Acoelomorphs are bilaterally symmetric small marine worms that lack a coelom and possess a digestive system with a single opening. Two alternative phylogenetic positions of this group within the animal tree are currently debated. In one view, Acoelomorpha is the sister group to all remaining Bilateria and as such, is a morphologically simple stepping stone in bilaterian evolution. In the other, the group is a lineage within the Deuterostomia, and therefore, has derived a simple morphology from a more complex ancestor. Acoels and the closely related Nemertodermatida and Xenoturbellida, which together form the Acoelomorpha, possess a very limited number of cell types. To further investigate the diversity and origin of mesodermal cell types we describe the expression pattern of 12 orthologs of bilaterian mesodermal markers including Six1/2, Twist, FoxC, GATA4/5/6, in the acoel Isodiametra pulchra. All the genes are expressed in stem cells (neoblasts), gonads, and at least subsets of the acoel musculature. Most are expressed in endomesodermal compartments of I. pulchra developing embryos similar to what has been described in cnidarians. Our molecular evidence indicates a very limited number of mesodermal cell types and suggests an endomesodermal origin of the gonads and the stem cell system. We discuss our results in light of the two prevailing phylogenetic positions of Acoelomorpha.
Chiodin, Marta; B?rve, Aina; Berezikov, Eugene; Ladurner, Peter; Martinez, Pedro; Hejnol, Andreas
Introduction Acoels are microscopic marine worms that have become the focus of renewed debate and research due to their placement at the base of the Bilateria by molecular phylogenies. To date, Isodiametra pulchra is the most promising “model acoel” as it can be cultured and gene knockdown can be performed with double-stranded RNA. Despite its well-known morphology data on the nervous system are scarce. Therefore we examined this organ using various microscopic techniques, including histology, conventional histochemistry, electron microscopy, and immunocytochemistry in combination with CLSM and discuss our results in light of recently established phylogenies. Results The nervous system of Isodiametra pulchra consists of a bilobed brain with a dorsal posterior commissure, a frontal ring and tracts, four pairs of longitudinal neurite bundles, as well as a supramuscular and submuscular plexus. Serotonin-like immunoreactivity (SLI) is displayed in parts of the brain, the longitudinal neurite bundles and a large part of the supramuscular plexus, while FMRFamide-like immunoreactivity (RFLI) is displayed in parts of the brain and a distinct set of neurons, the longitudinal neurite bundles and the submuscular plexus. Despite this overlap SLI and RFLI are never colocalized. Most remarkable though is the presence of a distinct functional neuro-muscular system consisting of the statocyst, tracts, motor neurons and inner muscles, as well as the presence of various muscles that differ with regard to their ultrastructure and innervation. Conclusions The nervous system of Isodiametra pulchra consists of an insunk, bilobed brain, a peripheral part for perception and innervation of the smooth body-wall musculature as well as tracts and motor neurons that together with pseudostriated inner muscles are responsible for steering and quick movements. The insunk, bilobed brains with two to three commissures found in numerous acoels are homologous and evolved from a ring-commissural brain that was present in the stem species of acoelomorphs. The acoelomorph brain is bipartite, consisting of a Six3/6-dependend animal pole nervous system that persists throughout adulthood and an axial nervous system that does not develop by exhibiting a staggered pattern of conserved regulatory genes as in other bilaterians but by a nested pattern of these genes. This indicates that acoelomorphs stem from an ancestor with a simple brain or with a biphasic life cycle.
BACKGROUND: Tissue plasticity and a substantial regeneration capacity based on stem cells are the hallmark of several invertebrate groups such as sponges, cnidarians and Platyhelminthes. Traditionally, Acoela were seen as an early branching clade within the Platyhelminthes, but became recently positioned at the base of the Bilateria. However, little is known on how the stem cell system in this new
Katrien De Mulder; Georg Kuales; Daniela Pfister; Maxime Willems; Bernhard Egger; Willi Salvenmoser; Marlene Thaler; Anne-Kathrin Gorny; Martina Hrouda; Gaëtan Borgonie; Peter Ladurner
Since first described, acoels were considered members of the flatworms (Platyhelminthes). However, no clear synapomorphies among the three large flatworm taxa - the Catenulida, the Acoelomorpha and the Rhabditophora - have been characterized to date. Molecular phylogenies, on the other hand, commonly positioned acoels separate from other flatworms. Accordingly, our own multi-locus phylogenetic analysis using 43 genes and 23 animal species places the acoel flatworm Isodiametra pulchra at the base of all Bilateria, distant from other flatworms. By contrast, novel data on the distribution and proliferation of stem cells and the specific mode of epidermal replacement constitute a strong synapomorphy for the Acoela plus the major group of flatworms, the Rhabditophora. The expression of a piwi-like gene not only in gonadal, but also in adult somatic stem cells is another unique feature among bilaterians. These two independent stem-cell-related characters put the Acoela into the Platyhelminthes-Lophotrochozoa clade and account for the most parsimonious evolutionary explanation of epidermal cell renewal in the Bilateria. Most available multigene analyses produce conflicting results regarding the position of the acoels in the tree of life. Given these phylogenomic conflicts and the contradiction of developmental and morphological data with phylogenomic results, the monophyly of the phylum Platyhelminthes and the position of the Acoela remain unresolved. By these data, both the inclusion of Acoela within Platyhelminthes, and their separation from flatworms as basal bilaterians are well-supported alternatives.
Arendt, Detlev; Borgonie, Gaetan; Funayama, Noriko; Gschwentner, Robert; Hartenstein, Volker; Hobmayer, Bert; Hooge, Matthew; Hrouda, Martina; Ishida, Sachiko; Kobayashi, Chiyoko; Kuales, Georg; Nishimura, Osamu; Pfister, Daniela; Rieger, Reinhard; Salvenmoser, Willi; Smith, Julian; Technau, Ulrich; Tyler, Seth; Agata, Kiyokazu; Salzburger, Walter; Ladurner, Peter
CORAL is a language for specifying properties of ACOEL, a component-oriented extensional language. The design of CORAL is based on input\\/output automata and type state. The properties of ACOEL components that need to be verified are specified using CORAL. A verification en- gine will then crawl through CORAL and verify whether ACOEL can be safely executed or not. In this
Vugranam C. Sreedhar
Summary A cytological (light microscopical, cytochemical and fine structural) analysis of the cellular organization of the acoel turbellarianConvoluta convoluta (Abildgaard) is presented. The controversial problem as to the cellular organization has been clarified. The animal has been found to be composed of cells, and contrary to what is usually supposed it is not syncytially or plasmodially organized.
Knud Jørgen Pedersen
The localisation of halogenated furanones, the biologically active secondary metabolites from the red alga Delisea pulchra (Greville), was determined by a combination of fluorescence microscopy, culture studies and quantitative chemical analyses.\\u000a All types of evidence showed that furanones are localised in the central vesicle of gland cells in D. pulchra. These cells release furanones onto the surface of the plant,
S. A. Dworjanyn; R. De Nys; P. D. Steinberg
Our interest in the red alga Delisea pulchra (=D.fimbriata) (Greville) Montagne 1844 (Rhodophyceae, Bonnemaisoniales, Bonnemaisoniaceace) was stimulated by its activity in the biosssays done at Wyeth Pharmaceuticals. Halogenated compounds from D. pulchra interfere with Gram-negative bacterial signaling systems, affect the growth of Gram-positive bacteria, inhibit quorum sensing and swarming motility of marine bacteria (inhibit bacterial communication). They also inhibit surface
As a consequence of anthropogenic CO2 emissions, oceans are becoming more acidic, a phenomenon known as ocean acidification. Many marine species predicted to be sensitive to this stressor are photosymbiotic, including corals and foraminifera. However, the direct impact of ocean acidification on the relationship between the photosynthetic and nonphotosynthetic organism remains unclear and is complicated by other physiological processes known to be sensitive to ocean acidification (e.g. calcification and feeding). We have studied the impact of extreme pH decrease/pCO2 increase on the complete life cycle of the photosymbiotic, non-calcifying and pure autotrophic acoel worm, Symsagittifera roscoffensis. Our results show that this species is resistant to high pCO2 with no negative or even positive effects on fitness (survival, growth, fertility) and/or photosymbiotic relationship till pCO2 up to 54 K µatm. Some sub-lethal bleaching is only observed at pCO2 up to 270 K µatm when seawater is saturated by CO2. This indicates that photosymbiosis can be resistant to high pCO2. If such a finding would be confirmed in other photosymbiotic species, we could then hypothesize that negative impact of high pCO2 observed on other photosymbiotic species such as corals and foraminifera could occur through indirect impacts at other levels (calcification, feeding).
Dupont, Sam; Moya, Aurelie; Bailly, Xavier
As a consequence of anthropogenic CO? emissions, oceans are becoming more acidic, a phenomenon known as ocean acidification. Many marine species predicted to be sensitive to this stressor are photosymbiotic, including corals and foraminifera. However, the direct impact of ocean acidification on the relationship between the photosynthetic and nonphotosynthetic organism remains unclear and is complicated by other physiological processes known to be sensitive to ocean acidification (e.g. calcification and feeding). We have studied the impact of extreme pH decrease/pCO? increase on the complete life cycle of the photosymbiotic, non-calcifying and pure autotrophic acoel worm, Symsagittifera roscoffensis. Our results show that this species is resistant to high pCO? with no negative or even positive effects on fitness (survival, growth, fertility) and/or photosymbiotic relationship till pCO? up to 54 K µatm. Some sub-lethal bleaching is only observed at pCO? up to 270 K µatm when seawater is saturated by CO?. This indicates that photosymbiosis can be resistant to high pCO?. If such a finding would be confirmed in other photosymbiotic species, we could then hypothesize that negative impact of high pCO? observed on other photosymbiotic species such as corals and foraminifera could occur through indirect impacts at other levels (calcification, feeding). PMID:22253736
Dupont, Sam; Moya, Aurélie; Bailly, Xavier
REVERSAL of phototaxis has been noted in a number of animals and attributed to fright, hunger and food and other chemical stimuli. The only case known to me in which the direction of phototaxis is determined by the salinity of the environment is provided by the larvæ of Polydora pulchra, Carazzi, previously recorded1 from the plaice ponds at the Marine
M. R. Ranade
In this study the antifouling activity was investigated of a series of chemically related, halogenated furanones isolated from Delisea pulchra (Greville) Montagne, a red alga which is rarely fouled in the field. The metabolites were tested in laboratory assays against representatives of the three major groups of fouling organisms, the barnacle Balanus amphitrite amphitirite Darwin, the macroalga Ulva lactuca Linnaeus
R. De Nys; P. D. Steinberg; P. Willemsen; S. A. Dworjanyn; C. L. Gabelish; R. J. King
Five plasmids occur in the red alga Porphyra pulchra. The two larger ones (6859 and 6427 bp) differ in their sequences. The three smaller (1896, 2100, and 2102 bp) have sequences\\u000a that are similar to one another. These plasmids are circular, double-stranded DNA, present in high copy number, and maintained\\u000a in this organism through successive generations of laboratory culture. Sequence
D. A. Moon; Lynda J. Goff
Halogenated furanones produced by the benthic marine macroalga Delisea pulchra inhibit swarming motility of Serratia liquefaciens MG1. This study demonstrates that exogenously added furanones control transcription of the quorum sensing regulated gene swrA in competition with the cognate signal molecule N-butanoyl-L-homoserine lactone. This in turn results in reduced production of the surface-active compound serrawettin W2, which is crucial for surface
Thomas Bovbjerg Rasmussen; Michael Manefield; Jens Bo Andersen; Leo Eberl; Uffe Anthoni; Carsten Christophersen; Peter Steinberg; Staffan Kjelleberg; Michael Givskov
Summary Background Tidal (12.4 hr) cycles of behavior and physiology adapt intertidal organisms to temporally complex coastal environments, yet their underlying mechanism is unknown. However, the very existence of an independent “circatidal” clock has been disputed, and it has been argued that tidal rhythms arise as a submultiple of a circadian clock, operating in dual oscillators whose outputs are held in antiphase i.e., ?12.4 hr apart. Results We demonstrate that the intertidal crustacean Eurydice pulchra (Leach) exhibits robust tidal cycles of swimming in parallel to circadian (24 hr) rhythms in behavioral, physiological and molecular phenotypes. Importantly, ?12.4 hr cycles of swimming are sustained in constant conditions, they can be entrained by suitable stimuli, and they are temperature compensated, thereby meeting the three criteria that define a biological clock. Unexpectedly, tidal rhythms (like circadian rhythms) are sensitive to pharmacological inhibition of Casein kinase 1, suggesting the possibility of shared clock substrates. However, cloning the canonical circadian genes of E. pulchra to provide molecular markers of circadian timing and also reagents to disrupt it by RNAi revealed that environmental and molecular manipulations that confound circadian timing do not affect tidal timing. Thus, competent circadian timing is neither an inevitable nor necessary element of tidal timekeeping. Conclusions We demonstrate that tidal rhythms are driven by a dedicated circatidal pacemaker that is distinct from the circadian system of E. pulchra, thereby resolving a long-standing debate regarding the nature of the circatidal mechanism.
