Convergent evolution of RFX transcription factors and ciliary genes predated the origin of metazoans

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Chen Nansheng

2010-05-01

Full Text Available Abstract Background Intraflagellar transport (IFT genes, which are critical for the development and function of cilia and flagella in metazoans, are tightly regulated by the Regulatory Factor X (RFX transcription factors (TFs. However, how and when their evolutionary relationship was established remains unknown. Results We have identified evidence suggesting that RFX TFs and IFT genes evolved independently and their evolution converged before the first appearance of metazoans. Both ciliary genes and RFX TFs exist in all metazoans as well as some unicellular eukaryotes. However, while RFX TFs and IFT genes are found simultaneously in all sequenced metazoan genomes, RFX TFs do not co-exist with IFT genes in most pre-metazoans and thus do not regulate them in these organisms. For example, neither the budding yeast nor the fission yeast possesses cilia although both have well-defined RFX TFs. Conversely, most unicellular eukaryotes, including the green alga Chlamydomonas reinhardtii, have typical cilia and well conserved IFT genes but lack RFX TFs. Outside of metazoans, RFX TFs and IFT genes co-exist only in choanoflagellates including M. brevicollis, and only one fungus Allomyces macrogynus of the 51 sequenced fungus genomes. M. brevicollis has two putative RFX genes and a full complement of ciliary genes. Conclusions The evolution of RFX TFs and IFT genes were independent in pre-metazoans. We propose that their convergence in evolution, or the acquired transcriptional regulation of IFT genes by RFX TFs, played a pivotal role in the establishment of metazoan.

Isolation of a substance activating foot formation in hydra

DEFF Research Database (Denmark)

Grimmelikhuijzen, C J; Schaller, H C

1977-01-01

-forming potential of the tissue (2) It does not accelerate head regeneration, nor do the head factors of hydra discovered by Schaller (1973) and Berking (1977) accelerate foot regeneration. We propose that the foot-activating substance is a morphogen responsible for foot formation in hydra. The foot activator can...

Metazoan Remaining Genes for Essential Amino Acid Biosynthesis: Sequence Conservation and Evolutionary Analyses

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Igor R. Costa

2014-12-01

Full Text Available Essential amino acids (EAA consist of a group of nine amino acids that animals are unable to synthesize via de novo pathways. Recently, it has been found that most metazoans lack the same set of enzymes responsible for the de novo EAA biosynthesis. Here we investigate the sequence conservation and evolution of all the metazoan remaining genes for EAA pathways. Initially, the set of all 49 enzymes responsible for the EAA de novo biosynthesis in yeast was retrieved. These enzymes were used as BLAST queries to search for similar sequences in a database containing 10 complete metazoan genomes. Eight enzymes typically attributed to EAA pathways were found to be ubiquitous in metazoan genomes, suggesting a conserved functional role. In this study, we address the question of how these genes evolved after losing their pathway partners. To do this, we compared metazoan genes with their fungal and plant orthologs. Using phylogenetic analysis with maximum likelihood, we found that acetolactate synthase (ALS and betaine-homocysteine S-methyltransferase (BHMT diverged from the expected Tree of Life (ToL relationships. High sequence conservation in the paraphyletic group Plant-Fungi was identified for these two genes using a newly developed Python algorithm. Selective pressure analysis of ALS and BHMT protein sequences showed higher non-synonymous mutation ratios in comparisons between metazoans/fungi and metazoans/plants, supporting the hypothesis that these two genes have undergone non-ToL evolution in animals.

Neurotensin-like immunoreactivity in the nervous system of hydra

DEFF Research Database (Denmark)

Grimmelikhuijzen, C J; Carraway, R E; Rökaeus, A

1981-01-01

Neurotensin-like immunoreactivity is found in nerve fibers present in all body regions of hydra. The nerve fibers are especially numerous in the ectoderm at the bases of the tentacles and in the ectoderm at a site just above the foot. Radioimmunoassays of acetic-acid extracts of hydra, using vari...

Molecular cloning of a preprohormone from Hydra magnipapillata containing multiple copies of Hydra-L Wamide (Leu-Trp-NH2) neuropeptides: evidence for processing at Ser and Asn residues

DEFF Research Database (Denmark)

Leviev, I; Williamson, M; Grimmelikhuijzen, C J

1997-01-01

The simple, freshwater polyp Hydra is often used as a model to study development in cnidarians. Recently, a neuropeptide, metamorphosis in a hydroid planula larva to become a polyp. Here, we have cloned a preprohormone...... from Hydra magnipapillata containing 11 (eight different) immature neuropeptide sequences that are structurally related to the metamorphosis-inducing neuropeptide from sea anermones. During the final phase of our cloning experiments, another research team independently isolated and sequenced five...... most frequent one being Gly-Pro-Pro-Pro-Gly-Leu-Trp-NH2; Hydra-LWamide l; three copies). Based on their structural similarities with the metamorphosis-inducing neuropeptide from sea anemones, the mature peptides derived from the Hydra-LWamide preprohormone are potential candidates for being...

Hydra-Ring: a computational framework to combine failure probabilities

Science.gov (United States)

Diermanse, Ferdinand; Roscoe, Kathryn; IJmker, Janneke; Mens, Marjolein; Bouwer, Laurens

2013-04-01

This presentation discusses the development of a new computational framework for the safety assessment of flood defence systems: Hydra-Ring. Hydra-Ring computes the failure probability of a flood defence system, which is composed of a number of elements (e.g., dike segments, dune segments or hydraulic structures), taking all relevant uncertainties explicitly into account. This is a major step forward in comparison with the current Dutch practice in which the safety assessment is done separately per individual flood defence section. The main advantage of the new approach is that it will result in a more balanced prioratization of required mitigating measures ('more value for money'). Failure of the flood defence system occurs if any element within the system fails. Hydra-Ring thus computes and combines failure probabilities of the following elements: - Failure mechanisms: A flood defence system can fail due to different failure mechanisms. - Time periods: failure probabilities are first computed for relatively small time scales (assessment of flood defense systems, Hydra-Ring can also be used to derive fragility curves, to asses the efficiency of flood mitigating measures, and to quantify the impact of climate change and land subsidence on flood risk. Hydra-Ring is being developed in the context of the Dutch situation. However, the computational concept is generic and the model is set up in such a way that it can be applied to other areas as well. The presentation will focus on the model concept and probabilistic computation techniques.

Substance P-like immunoreactivity in the nervous system of hydra

DEFF Research Database (Denmark)

Grimmelikhuijzen, C J; Balfe, A; Emson, P C

1981-01-01

Using immunocytochemistry we find substance P-like material in nerve cells of hydra. These nerve cells are situated in the ectoderm of the basal disk and tentacles. Radioimmunoassay of hydra extracts gives dilution curves parallel to that of synthetic substance P, from which it can be calculated ...

Collagen cross-linking: insights on the evolution of metazoan extracellular matrix.

Science.gov (United States)

Rodriguez-Pascual, Fernando; Slatter, David Anthony

2016-11-23

Collagens constitute a large family of extracellular matrix (ECM) proteins that play a fundamental role in supporting the structure of various tissues in multicellular animals. The mechanical strength of fibrillar collagens is highly dependent on the formation of covalent cross-links between individual fibrils, a process initiated by the enzymatic action of members of the lysyl oxidase (LOX) family. Fibrillar collagens are present in a wide variety of animals, therefore often being associated with metazoan evolution, where the emergence of an ancestral collagen chain has been proposed to lead to the formation of different clades. While LOX-generated collagen cross-linking metabolites have been detected in different metazoan families, there is limited information about when and how collagen acquired this particular modification. By analyzing telopeptide and helical sequences, we identified highly conserved, potential cross-linking sites throughout the metazoan tree of life. Based on this analysis, we propose that they have importantly contributed to the formation and further expansion of fibrillar collagens.

Archaea in metazoan diets: implications for food webs and biogeochemical cycling.

Science.gov (United States)

Thurber, Andrew R; Levin, Lisa A; Orphan, Victoria J; Marlow, Jeffrey J

2012-08-01

Although the importance of trophic linkages, including 'top-down forcing', on energy flow and ecosystem productivity is recognized, the influence of metazoan grazing on Archaea and the biogeochemical processes that they mediate is unknown. Here, we test if: (1) Archaea provide a food source sufficient to allow metazoan fauna to complete their life cycle; (2) neutral lipid biomarkers (including crocetane) can be used to identify Archaea consumers; and (3) archaeal aggregates are a dietary source for methane seep metazoans. In the laboratory, we demonstrated that a dorvilleid polychaete, Ophryotrocha labronica, can complete its life cycle on two strains of Euryarchaeota with the same growth rate as when fed bacterial and eukaryotic food. Archaea were therefore confirmed as a digestible and nutritious food source sufficient to sustain metazoan populations. Both strains of Euryarchaeota used as food sources had unique lipids that were not incorporated into O. labronica tissues. At methane seeps, sulfate-reducing bacteria that form aggregations and live syntrophically with anaerobic-methane oxidizing Archaea contain isotopically and structurally unique fatty acids (FAs). These biomarkers were incorporated into tissues of an endolithofaunal dorvilleid polychaete species from Costa Rica (mean bulk δ(13)C=-92±4‰; polar lipids -116‰) documenting consumption of archaeal-bacterial aggregates. FA composition of additional soft-sediment methane seep species from Oregon and California provided evidence that consumption of archaeal-bacterial aggregates is widespread at methane seeps. This work is the first to show that Archaea are consumed by heterotrophic metazoans, a trophic process we coin as 'archivory'.

Slow-cycling stem cells in hydra contribute to head regeneration

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Niraimathi Govindasamy

2014-11-01

Full Text Available Adult stem cells face the challenge of maintaining tissue homeostasis by self-renewal while maintaining their proliferation potential over the lifetime of an organism. Continuous proliferation can cause genotoxic/metabolic stress that can compromise the genomic integrity of stem cells. To prevent stem cell exhaustion, highly proliferative adult tissues maintain a pool of quiescent stem cells that divide only in response to injury and thus remain protected from genotoxic stress. Hydra is a remarkable organism with highly proliferative stem cells and ability to regenerate at whole animal level. Intriguingly, hydra does not display consequences of high proliferation, such as senescence or tumour formation. In this study, we investigate if hydra harbours a pool of slow-cycling stem cells that could help prevent undesirable consequences of continuous proliferation. Hydra were pulsed with the thymidine analogue 5-ethynyl-2′-deoxyuridine (EdU and then chased in the absence of EdU to monitor the presence of EdU-retaining cells. A significant number of undifferentiated cells of all three lineages in hydra retained EdU for about 8–10 cell cycles, indicating that these cells did not enter cell cycle. These label-retaining cells were resistant to hydroxyurea treatment and were predominantly in the G2 phase of cell cycle. Most significantly, similar to mammalian quiescent stem cells, these cells rapidly entered cell division during head regeneration. This study shows for the first time that, contrary to current beliefs, cells in hydra display heterogeneity in their cell cycle potential and the slow-cycling cells in this population enter cell cycle during head regeneration. These results suggest an early evolution of slow-cycling stem cells in multicellular animals.

An Atlas of annotations of Hydra vulgaris transcriptome.

Science.gov (United States)

Evangelista, Daniela; Tripathi, Kumar Parijat; Guarracino, Mario Rosario

2016-09-22

RNA sequencing takes advantage of the Next Generation Sequencing (NGS) technologies for analyzing RNA transcript counts with an excellent accuracy. Trying to interpret this huge amount of data in biological information is still a key issue, reason for which the creation of web-resources useful for their analysis is highly desiderable. Starting from a previous work, Transcriptator, we present the Atlas of Hydra's vulgaris, an extensible web tool in which its complete transcriptome is annotated. In order to provide to the users an advantageous resource that include the whole functional annotated transcriptome of Hydra vulgaris water polyp, we implemented the Atlas web-tool contains 31.988 accesible and downloadable transcripts of this non-reference model organism. Atlas, as a freely available resource, can be considered a valuable tool to rapidly retrieve functional annotation for transcripts differentially expressed in Hydra vulgaris exposed to the distinct experimental treatments. WEB RESOURCE URL: http://www-labgtp.na.icar.cnr.it/Atlas .

Evolution of the metazoan mitochondrial replicase.

Science.gov (United States)

Oliveira, Marcos T; Haukka, Jani; Kaguni, Laurie S

2015-03-03

The large number of complete mitochondrial DNA (mtDNA) sequences available for metazoan species makes it a good system for studying genome diversity, although little is known about the mechanisms that promote and/or are correlated with the evolution of this organellar genome. By investigating the molecular evolutionary history of the catalytic and accessory subunits of the mtDNA polymerase, pol γ, we sought to develop mechanistic insight into its function that might impact genome structure by exploring the relationships between DNA replication and animal mitochondrial genome diversity. We identified three evolutionary patterns among metazoan pol γs. First, a trend toward stabilization of both sequence and structure occurred in vertebrates, with both subunits evolving distinctly from those of other animal groups, and acquiring at least four novel structural elements, the most important of which is the HLH-3β (helix-loop-helix, 3 β-sheets) domain that allows the accessory subunit to homodimerize. Second, both subunits of arthropods and tunicates have become shorter and evolved approximately twice as rapidly as their vertebrate homologs. And third, nematodes have lost the gene for the accessory subunit, which was accompanied by the loss of its interacting domain in the catalytic subunit of pol γ, and they show the highest rate of molecular evolution among all animal taxa. These findings correlate well with the mtDNA genomic features of each group described above, and with their modes of DNA replication, although a substantive amount of biochemical work is needed to draw conclusive links regarding the latter. Describing the parallels between evolution of pol γ and metazoan mtDNA architecture may also help in understanding the processes that lead to mitochondrial dysfunction and to human disease-related phenotypes. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Comparison of HYDRA predictions to temperature data from two single-assembly spent fuel heat transfer tests

International Nuclear Information System (INIS)

McCann, R.A.

1986-12-01

The HYDRA computer code was used to simulate the thermal performance of an actual and a model spent fuel assembly. The HYDRA-predicted temperatures were then compared with measured data from two single-assembly test sections. The objective of this effort was to further verify the predictive capabilities of the HYDRA code for use in assessments of the hydrothermal performance of spent fuel dry storage systems. After HYDRA has been adequately evaluated and validated, the code will be documented to permit design and licensing safety analyses

Evolutionary Analysis of Minor Histocompatibility Genes In Hydra

KAUST Repository

Aalismail, Nojood

2016-01-01

In the present study we took initiative to study the self/nonself recognition in hydra and its relation to the immune response. Moreover, performing phylogenetic analysis to look for annotated immune genes in hydra gave us a potential to analyze the expression of minor histocompatibility genes that have been shown to play a major role in grafting and transplantation in mammals. Here we obtained the cDNA library that shows expression of minor histocompatibility genes and confirmed that the annotated sequences in databases are actually present. In addition, grafting experiments suggested, although still preliminary, that homograft showed less rejection response than in heterograft. Involvement of possible minor histocompatibility gene orthologous in immune response was examined by qPCR.

HYDRA Hyperspectral Data Research Application Tom Rink and Tom Whittaker

Science.gov (United States)

Rink, T.; Whittaker, T.

2005-12-01

HYDRA is a freely available, easy to install tool for visualization and analysis of large local or remote hyper/multi-spectral datasets. HYDRA is implemented on top of the open source VisAD Java library via Jython - the Java implementation of the user friendly Python programming language. VisAD provides data integration, through its generalized data model, user-display interaction and display rendering. Jython has an easy to read, concise, scripting-like, syntax which eases software development. HYDRA allows data sharing of large datasets through its support of the OpenDAP and OpenADDE server-client protocols. The users can explore and interrogate data, and subset in physical and/or spectral space to isolate key areas of interest for further analysis without having to download an entire dataset. It also has an extensible data input architecture to recognize new instruments and understand different local file formats, currently NetCDF and HDF4 are supported.

Development and population growth of Hydra viridissima Pallas, 1766 (Cnidaria, Hydrozoa in the laboratory

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FC. Massaro

Full Text Available Hydras, the most representative freshwater Cnidaria, are of common occurrence in bodies of water in every continent except Antarctica. This study was planned with the aim of maintaining a population of Hydra viridissima in laboratory culture to enable the determination of the individual and population growth-rates of this species, as well as its population doubling time and generation time, with a view to employing these common animals as test-organisms in ecotoxicological assays. The organisms were maintained in reconstituted water at 20 ± 2 °C, illuminated at 800 lux with a photoperiod of 12 hours light: 12 hours dark, and were fed on neonates of the cladoceran Ceriodaphnia silvestrii (3 or 4 neonates per hydra, 3 times a week. The individual growth-rate (k of the species was 0.43, the maximum length of the column 2.53 mm and the generation time 6.6 ± 1.5 days on average. The hydra population showed an intrinsic growth-rate (r of 0.0468, according to the fitted curve, and a doubling time of 14.8 ± 2.63 days. Hydra viridissima is easy to grow in the laboratory and performs well in the conditions used in this study. It is thus a promising candidate test-organism for ecotoxicological studies.

