme contains one molecule of thiamine pyrophosphate and four [4Fe-4S]2+,1+ and one [3Fe-4S]0,1+ cluster, as determined by iron analyses and EPR spectroscopy. Significant amounts of other metals such as copper and zinc were not detected. IOR was virtually inactive at 25 degrees C and exhibited optimal activity above 90 degrees C (at pH 8.0) and at pH 8.5-10.5 (at 80 degrees C). The enzyme was sensitive to inactivation by O2, losing 50% of its activity after exposure to air for 20 min at 23 degrees C, and was quite thermostable, with a half-life of activity at 80 degrees C (under anaerobic conditions) of about 80 min. The Km values (in microM) for indolepyruvate, p-hydroxyphenylpyruvate, phenylpyruvate, CoASH, and P. furiosus ferredoxin, the physiological electron carrier, were 250, 110, 90, 17, and 48, respectively. IOR was inhibited by KCN (apparent Ki = 7.5 mM), but not by CO (1 atm). An enzyme analogous to IOR has not been reported previously. Curiously, it has few properties in common with the pyruvate ferredoxin oxidoreductase of P. furiosus, even though the two enzymes catalyze virtually identical reactions. In fact, of known ketoacid oxidoreductases, the catalytic mechanism of IOR appears to be most similar to that of the pyruvate ferredoxin oxidoreductase from the hyperthermophilic bacterium Thermotoga maritima. PMID:8206994

Mai, X; Adams, M W

1994-06-17

378

The applicability of OSL as a sedimentological proxy: new avenues to distinguish extreme events  

NASA Astrophysics Data System (ADS)

Signature underwater tsunami deposits have been relatively recently found in the upper Mediterranean shelf offshore Israel. They have been attributed as a potential cause for the demise of the ancient Roman city of Caesarea Maritima and its artificial Herodian harbour of Sebastos. Present annual large winter storm activity (2010-2011; waves heights up to 14 m) has severely impacted the area, showing increased coastal erosion and rigorous movement of nearshore sands, complicating the stratigraphical histories of the near offshore record. Recent sedimentological and geoarchaeological studies conducted in and around the harbour have been aimed to investigate extreme event characterization by different means, using Optically Stimulated Luminescence (OSL). A comparative study of modern and palaeo-storm sediments was launched in order to obtain physical correlation between offshore sediments, enabling further comparison with historical tsunami deposits, as well as modern and ancient sands emplaced during normal marine conditions. A suite of previously collected and identified sediment samples was selected from the same area where the modern storm analogues were collected. The palaeo-samples came from long-vertical hydraulic percussion cores (14-30 m depths) and small horizontal tubes pushed into excavated underwater sediment walls (2-12 m depths). The uniqueness of OSL relays on its capacity to date the last time a mineral grain was effectively exposed to sunlight, just prior to its burial. It is intrinsically related to final depositional process, which should reflect the completeness of the OSL signal resetting (zeroing process), evidenced by the normality and modality of the Equivalent Dose (DE) distribution. In Optical Dating, DE over-dispersion values have been used as a measure of inhomogeneitiy in the natural palaeo-dose of sediments. Such heterogeneity can be due to an array of causes, including insufficient zeroing during transport and deposition, or turbation processes after burial. Environments where sediments are well exposed to daylight at deposition (e.g. aeolian and some coastal) do not show extreme over-dispersion values but rather well clustered DE's as noted by probability-distribution plots. The degrees of variance and skewness of Gaussian or relative-probability distributions are intrinsically related to the scatter factor. Hence, the latter could be used to differentiate between depositional mechanisms and/or environmental settings. In this study, the single-aliquot regenerative-dose (SAR) protocol was used to measure the OSL signals from single grains of quartz from tsunami, storm and normal marine conditions deposits. Over-dispersion analyses were conducted on all samples. Preliminary results suggest the possibility of differentiating between all three types of deposits based on pre-established over-dispersion values and representative single-dose population distributions. Further comparative OSL experiments are currently being carried out on other known tsunamigenic analogues to further evaluate OSL signal behaviours and constrain the findings (2011 Tohoku Tsunami; 1979 night Petatlán Tsunami). Rather than a dating tool, OSL was used to identify signal patterns exclusive to known depositional conditions, in hope of applying it as sedimentological proxy in event stratigraphy and palaeoseismic tsunami research.

Lopez, G. I.