Zhang, Lin; Hastings, Michael H.; Green, Edward W.; Tauber, Eran; Sladek, Martin; Webster, Simon G.; Kyriacou, Charalambos P.; Wilcockson, David C.
Abstract We describe a new species of the bee genus Centris, Centris (Centris) byrsonimae Mahlmann & Oliveira sp. n., whose name has appeared as a nomen nudum in the literature since 1985. Further, a new species group of Centris s.str. is proposed, the pulchra group, based on morphological characters, which comprises the species Centris pulchra Moure, Oliveira & Viana, 2003 and Centris byrsonimae sp. n..Based on information from specimen labels studied and data from the literature, a list of plant species visited by the pulchra group is presented. The male genitalia and hidden metasomal sterna 7 and 8 of Centris pulchra are described for the first time. Typographic errors pertaining to the paratype labels reported in the original description of Centris pulchra are corrected. One female paratype of Centris pulchra is designated herein as a paratype of Centris byrsonimae sp. n. An updated list of species of Centris s.str. from northeastern Brazil is provided including references about geographic distributions as well as an identification key to the pulchra species group.
Mahlmann, Thiago; de Oliveira, Favizia Freitas
We describe a new species of the bee genus Centris, Centris (Centris) byrsonimae Mahlmann & Oliveira sp. n., whose name has appeared as a nomen nudum in the literature since 1985. Further, a new species group of Centris s.str. is proposed, the pulchra group, based on morphological characters, which comprises the species Centris pulchra Moure, Oliveira & Viana, 2003 and Centris byrsonimaesp. n..Based on information from specimen labels studied and data from the literature, a list of plant species visited by the pulchra group is presented. The male genitalia and hidden metasomal sterna 7 and 8 of Centris pulchra are described for the first time. Typographic errors pertaining to the paratype labels reported in the original description of Centris pulchra are corrected. One female paratype of Centris pulchra is designated herein as a paratype of Centris byrsonimaesp. n. An updated list of species of Centris s.str. from northeastern Brazil is provided including references about geographic distributions as well as an identification key to the pulchra species group. PMID:23459508
Mahlmann, Thiago; de Oliveira, Favízia Freitas
Background The hemolytic activity of skin secretions obtained by stimulating the frog Kaloula pulchra hainana with diethyl ether was tested using human, cattle, rabbit, and chicken erythrocytes. The skin secretions had a significant concentration-dependent hemolytic effect on erythrocytes. The hemolytic activity of the skin secretions was studied in the presence of osmotic protectants (polyethylene glycols and carbohydrates), cations (Mg2+, Ca2+, Ba2+, Cu2+, and K+), or antioxidants (ascorbic acid, reduced glutathione, and cysteine). Results Depending on their molecular mass, osmotic protectants effectively inhibited hemolysis. The inhibition of skin hemolysis was observed after treatment with polyethylene glycols (1000, 3400, and 6000 Da). Among divalent cations, only 1 mM Cu2+ markedly inhibited hemolytic activity. Antioxidant compounds slightly reduced the hemolytic activity. Conclusions The results suggested that skin secretions of K. pulchra hainana induce a pore-forming mechanism to form pores with a diameter of 1.36-2.0 nm rather than causing oxidative damage to the erythrocyte membrane.
Oogenesis in Typosyllis pulchra begins with a short proliferative gonial phase. Gonial clusters, consisting of six to eight syncytial sibling cells, are surrounded by gonial peritoneum and are eventually liberated into the coelom. At about the same time as the onset of the coelomic phase, one gonial cell in each cluster differentiates, begins to accumulate yolk and increases in size,
Albert E. Heacox; Paul C. Schroeder
Disease is increasingly viewed as a major factor in the ecology of marine communities and its impact appears to be increasing with environmental change, such as global warming. The temperate macroalga Delisea pulchra bleaches in Southeast Australia during warm summer periods, a phenomenon which previous studies have indicated is caused by a temperature induced bacterial disease. In order to better understand the ecology of this disease, the bacterial communities associated with threes type of samples was investigated using 16S rRNA gene and environmental shotgun sequencing: 1) unbleached (healthy) D. pulchra 2) bleached parts of D. pulchra and 3) apparently healthy tissue adjacent to bleached regions. Phylogenetic differences between healthy and bleached communities mainly reflected relative changes in the taxa Colwelliaceae, Rhodobacteraceae, Thalassomonas and Parvularcula. Comparative metagenomics showed clear difference in the communities of healthy and diseased D. pulchra as reflected by changes in functions associated with transcriptional regulation, cation/multidrug efflux and non-ribosomal peptide synthesis. Importantly, the phylogenetic and functional composition of apparently healthy tissue adjacent to bleached sections of the thalli indicated that changes in the microbial communities already occur in the absence of visible tissue damage. This shift in unbleached sections might be due to the decrease in furanones, algal metabolites which are antagonists of bacterial quorum sensing. This study reveals the complex shift in the community composition associated with bleaching of Delisea pulchra and together with previous studies is consistent with a model in which elevated temperatures reduce levels of chemical defenses in stressed thalli, leading to colonization or proliferation by opportunistic pathogens or scavengers. PMID:23226544
Fernandes, Neil; Steinberg, Peter; Rusch, Doug; Kjelleberg, Staffan; Thomas, Torsten
Disease is increasingly viewed as a major factor in the ecology of marine communities and its impact appears to be increasing with environmental change, such as global warming. The temperate macroalga Delisea pulchra bleaches in Southeast Australia during warm summer periods, a phenomenon which previous studies have indicated is caused by a temperature induced bacterial disease. In order to better understand the ecology of this disease, the bacterial communities associated with threes type of samples was investigated using 16S rRNA gene and environmental shotgun sequencing: 1) unbleached (healthy) D. pulchra 2) bleached parts of D. pulchra and 3) apparently healthy tissue adjacent to bleached regions. Phylogenetic differences between healthy and bleached communities mainly reflected relative changes in the taxa Colwelliaceae, Rhodobacteraceae, Thalassomonas and Parvularcula. Comparative metagenomics showed clear difference in the communities of healthy and diseased D. pulchra as reflected by changes in functions associated with transcriptional regulation, cation/multidrug efflux and non-ribosomal peptide synthesis. Importantly, the phylogenetic and functional composition of apparently healthy tissue adjacent to bleached sections of the thalli indicated that changes in the microbial communities already occur in the absence of visible tissue damage. This shift in unbleached sections might be due to the decrease in furanones, algal metabolites which are antagonists of bacterial quorum sensing. This study reveals the complex shift in the community composition associated with bleaching of Delisea pulchra and together with previous studies is consistent with a model in which elevated temperatures reduce levels of chemical defenses in stressed thalli, leading to colonization or proliferation by opportunistic pathogens or scavengers.
Fernandes, Neil; Steinberg, Peter; Rusch, Doug; Kjelleberg, Staffan; Thomas, Torsten
Four species of marine calcifying algae, the coccolithophores Calcidiscus leptoporus, Helicosphaera carteri, Syracosphaera pulchra and Umbilicosphaera foliosa were grown in laboratory cultures under temperatures varying between 14 and 23 °C, and one species, C. leptoporus, under varying [CO 32-], ranging from 105 to 219 ?mol/kg. Calcium isotope compositions of the coccoliths resemble in both absolute fractionation and temperature sensitivity previous calibrations of marine calcifying species e.g. Emiliania huxleyi (coccolithophores) and Orbulina universa (planktonic foraminifera) as well as inorganically precipitated CaCO 3, but also reveal small species specific differences. In contrast to inorganically precipitated calcite, but similar to E. huxleyi and O. universa, the carbonate ion concentration of the medium has no statistically significant influence on the Ca isotope fractionation of C. leptoporus coccoliths; however, combined data of E. huxleyi and C. leptoporus indicate that the observed trends might be related to changes of the calcite saturation state of the medium. Since coccoliths constitute a significant portion of the global oceanic CaCO 3 export production, the Ca isotope fractionation in these biogenic structures is important for defining the isotopic composition of the Ca sink of the ocean, one of the key parameters for modelling changes to the marine Ca budget over time. For the present ocean our results are in general agreement with the previously postulated and applied mean value of the oceanic Ca sink (? sed) of about - 1.3‰, but the observed inter- and intra-species differences point to possible changes in ? sed through earth history, due to changing physico-chemical conditions of the ocean and shifts in floral and faunal assemblages.
Gussone, Nikolaus; Langer, Gerald; Geisen, Markus; Steel, Blair A.; Riebesell, Ulf
The mottled skate, Raja pulchra, is an economically valuable fish. However, due to a severe population decline, it is listed as a vulnerable species by the International Union for Conservation of Nature. To analyze its genetic structure and diversity, microsatellite markers were developed using 454 pyrosequencing. A total of 17,033 reads containing dinucleotide microsatellite repeat units (mean, 487 base pairs) were identified from 453,549 reads. Among 32 loci containing more than nine repeat units, 20 primer sets (62%) produced strong PCR products, of which 14 were polymorphic. In an analysis of 60 individuals from two R. pulchra populations, the number of alleles per locus ranged from 1–10, and the mean allelic richness was 4.7. No linkage disequilibrium was found between any pair of loci, indicating that the markers were independent. The Hardy–Weinberg equilibrium test showed significant deviation in two of the 28 single-loci after sequential Bonferroni’s correction. Using 11 primer sets, cross-species amplification was demonstrated in nine related species from four families within two classes. Among the 11 loci amplified from three other Rajidae family species; three loci were polymorphic. A monomorphic locus was amplified in all three Rajidae family species and the Dasyatidae family. Two Rajidae polymorphic loci amplified monomorphic target DNAs in four species belonging to the Carcharhiniformes class, and another was polymorphic in two Carcharhiniformes species.
Kang, Jung-Ha; Park, Jung-Youn; Jo, Hyun-Su
Nautella sp. R11, a member of the marine Roseobacter clade, causes a bleaching disease in the temperate-marine red macroalga, Delisea pulchra. To begin to elucidate the molecular mechanisms underpinning the ability of Nautella sp. R11 to colonize, invade and induce bleaching of D. pulchra, we sequenced and analyzed its genome. The genome encodes several factors such as adhesion mechanisms, systems for the transport of algal metabolites, enzymes that confer resistance to oxidative stress, cytolysins, and global regulatory mechanisms that may allow for the switch of Nautella sp. R11 to a pathogenic lifestyle. Many virulence effectors common in phytopathogenic bacteria are also found in the R11 genome, such as the plant hormone indole acetic acid, cellulose fibrils, succinoglycan and nodulation protein L. Comparative genomics with non-pathogenic Roseobacter strains and a newly identified pathogen, Phaeobacter sp. LSS9, revealed a patchy distribution of putative virulence factors in all genomes, but also led to the identification of a quorum sensing (QS) dependent transcriptional regulator that was unique to pathogenic Roseobacter strains. This observation supports the model that a combination of virulence factors and QS-dependent regulatory mechanisms enables indigenous members of the host alga's epiphytic microbial community to switch to a pathogenic lifestyle, especially under environmental conditions when innate host defence mechanisms are compromised.