THM-GTRF: New Spider meshes, New Hydra-TH runs

Energy Technology Data Exchange (ETDEWEB)

Bakosi, Jozsef [Los Alamos National Laboratory; Christon, Mark A. [Los Alamos National Laboratory; Francois, Marianne M. [Los Alamos National Laboratory; Lowrie, Robert B. [Los Alamos National Laboratory; Nourgaliev, Robert [Los Alamos National Laboratory

2012-06-20

Progress is reported on computational capabilities for the grid-to-rod-fretting (GTRF) problem of pressurized water reactors. Numeca's Hexpress/Hybrid mesh generator is demonstrated as an excellent alternative to generating computational meshes for complex flow geometries, such as in GTRF. Mesh assessment is carried out using standard industrial computational fluid dynamics practices. Hydra-TH, a simulation code developed at LANL for reactor thermal-hydraulics, is demonstrated on hybrid meshes, containing different element types. A series of new Hydra-TH calculations has been carried out collecting turbulence statistics. Preliminary results on the newly generated meshes are discussed; full analysis will be documented in the L3 milestone, THM.CFD.P5.05, Sept. 2012.

Detection of CO emission in Hydra 1 cluster galaxies

International Nuclear Information System (INIS)

Huchtmeier, W.K.

1990-01-01

A survey of bright Hydra cluster spiral galaxies for the CO(1-0) transition at 115 GHz was performed with the 15m Swedish-ESO submillimeter telescope (SEST). Five out of 15 galaxies observed have been detected in the CO(1-0) line. The largest spiral galaxy in the cluster, NGC 3312, got more CO than any spiral of the Virgo cluster. This Sa-type galaxy is optically largely distorted and disrupted on one side. It is a good candidate for ram pressure stripping while passing through the cluster's central region. A comparison with global CO properties of Virgo cluster spirals shows a relatively good agreement with the detected Hydra cluster galaxies

LRPPRC is a mitochondrial matrix protein that is conserved in metazoans

International Nuclear Information System (INIS)

Sterky, Fredrik H.; Ruzzenente, Benedetta; Gustafsson, Claes M.; Samuelsson, Tore; Larsson, Nils-Goeran

2010-01-01

Research highlights: → LRPPRC orthologs are restricted to metazoans. → LRPPRC is imported to the mitochondrial matrix. → No evidence of nuclear isoform. -- Abstract: LRPPRC (also called LRP130) is an RNA-binding pentatricopeptide repeat protein. LRPPRC has been recognized as a mitochondrial protein, but has also been shown to regulate nuclear gene transcription and to bind specific RNA molecules in both the nucleus and the cytoplasm. We here present a bioinformatic analysis of the LRPPRC primary sequence, which reveals that orthologs to the LRPPRC gene are restricted to metazoan cells and that all of the corresponding proteins contain mitochondrial targeting signals. To address the subcellular localization further, we have carefully analyzed LRPPRC in mammalian cells and identified a single isoform that is exclusively localized to mitochondria. The LRPPRC protein is imported to the mitochondrial matrix and its mitochondrial targeting sequence is cleaved upon entry.

+ 6 TEKSTER. KARTOGRAFI HYDRA 2013 #3

DEFF Research Database (Denmark)

Dinesen, Cort Ross

2013-01-01

+6 TEKSTER #3 indeholder en række indlæg, der er relateret til 14 NYE LANDSKABER/HYDRA 9, 2012 #1. Arbejdet med topologien og kartografien omkring tre urbane udsnit i Berlin, Paris og Tokyo har ført til en række udgivelser i GRID og følges op her med en række betragtninger, der perspektiverer denne...

β-Catenin acts in a position-independent regeneration response in the simple eumetazoan Hydra.

Science.gov (United States)

Gufler, S; Artes, B; Bielen, H; Krainer, I; Eder, M-K; Falschlunger, J; Bollmann, A; Ostermann, T; Valovka, T; Hartl, M; Bister, K; Technau, U; Hobmayer, B

2018-01-15

Wnt/β-Catenin signaling plays crucial roles in regenerative processes in eumetazoans. It also acts in regeneration and axial patterning in the simple freshwater polyp Hydra, whose morphallactic regenerative capacity is unparalleled in the animal kingdom. Previous studies have identified β-catenin as an early response gene activated within the first 30min in Hydra head regeneration. Here, we have studied the role of β-Catenin in more detail. First, we show that nuclear β-Catenin signaling is required for head and foot regeneration. Loss of nuclear β-Catenin function blocks head and foot regeneration. Transgenic Hydra tissue, in which β-Catenin is over-expressed, regenerates more heads and feet. In addition, we have identified a set of putative β-Catenin target genes by transcriptional profiling, and these genes exhibit distinct expression patterns in the hypostome, in the tentacles, or in an apical gradient in the body column. All of them are transcriptionally up-regulated in the tips of early head and foot regenerates. In foot regenerates, this is a transient response, and expression starts to disappear after 12-36h. ChIP experiments using an anti-HydraTcf antibody show Tcf binding at promoters of these targets. We propose that gene regulatory β-Catenin activity in the pre-patterning phase is generally required as an early regeneration response. When regenerates are blocked with iCRT14, initial local transcriptional activation of β-catenin and the target genes occurs, and all these genes remain upregulated at the site of both head and foot regeneration for the following 2-3 days. This indicates that the initial regulatory network is followed by position-specific programs that inactivate fractions of this network in order to proceed to differentiation of head or foot structures. brachyury1 (hybra1) has previously been described as early response gene in head and foot regeneration. The HyBra1 protein, however, appears in head regenerating tips not earlier

Bayesian inference of the metazoan phylogeny

DEFF Research Database (Denmark)

Glenner, Henrik; Hansen, Anders J; Sørensen, Martin V

2004-01-01

Metazoan phylogeny remains one of evolutionary biology's major unsolved problems. Molecular and morphological data, as well as different analytical approaches, have produced highly conflicting results due to homoplasy resulting from more than 570 million years of evolution. To date, parsimony has...

CIRCUMBINARY CHAOS: USING PLUTO'S NEWEST MOON TO CONSTRAIN THE MASSES OF NIX AND HYDRA

International Nuclear Information System (INIS)

Youdin, Andrew N.; Kratter, Kaitlin M.; Kenyon, Scott J.

2012-01-01

The Pluto system provides a unique local laboratory for the study of binaries with multiple low-mass companions. In this paper, we study the orbital stability of P4, the most recently discovered moon in the Pluto system. This newfound companion orbits near the plane of the Pluto-Charon (PC) binary, roughly halfway between the two minor moons Nix and Hydra. We use a suite of few body integrations to constrain the masses of Nix and Hydra, and the orbital parameters of P4. For the system to remain stable over the age of the solar system, the masses of Nix and Hydra likely do not exceed 5 × 10 16 kg and 9 × 10 16 kg, respectively. These upper limits assume a fixed mass ratio between Nix and Hydra at the value implied by their median optical brightness. Our study finds that stability is more sensitive to their total mass and that a downward revision of Charon's eccentricity (from our adopted value of 0.0035) is unlikely to significantly affect our conclusions. Our upper limits are an order of magnitude below existing astrometric limits on the masses of Nix and Hydra. For a density at least that of ice, the albedos of Nix and Hydra would exceed 0.3. This constraint implies they are icy, as predicted by giant impact models. Even with these low masses, P4 only remains stable if its eccentricity e ∼< 0.02. The 5:1 commensurability with Charon is particularly unstable, combining stability constraints with the observed mean motion places the preferred orbit for P4 just exterior to the 5:1 resonance. These predictions will be tested when the New Horizons satellite visits Pluto. Based on the results for the PC system, we expect that circumbinary, multi-planet systems will be more widely spaced than their singleton counterparts. Further, circumbinary exoplanets close to the three-body stability boundary, such as those found by Kepler, are less likely to have other companions nearby.

Optical identifications of IRAS point sources: the Fornax, Hydra I and Coma clusters

International Nuclear Information System (INIS)

Wang, G.; Leggett, S.K.; Savage, A.

1991-01-01

We present optical identifications for 66 IRAS point sources in the region of the Fornax cluster of galaxies, 106 IRAS point sources in the region of the Hydra I cluster of galaxies (Abell 1060) and 59 IRAS point sources in the region of the Coma cluster of galaxies (Abell 1656). Eight other sources in Hydra I do not have optical counterparts and are very probably due to infrared cirrus. Twenty-three (35 per cent) of the Fornax sources are associated with stars and 43 (65 per cent) with galaxies; 48 (42 per cent) of the Hydra I sources are associated with stars and 58 (51 per cent) with galaxies; 18 (31 per cent) of the Coma sources are associated with stars and 41 (69 per cent) with galaxies. The stellar and infrared cirrus surface density is consistent with the galactic latitude of each field. (author)

Innexin gap junctions in nerve cells coordinate spontaneous contractile behavior in Hydra polyps

KAUST Repository

Takaku, Yasuharu

2014-01-07

Nerve cells and spontaneous coordinated behavior first appeared near the base of animal evolution in the common ancestor of cnidarians and bilaterians. Experiments on the cnidarian Hydra have demonstrated that nerve cells are essential for this behavior, although nerve cells in Hydra are organized in a diffuse network and do not form ganglia. Here we show that the gap junction protein innexin-2 is expressed in a small group of nerve cells in the lower body column of Hydra and that an anti-innexin-2 antibody binds to gap junctions in the same region. Treatment of live animals with innexin-2 antibody eliminates gap junction staining and reduces spontaneous body column contractions. We conclude that a small subset of nerve cells, connected by gap junctions and capable of synchronous firing, act as a pacemaker to coordinate the contraction of the body column in the absence of ganglia.

Structural and Sequence Similarities of Hydra Xeroderma Pigmentosum A Protein to Human Homolog Suggest Early Evolution and Conservation

Directory of Open Access Journals (Sweden)

Apurva Barve

2013-01-01

Full Text Available Xeroderma pigmentosum group A (XPA is a protein that binds to damaged DNA, verifies presence of a lesion, and recruits other proteins of the nucleotide excision repair (NER pathway to the site. Though its homologs from yeast, Drosophila, humans, and so forth are well studied, XPA has not so far been reported from protozoa and lower animal phyla. Hydra is a fresh-water cnidarian with a remarkable capacity for regeneration and apparent lack of organismal ageing. Cnidarians are among the first metazoa with a defined body axis, tissue grade organisation, and nervous system. We report here for the first time presence of XPA gene in hydra. Putative protein sequence of hydra XPA contains nuclear localization signal and bears the zinc-finger motif. It contains two conserved Pfam domains and various characterized features of XPA proteins like regions for binding to excision repair cross-complementing protein-1 (ERCC1 and replication protein A 70 kDa subunit (RPA70 proteins. Hydra XPA shows a high degree of similarity with vertebrate homologs and clusters with deuterostomes in phylogenetic analysis. Homology modelling corroborates the very close similarity between hydra and human XPA. The protein thus most likely functions in hydra in the same manner as in other animals, indicating that it arose early in evolution and has been conserved across animal phyla.

Biological control of biofilms on membranes by metazoans.

Science.gov (United States)

Klein, Theresa; Zihlmann, David; Derlon, Nicolas; Isaacson, Carl; Szivak, Ilona; Weissbrodt, David G; Pronk, Wouter

2016-01-01

Traditionally, chemical and physical methods have been used to control biofouling on membranes by inactivating and removing the biofouling layer. Alternatively, the permeability can be increased using biological methods while accepting the presence of the biofouling layer. We have investigated two different types of metazoans for this purpose, the oligochaete Aelosoma hemprichi and the nematode Plectus aquatilis. The addition of these grazing metazoans in biofilm-controlled membrane systems resulted in a flux increase of 50% in presence of the oligochaetes (Aelosoma hemprichi), and a flux increase of 119-164% in presence of the nematodes (Plectus aquatilis) in comparison to the control system operated without metazoans. The change in flux resulted from (1) a change in the biofilm structure, from a homogeneous, cake-like biofilm to a more heterogeneous, porous structure and (2) a significant reduction in the thickness of the basal layer. Pyrosequencing data showed that due to the addition of the predators, also the community composition of the biofilm in terms of protists and bacteria was strongly affected. The results have implications for a range of membrane processes, including ultrafiltration for potable water production, membrane bioreactors and reverse osmosis. Copyright © 2015 Elsevier Ltd. All rights reserved.

Two-Step Evolution of Endosymbiosis between Hydra and Algae

KAUST Repository

Ishikawa, Masakazu; Shimizu, Hiroshi; Nozawa, Masafumi; Ikeo, Kazuho; Gojobori, Takashi

2016-01-01

In the Hydra vulgaris group, only 2 of the 25 strains in the collection of the National Institute of Genetics in Japan currently show endosymbiosis with green algae. However, whether the other non-symbiotic strains also have the potential to harbor

A comparison between Daphnia pulex and Hydra vulgaris as ...

African Journals Online (AJOL)

2017-04-02

Apr 2, 2017 ... dependence thereon, has led not only to valuable products ... effects, estimating environmental risk based on measured ... The LC50-values were statistically determined using the EPA Probit Analysis Model ..... and organic contaminants. ..... green algae on the response of Hydra viridissima (Pallas 1776).

Floating attenuator wave energy device: Wavegen HYDRA project

Energy Technology Data Exchange (ETDEWEB)

NONE

2004-07-01

This report describes research funded by the Department of Trade and Industry (DTI) into the feasibility of developing and constructing a floating attenuator wave energy device known as HYDRA following initial studies by Wavegen. HYDRA is a floating externally tensioned articulated raft wave energy generator based on work by Professor FJM Farley and colleagues during the 1980s. The project's first four work tasks confirmed the theoretical potential of the device but also highlighted significant practical problems in translating that potential into a viable design. It was therefore decided not to proceed further, i.e. not to construct and test a prototype device. The report provides a general description of the device and describes the results of the initial analysis and the first series of model tests. It then discusses device design and component testing and explains the methodology for determining device performance at a particular site and mathematical modelling of a one-third scale device. To help future research and development programmes, the report emphasises the generic problems associated with the development of wave devices.

FMRFamide-like immunoreactivity in the nervous system of Hydra

DEFF Research Database (Denmark)

Grimmelikhuijzen, C J; Dockray, G J; Schot, L P

1982-01-01

FMRFamide-like immunoreactivity has been localized in different parts of the hydra nervous system. Immunoreactivity occurs in nerve perikarya and processes in the ectoderm of the lower peduncle region near the basal disk, in the ectoderm of the hypostome and in the ectoderm of the tentacles...

Metazoan parasites of fishes from the Celestun coastal lagoon, Yucatan, Mexico.

Science.gov (United States)

Sosa-Medina, Trinidad; Vidal-Martínez, Víctor M; Aguirre-Macedo, M Leopoldina

2015-08-31

The aims of this study were to produce a checklist of the metazoan parasites of fishes from the Celestun coastal lagoon and to determine the degree of faunal similarity among the fishes based on the metazoan parasites they share. A checklist was prepared including all available records (1996-2014) of parasites of marine, brackish water and freshwater fishes of the area. All of these data were included in a presence/absence database and used to determine similarity via Jaccard's index. The results indicate the presence of 62 metazoan parasite species infecting 22 fish species. The number of metazoan parasite species found in the fishes from the Celestún lagoon is apparently the highest reported worldwide for a tropical coastal lagoon. The parasites included 12 species of adult digeneans, 27 digeneans in the metacercarial stage, 6 monogeneans, 3 metacestodes, 9 nematodes, 2 acanthocephalans, 2 crustaceans and 1 annelid. Forty parasite species were autogenic and 23 were allogenic and 1 unknown. The overall similarity among all of the species of fish with respect to the metazoan parasites they share was low (0.08 ± 0.12), with few similarity values above 0.4 being obtained. This low similarity was due primarily to the presence of suites of parasites exclusive to specific species of fish. The autogenic component of the parasite fauna (40 species) dominated the allogenic component (21 species). The most likely explanation for the large number of fish parasites found at Celestún is the good environmental condition of the lagoon, which allows the completion of parasite life cycles and free circulation of euryhaline fishes from the marine environment bringing marine parasites into the lagoon.

Metazoan-like signaling in a unicellular receptor tyrosine kinase

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Schultheiss Kira P

2013-02-01

Full Text Available Abstract Background Receptor tyrosine kinases (RTKs are crucial components of signal transduction systems in multicellular animals. Surprisingly, numerous RTKs have been identified in the genomes of unicellular choanoflagellates and other protists. Here, we report the first biochemical study of a unicellular RTK, namely RTKB2 from Monosiga brevicollis. Results We cloned, expressed, and purified the RTKB2 kinase, and showed that it is enzymatically active. The activity of RTKB2 is controlled by autophosphorylation, as in metazoan RTKs. RTKB2 possesses six copies of a unique domain (designated RM2 in its C-terminal tail. An isolated RM2 domain (or a synthetic peptide derived from the RM2 sequence served as a substrate for RTKB2 kinase. When phosphorylated, the RM2 domain bound to the Src homology 2 domain of MbSrc1 from M. brevicollis. NMR structural studies of the RM2 domain indicated that it is disordered in solution. Conclusions Our results are consistent with a model in which RTKB2 activation stimulates receptor autophosphorylation within the RM2 domains. This leads to recruitment of Src-like kinases (and potentially other M. brevicollis proteins and further phosphorylation, which may serve to increase or dampen downstream signals. Thus, crucial features of signal transduction circuitry were established prior to the evolution of metazoans from their unicellular ancestors.