2012-12-01

379

The 3.2 ? resolution structure of a Receptor:CheA:CheW signaling complex defines overlapping binding sites and key residue interactions within bacterial chemosensory arrays  

PubMed Central

Bacterial chemosensory arrays are composed of extended networks of chemoreceptors (also known as methyl-accepting chemotaxis proteins, MCPs), the histidine kinase CheA, and the adaptor protein CheW. Models of these arrays have been developed from cryoelectron microscopy, crystal structures of binary and ternary complexes, NMR spectroscopy, mutational data and biochemical studies. A new 3.2 Å resolution crystal structure of a T. maritima MCP protein interaction region in complex with the CheA kinase-regulatory module (P4–P5) and adaptor protein CheW provides sufficient detail to define residue contacts at the interfaces formed among the three proteins. As in a previous 4.5 Å resolution structure, CheA-P5 and CheW interact through conserved hydrophobic surfaces at the ends of their ?-barrels to from pseudo six-fold symmetric rings in which the two proteins alternate around the circumference. The interface between P5 subdomain 1 and CheW subdomain 2 was anticipated from previous studies, whereas the related interface between CheW subdomain 1 and P5 subdomain 2 has only been observed in these ring assemblies. The receptor forms an unexpected structure in that the helical hairpin tip of each subunit has “unzipped” into a continuous ?-helix; four such helices associate into a bundle and the tetramers bridge adjacent P5-CheW rings in the lattice through interactions with both P5 and CheW. P5 and CheW each bind a receptor helix with a groove of conserved hydrophobic residues between subdomains 1 and 2. P5 binds the receptor helix N-terminal to the tip region (lower site), whereas CheW binds the same helix with inverted polarity near the bundle end (upper site). Sequence comparisons among different evolutionary classes of chemotaxis proteins show that the binding partners undergo correlated changes at key residue positions that involve the lower site. Such evolutionary analyses argue that both CheW and P5 bind to the receptor tip at overlapping positions. Computational genomics further reveal that two distinct CheW proteins in Thermotogae utilize the analogous recognition motifs to couple different receptor classes to the same CheA kinase. Important residues for function previously identified by mutagenesis, chemical modification and biophysical approaches also map to these same interfaces. Thus, although the native CheW-receptor interaction is not observed in the present crystal structure, the bioinformatics and previous data predict key features of this interface. The companion study of the P5-receptor interface in native arrays (Piasta et al. (2013) Biochemistry; Companion paper) shows that, despite the non-native receptor fold in the present crystal structure, the local helix-in-groove contacts of the crystallographic P5-receptor interaction are present in native arrays and are essential for receptor regulation of kinase activity. PMID:23668907

Li, Xiaoxiao; Fleetwood, Aaron D.; Bayas, Camille; Bilwes, Alexandrine M.; Ortega, Davi R.; Falke, Joseph J.; Zhulin, Igor B.; Crane, Brian R.

2013-01-01

380

Remediation of heavy metal contaminated sites in the Venice lagoon and conterminous areas (Northern Italy)  

NASA Astrophysics Data System (ADS)

The lagoon of Venice and the conterminous land are affected by heavy contamination of anthropogenic origin, and for this reason the whole area has been classified as site of national interest, and must be restored. Heavy metals (As, Cd, Cr, Cu, Hg, Mn, Pb, Sb, Se, Zn) and organic compounds (IPA, PCB, Dioxine) have been identified as the main contaminants at various sites, owing to agriculture and industrial wastes discharged on soils and convoyed to the lagoon. Five case studies of soil remediation are here reported. S. Giuliano is a former palustrine area reclaimed since the 60's with various human transported materials (HTM). In this area, hot spots overpassing the reference limits for residential and green areas have been recorded for Cd, Cu, Pb, Zn and IPA. Campalto is a site bordering the Venice lagoon and subjected to oscillating water level, that enhances metal mobility; diffuse contamination by heavy metals, particularly Pb, has been recorded at this site, utilized since 30 years for military and sport (skate) activities. Marghera is dramatically famous for its numerous factories and for oil refineries that affected the lagoon sediments since the 50's. Sediments proved heavily contaminated by As (up to 137 mgkg-1), Cd (57 mgkg-1), Hg (30mgkg-1), Ni, Pb (700 mgkg-1), Zn (5818 mgkg-1). Murano is a small island where many glass factories (the most famous all over the world) are running since XIII century. Glass is stained with several metals and, moreover, some substances are used to regulate fusion temperature, purity, etc., and therefore the surrounding environment is heavily contaminated by these substances. Mean concentrations of As (429 mgkg-1), Cd (1452 mgkg-1), Pb (749 mgkg-1), Zn (1624 mgkg-1), Se (341 mgkg-1), Sb (74 mgkg-1) widely overpass the reference values for both residential and industrial areas in national guidelines. Molo Serbatoi is a former oil container currently under restoration in the port of Venice. Soil contamination by As, Hg, Zn and IPA was recorded, while groundwater proved to be contaminated by As, Cd, Cr, Hg, Pb, Cu, Se, Ni, Mn, Sb, Fe. Restoration of the studied sites has been carried out by phytoremediation with native or exotic vegetation (Fragmites australis, Juncus lacustris,Puccinellia palustris, Limonium serotinum, Salicornia glauca, Spartina maritima, Pteris vittata) or cultivated plants (Heliantus annuus, Zea mais, Brassica napus, Brassica juncea). Results are somewhat contradictory. At S. Giuliano, the exotic fern (Pteris vittata), consistently with data from current literature, showed high ability to accumulate As, particularly in aerial parts. At Campalto, native vegetation proved ineffective for phytoextraction, but suitable for phytostabilization, owing to a root barrier effect. In the lagoon sediments from Marghera, Spartina proved more effective than Fragmites to uptake metals, while cultivated plants could not survive to high heavy metal concentrations. At Murano, Pteris vittata proved highly effective to accumulate As, but also resistant to elevated concentrations of co-existing metals (Cd, Pb, Se, Zn), with clear signals of growth sufference and a drastic reduction of sorption capacity only in the presence of very high Cd concentration. At Molo Serbatoi, phytoremediation could not be applied in absence of a chelating agent (e.g. EDTA), which could enhance metal mobilization: therefore, soil has been stored, selected and finally (the most contaminated part) delivered to a landfill, while groundwater will be remediated by bioremediation techniques.