Fernandes, Neil; Case, Rebecca J.; Longford, Sharon R.; Seyedsayamdost, Mohammad R.; Steinberg, Peter D.; Kjelleberg, Staffan; Thomas, Torsten
A refinery located on the slopes of a mountain range in the city of Cubatão (SE-Brazil) is the main source of sulfur dioxide (SO(2)) in the region. For this reason, the refinery replaced a system in which energy was produced from crude oil combustion in boilers with a system of energy and vapor co-generation in a thermoelectric power plant fueled by natural gas. The aim of this study was to investigate the responses of Tibouchina pulchra to the fuel switching. Saplings planted in pots were distributed throughout monitoring sites around the polluting source (sites I, II, III and IV) and in a site (V) far from emissions. Changes on the plants responses occur along the three fuel switching phases. During the last phase, increased carbon assimilation (Asat) and decreased stomatal conductance (gs) were observed in plants growing in sites II and III; as a consequence, intrinsic water use efficiency (iWUE) increased. However, the increase in Asat did not promote growth increase suggesting that changes at the refinery did not result in better air quality, but only in a change in the main contaminants. PMID:23352657
Silva, Daiane T; Moraes, Regina M
Insect galls may present nutritive tissues with distinct cytological features related to the order of the gall inducer. Galling Lepidoptera larvae chew plant cells and induce the redifferentiation of parenchymatic cells into nutritive ones. The nutritive cells in the galls induced by a microlepidoptera on the leaves of Tibouchina pulchra (Cham.) Cogn. (Melastomataceae) are organelle-rich, with developed Golgi apparatus, endoplasmic reticulum, ribosomes, polyribosomes, mitochondria, plastids, and one great central or several fragmented vacuoles. The nonobservance of the nuclei in the nutritive cells deserves special attention, and confers a similarity between the nutritive cells and the vascular conductive ones. The great amount of rough endoplasmic reticulum, ribosomes, polyribosomes, and mitochondria is indicative of the high metabolic status of these cells. They are vascular cambium-like, with high protein synthesis and lipid storage. The proteins are essential to enzymatic metabolism, and secondarily, to larvae nutrition, similarly to the lipid droplets which confer energetic profile to these nutritive cells. The living enucleated cells receive mRNA from their neighbor ones, which may support the high metabolic profile of endoplasmic reticulum and ribosomes observed in galls. Thus, the nutritive cells are stimulated by the galling larvae activity, generating a new cell type, whose redifferentiation includes a mix of intrinsic and common plant pathways. PMID:23779213
Vecchi, Claudia; Menezes, Nanuza Luiza; Oliveira, Denis Coelho; Ferreira, Bruno Garcia; Isaias, Rosy Mary Santos
The effect of 17-methoxyl-7-hydroxy-benzene-furanchalcone isolated from the roots of Millettia pulchra (Benth.) Kurz var. Laxior (Dunn) Z. Wei on rat myocardial ischemia has been investigated. An in vitro cardiocyte apoptosis model and an in vivo myocardial ischemia model were used to elucidate the mechanism of 17-methoxyl-7-hydroxy-benzene-furanchalcone. In contrast to hydrogen peroxide (H2O2, 100 µmol/L), 17-methoxyl-7-hydroxy-benzene-furanchalcone in vitro (255 and 510 µmol/L) increased the quantity of total superoxide dismutase and the protein expression of B cell lymphoma/leukemia-2, while it inhibited cardiocyte apoptosis, the release of malondialdehyde and tumor necrosis factor ?, and protein expression of nuclear factor ? Bp65 and Bcl-2-associated X protein. Furthermore, pretreatment with MHBFC in vivo (10 and 20 mg/kg) decreased heart rate, systolic pressure, diastolic pressure, average pressure, left ventricular systolic pressure, the largest upstroke velocity of the left ventricular pressure (+ dp/dtmax), total antioxidative capability, myoglobin isoenzyme of creatine kinase, and inducible nitric oxide synthase, while it increased endothelial nitric oxide synthase, ATPases, left ventricular diastolic pressure, left ventricular end-diastolic pressure, the largest descendent velocity of the left ventricular pressure (-dp/dtmax) and the interval from the beginning of left ventricular contraction to +dp/dtmax (t - dp/dtmax), all in a dose-dependent manner. Our present results suggest that 17-methoxyl-7-hydroxy-benzene-furanchalcone is an attractive antimyocardial ischemia agent mostly because of its negative heart rate and negative inotropic effects, the reduction in myocardial oxidative damage, and the modulating expression of genes associated with apoptosis, which improves diastolic function. PMID:22700048
Jian, Jie; Qing, Feizhang; Zhang, Shijun; Huang, Jianchun; Huang, Renbin
Determination of five flavonoids in different parts of Fordia cauliflora by ultra performance liquid chromatography/triple-quadrupole mass spectrometry and chemical comparison with the root of Millettia pulchra var. laxior
Background The root of Fordia cauliflora Hemsl (FC) has long been used in southern China for the treatment of rheumatism, bruises, dementia in children, and valetudinarianism. However, sometimes it is mixed with other parts. And it has always been confused with the root of Millettia pulchra (Benth.) Kurz var. laxior (Dunn) Z. Wei (MP) by the local people. The chemical differences between the two ethnic drugs are not clear until now. The aim of this study is to develop a precise and accurate method to characterize and quantify multiple chemical components of FC, which is helpful for the quality evaluation and identification of FC. Results A method coupling ultra performance liquid chromatography (UPLC) with triple-quadrupole mass spectrometry (QqQ-MS) was first developed for simultaneous determination of five flavonoids in different parts of FC and the root of MP, based on a UPLC-diode array detection (DAD) fingerprint method. All calibration curves showed good linearity (R2>0.99) within test ranges. The overall LOD and LOQ were lower than 2.5 ng/mL and 5.0 ng/mL, respectively. The RSDs for intra- and inter-day of five analytes were less than 2.83% and 3.04%, respectively. Recovery studies for the quantified compounds were found to be within the range 93.6-99.8% with RSD less than 5.73%. The results suggest that the root, traditionally used medicinal part, yields the highest flavanoid content in FC. Pachycarin A, 3?,4?-dimethoxy(2??,3??:7,8) furanoflavone, karanjachromene and isoderricin A can be used to differentiate between FC and MP samples. Conclusions The present method is specific, precise and reliable, and is suitable for characterizing and quantifying multiple chemical components of FC.
Convolutriloba longifissura is a red flatworm with white dots that harbors unicellular green algae within its body. The red pigment of the flatworm that is present in round cells is soluble in ethanol or acetone, whereas the white pigment contained in the crystalline (retractile) platelets of amoeboid-shaped cells is soluble in 1% NH4OH. These two types of pigment cells form the body coloration and are probably involved in light protection of the algal symbionts, as many algal cells are distributed beneath the body wall and some are in the highly vacuolated parenchyma. The ultrastructural features of these cells suggest a close relationship with Tetraselmis spp. The morphology of sagittocysts within the mantle is also described by means of scanning and transmission electron microscopy. PMID:18271640
Hirose, Euichi; Hirose, Mamiko
The neuroarchitecture of Acoela has been at the center of morphological debates. Some authors, using immunochemical tools,\\u000a suggest that the nervous system in Acoela is organized as a commissural brain that bears little resemblance to the central,\\u000a ganglionic type brain of other flatworms, and bilaterians in general. Others, who used histological staining on paraffin sections,\\u000a conclude that it is a
Amandine Bery; Albert Cardona; Pedro Martinez; Volker Hartenstein
Submarine groundwater discharge (SGD) occurs in intertidal areas, representing a largely unquantified source of solute fluxes to adjacent coastal zones, with nitrogen being constantly the keynote chemical of concern. In Olhos de Água SGD is present as groundwater springs or merely sub-aerial runoff. The occurrence of the flatworm Symsagittifera roscoffensis is described for the first time in Olhos de Água in connection to seepage flows. To assess the impact of this symbiotic flatworm on the nitrogen associated to groundwater discharge flow at the beach, nitrate uptake experiments were conducted in laboratory microcosms. Our results show that S. roscoffensis actively uptakes nitrate at different rates depending on light availability, with rates ?10times higher than that of its symbiotic microalgae alone. This supports the hypothesis thatS. roscoffensis could be an important in situ nitrate interceptor, potentially playing a biological role on the transformation of groundwater-borne nitrate loads at the land-ocean boundary. PMID:23948093
Carvalho, Liliana F; Rocha, Carlos; Fleming, Alexandra; Veiga-Pires, Cristina; Aníbal, Jaime
As a part of an investigations on the lipid metabolism in Platyhelminthes, the acoel Convoluta roscoffensis, which harbors the green alga Platymonas convoluta as a symbiont, was studied. Isotopic tracer experiments established that the acoel lacks the ability to synthesize de novo long-chain saturated and unsaturated fatty acids and depends on its algal symbiont for these compounds. The acoel's fatty acid composition closely resembles that of the alga but differs from those of other animals; the acoel's polyunsaturated fatty acids are of the plant type (omega 3 family) rather than of the animal type (omega 6 family). The acoel also lacks the ability to synthesize sterols de novo. It contains 24-methylenecholesterol synthesized by the algae and, in addition, significant amounts of cholesterol, which is probably a host modification product of the algal sterol. With fatty acids provided by the symbiont, the acoel has the ability to synthesize its own complex lipids. The acoel contains relatively large amounts of triglyceride, phosphatidylcholine, and ethanolamine plasmalogen. These compounds are either not present at all or present only in minute amounts in the symbiotic alga. Since acoels belong to the most primitive forms of the present-day flatworms, the observed metabolic defects in this organism suggest that mechanisms for the biosynthesis of fatty acids and sterols were lost early during the evolution of the Platyhelminthes, and that this phenomenon is widespread within the phylum. PMID:465514
Meyer, H; Provasoli, L; Meyer, F
A dark brown acoel has been collected for a number of years in bottom mud samples from Great Harbor and Buzzards Bay near Woods Hole, Massachusetts for use in class and experimental work. In the summer of 1965 I found a large population of the same species living intertidally in the salt marsh bordering Barn stable Harbor near West Dennis,
Conventional wisdom suggests that bilateral organisms arose from ancestors that were radially, rather than bilaterally, symmetrical and, therefore, had a single body axis and no mesoderm. The two main hypotheses on how this transformation took place consider either a simple organism akin to the planula larva of extant cnidarians or the acoel Platyhelminthes (planuloid-acoeloid theory), or a rather complex organism
Pere Martinez; Jordi Paps; Marta Riutort
Background Acoels are simply organized unsegmented worms, lacking hindgut and anus. Several publications over recent years challenge the long-held view that acoels are early offshoots of the flatworms. Instead a basal position as sister group to all other bilaterian animals was suggested, mainly based on molecular evidence. This led to the view that features of acoels might reflect those of the last common ancestor of Bilateria, and resulted in several evo-devo studies trying to interpret bilaterian evolution using acoels as a proxy model for the "Urbilateria". Results We describe the first complete mitochondrial genome sequence of a member of the Acoela, Symsagittifera roscoffensis. Gene content and circular organization of the mitochondrial genome does not significantly differ from other bilaterian animals. However, gene order shows no similarity to any other mitochondrial genome within the Metazoa. Phylogenetic analyses of concatenated alignments of amino acid sequences from protein coding genes support a position of Acoela and Nemertodermatida as the sister group to all other Bilateria. Our data provided no support for a sister group relationship between Xenoturbellida and Acoela or Acoelomorpha. The phylogenetic position of Xenoturbella bocki as sister group to or part of the deuterostomes was also unstable. Conclusions Our phylogenetic analysis supports the view that acoels and nemertodermatids are the earliest divergent extant lineage of Bilateria. As such they remain a valid source for seeking primitive characters present in the last common ancestor of Bilateria. Gene order of mitochondrial genomes seems to be very variable among Acoela and Nemertodermatida and the groundplan for the metazoan mitochondrial genome remains elusive. More data are needed to interpret mitochondrial genome evolution at the base of Bilateria.