CIRCUMBINARY CHAOS: USING PLUTO'S NEWEST MOON TO CONSTRAIN THE MASSES OF NIX AND HYDRA

Energy Technology Data Exchange (ETDEWEB)

Youdin, Andrew N.; Kratter, Kaitlin M.; Kenyon, Scott J. [Harvard-Smithsonian Center for Astrophysics, 60 Garden St., Cambridge, MA 02138 (United States)

2012-08-10

The Pluto system provides a unique local laboratory for the study of binaries with multiple low-mass companions. In this paper, we study the orbital stability of P4, the most recently discovered moon in the Pluto system. This newfound companion orbits near the plane of the Pluto-Charon (PC) binary, roughly halfway between the two minor moons Nix and Hydra. We use a suite of few body integrations to constrain the masses of Nix and Hydra, and the orbital parameters of P4. For the system to remain stable over the age of the solar system, the masses of Nix and Hydra likely do not exceed 5 Multiplication-Sign 10{sup 16} kg and 9 Multiplication-Sign 10{sup 16} kg, respectively. These upper limits assume a fixed mass ratio between Nix and Hydra at the value implied by their median optical brightness. Our study finds that stability is more sensitive to their total mass and that a downward revision of Charon's eccentricity (from our adopted value of 0.0035) is unlikely to significantly affect our conclusions. Our upper limits are an order of magnitude below existing astrometric limits on the masses of Nix and Hydra. For a density at least that of ice, the albedos of Nix and Hydra would exceed 0.3. This constraint implies they are icy, as predicted by giant impact models. Even with these low masses, P4 only remains stable if its eccentricity e {approx}< 0.02. The 5:1 commensurability with Charon is particularly unstable, combining stability constraints with the observed mean motion places the preferred orbit for P4 just exterior to the 5:1 resonance. These predictions will be tested when the New Horizons satellite visits Pluto. Based on the results for the PC system, we expect that circumbinary, multi-planet systems will be more widely spaced than their singleton counterparts. Further, circumbinary exoplanets close to the three-body stability boundary, such as those found by Kepler, are less likely to have other companions nearby.

The mitochondrial inner membrane AAA metalloprotease family in metazoans.

Science.gov (United States)

Juhola, M K; Shah, Z H; Grivell, L A; Jacobs, H T

2000-09-15

Three metalloproteases belonging to the AAA superfamily (Yme1p, Afg3p and Rca1p) are involved in protein turnover and respiratory chain complex assembly in the yeast inner mitochondrial membrane. Analysis of the completed genome sequences of Caenorhabditis elegans and Drosophila melanogaster indicates that this gene family typically comprises 3-4 members in metazoans. Phylogenetic analysis reveals three main branches represented, respectively, by Saccharomyces cerevisiae YME1, human SPG7 (paraplegin) and S. cerevisiae AFG3 and RCA1. mt-AAA metalloproteases are weak candidates for several previously studied Drosophila mutants. A full elucidation of the cellular and physiological roles of mt-AAA metalloproteases in metazoans will require the creation of targeted mutations.

Advances in HYDRA and its application to simulations of Inertial Confinement Fusion targets

Science.gov (United States)

Marinak, M. M.; Kerbel, G. D.; Koning, J. M.; Patel, M. V.; Sepke, S. M.; Brown, P. N.; Chang, B.; Procassini, R.; Veitzer, S. A.

2008-11-01

We will outline new capabilities added to the HYDRA 2D/3D multiphysics ICF simulation code. These include a new SN multigroup radiation transport package (1D), constitutive models for elastic-plastic (strength) effects, and a mix model. A Monte Carlo burn package is being incorporated to model diagnostic signatures of neutrons, gamma rays and charged particles. A 3D MHD package that treats resistive MHD is available. Improvements to HYDRA's implicit Monte Carlo photonics package, including the addition of angular biasing, now enable integrated hohlraum simulations to complete in substantially shorter time. The heavy ion beam deposition package now includes a new model for ion stopping power developed by the Tech-X Corporation, with improved accuracy below the Bragg peak. Examples will illustrate HYDRA's enhanced capabilities to simulate various aspects of inertial confinement fusion targets.This work was performed under the auspices of the Lawrence Livermore National Security, LLC, (LLNS) under Contract No. DE-AC52-07NA27344. The work of Tech-X personnel was funded by the Department of Energy under Small Business Innovation Research Contract No. DE-FG02-03ER83797.

Rolling circle amplification of metazoan mitochondrialgenomes

Energy Technology Data Exchange (ETDEWEB)

Simison, W. Brian; Lindberg, D.R.; Boore, J.L.

2005-07-31

Here we report the successful use of rolling circle amplification (RCA) for the amplification of complete metazoan mt genomes to make a product that is amenable to high-throughput genome sequencing techniques. The benefits of RCA over PCR are many and with further development and refinement of RCA, the sequencing of organellar genomics will require far less time and effort than current long PCR approaches.

Characterizing TW Hydra

Science.gov (United States)

Sokal, Kimberly R.; Deen, Casey P.; Mace, Gregory N.; Lee, Jae-Joon; Oh, Heeyoung; Kim, Hwihyun; Kidder, Benjamin T.; Jaffe, Daniel T.

2018-02-01

At 60 pc, TW Hydra (TW Hya) is the closest example of a star with a gas-rich protoplanetary disk, though TW Hya may be relatively old (3–15 Myr). As such, TW Hya is especially appealing for testing our understanding of the interplay between stellar and disk evolution. We present a high-resolution near-infrared spectrum of TW Hya obtained with the Immersion GRating INfrared Spectrometer (IGRINS) to re-evaluate the stellar parameters of TW Hya. We compare these data to synthetic spectra of magnetic stars produced by MoogStokes, and use sensitive spectral line profiles to probe the effective temperature, surface gravity, and magnetic field. A model with {T}{eff}=3800 K, {log} g=4.2, and B=3.0 kG best fits the near-infrared spectrum of TW Hya. These results correspond to a spectral type of M0.5 and an age of 8 Myr, which is well past the median life of gaseous disks.

Hydra: A web-based system for cardiovascular analysis, diagnosis and treatment.

Science.gov (United States)

Novo, J; Hermida, A; Ortega, M; Barreira, N; Penedo, M G; López, J E; Calvo, C

2017-02-01

Cardiovascular (CV) risk stratification is a highly complex process involving an extensive set of clinical trials to support the clinical decision-making process. There are many clinical conditions (e.g. diabetes, obesity, stress, etc.) that can lead to the early diagnosis or establishment of cardiovascular disease. In order to determine all these clinical conditions, a complete set of clinical patient analyses is typically performed, including a physical examination, blood analysis, electrocardiogram, blood pressure (BP) analysis, etc. This article presents a web-based system, called Hydra, which integrates a full and detailed set of services and functionalities for clinical decision support in order to help and improve the work of clinicians in cardiovascular patient diagnosis, risk assessment, treatment and monitoring over time. Hydra integrates a number of different services: a service for inputting all the information gathered by specialists (physical examination, habits, BP, blood analysis, electrocardiogram, etc.); a tool to automatically determine the CV risk stratification, including well-known standard risk stratification tables; and, finally, various tools to incorporate, analyze and graphically present the records of the ambulatory BP monitoring that provides BP analysis over a given period of time (24 or 48 hours). In addition, the platform presents a set of reports derived from all the information gathered from the patient in order to support physicians in their clinical decisions. Hydra was tested and validated in a real domain. In particular, internal medicine specialists at the Hypertension Unit of the Santiago de Compostela University Hospital (CHUS) validated the platform and used it in different clinical studies to demonstrate its utility. It was observed that the platform increased productivity and accuracy in the assessment of patient data yielding a cost reduction in clinical practice. This paper proposes a complete platform that includes

Molecular Characterization of a Catalase from Hydra vulgaris

Science.gov (United States)

Dash, Bhagirathi; Phillips, Timothy D.

2012-01-01

Catalase, an antioxidant and hydroperoxidase enzyme protects the cellular environment from harmful effects of hydrogen peroxide by facilitating its degradation to oxygen and water. Molecular information on a cnidarian catalase and/or peroxidase is, however, limited. In this work an apparent full length cDNA sequence coding for a catalase (HvCatalase) was isolated from Hydra vulgaris using 3’- and 5’- (RLM) RACE approaches. The 1859 bp HvCatalase cDNA included an open reading frame of 1518 bp encoding a putative protein of 505 amino acids with a predicted molecular mass of 57.44 kDa. The deduced amino acid sequence of HvCatalase contained several highly conserved motifs including the heme-ligand signature sequence RLFSYGDTH and the active site signature FXRERIPERVVHAKGXGA. A comparative analysis showed the presence of conserved catalytic amino acids [His(71), Asn(145), and Tyr(354)] in HvCatalase as well. Homology modeling indicated the presence of the conserved features of mammalian catalase fold. Hydrae exposed to thermal, starvation, metal and oxidative stress responded by regulating its catalase mRNA transcription. These results indicated that the HvCatalase gene is involved in the cellular stress response and (anti)oxidative processes triggered by stressor and contaminant exposure. PMID:22521743

Implementation of GENSEC section from HYDRA 3.40 system on IBM 370/135 (DOS/VS 34.0)

International Nuclear Information System (INIS)

Ponta, T.

1984-07-01

In High Energy Physics, processing and interpretation of experimental data, supplied by track-particle detectors, are made by means of HYDRA system. We present here the implementation on IBM 370/135 (DOS/VS 34.0) (belonqing to Central Institute of Physics) of General Section (GENSEC) from HYDRA system, paying a special attention to the description of the 176 routines of this section, in order to facilitate their use on the computer. (author)

The Skeleton Forming Proteome of an Early Branching Metazoan: A Molecular Survey of the Biomineralization Components Employed by the Coralline Sponge Vaceletia Sp.

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Juliane Germer

Full Text Available The ability to construct a mineralized skeleton was a major innovation for the Metazoa during their evolution in the late Precambrian/early Cambrian. Porifera (sponges hold an informative position for efforts aimed at unraveling the origins of this ability because they are widely regarded to be the earliest branching metazoans, and are among the first multi-cellular animals to display the ability to biomineralize in the fossil record. Very few biomineralization associated proteins have been identified in sponges so far, with no transcriptome or proteome scale surveys yet available. In order to understand what genetic repertoire may have been present in the last common ancestor of the Metazoa (LCAM, and that may have contributed to the evolution of the ability to biocalcify, we have studied the skeletal proteome of the coralline demosponge Vaceletia sp. and compare this to other metazoan biomineralizing proteomes. We bring some spatial resolution to this analysis by dividing Vaceletia's aragonitic calcium carbonate skeleton into "head" and "stalk" regions. With our approach we were able to identify 40 proteins from both the head and stalk regions, with many of these sharing some similarity to previously identified gene products from other organisms. Among these proteins are known biomineralization compounds, such as carbonic anhydrase, spherulin, extracellular matrix proteins and very acidic proteins. This report provides the first proteome scale analysis of a calcified poriferan skeletal proteome, and its composition clearly demonstrates that the LCAM contributed several key enzymes and matrix proteins to its descendants that supported the metazoan ability to biocalcify. However, lineage specific evolution is also likely to have contributed significantly to the ability of disparate metazoan lineages to biocalcify.

Metazoan operons accelerate recovery from growth arrested states

Science.gov (United States)

Zaslaver, Alon; Baugh, L. Ryan; Sternberg, Paul W.

2011-01-01

Summary Existing theories explain why operons are advantageous in prokaryotes, but their occurrence in metazoans is an enigma. Nematode operon genes, typically consisting of growth genes, are significantly up-regulated during recovery from growth-arrested states. This expression pattern is anti-correlated to non-operon genes consistent with a competition for transcriptional resources. We find that transcriptional resources are initially limiting during recovery, and that recovering animals are highly sensitive to any additional decrease in transcriptional resources. Operons become advantageous because by clustering growth genes into operons, fewer promoters compete for the limited transcriptional machinery, effectively increasing the concentration of transcriptional resources, and accelerating recovery. Mathematical modeling reveals how a moderate increase in transcriptional resources can substantially enhance transcription rate and recovery. This design principle occurs in different nematodes and the chordate C. intestinalis. As transition from arrest to rapid growth is shared by many metazoans, operons could have evolved to facilitate these processes. PMID:21663799

Fibrous mini-collagens in hydra nematocysts.

Science.gov (United States)

Holstein, T W; Benoit, M; Herder, G V; David, C N; Wanner, G; Gaub, H E

1994-07-15

Nematocysts (cnidocysts) are exocytotic organelles found in all cnidarians. Here, atomic force microscopy and field emission scanning electron microscopy reveal the structure of the nematocyst capsule wall. The outer wall consists of globular proteins of unknown function. The inner wall consists of bundles of collagen-like fibrils having a spacing of 50 to 100 nanometers and cross-striations at intervals of 32 nanometers. The fibrils consist of polymers of "mini-collagens," which are abundant in the nematocysts of Hydra. The distinct pattern of mini-collagen fibers in the inner wall can provide the tensile strength necessary to withstand the high osmotic pressure (15 megapascals) in the capsules.

Hydra: software for tailored processing of H/D exchange data from MS or tandem MS analyses

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Bennett Melissa

2009-05-01

Full Text Available Abstract Background Hydrogen/deuterium exchange mass spectrometry (H/DX-MS experiments implemented to characterize protein interaction and protein folding generate large quantities of data. Organizing, processing and visualizing data requires an automated solution, particularly when accommodating new tandem mass spectrometry modes for H/DX measurement. We sought to develop software that offers flexibility in defining workflows so as to support exploratory treatments of H/DX-MS data, with a particular focus on the analysis of very large protein systems and the mining of tandem mass spectrometry data. Results We present a software package ("Hydra" that supports both traditional and exploratory treatments of H/DX-MS data. Hydra's software architecture tolerates flexible data analysis procedures by allowing the addition of new algorithms without significant change to the underlying code base. Convenient user interfaces ease the organization of raw data files and input of peptide data. After executing a user-defined workflow, extracted deuterium incorporation values can be visualized in tabular and graphical formats. Hydra also automates the extraction and visualization of deuterium distribution values. Manual validation and assessment of results is aided by an interface that aligns extracted ion chromatograms and mass spectra, while providing a means of rapidly reprocessing the data following manual adjustment. A unique feature of Hydra is the automated processing of tandem mass spectrometry data, demonstrated on a large test data set in which 40,000 deuterium incorporation values were extracted from replicate analysis of approximately 1000 fragment ions in one hour using a typical PC. Conclusion The customizable workflows and user-friendly interfaces of Hydra removes a significant bottleneck in processing and visualizing H/DX-MS data and helps the researcher spend more time executing new experiments and interpreting results. This increased

Impact of cycling cells and cell cycle regulation on Hydra regeneration.

Science.gov (United States)

Buzgariu, Wanda; Wenger, Yvan; Tcaciuc, Nina; Catunda-Lemos, Ana-Paula; Galliot, Brigitte

2018-01-15

Hydra tissues are made from three distinct populations of stem cells that continuously cycle and pause in G2 instead of G1. To characterize the role of cell proliferation after mid-gastric bisection, we have (i) used flow cytometry and classical markers to monitor cell cycle modulations, (ii) quantified the transcriptomic regulations of 202 genes associated with cell proliferation during head and foot regeneration, and (iii) compared the impact of anti-proliferative treatments on regeneration efficiency. We confirm two previously reported events: an early mitotic wave in head-regenerating tips, when few cell cycle genes are up-regulated, and an early-late wave of proliferation on the second day, preceded by the up-regulation of 17 cell cycle genes. These regulations appear more intense after mid-gastric bisection than after decapitation, suggesting a position-dependent regulation of cell proliferation during head regeneration. Hydroxyurea, which blocks S-phase progression, delays head regeneration when applied before but not after bisection. This result is consistent with the fact that the Hydra central region is enriched in G2-paused adult stem cells, poised to divide upon injury, thus forming a necessary constitutive pro-blastema. However a prolonged exposure to hydroxyurea does not block regeneration as cells can differentiate apical structures without traversing S-phase, and also escape in few days the hydroxyurea-induced S-phase blockade. Thus Hydra head regeneration, which is a fast event, is highly plastic, relying on large stocks of adult stem cells paused in G2 at amputation time, which immediately divide to proliferate and/or differentiate apical structures even when S-phase is blocked. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Innexin gap junctions in nerve cells coordinate spontaneous contractile behavior in Hydra polyps

KAUST Repository

Takaku, Yasuharu; Hwang, Jung Shan; Wolf, Alexander; Bö ttger, Angelika; Shimizu, Hiroshi; David, Charles N.; Gojobori, Takashi

2014-01-01

Nerve cells and spontaneous coordinated behavior first appeared near the base of animal evolution in the common ancestor of cnidarians and bilaterians. Experiments on the cnidarian Hydra have demonstrated that nerve cells are essential

Molecular Characterization of a Catalase from Hydra vulgaris

OpenAIRE

Dash, Bhagirathi; Phillips, Timothy D.