Bini, Claudio; Wahsha, Mohammad; Fontana, Silvia; Maleci, Laura

2013-04-01

381

Threatened and Endangered Species Survey for Patrick Air Force Base, Florida  

NASA Technical Reports Server (NTRS)

A review of previous environmental work conducted at Patrick Air Force Base (PAFB) indicated that several threatened, endangered, or species of special concern occurred or had the potential to occur there. This study was implemented to collect more information on protected species at PAFB. A map of landcover types was prepared for PAFB using aerial photography, groundtruthing, and a geographic information system (GIS). Herbaceous vegetation was the most common vegetation type. The second most abundant vegetation type was disturbed shrubs/exotics. The beach and associated dune vegetation comprised 3.2% of the land area, but was the most extensive natural community within PAFB. A few isolated mangrove communities exist along the Banana River. Seventy-seven species of vascular plants occurred on the dunes, including four species listed by state agencies: spider lily (Hymenocallis latifolia), prickly pear cactus (Opuntia stricta), beach star (Remirea maritima), and inkberry (Scaevola plumien). Surveys of other habitats revealed eighty-four species of vascular plants including two state-listed species: spider lily and prickly pear cactus. Many of these areas are dominated by invasive, exotic species, particularly Brazilian pepper (Schinus terebinthifolius) and Australian pine (Casuarina equisetifolia), and native species of open or disturbed sites such as camphorweed (Heterotheca subaxillaris) and beardgrass (Andropogon spp.). Due to the isolation of PAFB from other natural areas, most exotic plant populations on the base are not an immediate threat to intact native plant communities. Dune habitat was surveyed for the southeastem beach mouse (Peromyscus polionotus niveiventris) by quarterly trapping along eight 100 m transects. No beach mice were found. The limited extent of dune habitat, its fragmented condition, and the isolation of PAFB from extant populations of the beach mouse probably accounts for its absence. Surveys of birds on PAFB found an avifauna characteristic of species that occur in the Indian River Lagoon system. Twenty-five species of waterbirds were observed during quarterly surveys on PAFB, including five species listed as species of special concern by the state of Florida: Snowy Egret (Egretta thula), Little Blue Heron (Egretta caerulea), Tricolored Heron (Egretta tricolo4, White Ibis (Eudocimus albus), and Brown Pelican (Pelecanus occidentalis). The Golf Course was used extensively by almost all species of waterbirds on PAFB. Twenty-two species of shorebirds were observed on PAFB. Although no listed species were observed, the potential exists for several protected species of shorebirds to use the beach at PAFB during some parts of the year. The Airfield runways and associated grass areas were important sites at PAFB for loafing and feeding for some shorebirds. Surveys of rooftop nesting by Least Terns (Stema antillarum) on PAFB found a large colony on a rooftop in the PAFB Industrial Area. This colony produced some independent young. Two rooftop Least Tern colonies reported from previous years were inactive during 1996. A small number of Black Skimmers (Rhynchops nigee attempted to nest at the Least Ten colony but were unsuccessful. Surveys for the gopher tortoise (Gopherus polyphemus) revealed burrows and tortoises only at the Waste Study Site; five burrows and three tortoises were observed. No Florida scrub lizards (Sceloporus woodi), eastern indigo snakes (Drymarchon corais couperl), or diamondback terrapins (Malademys terrapin terrapin) were observed. American alligators (Alligator mississippiensis) were observed on the Golf Course and using ditches, ponds, and areas along the Banana River. The amount of dune habitat could be expanded by not mowing areas adjacent to the dunes to allow dune species to colonize and expand. Planting dune species as part of the beach renourishment project will also increase this habitat. Exotic plants dominate several areas on the base and are used by threatened, endangered, and species of special concern. However, the use of native vegetation in landscaping projects thro

Oddy, Donna M.; Stolen, Eric D.; Schmalzer, Paul A.; Larson, Vickie L.; Hall, Patrice; Hensley, Melissa A.

1997-01-01