Determination of total sulfur in lichens and plants by combustion-infrared analysis. [Medicago sativa L. ; Vitis labruscana Bailey; Festuca sp. ; Fraxinum pennsylvanica Marsh. ; Paremelia chlorochroa Tuck. ; P. sulcata Tayl. ; Juniperus scopulorum Sarg. ; Artemisia tridentata Nuttl; Lycopersicum esculentum Mill. ; Triticum compactum Host; Agropyron smithii Rydb. ; Salix pulchra Cham
Sulfur was determined in plants and lichens by combustion of the sample and infrared detection of evolved sulfur dioxide using an automated sulfur analyzer. Vanadium pentaoxide was used as a combustion accelerator. Pelletization of the sample prior to combustion was not found to be advantageous. Washing studies showed that leaching of sulfur was not a major factor in the sample preparation. The combustion-IR analysis usually gave higher sulfur content than the turbidimetric analysis as well as shorter analysis time. Relative standard deviations of less than 7% were obtained by the combustion-IR technique when sulfur levels in plant material range from 0.05 to 0.70%. Determination of sulfur in National Bureau of Standards botanical reference materials showed good agreement between the combustion-IR technique and other instrumental procedures. Seven NBS botanical reference materials were analyzed.
Jackson, L.L.; Engleman, E.E.; Peard, J.L.
Eight anuran species were recorded for the first time in Guam in the period May 2003-December 2005, all apparently the result of arrivals to the island since 2000. Three of the eight species (Rana guentheri, Polypedates megacephalus, and Eleutherodactylus planirostris) had well-established breeding populations by 2005. A further three (Fejervarya cf. limnocharis, Fejervarya cancri- vora, and Microhyla pulchra) were recorded
Michelle T. Christy; Craig S. Clark; David E. Gee II; Diane Vice; Daniel S. Vice; Mitchell P. Warner; Claudine L. Tyrrell; Gordon H. Rodda; Julie A. Savidge
Differences in resistance to powdery mildew were observed on detached leaf disks of six flowering dogwood lines inoculated with conidia of Erysiphe pulchra. Significant differences (P < 0.02) in germinated conidia with branched hyphae, infection efficiency, latent period and sporulation were detecte...
Fossil record of holococcoliths and selected hetero-holococcolith associations from the Mediterranean (Holocene–late Pleistocene): Evaluation of carbonate diagenesis and palaeoecological–palaeocenographic implications
The Holocene–late Pleistocene distribution of holococcoliths, is quantified by light microscopy from cores from the Western Mediterranean, the Aegean Sea and eight eastern Mediterranean cores recovering sapropel S1. The diversity of fossil holococcoliths is much lower than is seen in the plankton, indicating selective preservation. However the holococcolith phases of Syracosphaera pulchra and Helicosphaera carteri are abundantly preserved allowing a
Daniela Crudeli; Jeremy R. Young; Elisabetta Erba; Markus Geisen; Patrizia Ziveri; Gert J. de Lange; Caroline P. Slomp
In this paper, nine new fossil species of Trichoptera in Dominican amber are described: An- tillopsyche auricula n. sp., Antillopsyche digitus n. sp., Atopsyche perlucida n. sp., Calosopsyche palaeoelegans n. sp., Cernotina pulchra n. sp., Chimarra (Chimarrita) palaenova n. sp., Cubanoptila longiscapa n. sp., Macronema hispaniola n. sp., Phylloicus velteni n. sp. Thus 31 fossil species are verified in Dominican
To control biofilms, we have synthesized the natural biofilm inhibitor (5Z)-4-bromo-5- (bromomethylene) -3-butyl-2(5H)-furanone from the red alga Delisea pulchra and determined that it functions by disrupting quorum sensing in Vibrio harveyi by blocking a...
T. K. Wood
Floral color changes are common among Melastomataceae and have been interpreted as a warning mechanism for bees to avoid old flowers, albeit increasing long-distance flower display. Here the reproductive systems of Tibouchina pulchra and T. sellowiana were investigated by controlled pollinations. Their pollinators were identified, and experiments on floral color and fragrance changes were conduced to verify if those changes
Adriana Couto Pereira; Juliana Bertolino da Silva; Renato Goldenberg; Gabriel A. R. Melo; Isabela Galarda Varassin
The red alga Delisea pulchra has been a model organism for antifoulants. Furanones are produced by the plant and delivered to the understanding the ecological role of secondary metabolites as natural surface at a concentration where they regulate bacterial colonisation and the settlement of epibiota. This biological understanding has led to the application of furanones as inhibitors of bacterial- and
R. de Nys; M. Givskov; N. Kumar; S. Kjelleberg; P. D. Steinberg
In California valley grasslands, Avena fatua L. and other exotic annual grasses have largely displaced native perennial bunchgrasses such as Elymus glaucus Buckley and Nassella pulchra (A. Hitchc.) Barkworth. The invasion success and continued dominance of the exotics has been generally attributed to changes\\u000a in disturbance regimes and the outcome of direct competition between species. Here, we report that exotic
Carolyn M. Malmstrom; April J. McCullough; Hope A. Johnson; Linsey A. Newton; Elizabeth T. Borer
Bilateria are currently subdivided into three superclades: Deuterostomia, Ecdysozoa, and Lophotrochozoa. Within this new taxonomic frame, acoelomate Platyhelminthes, for a long time held to be basal bilaterians, are now considered spiralian lophotrochozoans. However, recent 18S rDNA [small subunit (SSU)] analyses have shown Platyhelminthes to be polyphyletic with two of its orders, the Acoela and the Nemertodermatida, as the earliest extant bilaterians. To corroborate such position and avoid the criticisms of saturation and long-branch effects thrown on the SSU molecule, we have searched for independent molecular data bearing good phylogenetic information at deep evolutionary nodes. Here we report a phylogenetic analysis of DNA sequences from the myosin heavy chain type II (myosin II) gene from a large set of metazoans, including acoels and nemertodermatids. Our study demonstrates, both for the myosin II data set alone and for a combined SSU + myosin II data set, that Platyhelminthes are polyphyletic and that acoels and nemertodermatids are the extant earliest bilaterians. Hence, the common bilaterian ancestor was not, as currently held, large and complex but small, simple, and likely with direct development. This scenario has far-reaching implications for understanding the evolution of major body plans and for perceptions of the Cambrian evolutionary explosion.
Ruiz-Trillo, I.; Paps, J.; Loukota, M.; Ribera, C.; Jondelius, U.; Baguna, J.; Riutort, M.
We introduce PULCHRA, a fast and robust method for the reconstruction of full-atom protein models starting from a reduced protein representation. The algorithm is particularly suitable as an intermediate step between coarse grained model-based structure prediction and applications requiring an all-atom structure, such as molecular dynamics, protein-ligand docking, structure-based function prediction, or assessment of quality of the predicted structure. The accuracy of the method was tested on a set of high-resolution crystallographic structures, as well as on a set low-resolution protein decoys generated by a protein structure prediction algorithm TASSER. The method is implemented as a standalone program that is available for download from http://cssb.biology.gatech.edu/skolnick/files/PULCHRA
Rotkiewicz, Piotr; Skolnick, Jeffrey
We introduce PULCHRA, a fast and robust method for the reconstruction of full-atom protein models starting from a reduced protein representation. The algorithm is particularly suitable as an intermediate step between coarse-grained model-based structure prediction and applications requiring an all-atom structure, such as molecular dynamics, protein-ligand docking, structure-based function prediction, or assessment of quality of the predicted structure. The accuracy of the method was tested on a set of high-resolution crystallographic structures as well as on a set of low-resolution protein decoys generated by a protein structure prediction algorithm TASSER. The method is implemented as a standalone program that is available for download from http://cssb.biology.gatech.edu/skolnick/files/PULCHRA. PMID:18196502
Rotkiewicz, Piotr; Skolnick, Jeffrey
N-acyl-L-homoserine lactones (AHLs) are co-regulatory ligands required for control of the expression of genes encoding virulence traits in many Gram- negative bacterial species. Recent studies have indicated that AHLs modulate the cellular concentrations of LuxR-type regulatory proteins by binding and fortifying these proteins against proteolytic degradation (Zhu & Winans, 2001). Halogenated furanones produced by the macroalga Delisea pulchra inhibit AHL-dependent
Michael Manefield; Thomas Bovbjerg Rasmussen; Morten Henzter; Jens Bo Andersen; Peter Steinberg; Staffan Kjelleberg; Michael Givskov
Benthonic foraminiferal paleoecology of the Brasso Formation (Globorotalia fohsi lobata and Globorotalia fohsi robusta [N11 N12] Zones), Trinidad, West Indies: A transect through an oxygen minimum zone
Benthonic foraminifera indicate that part of the Middle Miocene Brasso Formation, central Trinidad (planktonic foraminiferal Zones N11 N12), was deposited during a regression. A stratigraphic sequence of five foraminiferal assemblages reflects changes in paleodepth and dissolved oxygen concentration and indicates that the relative fall in sea level brought the seabed into contact with an oxygen minimum zone (OMZ): (1) Assemblage 1 (Uvigerina quesqueyana, Siphonina pulchra) lived in upper bathyal, moderately oxygenated water beneath the OMZ; (2) Assemblage 2 (S. pulchra, Cassidulina laevigata, lesser Globocassidulina subglobosa) lived in outer neritic, moderately oxygenated water below the OMZ; (3) Assemblage 3 (U. subperegrina) occupied the outer neritic, lower margin of the OMZ; (4) Assemblage 4 (Brizalina subaenariensis, U. subperegrina) lived at the core of the OMZ and rates the lowest on the Benthonic Foraminiferal Oxygen Index; and (5) Assemblage 5 (middle-neritic species with few Uvigerina spp. and Brizalina spp.) lived in well-oxygenated water above the OMZ. The onset of the severest oxygen depletion was abrupt and occurred shortly after the N11 N12 boundary. Previous work on the Brasso Formation has reported a similar sequence of benthonic assemblages in planktonic foraminiferal Zones N8 N10. These assemblages may be useful for local correlation of the Brasso Formation.