2012-01-01

Catalase, an antioxidant and hydroperoxidase enzyme protects the cellular environment from harmful effects of hydrogen peroxide by facilitating its degradation to oxygen and water. Molecular information on a cnidarian catalase and/or peroxidase is, however, limited. In this work an apparent full length cDNA sequence coding for a catalase (HvCatalase) was isolated from Hydra vulgaris using 3’- and 5’- (RLM) RACE approaches. The 1859 bp HvCatalase cDNA included an open reading frame of 1518 bp ...

HYDRA-II: A hydrothermal analysis computer code: Volume 1, Equations and numerics

International Nuclear Information System (INIS)

McCann, R.A.

1987-04-01

HYDRA-II is a hydrothermal computer code capable of three-dimensional analysis of coupled conduction, convection, and thermal radiation problems. This code is especially appropriate for simulating the steady-state performance of spent fuel storage systems. The code has been evaluated for this application for the US Department of Energy's Commercial Spent Fuel Management Program. HYDRA-II provides a finite difference solution in Cartesian coordinates to the equations governing the conservation of mass, momentum, and energy. A cylindrical coordinate system may also be used to enclose the Cartesian coordinate system. This exterior coordinate system is useful for modeling cylindrical cask bodies. The difference equations for conservation of momentum are enhanced by the incorporation of directional porosities and permeabilities that aid in modeling solid structures whose dimensions may be smaller than the computational mesh. The equation for conservation of energy permits of modeling of orthotropic physical properties and film resistances. Several automated procedures are available to model radiation transfer within enclosures and from fuel rod to fuel rod. The documentation of HYDRA-II is presented in three separate volumes. This volume, Volume I - Equations and Numerics, describes the basic differential equations, illustrates how the difference equations are formulated, and gives the solution procedures employed. Volume II - User's Manual contains code flow charts, discusses the code structure, provides detailed instructions for preparing an input file, and illustrates the operation of the code by means of a model problem. The final volume, Volume III - Verification/Validation Assessments, presents results of numerical simulations of single- and multiassembly storage systems and comparisons with experimental data. 4 refs

Analysis of Schizosaccharomyces pombe mediator reveals a set of essential subunits conserved between yeast and metazoan cells

DEFF Research Database (Denmark)

Spåhr, H; Samuelsen, C O; Baraznenok, V

2001-01-01

. cerevisiae share an essential protein module, which associates with nonessential speciesspecific subunits. In support of this view, sequence analysis of the conserved yeast Mediator components Med4 and Med8 reveals sequence homology to the metazoan Mediator components Trap36 and Arc32. Therefore, 8 of 10...... essential genes conserved between S. pombe and S. cerevisiae also have a metazoan homolog, indicating that an evolutionary conserved Mediator core is present in all eukaryotic cells. Our data suggest a closer functional relationship between yeast and metazoan Mediator than previously anticipated....

Einstein observations of the Hydra A cluster and the efficiency of galaxy formation in groups and clusters

Science.gov (United States)

David, L. P.; Arnaud, K. A.; Forman, W.; Jones, C.

1990-01-01

The Einstein imaging proportional counter observations of the poor cluster of galaxies centered on the radio galaxy Hydra A are examined. From the surface brightness profile, it is found that the X-ray-emitting gas in the Hydra A cluster must be condensing out of the intracluster medium at a rate of 600 solar masses/yr. This is one of the largest mass deposition rates observed in a cluster of galaxies. The ratio of gas mass to stellar mass is compared for a variety of systems, showing that this ratio correlates with the gas temperature.

The putative Notch ligand HyJagged is a transmembrane protein present in all cell types of adult Hydra and upregulated at the boundary between bud and parent

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Tischer Susanne

2011-09-01

Full Text Available Abstract Background The Notch signalling pathway is conserved in pre-bilaterian animals. In the Cnidarian Hydra it is involved in interstitial stem cell differentiation and in boundary formation during budding. Experimental evidence suggests that in Hydra Notch is activated by presenilin through proteolytic cleavage at the S3 site as in all animals. However, the endogenous ligand for HvNotch has not been described yet. Results We have cloned a cDNA from Hydra, which encodes a bona-fide Notch ligand with a conserved domain structure similar to that of Jagged-like Notch ligands from other animals. Hyjagged mRNA is undetectable in adult Hydra by in situ hybridisation but is strongly upregulated and easily visible at the border between bud and parent shortly before bud detachment. In contrast, HyJagged protein is found in all cell types of an adult hydra, where it localises to membranes and endosomes. Co-localisation experiments showed that it is present in the same cells as HvNotch, however not always in the same membrane structures. Conclusions The putative Notch ligand HyJagged is conserved in Cnidarians. Together with HvNotch it may be involved in the formation of the parent-bud boundary in Hydra. Moreover, protein distribution of both, HvNotch receptor and HyJagged indicate a more widespread function for these two transmembrane proteins in the adult hydra, which may be regulated by additional factors, possibly involving endocytic pathways.

How to use Hydra as a model system to teach biology in the classroom.

Science.gov (United States)

Bossert, Patricia; Galliot, Brigitte

2012-01-01

As scientists it is our duty to fight against obscurantism and loss of rational thinking if we want politicians and citizens to freely make the most intelligent choices for the future generations. With that aim, the scientific education and training of young students is an obvious and urgent necessity. We claim here that Hydra provides a highly versatile but cheap model organism to study biology at any age. Teachers of biology have the unenviable task of motivating young people, who with many other motivations that are quite valid, nevertheless must be guided along a path congruent with a 'syllabus' or a 'curriculum'. The biology of Hydra spans the history of biology as an experimental science from Trembley's first manipulations designed to determine if the green polyp he found was plant or animal to the dissection of the molecular cascades underpinning, regeneration, wound healing, stemness, aging and cancer. It is described here in terms designed to elicit its wider use in classrooms. Simple lessons are outlined in sufficient detail for beginners to enter the world of 'Hydra biology'. Protocols start with the simplest observations to experiments that have been pretested with students in the USA and in Europe. The lessons are practical and can be used to bring 'life', but also rational thinking into the study of life for the teachers of students from elementary school through early university.

Development of the two-part pattern during regeneration of the head in hydra

DEFF Research Database (Denmark)

Bode, Matthias; Awad, T A; Koizumi, O

1988-01-01

The head of a hydra is composed of two parts, a domed hypostome with a mouth at the top and a ring of tentacles below. When animals are decapitated a new head regenerates. During the process of regeneration the apical tip passes through a transient stage in which it exhibits tentacle......-like characteristics before becoming a hypostome. This was determined from markers which appeared before morphogenesis took place. The first was a monoclonal antibody, TS-19, that specifically binds to the ectodermal epithelial cells of the tentacles. The second was an antiserum against the peptide Arg......-Phe-amide (RFamide), which in the head of hydra is specific to the sensory cells of the hypostomal apex and the ganglion cells of the lower hypostome and tentacles. The TS-19 expression and the ganglion cells with RFamide-like immunoreactivity (RLI) arose first at the apex and spread radially. Once the tentacles...

Oxytocin/vasopressin-like immunoreactivity is present in the nervous system of hydra

DEFF Research Database (Denmark)

Grimmelikhuijzen, C J; Dierickx, K; Boer, G J

1982-01-01

Nerve cells have been found in hydra, which react with antisera to oxytocin, vasopressin and mesotocin. These nerve cells have a high density in the ectoderm of basal disk and tentacles and lower density in the ectoderm of peduncle, gastric region and hypostome. A very small number of nerve cells...

Transient behaviour study program of research reactors fuel elements at the Hydra Pulse Reactor

International Nuclear Information System (INIS)

Khvostionov, V.E.; Egorenkov, P.M.; Malankin, P.V.

2004-01-01

Program on behavior study of research reactor Fuel Elements (FE) under transient regimes initiated by excessive reactivity insertion is being presented. Program would be realized at HYDRA pulse reactor at Russian Research Center 'Kurchatov Institute' (RRC 'K1'). HYDRA uses aqueous solution of uranyl sulfate (UO 2 SO 4 ) as a fuel. Up to 30 MJ of energy can be released inside the core during the single pulse, effective power pulse width varying from 2 to 10 ms. Reactor facility allows to investigate behaviour of FE consisting of different types of fuel composition, being developed according to Russian RERTR. First part of program is aimed at transient behaviour studying of FE MR, IRT-3M, WWR-M5 types containing meats based on dioxide uranium in aluminum matrix. Mentioned FEs use 90% and 36% enriched uranium. (author)

The TFIID components human TAF(II)140 and Drosophila BIP2 (TAF(II)155) are novel metazoan homologues of yeast TAF(II)47 containing a histone fold and a PHD finger.

Science.gov (United States)

Gangloff, Y G; Pointud, J C; Thuault, S; Carré, L; Romier, C; Muratoglu, S; Brand, M; Tora, L; Couderc, J L; Davidson, I

2001-08-01

The RNA polymerase II transcription factor TFIID comprises the TATA binding protein (TBP) and a set of TBP-associated factors (TAF(II)s). TFIID has been extensively characterized for yeast, Drosophila, and humans, demonstrating a high degree of conservation of both the amino acid sequences of the constituent TAF(II)s and overall molecular organization. In recent years, it has been assumed that all the metazoan TAF(II)s have been identified, yet no metazoan homologues of yeast TAF(II)47 (yTAF(II)47) and yTAF(II)65 are known. Both of these yTAF(II)s contain a histone fold domain (HFD) which selectively heterodimerizes with that of yTAF(II)25. We have cloned a novel mouse protein, TAF(II)140, containing an HFD and a plant homeodomain (PHD) finger, which we demonstrated by immunoprecipitation to be a mammalian TFIID component. TAF(II)140 shows extensive sequence similarity to Drosophila BIP2 (dBIP2) (dTAF(II)155), which we also show to be a component of Drosophila TFIID. These proteins are metazoan homologues of yTAF(II)47 as their HFDs selectively heterodimerize with dTAF(II)24 and human TAF(II)30, metazoan homologues of yTAF(II)25. We further show that yTAF(II)65 shares two domains with the Drosophila Prodos protein, a recently described potential dTAF(II). These conserved domains are critical for yTAF(II)65 function in vivo. Our results therefore identify metazoan homologues of yTAF(II)47 and yTAF(II)65.

Microarray Glycan Profiling Reveals Algal Fucoidan Epitopes in Diverse Marine Metazoans

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Armando A. Salmeán

2017-09-01

Full Text Available Despite the biological importance and pharmacological potential of glycans from marine organisms, there are many unanswered questions regarding their distribution, function, and evolution. Here we describe microarray-based glycan profiling of a diverse selection of marine animals using antibodies raised against fucoidan isolated from a brown alga. We demonstrate the presence of two fucoidan epitopes in six animals belonging to three phyla including Porifera, Molusca, and Chordata. We studied the spatial distribution of these epitopes in Cliona celata (“boring sponge” and identified their restricted localization on the surface of internal chambers. Our results show the potential of high-throughput screening and probes commonly used in plant and algal cell wall biology to study the diversity and distribution of glycan structures in metazoans.

High-Resolution Profiling of Drosophila Replication Start Sites Reveals a DNA Shape and Chromatin Signature of Metazoan Origins

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Federico Comoglio

2015-05-01

Full Text Available At every cell cycle, faithful inheritance of metazoan genomes requires the concerted activation of thousands of DNA replication origins. However, the genetic and chromatin features defining metazoan replication start sites remain largely unknown. Here, we delineate the origin repertoire of the Drosophila genome at high resolution. We address the role of origin-proximal G-quadruplexes and suggest that they transiently stall replication forks in vivo. We dissect the chromatin configuration of replication origins and identify a rich spatial organization of chromatin features at initiation sites. DNA shape and chromatin configurations, not strict sequence motifs, mark and predict origins in higher eukaryotes. We further examine the link between transcription and origin firing and reveal that modulation of origin activity across cell types is intimately linked to cell-type-specific transcriptional programs. Our study unravels conserved origin features and provides unique insights into the relationship among DNA topology, chromatin, transcription, and replication initiation across metazoa.

Horizontal gene transfer contributed to the evolution of extracellular surface structures: the freshwater polyp Hydra is covered by a complex fibrous cuticle containing glycosaminoglycans and proteins of the PPOD and SWT (sweet tooth families.

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Angelika Böttger

Full Text Available The single-cell layered ectoderm of the fresh water polyp Hydra fulfills the function of an epidermis by protecting the animals from the surrounding medium. Its outer surface is covered by a fibrous structure termed the cuticle layer, with similarity to the extracellular surface coats of mammalian epithelia. In this paper we have identified molecular components of the cuticle. We show that its outermost layer contains glycoproteins and glycosaminoglycans and we have identified chondroitin and chondroitin-6-sulfate chains. In a search for proteins that could be involved in organising this structure we found PPOD proteins and several members of a protein family containing only SWT (sweet tooth domains. Structural analyses indicate that PPODs consist of two tandem β-trefoil domains with similarity to carbohydrate-binding sites found in lectins. Experimental evidence confirmed that PPODs can bind sulfated glycans and are secreted into the cuticle layer from granules localized under the apical surface of the ectodermal epithelial cells. PPODs are taxon-specific proteins which appear to have entered the Hydra genome by horizontal gene transfer from bacteria. Their acquisition at the time Hydra evolved from a marine ancestor may have been critical for the transition to the freshwater environment.

Hydra II: A Faint and Compact Milky Way Dwarf Galaxy Found in the Survey of the Magellanic Stellar History

OpenAIRE

Martin, NF; Nidever, DL; Besla, G; Olsen, K; Walker, AR; Vivas, AK; Gruendl, RA; Kaleida, CC; Muñoz, RR; Blum, RD; Saha, A; Conn, BC; Bell, EF; Chu, YH; Cioni, MRL

2015-01-01

© 2015. The American Astronomical Society. All rights reserved.We present the discovery of a new dwarf galaxy, Hydra II, found serendipitously within the data from the ongoing Survey of the Magellanic Stellar History conducted with the Dark Energy Camera on the Blanco 4 m Telescope. The new satellite is compact (rh = 68 ± 11 pc) and faint (MV = -4.8 ± 0.3), but well within the realm of dwarf galaxies. The stellar distribution of Hydra II in the color-magnitude diagram is well-described by a m...

Constraints on genes shape long-term conservation of macro-synteny in metazoan genomes

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Putnam Nicholas H

2011-10-01

Full Text Available Abstract Background Many metazoan genomes conserve chromosome-scale gene linkage relationships (“macro-synteny” from the common ancestor of multicellular animal life 1234, but the biological explanation for this conservation is still unknown. Double cut and join (DCJ is a simple, well-studied model of neutral genome evolution amenable to both simulation and mathematical analysis 5, but as we show here, it is not sufficent to explain long-term macro-synteny conservation. Results We examine a family of simple (one-parameter extensions of DCJ to identify models and choices of parameters consistent with the levels of macro- and micro-synteny conservation observed among animal genomes. Our software implements a flexible strategy for incorporating genomic context into the DCJ model to incorporate various types of genomic context (“DCJ-[C]”, and is available as open source software from http://github.com/putnamlab/dcj-c. Conclusions A simple model of genome evolution, in which DCJ moves are allowed only if they maintain chromosomal linkage among a set of constrained genes, can simultaneously account for the level of macro-synteny conservation and for correlated conservation among multiple pairs of species. Simulations under this model indicate that a constraint on approximately 7% of metazoan genes is sufficient to constrain genome rearrangement to an average rate of 25 inversions and 1.7 translocations per million years.