Neuroglobins, previously thought to be restricted to vertebrate neurons, were detected in the brain of a photosymbiotic acoel, Symsagittifera roscoffensis, and in neurosensory cells of the jellyfish Clytia hemisphaerica. For the neuroglobin of S. roscoffensis, a member of a lineage that originated either at the base of the bilateria or of the deuterostome clade, we report the ligand binding properties, crystal structure at 2.3 ?, and brain immunocytochemical pattern. We also describe in situ hybridizations of two neuroglobins specifically expressed in differentiating nematocytes (neurosensory cells) and in statocytes (ciliated mechanosensory cells) of C. hemisphaerica, a member of the early branching animal phylum cnidaria. In silico searches using these neuroglobins as queries revealed the presence of previously unidentified neuroglobin-like sequences in most metazoan lineages. Because neural systems are almost ubiquitous in metazoa, the constitutive expression of neuroglobin-like proteins strongly supports the notion of an intimate association of neuroglobins with the evolution of animal neural systems and hints at the preservation of a vitally important function. Neuroglobins were probably recruited in the first protoneurons in early metazoans from globin precursors. Neuroglobins were identified in choanoflagellates, sponges, and placozoans and were conserved during nervous system evolution. Because the origin of neuroglobins predates the other metazoan globins, it is likely that neuroglobin gene duplication followed by co-option and subfunctionalization led to the emergence of globin families in protostomes and deuterostomes (i.e. convergent evolution). PMID:23288852
Lechauve, Christophe; Jager, Muriel; Laguerre, Laurent; Kiger, Laurent; Correc, Gaëlle; Leroux, Cédric; Vinogradov, Serge; Czjzek, Mirjam; Marden, Michael C; Bailly, Xavier
Nowadays, beach nourishment is widely considered as a better alternative compared to the construction of hard structures to protect a sandy coast against detrimental erosive effects, both from an ecological and an engineering perspective. The rare studies conducted on the ecological impact of beach nourishment are short-term, post hoc monitoring investigations of the benthic macrofauna. Little is known of the biological processes during and after nourishment. To allow swift recolonization after nourishment, the characteristics of the nourished beach have to match the habitat demands of the benthic macrofauna. The sediment preference of the key intertidal species Scolelepis squamata, Eurydice pulchra, Bathyporeia pilosa and Bathyporeia sarsi, which dominate many West European sandy beaches, was investigated through laboratory experiments, both in single-species as well as combined-species treatments. While the former aimed at developing guidelines for impact mitigation of beach nourishment, the latter aimed at elucidating the role of biotic interactions in sediment preference. Results of the experiments indicated that B. pilosa and E. pulchra prefer the finest sediment, while B. sarsi had a broader preference and also occurred in medium-coarse sediments. However, the sediment preference of E. pulchra for fine sediments was not confirmed by other field and experimental studies. The polychaete S. squamata had the broadest preference and even showed a high occurrence in coarse sediments that are not naturally occurring on the sandy beaches where the animals were caught for this experiment. However, this polychaete is a cosmopolitan species, not only occurring on fine-grained beaches, but also on coarse-grained beaches worldwide. The preferences imply that beach nourishment with coarse sediment will have a major effect on B. pilosa while effects of coarse sediments on S. squamata will be minor. Finally, interspecific competition with the sympatrically occurring amphipod B. sarsi was found to change the sediment selection of the amphipod B. pilosa towards the coarser sediments where B. sarsi occurred in lower frequencies. PMID:23182894
Van Tomme, J; Vanden Eede, S; Speybroeck, J; Degraer, S; Vincx, M
An ethnobotanical study was conducted in the Wechiau Community Hippopotamus Sanctuary area in Ghana, through interviews and quadrate studies, to investigate the range and abundance of species used in the treatment of malaria. Forty-one species belonging to 17 families were encountered during the study. Of the 17 families studied Leguminosae and Anacardiaceae predominated in terms of number of species used to treat malaria. Eight plant species namely, Afraegle paniculata (Rutaceae), Haematostaphis barteri (Anacardiaceae), Indigo era pulchra (Leguminosae), Monanthotaxis sp. (Annonaceae), Ozoroa insignis (Anacardiaceae), Strychnos innocua (Loganiaceae), Strychnos spinosa (Loganiaceae) and Xeroderris stuhlmannii (Leguminosae) have not previously been documented for the treatment of malaria in Ghana. The results are discussed and recommendations made for future research to support the conservation and sustainable harvesting of the species reported to have medicinal properties. PMID:15894138
Asase, Alex; Oteng-Yeboah, Alfred A; Odamtten, George T; Simmonds, Monique S J
A literature-based taxonomic catalogue of the nemertean species (Phylum Nemertea) reported from Japanese waters is provided, listing 19 families, 45 genera, and 120 species as valid. Applications of the following species names to forms previously recorded from Japanese waters are regarded as uncertain: Amphiporus cervicalis, Amphiporus depressus, Amphiporus lactifloreus, Cephalothrix filiformis, Cephalothrix linearis, Cerebratulus fuscus, Lineus vegetus, Lineus bilineatus, Lineus gesserensis, Lineus grubei, Lineus longifissus, Lineus mcintoshii, Nipponnemertes pulchra, Oerstedia venusta, Prostoma graecense, and Prostoma grande. The identities of the taxa referred to by the following four nominal species require clarification through future investigations: Cosmocephala japonica, Dicelis rubra, Dichilus obscurus, and Nareda serpentina. The nominal species established from Japanese waters are tabulated. In addition, a brief history of taxonomic research on Japanese nemerteans is reviewed. PMID:17867829
Precipitation amounts and patterns at high latitude sites have been predicted to change as a result of global climatic changes. We addressed vegetation responses to three years of experimentally increased summer precipitation in two previously unaddressed tundra types: Betula nana-dominated shrub tundra (northeast Siberia) and a dry Sphagnum fuscum-dominated bog (northern Sweden). Positive responses to approximately doubled ambient precipitation (an increase of 200 mm year(-1)) were observed at the Siberian site, for B. nana (30 % larger length increments), Salix pulchra (leaf size and length increments) and Arctagrostis latifolia (leaf size and specific leaf area), but none were observed at the Swedish site. Total biomass production did not increase at either of the study sites. This study corroborates studies in other tundra vegetation types and shows that despite regional differences at the plant level, total tundra plant productivity is, at least at the short or medium term, largely irresponsive to experimentally increased summer precipitation. PMID:22864700
Keuper, Frida; Parmentier, Frans-Jan W; Blok, Daan; van Bodegom, Peter M; Dorrepaal, Ellen; van Hal, Jurgen R; van Logtestijn, Richard S P; Aerts, Rien
Benthic biological samples were taken in 1977 from the vicinity of the Farallon Islands radioactive waste disposal sites for characterization of the infaunal macroinvertebrates and foraminifera. A total of 120 invertebrate species were collected, of which 75 species (63 percent) were polychaetes. Forty-three of these polychaete species have not previously been reported from depths greater than 1000m. A total of 1044 macroinvertebrate specimens were collected of which 54 percent were polychates. Only the nematods were present at all six benthic stations, but the community structure was dominated by the polychaetes Tauberia gracilis, Allia pulchra, Chaetozone setosa, and Cossura candida. Living and dead foraminifera were reported. The possible role of polychaetes in bioturbation and in the marine food chain is briefly discussed with respect to the various polychaete feeding mechanisms.
The purpose of this study was to apply probabilistic models to the mapping of the potential polychaeta habitat area in the Hwangdo tidal flat, Korea. Remote sensing techniques were used to construct spatial datasets of ecological environments and field observations were carried out to determine the distribution of macrobenthos. Habitat potential mapping was achieved for two polychaeta species, Prionospio japonica and Prionospio pulchra, and eight control factors relating to the tidal macrobenthos distribution were selected. These included the intertidal digital elevation model (DEM), slope, aspect, tidal exposure duration, distance from tidal channels, tidal channel density, spectral reflectance of the near infrared (NIR) bands and surface sedimentary facies from satellite imagery. The spatial relationships between the polychaeta species and each control factor were calculated using a frequency ratio and weights-of-evidence combined with geographic information system (GIS) data. The species were randomly divided into a training set (70%) to analyze habitat potential using frequency ratio and weights-of-evidence, and a test set (30%) to verify the predicted habitat potential map. The relationships were overlaid to produce a habitat potential map with a polychaeta habitat potential (PHP) index value. These maps were verified by comparing them to surveyed habitat locations such as the verification data set. For the verification results, the frequency ratio model showed prediction accuracies of 77.71% and 74.87% for P. japonica and P. pulchra, respectively, while those for the weights-of-evidence model were 64.05% and 62.95%. Thus, the frequency ratio model provided a more accurate prediction than the weights-of-evidence model. Our data demonstrate that the frequency ratio and weights-of-evidence models based upon GIS analysis are effective for generating habitat potential maps of polychaeta species in a tidal flat. The results of this study can be applied towards conservation and management initiatives for the macrofauna of tidal flats.
Choi, Jong-Kuk; Oh, Hyun-Joo; Koo, Bon Joo; Ryu, Joo-Hyung; Lee, Saro
During forest succession, litterfall nutrient fluxes increase significantly. The higher inputs of organic matter and nutrients through litterfall affects positively soil fertility and the species composition, which are essential components in forest restoration and management programs. In the present study, the input of nutrients to the forest soil via litterfall components was estimated for two sites of different development stages, in an early successional alluvial rain forest in Brazil. Litterfall returned to the soil, in kg/ha, ca. 93 N, 79 Ca, 24 K, 15 Mg, 6 P, 1.7 Mn, 0.94 Fe, 0.18 Zn, 0.09 Cu and 11.2 Al, in the site where trees were more abundant and had higher values of basal area. In the other area, where trees where less abundant and values of basal area were comparatively low, litterfall returned < 50% of those amounts to the forest soil, except for Al. The amount of Al that returned to the soil was similar in both areas due to the high contribution of Tibouchina pulchra (82% of Al returned). Comparatively, high proportion of three dominant native tree species (Myrsine coriacea, T. pulchra and Cecropia pachystachya) explained better litter nutrient use efficiency (mainly N and P) in the site with the least advanced successional stage. Although litterfall of these species show lower nutrient concentrations than the other tree species, their nutrient fluxes were high in both sites, indicating a certain independence from soil essential nutrients. Such feature of the native species is very advantageous and should be considered in forest restoration programs. PMID:22208099
Scheer, Maurício Bergamini; Gatti, Gustavo; Wisniewski, Celina
Within a small arctic tundra watershed located on the north slope of Alaska, we asked if plant abundance and physiological performance are linked to hillslope position by the hydrologic processes controlling nutrient availability. Our prediction was that down slope sites and within water track sites should have the greatest nutrient availability resulting in the highest photosynthetic capacity and productivity. To examine these relationships, two transects were established in the Imnavait Creek watershed, running from the northern ridge crest to a beaded stream. In total, 16 sites, one water track (WT) and one non water track (NWT), from 8 locations, each 100 m apart were examined. At each site, soil moisture, thaw depth, canopy water status (from spectral reflectance) and species diversity were recorded. Chlorophyll fluorescence was used assess the maximum capacity of each species to transport electrons within the photosynthetic membranes of individual leaves (ETRMAX), a variable we expect to reflect both leaf N and general photosynthetic capacity. Significant differences were found within and among the major functional groups of plants growing in the watershed. In the two deciduous shrubs, Betula nana and Salix pulchra, ETRMAX generally decreased down slope but no significant difference were found between the WT and NWT sites. By contrast, ETRMAX in Rubus chamaemors, also a deciduous species, showed an initial decrease at the first two locations, but then remained constant further down slope and between WT and NWT sites. In the evergreen plants, Ledum palustre differed in that the maximum ETRMAX was found at the mid-slope locations while Vaccinium vitis-idaea had a characteristic decrease in ETRMAX down slope, with a large difference between WT and NWT at the first location. The forb Petasites frigidus displayed a unique pattern, with large difference in ETRMAX between WT and NWT at sites 4 and 5, the last two locations at which this species could be found. Finally, the only graminoid species studied, Eriophorum vaginatu, ETRMAX decrease down slope in a linear fashion and had the highest absolute ETRMAX. Additionally leaf gas-exchange was measured in Salix pulchra and leaf N and canopy reflectance was measured at each site. Together, our results demonstrate that while hillsope position has a significant effect on the physiology, growth and diversity of species, the relationships were not as hypothesized. Clearly other ecological, morphological or environmental factors are contributing to the productivity of the watershed and ultimately impacting the biogeochemistry of this important ecosystem.
Griffin, K. L.; Epstein, D. J.; Shapiro, J. B.; Boelman, N. T.; Stieglitz, M.
Deep Sea Drilling Project Site 480 (27??54.10???N, 111??39.34???W; 655 m water depth) contains a high resolution record of paleoceanographic change of the past 15 000 years for the Guaymas Basin, a region of very high diatom productivity within the central Gulf of California. Analyses of diatoms and silicoflagellates were completed on samples spaced every 40-50 yr, whereas ICP-AES geochemical analyses were completed on alternate samples (sample spacing 80-100 yr). The B??lling-Aller??d interval (14.6-12.9 ka) (note, ka refers to 1000 calendar years BP throughout this report) is characterized by an increase in biogenic silica and a decline in calcium carbonate relative to surrounding intervals, suggesting conditions somewhat similar to those of today. The Younger Dryas event (12.9-11.6 ka) is marked by a major drop in biogenic silica and an increase in calcium carbonate. Increasing relative percentage contributions of Azpeitia nodulifera and Dictyocha perlaevis (a tropical diatom and silicoflagellate, respectively) and reduced numbers of the silicoflagellate Octactis pulchra are supportive of reduced upwelling of nutrient-rich waters. Between 10.6 and 10.0 ka, calcium carbonate and A. nodulifera abruptly decline at DSDP 480, while Roperia tesselata, a diatom indicative of winter upwelling in the modern-day Gulf, increases sharply in numbers. A nearly coincident increase in the silicoflagellate Dictyocha stapedia suggests that waters above DSDP 480 were more similar to the cooler and slightly more saline waters of the northern Gulf during much of the early and middle parts of the Holocene (???10 to 3.2 ka). At about 6.2 ka a stepwise increase in biogenic silica and the reappearance of the tropical diatom A. nodulifera marks a major change in oceanographic conditions in the Gulf. A winter shift to more northwesterly winds may have occurred at this time along with the onset of periodic northward excursions (El Nin??o-driven?) of the North Equatorial Countercurrent during the summer. Beginning between 2.8 and 2.4 ka, the amplitude of biogenic silica and wt% Fe, Al, and Ti (proxies of terrigenous input) increase, possibly reflecting intensification of ENSO cycles and the establishment of modern oceanographic conditions in the Gulf. Increased numbers of O. pulchra after 2.8 ka suggest enhanced spring upwelling. ?? 2003 Elsevier B.V. All rights reserved.
Barron, J. A.; Bukry, D.; Bischoff, J. L.
Three aviculariine genera endemic to Brazil are revised. Typhochlaena C. L. Koch, 1850 is resurrected, including five species; Pachistopelma Pocock, 1901 includes two species; and Iridopelma Pocock, 1901, six species. Nine species are newly described: Typhochlaena ammasp. n., Typhochlaena costaesp. n., Typhochlaena curumimsp. n., Typhochlaena paschoalisp. n., Pachistopelma bromelicolasp. n., Iridopelma katiaesp. n., Iridopelma marcoisp. n., Iridopelma oliveiraisp. n. and Iridopelma vaninisp. n. Three new synonymies are established: Avicularia pulchra Mello-Leitão, 1933 and Avicularia recifiensis Struchen & Brändle, 1996 are junior synonyms of Pachistopelma rufonigrum Pocock, 1901 syn. n., and Avicularia palmicola Mello-Leitão, 1945 is a junior synonym of Iridopelma hirsutum Pocock, 1901 syn. n.Pachistopelma concolor Caporiacco, 1947 is transferred to Tapinauchenius Ausserer, 1871, making the new combination Tapinauchenius concolor (Caporiacco, 1947)comb. n. Lectotypes are newly designed for Pachistopelma rufonigrum Pocock, 1901 , Iridopelma hirsutum Pocock, 1901 and Pachistopelma concolor Caporiacco, 1947. Cladistic analyses using both equal and implied weights were carried out with a matrix comprising 62 characters and 38 terminal taxa. The chosen cladogram found with X-Pee-Wee and concavity 6 suggests they are monophyletic. All species are keyed and mapped and information on species habitat and area cladograms are presented. Discussion on biogeography and conservation is provided. PMID:23166476
Under bleaching conditions, corals lose their symbiotic zooxanthellae, and thus, the ability to synthesize fatty acids (FAs) from photosynthetically derived carbon. This study investigated the lipid content and FA composition in healthy and bleached corals from the Odo reef flat in Okinawa, southern Japan, following a bleaching event. It was hypothesized that the FA composition and abundance would change as algae are lost or die, and possibly microbial abundance would increase in corals as a consequence of bleaching. The lipid content and FA composition of three healthy coral species ( Pavona frondifera, Acropora pulchra, and Goniastrea aspera) and of partially bleached and completely bleached colonies of P. frondifera were examined. The FA composition did not differ among healthy corals, but differed significantly among healthy, partially bleached, and completely bleached specimens of P. frondifera. Completely bleached corals contained significantly lower lipid and total FA content, as well as lower relative amounts of polyunsaturated FAs and higher relative amounts of saturated FAs, than healthy and partially bleached corals. Furthermore, there was a significantly higher relative concentration of monounsaturated FAs and odd-numbered branched FAs in completely bleached corals, indicating an increase in bacterial colonization in the bleached corals.
Bachok, Zainudin; Mfilinge, Prosper; Tsuchiya, Makoto
Abstract Three aviculariine genera endemic to Brazil are revised. Typhochlaena C. L. Koch, 1850 is resurrected, including five species; Pachistopelma Pocock, 1901 includes two species; and Iridopelma Pocock, 1901, six species. Nine species are newly described: Typhochlaena amma sp. n., Typhochlaena costae sp. n., Typhochlaena curumim sp. n., Typhochlaena paschoali sp. n., Pachistopelma bromelicola sp. n., Iridopelma katiae sp. n., Iridopelma marcoi sp. n., Iridopelma oliveirai sp. n. and Iridopelma vanini sp. n. Three new synonymies are established: Avicularia pulchra Mello-Leitão, 1933 and Avicularia recifiensis Struchen & Brändle, 1996 are junior synonyms of Pachistopelma rufonigrum Pocock, 1901 syn. n., and Avicularia palmicola Mello-Leitão, 1945 is a junior synonym of Iridopelma hirsutum Pocock, 1901 syn. n. Pachistopelma concolor Caporiacco, 1947 is transferred to Tapinauchenius Ausserer, 1871, making the new combination Tapinauchenius concolor (Caporiacco, 1947) comb. n. Lectotypes are newly designed for Pachistopelma rufonigrum Pocock, 1901 , Iridopelma hirsutum Pocock, 1901 and Pachistopelma concolor Caporiacco, 1947. Cladistic analyses using both equal and implied weights were carried out with a matrix comprising 62 characters and 38 terminal taxa. The chosen cladogram found with X-Pee-Wee and concavity 6 suggests they are monophyletic. All species are keyed and mapped and information on species habitat and area cladograms are presented. Discussion on biogeography and conservation is provided.
Phylogenetic relationships were studied in the genus Cyanolyca, an assemblage of jays distributed from Mexico south to Bolivia. Given its fragmented distribution along the humid forests of the Neotropics, the genus Cyanolyca is a model group for exploring hypotheses on biogeography and speciation. Phylogenetic analyses were based on two mitochondrial and three nuclear loci; taxon sampling includes all species in the genus and most subspecies. Maximum parsimony, maximum likelihood, and Bayesian analyses produced trees that were congruent and highly robust at both terminal and deep nodes of the phylogeny. Cyanolyca comprises two major clades: one contains the Mesoamerican "dwarf" jays, and the other consists of two main groups--C. cucullata+C. pulchra and the "core" South American species. Prior hypotheses of relationships were explored statistically using Maximum Likelihood and Bayesian approaches. Dispersal-Vicariance analysis revealed the importance of the Northern Andes as a major center for biological diversification, and the effects of dispersal across the Panamanian Land Bridge in the composition of South American and Mesoamerican avifaunas. Phylogenetic patterns are highly congruent with an allopatric mode of speciation. Implications of these results are discussed in the context of the biogeography of Neotropical montane forests. PMID:19135159
Two new species of the taxonomically confused genus Amphisiella were isolated from brackish-water habitats in southern China, and their morphology and morphogenesis were investigated. The genes coding for small subunit (SSU) rRNA were sequenced in each species and included in a phylogenetic analysis with all data available from nominal species of Amphisiella and related hypotrichs. Both new species are diagnosed by an elongate body shape, yellow-brown/grey-brown cell color, one kind of cortical granule, and two macronuclear nodules. The cortical granules in A. pulchra sp. n. are grouped in small clusters which are irregularly distributed both ventrally and dorsally; in A. candida sp. n., they are irregularly and sparsely distributed ventrally and form longitudinal stripes dorsally. The ontogenetic processes of both species show similarities to those of other congeners. Phylogenetic trees based on SSU rRNA gene sequences suggest that the family Amphisiellidae is a paraphyletic assemblage. The results further demonstrate that two isolates identified as Amphisiella annulata (DQ832260 and GU170843) are very likely cryptic species, and a sequence identified as A. milnei (DQ845293) may belong to a genus other than Amphisiella. PMID:23295032
Chen, Xumiao; Shao, Chen; Lin, Xiaofeng; Clamp, John C; Song, Weibo
The taxonomy of the genus Turris Batsch, 1789, type genus of the family Turridae, widespread in shallow-water habitats of tropic Indo-Pacific, is revised. A total of 31 species of Turris, are here recognized as valid. New species described: Turris chaldaea, Turris clausifossata, Turris guidopoppei, Turris intercancellata, Turris kantori, T. kathiewayae. Homonym renamed: Turris bipartita nom. nov. for Pleurotoma variegata Kiener, 1839 (non Philippi, 1836). New synonymies: Turris ankaramanyensis Bozzetti, 2006 = Turris tanyspira Kilburn, 1975; Turris imperfecti, T. nobilis, T. pulchra and T. tornatum Röding, 1798, and Turris assyria Olivera, Seronay & Fedosov, 2010 = T. babylonia; Turris dollyi Olivera, 2000 = Pleurotoma crispa Lamarck, 1816; Turris totiphyllis Olivera, 2000 = Turris hidalgoi Vera-Peláez, Vega-Luz & Lozano-Francisco, 2000; Turris kilburni Vera-Peláez, Vega-Luz & Lozano-Francisco, 2000 = Turris pagasa Olivera, 2000; Turris (Annulaturris) munizi Vera-Peláez, Vega-Luz & Lozano-Francisco, 2000 = Gemmula lululimi Olivera, 2000. Revised status: Turris intricata Powell, 1964, Pleurotoma variegata Kiener, 1839 (non Philippi, 1836) and Pleurotoma yeddoensis Jousseaume, 1883, are regarded as full species (not subspecies of Turris crispa). Neotype designated: For Pleurotoma garnonsii Reeve, 1843, to distinguish it from Turris garnonsii of recent authors, type locality emended to Zanzibar. New combination: Turris orthopleura Kilburn, 1983, is transferred to genus Makiyamaia, family Clavatulidae.
Kilburn, Richard N.; Fedosov, Alexander E.; Olivera, Baldomero M.
So-called "typical" behavioural responses of coastal animals to particular stimuli have previously been shown often to vary cyclically in phase with diel or tidal cycles in the environment. Less well-studied are differences in the behaviour of adults and juveniles of the same species at the same time of day or tidal state, or in response to the same stimulus. Experimental studies of such differences in behaviour are reviewed and compared for three species of beach crustaceans, namely, the crab Carcinus maenas, the isopod Eurydice pulchra and the amphipod Orchestoidea tuberculata. Juvenile, but not adult, Carcinus will entrain circatidal rhythmicity after exposure to artificial tidal cycles of immersion/emersion; juvenile, but not adult, Eurydice express pronounced free-running circatidal swimming rhythms at neap tides as well as at springs; and, in Orchestoidea, juveniles and adults express patterns of daily locomotor activity that are complementary, both on the shore and in the laboratory. These ontogenetic differences are discussed in relation to distributional and behavioural differences between adults and juveniles in each species, drawing attention to their adaptive significance and wider implications for coastal management and conservation.
Naylor, E.; Kennedy, F.