Hydratools manual version 1.0, documentation for a MATLAB®-based post-processing package for the Sontek Hydra

Science.gov (United States)

Martini, Marinna A.; Sherwood, Chris; Horwitz, Rachel; Ramsey, Andree; Lightsom, Fran; Lacy, Jessie; Xu, Jingping

2006-01-01

The Sediment Transport Instrumentation Group (STG) at the U.S. Geological Survey (USGS) Woods Hole Science Center has a long-standing comitment to providing scientists with high quality oceanographic data. To meet this commitment, STG personnel are vigilant in checking data as well as hardware for signs of instrument malfunction. STG data sets are accompanied by processing histories to detail data processing procedures that may have modified the natural data signal while removing noise from the data. The history also allows the data to be reprocessed in the ligth of new insight into instrument function and moored conditions. This toolbox was compiled to meet these data quality commitments for data generated by Sontek Hydra systems using both ADV and PCADP probes. In the mid 1900's, the USGS Coastal and Marine Program began frequent deployments of Sontek Hydra systems in support of projects in estuaries, coastal, and continental shelf regions nationwide. Hydra data sets are large and complex in structure, and existing processing and editing tools consisted of fragments of MATLAB code written by USGS scientists to satisfy personal research needs. This code did not meet STG quality control criteria. This toolbox permits engineers and scientists to monitor data quality by: 1.\tprocessing data with interactive critical review;

DISTANCE AND KINEMATICS OF THE TW HYDRAE ASSOCIATION FROM PARALLAXES

Energy Technology Data Exchange (ETDEWEB)

Weinberger, Alycia J.; Boss, Alan P. [Department of Terrestrial Magnetism, Carnegie Institution of Washington, 5241 Broad Branch Road NW, Washington, DC 20015 (United States); Anglada-Escude, Guillem, E-mail: weinberger@dtm.ciw.edu [Institut fuer Astrophysik, Universitaet Goettingen, Friedrich-Hund-Platz 1, 37077 Goettingen (Germany)

2013-01-10

From common proper motion and signatures of youth, researchers have identified about 30 members of a putative TW Hydrae Association. Only four of these had parallactic distances from Hipparcos. We have measured parallaxes and proper motions for 14 primary members. We combine these with literature values of radial velocities to show that the Galactic space motions of the stars, with the exception of TWA 9 and 22, are parallel and do not indicate convergence at a common formation point sometime in the last few million years. The space motions of TWA 9 and 22 do not agree with the others and indicate that they are not TWA members. The median parallax is 18 mas or 56 pc. We further analyze the stars' absolute magnitudes on pre-main-sequence evolutionary tracks and find a range of ages with a median of 10.1 Myr and no correlation between age and Galactic location. The TWA stars may have formed from an extended and filamentary molecular cloud but are not necessarily precisely coeval.

Concatenated analysis sheds light on early metazoan evolution and fuels a modern "urmetazoon" hypothesis.

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Bernd Schierwater

2009-01-01

Full Text Available For more than a century, the origin of metazoan animals has been debated. One aspect of this debate has been centered on what the hypothetical "urmetazoon" bauplan might have been. The morphologically most simply organized metazoan animal, the placozoan Trichoplax adhaerens, resembles an intriguing model for one of several "urmetazoon" hypotheses: the placula hypothesis. Clear support for a basal position of Placozoa would aid in resolving several key issues of metazoan-specific inventions (including, for example, head-foot axis, symmetry, and coelom and would determine a root for unraveling their evolution. Unfortunately, the phylogenetic relationships at the base of Metazoa have been controversial because of conflicting phylogenetic scenarios generated while addressing the question. Here, we analyze the sum of morphological evidence, the secondary structure of mitochondrial ribosomal genes, and molecular sequence data from mitochondrial and nuclear genes that amass over 9,400 phylogenetically informative characters from 24 to 73 taxa. Together with mitochondrial DNA genome structure and sequence analyses and Hox-like gene expression patterns, these data (1 provide evidence that Placozoa are basal relative to all other diploblast phyla and (2 spark a modernized "urmetazoon" hypothesis.

Concatenated analysis sheds light on early metazoan evolution and fuels a modern "urmetazoon" hypothesis.

Science.gov (United States)

Schierwater, Bernd; Eitel, Michael; Jakob, Wolfgang; Osigus, Hans-Jürgen; Hadrys, Heike; Dellaporta, Stephen L; Kolokotronis, Sergios-Orestis; Desalle, Rob

2009-01-27

For more than a century, the origin of metazoan animals has been debated. One aspect of this debate has been centered on what the hypothetical "urmetazoon" bauplan might have been. The morphologically most simply organized metazoan animal, the placozoan Trichoplax adhaerens, resembles an intriguing model for one of several "urmetazoon" hypotheses: the placula hypothesis. Clear support for a basal position of Placozoa would aid in resolving several key issues of metazoan-specific inventions (including, for example, head-foot axis, symmetry, and coelom) and would determine a root for unraveling their evolution. Unfortunately, the phylogenetic relationships at the base of Metazoa have been controversial because of conflicting phylogenetic scenarios generated while addressing the question. Here, we analyze the sum of morphological evidence, the secondary structure of mitochondrial ribosomal genes, and molecular sequence data from mitochondrial and nuclear genes that amass over 9,400 phylogenetically informative characters from 24 to 73 taxa. Together with mitochondrial DNA genome structure and sequence analyses and Hox-like gene expression patterns, these data (1) provide evidence that Placozoa are basal relative to all other diploblast phyla and (2) spark a modernized "urmetazoon" hypothesis.

Metazoan Parasite Infracommunities in Five Sciaenids from the Central Peruvian Coast

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Oliva Marcelo E

1998-01-01

Full Text Available Parasitological analysis of 237 Menticirrhus ophicephalus, 124 Paralonchurus peruanus, 249 Sciaena deliciosa, 50 Sciaena fasciata and 308 Stellifer minor from Callao (Perú yielded 37 species of metazoan parasites (14 Monogenea, 11 Copepoda, 4 Nematoda, 3 Acanthocephala, 1 Digenea, 1 Aspidobothrea, 1 Eucestoda, 1 Isopoda and 1 Hirudinea. Only one species, the copepoda Bomolochus peruensis, was common to all five hosts. The majority of the components of the infracommunities analyzed are ectoparasites. The Brillouin index (H and evenness (J´ were applied to the fully sampled metazoan parasite infracommunities. High values of prevalence and mean abundance of infection are associated to the polyonchoinean monogeneans; the low values of J' reinforce the strong dominance of this group in the studied communities. The paucity of the endoparasite fauna may be a consequence of the unstable environment due to an upwelling system, aperiodically affected by the El Niño Southern Oscillation phenomena.

The protist, Monosiga brevicollis, has a tyrosine kinase signaling network more elaborate and diverse than found in any known metazoan.

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Manning, Gerard; Young, Susan L; Miller, W Todd; Zhai, Yufeng

2008-07-15

Tyrosine kinase signaling has long been considered a hallmark of intercellular communication, unique to multicellular animals. Our genomic analysis of the unicellular choanoflagellate Monosiga brevicollis discovers a remarkable count of 128 tyrosine kinases, 38 tyrosine phosphatases, and 123 phosphotyrosine (pTyr)-binding SH2 proteins, all higher counts than seen in any metazoan. This elaborate signaling network shows little orthology to metazoan counterparts yet displays many innovations reminiscent of metazoans. These include extracellular domains structurally related to those of metazoan receptor kinases, alternative methods for membrane anchoring and phosphotyrosine interaction in cytoplasmic kinases, and domain combinations that link kinases to small GTPase signaling and transcription. These proteins also display a wealth of combinations of known signaling domains. This uniquely divergent and elaborate signaling network illuminates the early evolution of pTyr signaling, explores innovative ways to traverse the cellular signaling circuitry, and shows extensive convergent evolution, highlighting pervasive constraints on pTyr signaling.

Systematic analysis and evolution of 5S ribosomal DNA in metazoans.

Science.gov (United States)

Vierna, J; Wehner, S; Höner zu Siederdissen, C; Martínez-Lage, A; Marz, M

2013-11-01

Several studies on 5S ribosomal DNA (5S rDNA) have been focused on a subset of the following features in mostly one organism: number of copies, pseudogenes, secondary structure, promoter and terminator characteristics, genomic arrangements, types of non-transcribed spacers and evolution. In this work, we systematically analyzed 5S rDNA sequence diversity in available metazoan genomes, and showed organism-specific and evolutionary-conserved features. Putatively functional sequences (12,766) from 97 organisms allowed us to identify general features of this multigene family in animals. Interestingly, we show that each mammal species has a highly conserved (housekeeping) 5S rRNA type and many variable ones. The genomic organization of 5S rDNA is still under debate. Here, we report the occurrence of several paralog 5S rRNA sequences in 58 of the examined species, and a flexible genome organization of 5S rDNA in animals. We found heterogeneous 5S rDNA clusters in several species, supporting the hypothesis of an exchange of 5S rDNA from one locus to another. A rather high degree of variation of upstream, internal and downstream putative regulatory regions appears to characterize metazoan 5S rDNA. We systematically studied the internal promoters and described three different types of termination signals, as well as variable distances between the coding region and the typical termination signal. Finally, we present a statistical method for detection of linkage among noncoding RNA (ncRNA) gene families. This method showed no evolutionary-conserved linkage among 5S rDNAs and any other ncRNA genes within Metazoa, even though we found 5S rDNA to be linked to various ncRNAs in several clades.

Metazoan parasites of Brama australis from southern Chile: a tool for stock discrimination?

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Oliva, M E; Espinola, J F; Ñacari, L A

2016-03-01

The metazoan parasites of 403 specimens of the southern ray's bream Brama australis from three localities in southern Chile (Lebu 36° 70' S; 73° 40' W, Calbuco 41° 50' S; 73° 08' W and Punta Arenas 53° 10' S; 70° 50' W) were recorded. More than 23 400 parasite specimens belonging to 12 taxa were registered. Metazoan parasites were dominated by the copepod Hatschekia conifera, constituting 97% of the total number of parasites; the larval cestode Hepatoxylon trichiuri was the second most important parasite (2·1% of the total number of parasites). The remaining 10 species constituted parasites. Parasitological evidence, based on univariate and multivariate analysis, does not support the existence of discrete stocks in the studied zone. © 2016 The Fisheries Society of the British Isles.

Prolonged decay of molecular rate estimates for metazoan mitochondrial DNA

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Martyna Molak

2015-03-01

Full Text Available Evolutionary timescales can be estimated from genetic data using the molecular clock, often calibrated by fossil or geological evidence. However, estimates of molecular rates in mitochondrial DNA appear to scale negatively with the age of the clock calibration. Although such a pattern has been observed in a limited range of data sets, it has not been studied on a large scale in metazoans. In addition, there is uncertainty over the temporal extent of the time-dependent pattern in rate estimates. Here we present a meta-analysis of 239 rate estimates from metazoans, representing a range of timescales and taxonomic groups. We found evidence of time-dependent rates in both coding and non-coding mitochondrial markers, in every group of animals that we studied. The negative relationship between the estimated rate and time persisted across a much wider range of calibration times than previously suggested. This indicates that, over long time frames, purifying selection gives way to mutational saturation as the main driver of time-dependent biases in rate estimates. The results of our study stress the importance of accounting for time-dependent biases in estimating mitochondrial rates regardless of the timescale over which they are inferred.

Wnt and TGF-beta expression in the sponge Amphimedon queenslandica and the origin of metazoan embryonic patterning.

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Maja Adamska

2007-10-01

Full Text Available The origin of metazoan development and differentiation was contingent upon the evolution of cell adhesion, communication and cooperation mechanisms. While components of many of the major cell signalling pathways have been identified in a range of sponges (phylum Porifera, their roles in development have not been investigated and remain largely unknown. Here, we take the first steps toward reconstructing the developmental signalling systems used in the last common ancestor to living sponges and eumetazoans by studying the expression of genes encoding Wnt and TGF-beta signalling ligands during the embryonic development of a sponge.Using resources generated in the recent sponge Amphimedon queenslandica (Demospongiae genome project, we have recovered genes encoding Wnt and TGF-beta signalling ligands that are critical in patterning metazoan embryos. Both genes are expressed from the earliest stages of Amphimedon embryonic development in highly dynamic patterns. At the time when the Amphimedon embryos begin to display anterior-posterior polarity, Wnt expression becomes localised to the posterior pole and this expression continues until the swimming larva stage. In contrast, TGF-beta expression is highest at the anterior pole. As in complex animals, sponge Wnt and TGF-beta expression patterns intersect later in development during the patterning of a sub-community of cells that form a simple tissue-like structure, the pigment ring. Throughout development, Wnt and TGF-beta are expressed radially along the anterior-posterior axis.We infer from the expression of Wnt and TGF-beta in Amphimedon that the ancestor that gave rise to sponges, cnidarians and bilaterians had already evolved the capacity to direct the formation of relatively sophisticated body plans, with axes and tissues. The radially symmetrical expression patterns of Wnt and TGF-beta along the anterior-posterior axis of sponge embryos and larvae suggest that these signalling pathways

Male and female stem cells and sex reversal in Hydra polyps

OpenAIRE

Bosch, Thomas C. G.; David, Charles N.

1986-01-01

Single interstitial stem cells of male polyps of Hydra magnipapillata give rise to clones that differentiate either male or female gametes. To test the sexual stability of these clones, stem cells were recloned. The results indicate that stem cells from female clones are stable in their sexual differentiation capacity; male stem cells, by comparison, switch sexual phenotype at the rate of 10-2 per cell per generation. As a result, female polyps contain only female stem cells; male polyps cont...

HYDRA-3D: a model for studying hydrogen transport in containments

International Nuclear Information System (INIS)

Prakash, P.; Mishra, A.; Das, M.; Srinivasan, G.R.

1994-01-01

The development of a 3D computer code HYDRA-3D for studying hydrogen transport in containment systems is described in this paper. The time-dependent conservation equations for mixture mass, mixture momentum, mixture energy and species mass are solved using finite difference technique. Effects of molecular diffusion and turbulence have been taken into account. Sample calculations involving steam injection in a cubical compartment show reasonable trends in pressure and species concentrations throughout the computation domain. (author). 5 refs., 6 figs

An efficient method to find potentially universal population genetic markers, applied to metazoans

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Chenuil Anne

2010-09-01

Full Text Available Abstract Background Despite the impressive growth of sequence databases, the limited availability of nuclear markers that are sufficiently polymorphic for population genetics and phylogeography and applicable across various phyla restricts many potential studies, particularly in non-model organisms. Numerous introns have invariant positions among kingdoms, providing a potential source for such markers. Unfortunately, most of the few known EPIC (Exon Primed Intron Crossing loci are restricted to vertebrates or belong to multigenic families. Results In order to develop markers with broad applicability, we designed a bioinformatic approach aimed at avoiding multigenic families while identifying intron positions conserved across metazoan phyla. We developed a program facilitating the identification of EPIC loci which allowed slight variation in intron position. From the Homolens databases we selected 29 gene families which contained 52 promising introns for which we designed 93 primer pairs. PCR tests were performed on several ascidians, echinoderms, bivalves and cnidarians. On average, 24 different introns per genus were amplified in bilaterians. Remarkably, five of the introns successfully amplified in all of the metazoan genera tested (a dozen genera, including cnidarians. The influence of several factors on amplification success was investigated. Success rate was not related to the phylogenetic relatedness of a taxon to the groups that most influenced primer design, showing that these EPIC markers are extremely conserved in animals. Conclusions Our new method now makes it possible to (i rapidly isolate a set of EPIC markers for any phylum, even outside the animal kingdom, and thus, (ii compare genetic diversity at potentially homologous polymorphic loci between divergent taxa.

Towards a Full Braginskii Formulation in HYDRA

Science.gov (United States)

Koning, Joseph

2014-10-01

The magnetic field package in the ICF radiation transport simulation code HYDRA currently contains a resistive MHD solver and includes the dielectric pressure source term, anisotropic electron thermal conduction and magnetic field effects on alpha charged particle transport. This package has been improved with the addition of Nernst and Hall terms implemented using a discrete differential forms method. The Nernst magnetic term includes a limiting method for any large thermal or magnetic gradients. The Nernst thermal term results in a non-symmetric matrix solved using GMRES. The Hall term is discretized using methods based on constrained transport magnetic advection. All of the terms utilize discrete differential forms methods to maintain zero magnetic divergence exactly while properly treating the appropriate continuity of all vector field terms. Prepared by LLNL under Contract DE-AC52-07NA27344. Partial Funding provided by Sandia National Laboratory.

More than just orphans: are taxonomically-restricted genes important in evolution?

Science.gov (United States)

Khalturin, Konstantin; Hemmrich, Georg; Fraune, Sebastian; Augustin, René; Bosch, Thomas C G

2009-09-01

Comparative genome analyses indicate that every taxonomic group so far studied contains 10-20% of genes that lack recognizable homologs in other species. Do such 'orphan' or 'taxonomically-restricted' genes comprise spurious, non-functional ORFs, or does their presence reflect important evolutionary processes? Recent studies in basal metazoans such as Nematostella, Acropora and Hydra have shed light on the function of these genes, and now indicate that they are involved in important species-specific adaptive processes. Here we focus on evidence from Hydra suggesting that taxonomically-restricted genes play a role in the creation of phylum-specific novelties such as cnidocytes, in the generation of morphological diversity, and in the innate defence system. We propose that taxon-specific genes drive morphological specification, enabling organisms to adapt to changing conditions.

Boolean logic and character state identity: pitfalls of character coding in metazoan cladistics

NARCIS (Netherlands)

Jenner, Ronald A.