Novel molecular tools have been constructed which allow for in situ detection of N-acyl homoserine lactone (AHL)-mediated quorum sensing in Pseudomonas aeruginosa biofilms. The reporter responds to AHL activation of LasR by expression of an unstable version of the green-fluorescent protein (Gfp). Gfp-based reporter technology has been applied for non-destructive, single-cell-level detection of quorum sensing in laboratory-based P. aeruginosa biofilms. It is reported that a synthetic halogenated furanone compound, which is a derivative of the secondary metabolites produced by the Australian macroalga Delisea pulchra, is capable of interfering with AHL-mediated quorum sensing in P. aeruginosa. It is demonstrated that the furanone compound specifically represses expression of a PlasB-gfp reporter fusion without affecting growth or protein synthesis. In addition, it reduces the production of important virulence factors, indicating a general effect on target genes of the las quorum sensing circuit. The furanone was applied to P. aeruginosa biofilms established in biofilm flow chambers. The Gfp-based analysis reveals that the compound penetrates microcolonies and blocks cell signalling and quorum sensing in most biofilm cells. The compound did not affect initial attachment to the abiotic substratum. It does, however, affect the architecture of the biofilm and enhances the process of bacterial detachment, leading to a loss of bacterial biomass from the substratum. PMID:11782502
Hentzer, Morten; Riedel, Kathrin; Rasmussen, Thomas B; Heydorn, Arne; Andersen, Jens Bo; Parsek, Matthew R; Rice, Scott A; Eberl, Leo; Molin, Søren; Høiby, Niels; Kjelleberg, Staffan; Givskov, Michael
This study describes the dynamics of phytoplankton in relation to environmental factors in coastal waters of the north-eastern Adriatic Sea. The distant Po River's influence is rarely noted on the eastern coastal part of the northern Adriatic, but it does trigger the crucial alternations in the community, e.g. mass development of diatoms in July 2009. A highly variable ecosystem, like the northern Adriatic, sustains high species diversity. Even though quite a few species were present for more than several months, we identified the seminal species of the seasonal succession. During spring Prorocentrum micans, Leptocylindrus minimus, Chaetoceros throndsenii, Ceratium furca and Ceratium fusus were most characteristic. These species thrive in low salinity and mixed waters. Typical summer diatom species were Chaetoceros vixvisibilis and Proboscia alata, while Rhabdosphaera clavigera and Syracosphaera pulchra were identified as distinctive summer coccolithophorids. All the summer species preferred warmer waters with low nitrate and low silica content. The autumn community was characterised by species such as Calciosolenia murrayi, Chaetoceros socialis, Asterionellopsis glacialis, and Lioloma pacificum. These species were related not only to high nutrient conditions, but also to low Po River influence. In winter a prevalence of large diatoms Thalassiosira rotula, Neocalyptrella robusta and Pseudosolenia calcar-avis was recorded. The winter assemblage was characterised by species of cold water preference able to grow in well mixed conditions.
Godrijan, Jelena; Mari?, Daniela; Tomaži?, Igor; Precali, Robert; Pfannkuchen, Martin
Canopy-forming shrubs are reported to be increasing at sites around the circumpolar Arctic. Our results indicate expansion in canopy cover and height of willows on Herschel Island located at 70 degrees north on the western Arctic coast of the Yukon Territory. We examined historic photographs, repeated vegetation surveys, and conducted monitoring of long-term plots and found evidence of increases of each of the dominant canopy-forming willow species (Salix richardsonii, Salix glauca and Salix pulchra), during the twentieth century. A simple model of patch initiation indicates that the majority of willow patches for each of these species became established between 1910 and 1960, with stem ages and maximum growth rates indicating that some patches could have established as late as the 1980s. Collectively, these results suggest that willow species are increasing in canopy cover and height on Herschel Island. We did not find evidence that expansion of willow patches is currently limited by herbivory, disease, or growing conditions. PMID:21954724
Myers-Smith, Isla H; Hik, David S; Kennedy, Catherine; Cooley, Dorothy; Johnstone, Jill F; Kenney, Alice J; Krebs, Charles J
Background Common structural biology methods (i.e., NMR and molecular dynamics) often produce ensembles of molecular structures. Consequently, averaging of 3D coordinates of molecular structures (proteins and RNA) is a frequent approach to obtain a consensus structure that is representative of the ensemble. However, when the structures are averaged, artifacts can result in unrealistic local geometries, including unphysical bond lengths and angles. Results Herein, we describe a method to derive representative structures while limiting the number of artifacts. Our approach is based on a Monte Carlo simulation technique that drives a starting structure (an extended or a 'close-by' structure) towards the 'averaged structure' using a harmonic pseudo energy function. To assess the performance of the algorithm, we applied our approach to C? models of 1364 proteins generated by the TASSER structure prediction algorithm. The average RMSD of the refined model from the native structure for the set becomes worse by a mere 0.08 Å compared to the average RMSD of the averaged structures from the native structure (3.28 Å for refined structures and 3.36 A for the averaged structures). However, the percentage of atoms involved in clashes is greatly reduced (from 63% to 1%); in fact, the majority of the refined proteins had zero clashes. Moreover, a small number (38) of refined structures resulted in lower RMSD to the native protein versus the averaged structure. Finally, compared to PULCHRA , our approach produces representative structure of similar RMSD quality, but with much fewer clashes. Conclusion The benchmarking results demonstrate that our approach for removing averaging artifacts can be very beneficial for the structural biology community. Furthermore, the same approach can be applied to almost any problem where averaging of 3D coordinates is performed. Namely, structure averaging is also commonly performed in RNA secondary prediction , which could also benefit from our approach.
KC, Dukka B
In the present study we investigated inter-annual coral disease dynamics, in situ disease progression rates, and disease-associated coral tissue mortality in the Wakatobi Marine National Park (WMNP) situated in the coral triangle in South-East Sulawesi, Indonesia. In 2005, only 2 known syndromes were recorded within the sampling area transect surveys: white syndrome (WS; 0.42% prevalence) and growth anomalies (GA; 0.15% prevalence), whilst 4 diseases were recorded in 2007: WS (0.19%), Porites ulcerative white spot disease (PUWS; 0.08%), GA (0.05%) and black band disease (BBD; 0.02%). Total disease prevalence decreased from 0.57% in 2005 to 0.33% in 2007. In addition to prevalence surveys, in situ progression rates of 4 diseases were investigated in 2007: BBD on Pachyseris foliosa, P. rugosa and Diploastrea heliopora, WS on Acropora clathrata, and brown band (BrB) and skeletal eroding band (SEB) diseases on Acropora pulchra. BrB and WS had the highest progression rates, 1.2 +/- 0.36 and 1.1 +/- 0.07 cm d(-1), respectively, indicating that diseases may have a significant impact on local Acropora populations. BBD had the lowest progression rate (0.39 +/- 0.14 cm d(-1)). WS caused the most severe recorded total tissue mortality: 53 923 cm2 over a period of 36 d. Sedimentation and coral cover were studied and a highly significant drop in coral cover was observed. This study provides the first documentation of spatio-temporal coral disease dynamics from Indonesia. Despite low total disease prevalence, progression rates comparable to the ones observed in the Caribbean and Australia indicate that diseases may threaten the reef framework in some locations and add to the degradation of coral reefs in a region already at high risk from anthropogenic impacts. PMID:20095246
Haapkylä, Jessica; Unsworth, Richard K F; Seymour, Adrian S; Melbourne-Thomas, Jessica; Flavell, Mike; Willis, Bette L; Smith, David J
Plankton samples collected in November 2002, February, May and August 2003 were used to examine seasonal variation in tidal exchange of zooplankton biomass, abundance and species composition between Lough Hyne Marine Nature Reserve and the adjacent Atlantic coast. Micro- to mesozooplankton were collected by pump over 24-h sampling periods during spring and neap tides from the narrow channel connecting the semi-enclosed water body to the Atlantic. Sample biomass (dry weight) and total zooplankton abundance peaked in the summer and were lowest in winter, showing a positive relationship with temperature. Zooplankton biomass, total abundance and numbers of holo- and meroplankton revealed import during some diel cycles and export in others. However, the tidal import of these planktonic components was generally dominant, especially during May. The greatest import of numbers of holoplankters and meroplanktonic larvae occurred during May and August, respectively. There was no significant variation in sample biomass between periods of light and dark, but some variation in zooplankton abundance could be explained by this diel periodicity. Significant differences in sample assemblage composition between flood and ebb tide samples were always observed, except during winter neap tides. There was a net import of the copepods Temora longicornis and Oithona helgolandica and the larval stages of Mytilus edulis during spring and summer. Proceraea cornuta and Capitellid trochophores were imported during winter, and a hydrozoan of the genus Obelia during the spring spring tides. Seasonal export from the lough was shown by Pseudopolydora pulchra larvae (autumn and spring), Serpulid trochophores (autumn) and veligers of the bivalve Anomia ephippium (summer). It is suggested that the direction of tidal exchange of meroplanktonic taxa is related to the distribution of the adult populations. Copepod naupliar stages dominated the assemblages except during May spring tides when the copepod Pseudocalanus elongatus made up over 22% of the abundance. The general import of micro- to mesozooplankton may, in part, explain the higher densities of this size-class of zooplankton within the semi-enclosed system of Lough Hyne.
Rawlinson, K. A.; Davenport, J.; Barnes, D. K. A.
Most of the studies on biological and ecological effects associated with brine discharge into the marine environment are related to the operation of desalination plants, for the production of freshwater. In this study we analysed the biological effects of a brine effluent from a completely different source, produced from the lixiviation of rock salt caves, for the creation of natural gas storage caverns. Lethal and sub-lethal endpoints following exposure to the brine were studied in a range of macrofauna species characteristic of the soft and hard bottom habitats in the vicinity of the discharge area, namely the isopod Eurydice pulchra, the annelids Sabellaria alveolata and Ophelia radiata, the sea-urchin Paracentrotus lividus and the bivalve Mytilus galloprovincialis. In a first series of experiments, brine, with salinity above 300, was diluted in distilled water to a salinity value close to that of the seawater in the discharge area (salinity 36) and, surprisingly, none of the exposed species was able to survive or develop into viable larvae. A second series of experiments exposed the species to brine diluted with seawater, simulating more realistic discharge circumstances. All the tested species at all the measured endpoints (adult survival, larval abnormal development, sperm fertilization success) showed negative biological effects in brine solutes always at a lower salinity than that of a salinity control obtained with concentrated seawater. The sub-lethal experiments with larval development of P. lividus, S. alveolata and M. galloprovincialis, and the fertilization success of P. lividus gave EC 50 values for the brine solute with salinity in the range of 40.9-43.5, whereas the EC 50 values for the concentrated seawater were in the range of salinity 44.2-49.0. It is hypothesised that differences in the ionic composition of the brine cause the inability of the species to tolerate the exposure to brine.
Quintino, Victor; Rodrigues, Ana Maria; Freitas, Rosa; Ré, Ana
Climate warming in the Arctic is predicted to result in the expansion of woody shrubs and increased frequency and size of tundra fires. How will fire influence this shrub expansion? Over a period of 32 years, following a 1977 tundra fire in the central Seward Peninsula, we sampled seven times the post-fire vegetation at eight permanently marked sites on a long (2 Km) hillslope (Nimrod Hill). We had previously sampled vegetation here in 1973 prior to the fire. By 2001, 24 years post-fire conspicuous willow shrubs (mostly Salix pulchra) had increased in numbers, size and cover over the entire slope in moist tussock-shrub tundra, well-drained heath, and wet meadow. Prior to fire, willow on this slope was largely restricted to small drainages or watertracks. Willows here have originated from both seed and vegetative resprouting - the latter mostly in moist tussock-shrub tundra from willows resprouting within one to three years post-fire. With fire-induced removal of vascular plant competition and Spagnum moss cover and litter in tussock-shrub tundra, both seedling and resprouting willows have grown rapidly to overtop tussocks by 30-40 cm. Similar rapid post-fire resprouting of willows has been observed in tussock-shrub tundra after the 2007 Anaktuvuk River tundra fire and after the 1977 tundra fires in the Noatak River basin. On Nimrod Hill the most striking willow expansion has occurred on the severely burned and well-drained backslope where willow establishment from seed 5-10 years after fire has resulted in up to 40% cover of rapidly growing willows of both upright and spreading growth form. At several sites along the slope there is evidence of continuing willow expansion from seedlings 24 to 32 years post-fire, when we might expect the effects of fire on seedbeds would have ceased. We conclude that tundra fire may promote shrub expansion in the Arctic.