2002-01-01

A critical study of the morphological data sets used for the most recent analyses of metazoan cladistics exposes a rather cavalier attitude towards character coding. Binary absence/presence coding is ubiquitous, but without any explicit justification. This uncompromising application of Boolean logic

“Is the Hydra the Enemy?” A Review of English Language as Hydra: Its Impacts on Non-English Language Cultures

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Corazon D. Villareal

2012-12-01

Full Text Available The book, part of the series on Linguistic Diversity and Language Rights of Multilingual Matters, seeks "to promote multilingualism as a resource, the maintenance of the linguistic diversity and development of and respect for linguistic human rights worldwide through the dissemination of theoretical and empirical research"(ii. The context for this advocacy is English whose domain is perceived to have reduced linguistic and cultural diversity; this encounter is the core concern of the book, as the title suggests. The contributors unabashedly articulate their disgust and rage against this hydra through a seemingly inexhaustible arsenal of metaphors - thief, bully, juggernaut,an intractable governess, "a partner in crime," "an overstaying auntie," etc. The tone is combative, sometimes veering dangerously close to simplistic name-calling and clichéd emotionalism. So it seems.

Testing whether Metazoan Tyrosine Loss Was Driven by Selection against Promiscuous Phosphorylation

Science.gov (United States)

Pandya, Siddharth; Struck, Travis J.; Mannakee, Brian K.; Paniscus, Mary; Gutenkunst, Ryan N.

2015-01-01

Protein tyrosine phosphorylation is a key regulatory modification in metazoans, and the corresponding kinase enzymes have diversified dramatically. This diversification is correlated with a genome-wide reduction in protein tyrosine content, and it was recently suggested that this reduction was driven by selection to avoid promiscuous phosphorylation that might be deleterious. We tested three predictions of this intriguing hypothesis. 1) Selection should be stronger on residues that are more likely to be phosphorylated due to local solvent accessibility or structural disorder. 2) Selection should be stronger on proteins that are more likely to be promiscuously phosphorylated because they are abundant. We tested these predictions by comparing distributions of tyrosine within and among human and yeast orthologous proteins. 3) Selection should be stronger against mutations that create tyrosine versus remove tyrosine. We tested this prediction using human population genomic variation data. We found that all three predicted effects are modest for tyrosine when compared with the other amino acids, suggesting that selection against deleterious phosphorylation was not dominant in driving metazoan tyrosine loss. PMID:25312910

Cyclic [G(2',5')pA(3',5')p] is the metazoan second messenger produced by DNA-activated cyclic GMP-AMP synthase.

Science.gov (United States)

Gao, Pu; Ascano, Manuel; Wu, Yang; Barchet, Winfried; Gaffney, Barbara L; Zillinger, Thomas; Serganov, Artem A; Liu, Yizhou; Jones, Roger A; Hartmann, Gunther; Tuschl, Thomas; Patel, Dinshaw J

2013-05-23

Recent studies identified cyclic GMP-AMP (cGAMP) as a metazoan second messenger triggering an interferon response. cGAMP is generated from GTP and ATP by cytoplasmic dsDNA sensor cGAMP synthase (cGAS). We combined structural, chemical, biochemical, and cellular assays to demonstrate that this second messenger contains G(2',5')pA and A(3',5')pG phosphodiester linkages, designated c[G(2',5')pA(3',5')p]. We show that, upon dsDNA binding, cGAS is activated through conformational transitions, resulting in formation of a catalytically competent and accessible nucleotide-binding pocket for generation of c[G(2',5')pA(3',5')p]. We demonstrate that cyclization occurs in a stepwise manner through initial generation of 5'-pppG(2',5')pA prior to cyclization to c[G(2',5')pA(3',5')p], with the latter positioned precisely in the catalytic pocket. Mutants of cGAS dsDNA-binding or catalytic pocket residues exhibit reduced or abrogated activity. Our studies have identified c[G(2',5')pA(3',5')p] as a founding member of a family of metazoan 2',5'-containing cyclic heterodinucleotide second messengers distinct from bacterial 3',5' cyclic dinucleotides. Copyright © 2013 Elsevier Inc. All rights reserved.

Evolution of mitochondrial power in vertebrate metazoans.

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Yasuhiro Kitazoe

Full Text Available BACKGROUND: Basal metabolic rate (BMR has a very strong body-mass (M dependence in an individual animal group, and BMR per unit mass (msBMR converges on a markedly narrow range even across major taxonomic groups. However, it is here a basic question in metazoan biology how much BMR per unit mitochondrion (mtBMR changes, and then whether mtBMR can be related to the original molecular mechanism of action of mt-encoded membrane proteins (MMPs playing a central role in cellular energy production. METHODOLOGY/PRINCIPAL FINDINGS: Analyzing variations of amino-acid compositions of MMPs across 13 metazoan animal groups, incorporating 2022 sequences, we found a strong inverse correlation between Ser/Thr composition (STC and hydrophobicity (HYD. A majority of animal groups showed an evolutionary pathway of a gradual increase in HYD and decrease in STC, whereas only the deuterostome lineage revealed a rapid decrease in HYD and increase in STC. The strongest correlations appeared in 5 large subunits (ND4, ND5, ND2, CO1, and CO3 undergoing dynamic conformational changes for the proton-pumping function. The pathway of the majority groups is well understood as reflecting natural selection to reduce mtBMR, since simply raising HYD in MMPs (surrounded by the lipid bilayer weakens their mobility and strengthens their stability. On the other hand, the marked decrease in HYD of the deuterostome elevates mtBMR, but is accompanied with their instability heightening a turnover rate of mitochondria and then cells. Interestingly, cooperative networks of interhelical hydrogen-bonds between motifs involving Ser and Thr residues can enhance MMP stability. CONCLUSION/SIGNIFICANCE: This stability enhancement lowers turnover rates of mitochondria/cells and may prolong even longevity, and was indeed founded by strong positive correlations of STC with both mtBMR and longevity. The lowest HYD and highest STC in Aves and Mammals are congruent with their very high mtBMR and long

Validity of HydraTrend reagent strips for the assessment of hydration status.

Science.gov (United States)

Abbey, Bryce M; Heelan, Kate A; Brown, Gregory A; Bartee, Rodrick T

2014-09-01

Hydration is used by athletic governing organizations for weight class eligibility. The measurement of urine specific gravity (USG) as a measure of hydration by reagent strips is a controversial issue. The purpose of this study was to determine the validity of HydraTrend reagent strips that facilitate the correction of USG for alkaline urine samples against refractometry for the assessment of USG. Fifty-one participants (33 males, age = 22.3 ± 1.3 years; 18 females, age = 22.4 ± 1.2 years) provided 84 urine samples. The samples were tested for USG using refractometry and reagent strips and for pH using reagent strips and a digital pH meter. Strong correlation coefficients were found between refractometry and reagent strips for USG (rs(82) = 0.812, p refractometry with USG >1.020, pass reagent strips with USG ≤1.020) occurred 39% (33/84) of the time and false negative results for National Federation of State High School Association (NFHS) requirements (fail refractometry with USG >1.025, pass reagent strips with USG ≤1.025) occurred 14% (12/84) of the time. There were no false positives (pass refractometry and fail reagent strips) for NCAA or NFHS requirements. These data show that refractometry and reagent strips have strong positive correlations. However, the risk of a false negative result leading to incorrect certification of euhydration status outweighs the benefits of the HydraTrend reagent strips for the measurement of USG.

ROS dependent copper toxicity in Hydra-biochemical and molecular study.

Science.gov (United States)

Zeeshan, Mohammed; Murugadas, Anbazhagan; Ghaskadbi, Surendra; Rajendran, Ramasamy Babu; Akbarsha, Mohammad Abdulkader

2016-01-01

Copper, an essential microelement, is known to be toxic to aquatic life at concentrations higher than that could be tolerated. Copper-induced oxidative stress has been documented in vitro, yet the in vivo effects of metal-induced oxidative stress have not been extensively studied in the lower invertebrates. The objective of the present study has been to find the effect of ROS-mediated toxicity of environmentally relevant concentrations of copper at organismal and cellular levels in Hydra magnipapillata. Exposure to copper at sublethal concentrations (0.06 and 0.1mg/L) for 24 or 48h resulted in generation of significant levels of intracellular reactive oxygen species (ROS). We infer that the free radicals here originate predominantly at the lysosomes but partly at the mitochondria also as visualized by H2-DHCFDA staining. Quantitative real-time PCR of RNA extracted from copper-exposed polyps revealed dose-dependent up-regulation of all antioxidant response genes (CAT, SOD, GPx, GST, GR, G6PD). Concurrent increase of Hsp70 and FoxO genes suggests the ability of polyps to respond to stress, which at 48h was not the same as at 24h. Interestingly, the transcript levels of all genes were down-regulated at 48h as compared to 24h incubation period. Comet assay indicated copper as a powerful genotoxicant, and the DNA damage was dose- as well as duration-dependent. Western blotting of proteins (Bax, Bcl-2 and caspase-3) confirmed ROS-mediated mitochondrial cell death in copper-exposed animals. These changes correlated well with changes in morphology, regeneration and aspects of reproduction. Taken together, the results indicate increased production of intracellular ROS in Hydra on copper exposure. Copyright © 2016 Elsevier Inc. All rights reserved.

High-resolution 3D simulations of NIF ignition targets performed on Sequoia with HYDRA

Science.gov (United States)

Marinak, M. M.; Clark, D. S.; Jones, O. S.; Kerbel, G. D.; Sepke, S.; Patel, M. V.; Koning, J. M.; Schroeder, C. R.

2015-11-01

Developments in the multiphysics ICF code HYDRA enable it to perform large-scale simulations on the Sequoia machine at LLNL. With an aggregate computing power of 20 Petaflops, Sequoia offers an unprecedented capability to resolve the physical processes in NIF ignition targets for a more complete, consistent treatment of the sources of asymmetry. We describe modifications to HYDRA that enable it to scale to over one million processes on Sequoia. These include new options for replicating parts of the mesh over a subset of the processes, to avoid strong scaling limits. We consider results from a 3D full ignition capsule-only simulation performed using over one billion zones run on 262,000 processors which resolves surface perturbations through modes l = 200. We also report progress towards a high-resolution 3D integrated hohlraum simulation performed using 262,000 processors which resolves surface perturbations on the ignition capsule through modes l = 70. These aim for the most complete calculations yet of the interactions and overall impact of the various sources of asymmetry for NIF ignition targets. This work was performed under the auspices of the Lawrence Livermore National Security, LLC, (LLNS) under Contract No. DE-AC52-07NA27344.

Tracking mechanical and morphological dynamics of regenerating Hydra tissue fragments using a two fingered micro-robotic hand

Science.gov (United States)

Veschgini, M.; Gebert, F.; Khangai, N.; Ito, H.; Suzuki, R.; Holstein, T. W.; Mae, Y.; Arai, T.; Tanaka, M.

2016-03-01

Regeneration of a tissue fragment of freshwater polyp Hydra is accompanied by significant morphological fluctuations, suggesting the generation of active forces. In this study, we utilized a two fingered micro-robotic hand to gain insights into the mechanics of regenerating tissues. Taking advantage of a high force sensitivity (˜1 nN) of our micro-hand, we non-invasively acquired the bulk elastic modulus of tissues by keeping the strain levels low (ɛ < 0.15). Moreover, by keeping the strain at a constant level, we monitored the stress relaxation of the Hydra tissue and determined both viscous modulus and elastic modulus simultaneously, following a simple Maxwell model. We further investigated the correlation between the frequency of force fluctuation and that of morphological fluctuation by monitoring one "tweezed" tissue and the other "intact" tissue at the same time. The obtained results clearly indicated that the magnitude and periodicity of the changes in force and shape are directly correlated, confirming that our two fingered micro-hand can precisely quantify the mechanics of soft, dynamic tissue during the regeneration and development in a non-invasive manner.

Quantitative distribution of metazoan meiofauna in continental margin sediments of the Skagerrak (Northeastern North Sea)

Science.gov (United States)

De Bovée, F.; Hall, P. O. J.; Hulth, S.; Hulthe, G.; Landén, A.; Tengberg, A.

1996-02-01

A quantitative survey of metazoan meiofauna in continental-margin sediments of the Skagerrak was carried out using virtually undisturbed sediment samples collected with a multiple corer. Altogether 11 stations distributed along and across the Norwegian Trench were occupied during three cruises. Abundance ranged from 155 to 6846 ind·10 cm -2 and revealed a sharply decreasing trend with increasing water depth. The densities were high on the upper part of the Danish margin (6846 ind·10 cm -2 at 194 m depth) and low in the central part of the deep Skagerrak (155 ind·10 cm -2 at 637 m depth). Also body lengths were significantly shorter on the Danish margin then elsewhere in the Skagerrak, indicating a greater importance of juveniles in this area. We suggest that the high densities may be explained by a stimulated renewal of the fauna, possibly induced by an adequate food supply. The low abundances found in sediments from the deepest part of the Norwegian Trench cannot be attributed to any lack of oxygen. We suggest that the low meiofaunal abundances are caused by a decrease in the food supply (accentuated in this area by lower sedimentation rates) and/or by the very high concentrations of dissolved manganese in the pore water of these sediments. The metazoan meiofauna was largely dominated by nematodes. Comparison of the respiration rates of the nematode population with the total benthic respiration (0.5 to 14%) suggests that the relative importance of metazoan meiofauna decreased with water depth.

Hydra meiosis reveals unexpected conservation of structural synaptonemal complex proteins across metazoans

OpenAIRE

Fraune, Johanna; Alsheimer, Manfred; Volff, Jean-Nicolas; Busch, Karoline; Fraune, Sebastian; Bosch, Thomas C. G.; Benavente, Ricardo

2012-01-01

The synaptonemal complex (SC) is a key structure of meiosis, mediating the stable pairing (synapsis) of homologous chromosomes during prophase I. Its remarkable tripartite structure is evolutionarily well conserved and can be found in almost all sexually reproducing organisms. However, comparison of the different SC protein components in the common meiosis model organisms Saccharomyces cerevisiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, and Mus musculus revealed...

Metazoan parasite communities: support for the biological invasion of Barbus barbus and its hybridization with the endemic Barbus meridionalis

Directory of Open Access Journals (Sweden)

L. Gettová

2016-11-01

Full Text Available Abstract Background Recently, human intervention enabled the introduction of Barbus barbus from the Rhône River basin into the Barbus meridionalis habitats of the Argens River. After an introduction event, parasite loss and lower infection can be expected in non-native hosts in contrast to native species. Still, native species might be endangered by hybridization with the incomer and the introduction of novel parasite species. In our study, we aimed to examine metazoan parasite communities in Barbus spp. populations in France, with a special emphasis on the potential threat posed by the introduction of novel parasite species by invasive B. barbus to local B. meridionalis. Methods Metazoan parasite communities were examined in B. barbus, B. meridionalis and their hybrids in three river basins in France. Microsatellites were used for the species identification of individual fish. Parasite abundance, prevalence, and species richness were compared. Effects of different factors on parasite infection levels and species richness were tested using GLM. Results Metazoan parasites followed the expansion range of B. barbus and confirmed its introduction into the Argens River. Here, the significantly lower parasite number and lower levels of infection found in B. barbus in contrast to B. barbus from the Rhône River supports the enemy release hypothesis. Barbus barbus × B. meridionalis hybridization in the Argens River basin was confirmed using both microsatellites and metazoan parasites, as hybrids were infected by parasites of both parental taxa. Trend towards higher parasite diversity in hybrids when compared to parental taxa, and similarity between parasite communities from the Barbus hybrid zone suggest that hybrids might represent “bridges” for parasite infection between B. barbus and B. meridionalis. Risk of parasite transmission from less parasitized B. barbus to more parasitized B. meridionalis indicated from our study in the Argens River

Melatonin Distribution Reveals Clues to Its Biological Significance in Basal Metazoans

Science.gov (United States)

Roopin, Modi; Levy, Oren

2012-01-01

Although nearly ubiquitous in nature, the precise biological significance of endogenous melatonin is poorly understood in phylogenetically basal taxa. In the present work, we describe insights into the functional role of melatonin at the most “basal” level of metazoan evolution. Hitherto unknown morphological determinants of melatonin distribution were evaluated in Nematostella vectensis by detecting melatonin immunoreactivity and examining the spatial gene expression patterns of putative melatonin biosynthetic and receptor elements that are located at opposing ends of the melatonin signaling pathway. Immuno-melatonin profiling indicated an elaborate interaction with reproductive tissues, reinforcing previous conjectures of a melatonin-responsive component in anthozoan reproduction. In situ hybridization (ISH) to putative melatonin receptor elements highlighted the possibility that the bioregulatory effects of melatonin in anthozoan reproduction may be mediated by interactions with membrane receptors, as in higher vertebrates. Another intriguing finding of the present study pertains to the prevalence of melatonin in centralized nervous structures. This pattern may be of great significance given that it 1) identifies an ancestral association between melatonin and key neuronal components and 2) potentially implies that certain effects of melatonin in basal species may be spread widely by regionalized nerve centers. PMID:23300630

The evolutionary portrait of metazoan NAD salvage.