From July 2001 to May 2005, seawater samples were collected once a week at a fixed station in Lisbon bay (38°41'N, 09°24'W) in order to describe the ecological dynamics of the coccolithophore community. The seasonal and interannual distribution patterns of the different species and their relationships with environmental parameters are addressed. The present work aimed to identify potential proxies for different local water bodies and environmental conditions. Throughout the period of study, the upwelling events were weak and progressively more persistent. High sea surface temperatures (SST) were observed earlier in the year; summers and winters were gradually warmer and colder, respectively. Salinity variations reflected the different weather conditions as they are strongly influenced by rainfall and thus by the Tagus river flow. The extended periods of weak upwelling and the overall increase in SST resulted in the development of phytoplankton populations as measured by chlorophyll a. However, the persistence of the upwelling, and thus shorter convergence periods, favoured other phytoplankton groups than coccolithophore populations as these decreased towards the end of the sampling period. The annual structure of the coccolithophore assemblage showed a pronounced and recurrent seasonal variability, mainly related with the intensity and persistence of upwelling. The highest cell densities were recorded from spring to autumn. An overall preference by most species for mature upwelled waters and low turbulent conditions was observed associated with high temperatures and salinities, although the species develop in different windows with mismatching maxima. The coccolithophores observed were capable of withstanding coastal processes such as turbulence and were well adapted to an environment rich in nutrients provided by both continental runoff and upwelling. The consistency of the results enabled local oceanographic tracers to be defined. Emiliania huxleyi and Gephyrocapsa species can be used as proxies of surface productivity waters during spring and summer while Coccolithus pelagicus indicates the presence of upwelling fronts. Calcidiscus leptoporus is a tracer of the convergence of subtropical oceanic waters onto the shelf, during winter while Coronosphaera mediterranea, Syracosphaera pulchra, Helicosphaera carteri and Rhabdosphaera clavigera revealed the presence of those waters during the short period that characterized the transition from upwelling to downwelling seasons.
Silva, A.; Palma, S.; Moita, M. T.
The Sr/Ca ratio of coccoliths was recently proposed as a potential indicator of past growth rates of coccolithophorids, marine algae, which play key roles in both the global carbonate and carbon cycles. We synthesize calibrations of this proxy through laboratory culture studies and analysis of monospecific coccolith assemblages from surface sediments. Cultures of coccolithophorids Helicosphaera carteri, Syracosphaera pulchra and Algirospira robusta confirm a 1-2% increase in Sr/Ca per degrees C previously identified in Emiliania huxleyi and Gephyrocapsa oceanica. This effect is not due merely to increases in growth rate with temperature and must be considered in palaeoceanographic studies. In light-limited cultures of E. huxleyi, Calcidiscus leptoporus and G. oceanica at constant temperature, coccolith Sr/Ca ratios vary by 10% across the range of possible growth and calcification rates for a given species. Among different species under similar culture conditions, Sr/Ca ratios vary by 30%. Although the highest ratios are in the cells with highest calcification and organic carbon fixation rates, at lower rates there is much scatter, indicating that different mechanisms control interspecific and intraspecific coccolith Sr/Ca variations. In field studies in the Equatorial Pacific and Somalia coastal region, coccolith Sr/Ca correlates with upwelling intensity and productivity. A more dynamic response is observed in larger coccoliths like C. leptoporus (23-55% variation in Sr/Ca) than in smaller coccoliths of G. oceanica or Florisphaera profunda (6-15% variation in Sr/Ca). This response suggests that, despite temperature effects, coccolith Sr/Ca has potential as an indicator of coccolithophorid productivity. If the variable Sr/Ca response of different species accurately reflects their variable productivity response to upwelling (and not different slopes of Sr/Ca with productivity), coccolith Sr/Ca could provide useful data on past changes in coccolith ecology. The mechanism of coccolith Sr/Ca variations remains poorly understood but is probably more closely tied to biochemical cycles during carbon acquisition than to chemical kinetic effects on Sr incorporation in the calcite coccolith crystals. PMID:12804301
Stoll, Heather M; Ziveri, Patricia; Geisen, Markus; Probert, Ian; Young, Jeremy R
We investigated the planktonic foraminiferal and calcareous nannofossil assemblages record of three late Pleistocene/Holocene box-cores from the western-central part of the Mediterranean Ridge. In particular we focused on the most significant faunal signals recorded before, during and after sapropel S-1 deposition. The interval preceding S-1 is characterised by an increasing trend of the two planktonic foraminiferal species Globorotalia inflata and Truncorotalia truncatulinoides usually related to a well developed cold and deep mixing layer. This is supported also by the rarity of warm coccolithophorid species such as Helicosphaera carteri, Rhabdosphaera claviger and Syracosphaera pulchra and by the presence of the deep dwelling species Florisphaera profunda. The beginning of S-1 is marked by the disappearance of the two last foraminiferal species and the significant increase of Globigerinoides ruber group, especially the rosea variety, usually considered indicative of warmer conditions. Warm species increase also within the coccolithophorid assemblage, while the upwelling species Reticulofenestra spp. suddenly decrease and remain low in the whole sapropel interval. According to a well known hypothesis, the occurrence of sapropel S-1 in correspondence of a Climatic Optimum stage is an expression of precipitation change in the low-latitude catchment of the Eastern Mediterranean Sea, where the African Monsoon provides moisture originating in the South Atlantic Ocean that discharges into the Eastern Mediterranean via Nile River (Emeis et al., 2000). The consistent decrease in the number of pteropod fragments in most of the sapropel S-1 interval in all the box-cores can be attributed to dissolution of the easily dissolvable aragonitic tests in the deep-sea acidic environment related to anoxic conditions. The sedimentary expression of the end of anoxia is the upper boundary of the oxidised level observed above visible S-1 in the three box-cores. Across this boundary we detect a small but well defined increase of Braarudosphaera bigelowii, the decrease of warm coccolithophorid species and the increase of Reticulofenestra spp. In addition we observe the reoccurrence of the planktonic foraminiferal species G. inflata and Neogloboquadrina pachyderma dextral and an evident decrease of G.ruber var. rosea . This suggests the end of the Holocene Climatic Optimum and the beginning of a cold and wet phase, probably correspondent to the Atlantic-Subboreal transition in continental environment (Stuiver and Reimer, 1993). References Emeis K. C., Sakamoto T., Wehausen R. and Brumsack H. J. (2000) - The sapropel record of the eastern Mediterranean Sea - results of Ocean Drilling Program Leg 160. Palaeo 3: 158, 371-395. Stùiver M. and Reimer P.J. (1993) - Extended 14C data base and revised CALIB 3.0 14C age calibration program. Radiocarbon: 35, 215-230.
Giunta, S.; Principato, M. S.; Corselli, C.; Negri, A.
High-resolution records of the past 2000??yr are compared in a north-south transect (28?? N to 24?? N) of three cores from the eastern slopes of the Guaymas, Carmen, and Pescadero Basins of the Gulf of California (hereafter referred to as the "Gulf"). Evenly-spaced samples from the varved sediments in each core allow sample resolution ranging from ?????16 to ?????37??yr. Diatoms and silicoflagellates capture the seasonal variation between a late fall to early spring period of high biosiliceous productivity, that is driven by northwest winds, and a summer period of warmer, more stratified waters during which these winds slacken and/or reverse direction (monsoonal flow). As these winds decrease, tropical waters enter the Gulf and spread northward. Individual samples represent a composite of 7 to 23??yr of deposition and are assumed to record the relative dominance of the winter vs. summer floral components. Intervals of enhanced summer incursion of tropical waters, alternating with periods of increased late fall to early spring biosiliceous productivity are recorded in all three cores. Regularly spaced cycles (?????100??yr duration) of Octactis pulchra, a silicoflagellate proxy for lower SST and high productivity, and Azpeitia nodulifera, a tropical diatom, occur between ?????A.D. 400 and ?????1700 in the more nearshore Carmen Basin core, NH01-21 (26.3?? N), suggesting a possible solar influence on coastal upwelling. Cores BAM80 E-17 (27.9?? N) and NH01-26 (24.3?? N) contain longer-duration cycles of diatoms and silicoflagellates. The early part of Medieval Climate Anomaly (?????A.D. 900 to 1200) is characterized by two periods of reduced productivity (warmer SST) with an intervening high productivity (cool) interval centered at ?????A.D. 1050. Reduced productivity and higher SST also characterize the record of the last ?????100 to 200??yr in these cores. Solar variability appears to be driving productivity cycles, as intervals of increased radiocarbon production (sunspot minima) correlate with intervals of enhanced productivity. It is proposed that increased winter cooling of the atmosphere above southwest U.S. during sunspot minima causes intensification of the northwest winds that blow down the Gulf during the late fall to early spring, leading to intensified overturn of surface waters and enhanced productivity. A new silicoflagellate species, Dictyocha franshepardii Bukry, is described and illustrated. ?? 2006 Elsevier B.V. All rights reserved.
Barron, J. A.; Bukry, D.
In 2005 willow leaves (all variants of Salix pulchra) and A-, B-, and C-horizon soils were sampled at 10 sites along a transect near the Quarry prospect and 11 sites along a transect near the Big Hurrah mine for the purpose of defining the spatial variability of elements and the regional geochemistry of willow and soil over Paleozoic metamorphic rocks potentially high in cadmium (Cd). Willow, a favorite browse of moose (Alces alces), has been shown by various investigators to bioaccumulate Cd. Moose in this region show clinical signs of tooth wear and breakage and are declining in population for unknown reasons. A trace element imbalance in their diet has been proposed as a possible cause for these observations. Cadmium, in high enough concentrations, is one dietary trace element that potentially could produce such symptoms. We report both the summary statistics for elements in willow and soils and the results of an unbalanced, one-way, hierarchical analysis of variance (ANOVA) (general linear model, GLM), which was constructed to measure the geochemical variability in willow (and soil) at various distance scales across the Paleozoic geologic unit high in bioavailable Cd. All of the geochemical data are presented in the Appendices. The two locations are separated by approximately 80 kilometers (km); sites within a location are approximately 0.5 kilometers apart. Duplicate soil samples collected within a site were separated by 0.05 km or slightly less. Results of the GLM are element specific and range from having very little regional variability to having most of their variance at the top (greater than 80 km) level. For willow, a significant proportion of the total variance occurred at the 'between locations' level for ash yield, barium (Ba), Cd, calcium (Ca), cobalt (Co), nickel (Ni), and zinc (Zn). For soils, concentrations of elements in all three soil horizons were similar in that most of the variability in the geochemical data occurred at the 'between locations' and the 'among sites at a location' GLM levels. Most of the variation in concentrations of Cd in soils occurred among sites (separated by 0.5 km) at both locations across all soil horizons and not between the two locations. Cd distribution across the landscape may be due to variation in soil mineralogy, especially the amount of graphite in soil, which has been associated with Cd. Although samples were collected on the same geologic unit, the geochemistry of soils was demonstrated to be uniform with depth but highly variable between locations separated by 80 km. This exploratory study establishes the presence of elevated levels of Cd in willow growing over Paleozoic bedrock in the Seward Peninsula. Further work is needed to definitively link these high Cd levels in willow browse to the health of moose.
Gough, L. P.; Lamothe, P. J.; Sanzolone, R. F.; Drew, L. J.; Maier, J. A. K.