Science.gov (United States)

Carneiro, João; Duarte-Pereira, Sara; Azevedo, Luísa; Castro, L Filipe C; Aguiar, Paulo; Moreira, Irina S; Amorim, António; Silva, Raquel M

2013-01-01

Nicotinamide Adenine Dinucleotide (NAD) levels are essential for cellular homeostasis and survival. Main sources of intracellular NAD are the salvage pathways from nicotinamide, where Nicotinamide phosphoribosyltransferases (NAMPTs) and Nicotinamidases (PNCs) have a key role. NAMPTs and PNCs are important in aging, infection and disease conditions such as diabetes and cancer. These enzymes have been considered redundant since either one or the other exists in each individual genome. The co-occurrence of NAMPT and PNC was only recently detected in invertebrates though no structural or functional characterization exists for them. Here, using expression and evolutionary analysis combined with homology modeling and protein-ligand docking, we show that both genes are expressed simultaneously in key species of major invertebrate branches and emphasize sequence and structural conservation patterns in metazoan NAMPT and PNC homologues. The results anticipate that NAMPTs and PNCs are simultaneously active, raising the possibility that NAD salvage pathways are not redundant as both are maintained to fulfill the requirement for NAD production in some species.

Different Endosymbiotic Interactions in Two Hydra Species Reflect the Evolutionary History of Endosymbiosis

KAUST Repository

Ishikawa, Masakazu

2016-06-19

Endosymbiosis is an important evolutionary event for organisms, and there is widespread interest in understanding the evolution of endosymbiosis establishment. Hydra is one of the most suitable organisms for studying the evolution of endosymbiosis. Within the genus Hydra, H. viridissima and H. vulgaris show endosymbiosis with green algae. Previous studies suggested that the endosymbiosis in H. vulgaris took place much more recently than that in H. viridissima, noting that the establishment of the interaction between H. vulgaris and its algae is not as stable as in H. viridissima. To investigate the on-going process of endosymbiosis, we first compared growth and tolerance to starvation in symbiotic and aposymbiotic polyps of both species. The results revealed that symbiotic H. viridissima had a higher growth rate and greater tolerance to starvation than aposymbiotic polyps. By contrast, growth of symbiotic H. vulgaris was identical to that of aposymbiotic polyps, and symbiotic H. vulgaris was less tolerant to starvation. Moreover, our gene expression analysis showed a pattern of differential gene expression in H. viridissima similar to that in other endosymbiotically established organisms, and contrary to that observed in H. vulgaris. We also showed that H. viridissima could cope with oxidative stress that caused damage, such as cell death, in H. vulgaris. These observations support the idea that oxidative stress related genes play an important role in the on-going process of endosymbiosis evolution. The different evolutionary stages of endosymbiosis studied here provide a deeper insight into the evolutionary processes occurring toward a stable endosymbiosis.

Different Endosymbiotic Interactions in Two Hydra Species Reflect the Evolutionary History of Endosymbiosis

KAUST Repository

Ishikawa, Masakazu; Yuyama, Ikuko; Shimizu, Hiroshi; Nozawa, Masafumi; Ikeo, Kazuho; Gojobori, Takashi

2016-01-01

Endosymbiosis is an important evolutionary event for organisms, and there is widespread interest in understanding the evolution of endosymbiosis establishment. Hydra is one of the most suitable organisms for studying the evolution of endosymbiosis. Within the genus Hydra, H. viridissima and H. vulgaris show endosymbiosis with green algae. Previous studies suggested that the endosymbiosis in H. vulgaris took place much more recently than that in H. viridissima, noting that the establishment of the interaction between H. vulgaris and its algae is not as stable as in H. viridissima. To investigate the on-going process of endosymbiosis, we first compared growth and tolerance to starvation in symbiotic and aposymbiotic polyps of both species. The results revealed that symbiotic H. viridissima had a higher growth rate and greater tolerance to starvation than aposymbiotic polyps. By contrast, growth of symbiotic H. vulgaris was identical to that of aposymbiotic polyps, and symbiotic H. vulgaris was less tolerant to starvation. Moreover, our gene expression analysis showed a pattern of differential gene expression in H. viridissima similar to that in other endosymbiotically established organisms, and contrary to that observed in H. vulgaris. We also showed that H. viridissima could cope with oxidative stress that caused damage, such as cell death, in H. vulgaris. These observations support the idea that oxidative stress related genes play an important role in the on-going process of endosymbiosis evolution. The different evolutionary stages of endosymbiosis studied here provide a deeper insight into the evolutionary processes occurring toward a stable endosymbiosis.

[Metazoan parasites of Micropterus salmoides (Centrarchidae: Perciformes) from reservoirs of Nuevo León, México and their association with condition factor and gender].

Science.gov (United States)

Galaviz S, Lucio; Escobar G, Baldemar; Iruegas B, Francisco Javier; Molina, Zinnia Judith

2016-06-01

The largemouth bass Micropterus salmoides is a very valuable fish species for aquaculture and sport fishing; however, there are no systematic studies on fish metazoan parasites in Mexico. The main objective of the present study was to describe the prevalence, abundance, and intensity of M. salmoides metazoan parasites, and their association with fish condition factor and gender. The sample size was composed by 672 hosts, collected between 2011-2013 from the following reservoirs of Nuevo Leon, México: Rodrigo Gómez dam (“La Boca”, LB), Cuchillo-Solidaridad dam (CS), Salinillas lagoon (LS), Mariano Escobedo dam (“Sombreretillo”, S), and José López Portillo dam (“Cerro Prieto”, CP). Living fish were transported to the laboratory; sizes and weights were then recorded to calculate the Fulton condition factor (k). If possible, gender was also recorded. Parasites were detected under stereoscopy, recollected and preserved by traditional techniques. Statistical analysis of association between parasitic load, gender, and Fulton condition factor were calculated, using the X2 and the Student-t tests. Results showed that 12 different metazoans were identified, two flukes (Posthodiplostomum minimum centrarchi and Phyllodistomum pearsei), one tapeworm (Proteocephalus ambloplitis), three roundworms (Contracaecum sp., Spinitectus carolini and Philometra nodulosa), two acantocephalan (Neoechinorhynchus cylindratus and Arhythmorhynchus sp.), one leech (Myzobdella moorei), and three copepods (Ergasilus versicolor; Ergasilus arthrosis and Ergasilus cerastes). HSD Tukey test showed that infected fish from LB were significantly different than LS, CS, CP, and S (PParasites most commonly collected in all five locations were P. m. centrarchi, Contracaecum sp. and E. versicolor. The frequency of P. m. centrarchi was highly significant (Pparasites; furthermore, this parasite showed the highest prevalence (97.5 %), abundance (10.12-83.6), and intensity (15.44-88.5). Statistical

Reconsidering regeneration in metazoans: an evo-devo approach

Directory of Open Access Journals (Sweden)

Stefano eTiozzo

2015-06-01

Full Text Available Regeneration of body structures is an ability widely but unevenly distributed amongst the animal kingdom. Understanding regenerative biology in metazoans means understanding the multiplicity of the cellular and molecular mechanisms that lead to the differentiation, morphogenesis and ultimately the development of a particular regenerating unit. In this manuscript we critically assess the evolutionary considerations suggesting that regeneration is an ancestral trait rather than a mechanism independently evolved in different taxa. As a general method to test evolutionary hypothesis on regeneration, we propose mechanistically dissecting the regenerative processes according to its conserved chronological steps: wound healing, mobilization of cell precursors and morphogenesis. We then suggest interpreting regenerative biology from an evo-devo perspective, proposing a possible theoretical framework and experimental approaches without necessarily invoking a common origin or only multiple losses of regenerative capabilities.

2'-phosphodiesterase and 2',5'-oligoadenylate synthetase activities in the lowest metazoans, sponge [porifera

DEFF Research Database (Denmark)

Saby, Emilie; Poulsen, Jesper Buchhave; Justesen, Just

2009-01-01

Sponges [porifera], the most ancient metazoans, contain modules related to the vertebrate immune system, including the 2′,5′-oligoadenylate synthetase (OAS). The components of the antiviral 2′,5′-oligoadenylate (2–5A) system (OAS, 2′-Phosphodiesterase (2′-PDE) and RNAse L) of vertebrates have...... not all been identified in sponges. Here, we demonstrate for the first time that in addition to the OAS activity, sponges possess a 2′-PDE activity, which highlights the probable existence of a premature 2–5A system. Indeed, Suberites domuncula and Crella elegans exhibited this 2–5A degrading activity....... Upon this finding, two out of three elements forming the 2–5A system have been found in sponges, only a endoribonuclease, RNAse L or similar, has to be found. We suspect the existence of a complex immune system in sponges, besides the self/non-self recognition system and the use of phagocytosis...

2'-phosphodiesterase and 2',5'-oligoadenylate synthetase activities in the lowest metazoans, sponge [porifera].

Science.gov (United States)

Saby, Emilie; Poulsen, Jesper Buchhave; Justesen, Just; Kelve, Merike; Uriz, Maria Jesus

2009-01-01

Sponges [porifera], the most ancient metazoans, contain modules related to the vertebrate immune system, including the 2',5'-oligoadenylate synthetase (OAS). The components of the antiviral 2',5'-oligoadenylate (2-5A) system (OAS, 2'-Phosphodiesterase (2'-PDE) and RNAse L) of vertebrates have not all been identified in sponges. Here, we demonstrate for the first time that in addition to the OAS activity, sponges possess a 2'-PDE activity, which highlights the probable existence of a premature 2-5A system. Indeed, Suberites domuncula and Crella elegans exhibited this 2-5A degrading activity. Upon this finding, two out of three elements forming the 2-5A system have been found in sponges, only a endoribonuclease, RNAse L or similar, has to be found. We suspect the existence of a complex immune system in sponges, besides the self/non-self recognition system and the use of phagocytosis and secondary metabolites against pathogens.

BAYESIAN ANALYSIS TO IDENTIFY NEW STAR CANDIDATES IN NEARBY YOUNG STELLAR KINEMATIC GROUPS

International Nuclear Information System (INIS)

Malo, Lison; Doyon, René; Lafrenière, David; Artigau, Étienne; Gagné, Jonathan; Baron, Frédérique; Riedel, Adric

2013-01-01

We present a new method based on a Bayesian analysis to identify new members of nearby young kinematic groups. The analysis minimally takes into account the position, proper motion, magnitude, and color of a star, but other observables can be readily added (e.g., radial velocity, distance). We use this method to find new young low-mass stars in the β Pictoris and AB Doradus moving groups and in the TW Hydrae, Tucana-Horologium, Columba, Carina, and Argus associations. Starting from a sample of 758 mid-K to mid-M (K5V-M5V) stars showing youth indicators such as Hα and X-ray emission, our analysis yields 214 new highly probable low-mass members of the kinematic groups analyzed. One is in TW Hydrae, 37 in β Pictoris, 17 in Tucana-Horologium, 20 in Columba, 6 in Carina, 50 in Argus, 32 in AB Doradus, and the remaining 51 candidates are likely young but have an ambiguous membership to more than one association. The false alarm rate for new candidates is estimated to be 5% for β Pictoris and TW Hydrae, 10% for Tucana-Horologium, Columba, Carina, and Argus, and 14% for AB Doradus. Our analysis confirms the membership of 58 stars proposed in the literature. Firm membership confirmation of our new candidates will require measurement of their radial velocity (predicted by our analysis), parallax, and lithium 6708 Å equivalent width. We have initiated these follow-up observations for a number of candidates, and we have identified two stars (2MASSJ01112542+1526214, 2MASSJ05241914-1601153) as very strong candidate members of the β Pictoris moving group and one strong candidate member (2MASSJ05332558-5117131) of the Tucana-Horologium association; these three stars have radial velocity measurements confirming their membership and lithium detections consistent with young age.

Hydra II: A Faint and Compact Milky Way Dwarf Galaxy Found in the Survey of the Magellanic Stellar History

NARCIS (Netherlands)

Martin, Nicolas F.; Nidever, David L.; Besla, Gurtina; Olsen, Knut; Walker, Alistair R.; Vivas, A. Katherina; Gruendl, Robert A.; Kaleida, Catherine C.; Muñoz, Ricardo R.; Blum, Robert D.; Saha, Abhijit; Conn, Blair C.; Bell, Eric F.; Chu, You-Hua; Cioni, Maria-Rosa L.; de Boer, Thomas J. L.; Gallart, Carme; Jin, Shoko; Kunder, Andrea; Majewski, Steven R.; Martinez-Delgado, David; Monachesi, Antonela; Monelli, Matteo; Monteagudo, Lara; Noël, Noelia E. D.; Olszewski, Edward W.; Stringfellow, Guy S.; van der Marel, Roeland P.; Zaritsky, Dennis

We present the discovery of a new dwarf galaxy, Hydra II, found serendipitously within the data from the ongoing Survey of the Magellanic Stellar History conducted with the Dark Energy Camera on the Blanco 4 m Telescope. The new satellite is compact ({{r}h}=68 ± 11 pc) and faint ({{M}V}=-4.8 ± 0.3),

The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation

OpenAIRE

Malik, Sohail; Roeder, Robert G.

2010-01-01

The Mediator is an evolutionarily conserved, multiprotein complex that is a key regulator of protein-coding genes. In metazoan cells, multiple pathways that are responsible for homeostasis, cell growth and differentiation converge on the Mediator through transcriptional activators and repressors that target one or more of the almost 30 subunits of this complex. Besides interacting directly with RNA polymerase II, Mediator has multiple functions and can interact with and coordinate the action ...

A Multi-Year Plan for Enhancing Turbulence Modeling in Hydra-TH Revised and Updated Version 2.0

Energy Technology Data Exchange (ETDEWEB)

Smith, Thomas M. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Berndt, Markus [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Baglietto, Emilio [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Magolan, Ben [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

2015-10-01

The purpose of this report is to document a multi-year plan for enhancing turbulence modeling in Hydra-TH for the Consortium for Advanced Simulation of Light Water Reactors (CASL) program. Hydra-TH is being developed to the meet the high- fidelity, high-Reynolds number CFD based thermal hydraulic simulation needs of the program. This work is being conducted within the thermal hydraulics methods (THM) focus area. This report is an extension of THM CASL milestone L3:THM.CFD.P10.02 [33] (March, 2015) and picks up where it left off. It will also serve to meet the requirements of CASL THM level three milestone, L3:THM.CFD.P11.04, scheduled for completion September 30, 2015. The objectives of this plan will be met by: maturation of recently added turbulence models, strategic design/development of new models and systematic and rigorous testing of existing and new models and model extensions. While multi-phase turbulent flow simulations are important to the program, only single-phase modeling will be considered in this report. Large Eddy Simulation (LES) is also an important modeling methodology. However, at least in the first year, the focus is on steady-state Reynolds Averaged Navier-Stokes (RANS) turbulence modeling.

Advances in HYDRA and its applications to simulations of inertial confinement fusion targets

Directory of Open Access Journals (Sweden)

Marinak M.M.

2013-11-01

Full Text Available A new set of capabilities has been implemented in the HYDRA 2D/3D multiphysics inertial confinement fusion simulation code. These include a Monte Carlo particle transport library. It models transport of neutrons, gamma rays and light ions, as well as products they generate from nuclear and coulomb collisions. It allows accurate simulations of nuclear diagnostic signatures from capsule implosions. We apply it to here in a 3D simulation of a National Ignition Facility (NIF ignition capsule which models the full capsule solid angle. This simulation contains a severely rough ablator perturbation and provides diagnostics signatures of capsule failure due to excessive instability growth.

The evolutionary portrait of metazoan NAD salvage.

Directory of Open Access Journals (Sweden)

João Carneiro

Full Text Available Nicotinamide Adenine Dinucleotide (NAD levels are essential for cellular homeostasis and survival. Main sources of intracellular NAD are the salvage pathways from nicotinamide, where Nicotinamide phosphoribosyltransferases (NAMPTs and Nicotinamidases (PNCs have a key role. NAMPTs and PNCs are important in aging, infection and disease conditions such as diabetes and cancer. These enzymes have been considered redundant since either one or the other exists in each individual genome. The co-occurrence of NAMPT and PNC was only recently detected in invertebrates though no structural or functional characterization exists for them. Here, using expression and evolutionary analysis combined with homology modeling and protein-ligand docking, we show that both genes are expressed simultaneously in key species of major invertebrate branches and emphasize sequence and structural conservation patterns in metazoan NAMPT and PNC homologues. The results anticipate that NAMPTs and PNCs are simultaneously active, raising the possibility that NAD salvage pathways are not redundant as both are maintained to fulfill the requirement for NAD production in some species.

Potential interactions between metazoan parasites of the Mayan catfish Ariopsis assimilis and chemical pollution in Chetumal Bay, Mexico.

Science.gov (United States)

Vidal-Martínez, V M; Aguirre-Macedo, M L; Noreña-Barroso, E; Gold-Bouchot, G; Caballero-Pinzón, P I

2003-06-01

The effect of pollutants on the intensity of infection of metazoan parasites in the Mayan catfish, Ariopsis assimilis was investigated. Data were collected on pollutants and metazoan parasites from 76 catfish from five localities in Chetumal Bay in October, 1996. Nineteen pollutants (pesticides, polychlorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs)) were found in the catfish livers. Heavy metal content was not determined. Nineteen metazoan parasite species were recovered. After controlling for fish length and sampling station, there was a significant negative linear relationship between the intensity of the larval digenean Mesostephanus appendiculatoides and 1,1,1,-trichloro-2,2-bis (4-chlorophenyl) ethane (DDT) concentrations. This negative relationship may be explained either by the effect of the pesticide on the mortality of (i) free-living larval forms, (ii) metacercariae in the fish, (iii) infected fish or (iv) intermediate host snails. There were significant differences between fish parasitized and not parasitized with M. appendiculatoides with respect to their DDT concentrations. There were also significant differences between the variances of the mean Clark's coefficient of condition values between catfish parasitized and not parasitized by M. appendiculatoides, with the variance of non-parasitized catfish being significantly larger. The results provided statistical evidence that DDT has a detrimental effect on M. appendiculatoides infection intensity. Furthermore, the significantly larger variance value of Clark's coefficient for non-parasitized fish suggested that DDT affects both the parasite and general host condition.

The backbone of the post-synaptic density originated in a unicellular ancestor of choanoflagellates and metazoans

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Manuel Michaël

2010-02-01

Full Text Available Abstract Background Comparative genomics of the early diverging metazoan lineages and of their unicellular sister-groups opens new window to reconstructing the genetic changes which preceded or accompanied the evolution of multicellular body plans. A recent analysis found that the genome of the nerve-less sponges encodes the homologues of most vertebrate post-synaptic proteins. In vertebrate excitatory synapses, these proteins assemble to form the post-synaptic density, a complex molecular platform linking membrane receptors, components of their signalling pathways, and the cytoskeleton. Newly available genomes from Monosiga brevicollis (a member of Choanoflagellata, the closest unicellular relatives of animals and Trichoplax adhaerens (a member of Placozoa: besides sponges, the only nerve-less metazoans offer an opportunity to refine our understanding of post-synaptic protein evolution. Results Searches for orthologous proteins and reconstruction of gene gains/losses based on the taxon phylogeny indicate that post-synaptic proteins originated in two main steps. The backbone scaffold proteins (Shank, Homer, DLG and some of their partners were acquired in a unicellular ancestor of choanoflagellates and metazoans. A substantial additional set appeared in an exclusive ancestor of the Metazoa. The placozoan genome contains most post-synaptic genes but lacks some of them. Notably, the master-scaffold protein Shank might have been lost secondarily in the placozoan lineage. Conclusions The time of origination of most post-synaptic proteins was not concomitant with the acquisition of synapses or neural-like cells. The backbone of the scaffold emerged in a unicellular context and was probably not involved in cell-cell communication. Based on the reconstructed protein composition and potential interactions, its ancestral function could have been to link calcium signalling and cytoskeleton regulation. The complex later became integrated into the evolving

A Rough Guide to Metabolite Identification Using High Resolution Liquid Chromatography Mass Spectrometry in Metabolomic Profiling in Metazoans

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David G Watson

2013-01-01

Full Text Available Compound identification in mass spectrometry based metabolomics can be a problem but sometimes the problem seems to be presented in an over complicated way. The current review focuses on metazoans where the range of metabolites is more restricted than for example in plants. The focus is on liquid chromatography with high resolution mass spectrometry where it is proposed that most of the problems in compound identification relate to structural isomers rather than to isobaric compounds. Thus many of the problems faced relate to separation of isomers, which is usually required even if fragmentation is used to support structural identification. Many papers report the use of MS/MS or MS2 as an adjunct to the identification of known metabolites but there a few examples in metabolomics studies of metazoans of complete structure elucidation of novel metabolites or metabolites where no authentic standards are available for comparison.

3D integrated HYDRA simulations of hohlraums including fill tubes

Science.gov (United States)

Marinak, M. M.; Milovich, J.; Hammel, B. A.; Macphee, A. G.; Smalyuk, V. A.; Kerbel, G. D.; Sepke, S.; Patel, M. V.

2017-10-01

Measurements of fill tube perturbations from hydro growth radiography (HGR) experiments on the National Ignition Facility show spoke perturbations in the ablator radiating from the base of the tube. These correspond to the shadow of the 10 μm diameter glass fill tube cast by hot spots at early time. We present 3D integrated HYDRA simulations of these experiments which include the fill tube. Meshing techniques are described which were employed to resolve the fill tube structure and associated perturbations in the simulations. We examine the extent to which the specific illumination geometry necessary to accommodate a backlighter in the HGR experiment contributes to the spoke pattern. Simulations presented include high resolution calculations run on the Trinity machine operated by the Alliance for Computing at Extreme Scale (ACES) partnership. This work was performed under the auspices of the Lawrence Livermore National Security, LLC, (LLNS) under Contract No. DE-AC52-07NA27344.

Tests of experimental fuel elements by the method of nuclear-thermal pulse loadings in 'HYDRA' reactor

International Nuclear Information System (INIS)

Nastoyashchaya, O.V.; Lebedev, Yu. M.; Chechurov, A.M.; Khvostionov, Ye

1997-01-01

The results of tests of experimental fuel elements with uranium dioxide fuel composition embedded in Al and Zr matrix with the enrichment from 90% to 36% in respect to U-235 performed at the pulse 'HYDRA' reactor are presented in this paper. Testing is performed in the frame-work of extensive research program studying the behavior of fuel elements (FE) of research and mini nuclear power systems in case of practically immediate energy release in the fuel taking place during the RIA-type accidents. Duration of the neutron pulse when testing in 'HYDRA' reactor is from 7 to 20 ms. The methods of diagnostics of the state of FE prior to and after testing in the reactor are developed and verified. Mathematical model describing temperature fields inside the FE in the process of testing. and accounting for non-uniformity of fuel composition has been developed in order to summarize experimental results. Experimental data on the limiting values of the energy density leading to deformation and degradation of FE depending on the type of fuel composition have been obtained and the mechanisms for the development of these processes have been determined. The nature of physical-chemical processes taking place in the fuel composition and fuel cladding depending on material composition under different levels of energy deposition is demonstrated. The data on hydrogen generation and radioactive product release out of fuel after failure of FE are presented. (author)

Drosophila protein interaction map (DPiM): a paradigm for metazoan protein complex interactions.

Science.gov (United States)

Guruharsha, K G; Obar, Robert A; Mintseris, Julian; Aishwarya, K; Krishnan, R T; Vijayraghavan, K; Artavanis-Tsakonas, Spyros

2012-01-01

Proteins perform essential cellular functions as part of protein complexes, often in conjunction with RNA, DNA, metabolites and other small molecules. The genome encodes thousands of proteins but not all of them are expressed in every cell type; and expressed proteins are not active at all times. Such diversity of protein expression and function accounts for the level of biological intricacy seen in nature. Defining protein-protein interactions in protein complexes, and establishing the when, what and where of potential interactions, is therefore crucial to understanding the cellular function of any protein-especially those that have not been well studied by traditional molecular genetic approaches. We generated a large-scale resource of affinity-tagged expression-ready clones and used co-affinity purification combined with tandem mass-spectrometry to identify protein partners of nearly 5,000 Drosophila melanogaster proteins. The resulting protein complex "map" provided a blueprint of metazoan protein complex organization. Here we describe how the map has provided valuable insights into protein function in addition to generating hundreds of testable hypotheses. We also discuss recent technological advancements that will be critical in addressing the next generation of questions arising from the map.

Cyclic [G(2′,5′)pA(3′,5′)p] Is the Metazoan Second Messenger Produced by DNA-Activated Cyclic GMP-AMP Synthase

Science.gov (United States)

Gao, Pu; Ascano, Manuel; Wu, Yang; Barchet, Winfried; Gaffney, Barbara L.; Zillinger, Thomas; Serganov, Artem A.; Liu, Yizhou; Jones, Roger A.; Hartmann, Gunther; Tuschl, Thomas; Patel, Dinshaw J.

2015-01-01

SUMMARY Recent studies identified cyclic GMP-AMP (cGAMP) as a metazoan second messenger triggering an interferon response. cGAMP is generated from GTP and ATP by cytoplasmic dsDNA sensor cGAMP synthase (cGAS). We combined structural, chemical, biochemical, and cellular assays to demonstrate that this second messenger contains G(2′,5′)pA and A(3′,5′)pG phosphodiester linkages, designated c[G(2′,5′) pA(3′,5′)p]. We show that, upon dsDNA binding, cGAS is activated through conformational transitions, resulting in formation of a catalytically competent and accessible nucleotide-binding pocket for generation of c[G(2′,5′)pA(3′,5′)p]. We demonstrate that cyclization occurs in a stepwise manner through initial generation of 5′-pppG(2′,5′)pA prior to cyclization to c[G(2′,5′)pA(3′,5′)p], with the latter positioned precisely in the catalytic pocket. Mutants of cGAS dsDNA-binding or catalytic pocket residues exhibit reduced or abrogated activity. Our studies have identified c[G(2′,5′)pA(3′,5′)p] as a founding member of a family of metazoan 2′,5′-containing cyclic heterodinucleotide second messengers distinct from bacterial 3′,5′ cyclic dinucleotides. PMID:23647843

Metazoan parasite infracommunities of Florida pompano (Trachinotus carolinus) from the coast of the Yucatan Peninsula, Mexico.

Science.gov (United States)

Sánchez-Ramírez, Claudia; Vidal-Martínez, Victor M

2002-12-01

Metazoan parasite infracommunities of the Florida pompano (Trachinotus carolinus) were studied in terms of species composition, species richness, diversity, numerical dominance, and similarity. Seventy-five fishes were collected from 4 localities along the Yucatan Peninsula coast and 24 parasite species recovered. Most were digeneans (8 species) and nematodes (7). Other species were monogeneans (3). aspidogastreans (2), cestodes (1), acanthocephalans (1), and crustaceans (2). Only 4 species were common in at least I locality. Mean values for species richness, abundance, diversity, numerical dominance, and similarity in total (all species in the individual fish), gastrointestinal, and ectoparasite infracommunities were within ranges observed for most helminth infracommunities of marine fishes from temperate and tropical latitudes. These infracommunities had low species richness, abundance, diversity, and predictability (except ectoparasite infracommunities) and high dominance. Within the predictable element (common species), the specialist monogenean Pseudobicotylophora atlantica was the main reason for the increase in predictability because it was the only common species at all 4 localities. Host feeding habits, the distribution of intermediate hosts and infective stages, the local species pool, and a phylogenetic component seem to be determining the characteristics of these metazoan parasite infracommunities.

The tubulins of animals, plants, fungi and protists implications for metazoan evolution

Science.gov (United States)

Little, Melvyn; Ludueña, Richard F.; Morejohn, Louis C.; Asnes, Clara; Hoffman, Eugene

1984-03-01

α-Tubulin subunits from trout (S. gairdneri) sperm tails, sea urchin (S. purpuratus) cilia, protistan alga (C. elongatum) flagella and rose (Paul's Scarlet) cytoplasm have been characterized by limited proteolytic cleavage with the enzymeStaphylococcus aureus protease and electrophoresis of the digestion products on SDS-PAGE. The resulting patterns corresponded to either of two major types representative of animal and non-animal α-tubulins, respectively. A total of 28 α-tubulins have now been characterized by this method. They are classified in this paper according to the type of cleavage pattern generated by the enzymeS. aureus protease. The implications of these results for metazoan evolution are discussed.

Toxicity of water and sediment from stormwater retarding basins to Hydra hexactinella

DEFF Research Database (Denmark)

Rosenkrantz, Rikke Tjørnhøj; Pollino, Carmel A.; Nugegoda, Dayanthi

2008-01-01

of 50 ml/L and 100 ml/L, while the 7 h pulse exposure caused a significant increase in the mean population growth rate compared to the control. Water samples from the two other retarding basins were found non-toxic to H. hexactinella. This is the first study to employ sediment tests with Hydra spp....... on stormwater sediments and a lower population growth rate was observed for organisms exposed to sediment from the Avoca St retarding basins. The behavioral study showed that H. hexactinella tended to avoid the sediment-water interface when exposed to sediment from all retarding basins, compared...... to the reference sediment. Further work is needed to determine the long-term effects of stormwater polluted sediments and acute effects due to organism exposure to short-term high concentrations during rain events. (C) 2008 Elsevier Ltd. All rights reserved....

Reassessing Domain Architecture Evolution of Metazoan Proteins: The Contribution of Different Evolutionary Mechanisms

Directory of Open Access Journals (Sweden)

Laszlo Patthy

2011-08-01

Full Text Available In the accompanying papers we have shown that sequence errors of public databases and confusion of paralogs and epaktologs (proteins that are related only through the independent acquisition of the same domain types significantly distort the picture that emerges from comparison of the domain architecture (DA of multidomain Metazoan proteins since they introduce a strong bias in favor of terminal over internal DA change. The issue of whether terminal or internal DA changes occur with greater probability has very important implications for the DA evolution of multidomain proteins since gene fusion can add domains only at terminal positions, whereas domain-shuffling is capable of inserting domains both at internal and terminal positions. As a corollary, overestimation of terminal DA changes may be misinterpreted as evidence for a dominant role of gene fusion in DA evolution. In this manuscript we show that in several recent studies of DA evolution of Metazoa the authors used databases that are significantly contaminated with incomplete, abnormal and mispredicted sequences (e.g., UniProtKB/TrEMBL, EnsEMBL and/or the authors failed to separate paralogs and epaktologs, explaining why these studies concluded that the major mechanism for gains of new domains in metazoan proteins is gene fusion. In contrast with the latter conclusion, our studies on high quality orthologous and paralogous Swiss-Prot sequences confirm that shuffling of mobile domains had a major role in the evolution of multidomain proteins of Metazoa and especially those formed in early vertebrates.

Metazoan endoparasites of Pygocentrus nattereri (Characiformes: Serrasalminae in the Negro River, Pantanal, Brazil

Directory of Open Access Journals (Sweden)

Wagner Vicentin

Full Text Available In the period of October 2007 to August 2008, 152 specimens ofPygocentrus nattereri were caught in the Negro River in the Nhecolândia region, central Pantanal wetland, State of Mato Grosso do Sul, Brazil. The specimens were necropsied and a total of 4,212 metazoan endoparasites were recovered, belonging to 10 taxons:Procamallanus (Spirocamallanusinopinatus, Philometridae gen. sp.,Eustrongylides sp., Brevimulticaecum sp.,Contracaecum sp. (Nematoda, Echinorhynchus paranensis (Acanthocephala, Leiperia gracile,Sebekia oxycephala, Subtriquetra sp. 1 andSubtriquetra sp. 2 (Pentastomida. This is the first record of two parasite species from P. nattereri: E. paranensis and L. gracile.

Taxonomy and ecology of metazoan parasites of otariids from Patagonia, Argentina : adult and infective stages

OpenAIRE

Hernández Orts, Jesús Servando

2013-01-01

At present, the metazoan parasite fauna of most species of otariids is generally poorly known, in part because these marine mammals are mostly protected and, therefore, sampling is limited to specimens stranded on the coast or captured as by-catch in fisheries. Similar problems also occur for the larval stages of gastrointestinal helminths of otariids. For most of these parasite species, the specific identity of the intermediate/paratenic of hosts is unknown and, therefore, many stages of the...

Gene duplication and neo-functionalization in the evolutionary and functional divergence of the metazoan copper transporters Ctr1 and Ctr2.

Science.gov (United States)

Logeman, Brandon L; Wood, L Kent; Lee, Jaekwon; Thiele, Dennis J

2017-07-07

Copper is an essential element for proper organismal development and is involved in a range of processes, including oxidative phosphorylation, neuropeptide biogenesis, and connective tissue maturation. The copper transporter (Ctr) family of integral membrane proteins is ubiquitously found in eukaryotes and mediates the high-affinity transport of Cu + across both the plasma membrane and endomembranes. Although mammalian Ctr1 functions as a Cu + transporter for Cu acquisition and is essential for embryonic development, a homologous protein, Ctr2, has been proposed to function as a low-affinity Cu transporter, a lysosomal Cu exporter, or a regulator of Ctr1 activity, but its functional and evolutionary relationship to Ctr1 is unclear. Here we report a biochemical, genetic, and phylogenetic comparison of metazoan Ctr1 and Ctr2, suggesting that Ctr2 arose over 550 million years ago as a result of a gene duplication event followed by loss of Cu + transport activity. Using a random mutagenesis and growth selection approach, we identified amino acid substitutions in human and mouse Ctr2 proteins that support copper-dependent growth in yeast and enhance copper accumulation in Ctr1 -/- mouse embryonic fibroblasts. These mutations revert Ctr2 to a more ancestral Ctr1-like state while maintaining endogenous functions, such as stimulating Ctr1 cleavage. We suggest key structural aspects of metazoan Ctr1 and Ctr2 that discriminate between their biological roles, providing mechanistic insights into the evolutionary, biochemical, and functional relationships between these two related proteins. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Performance of single and concatenated sets of mitochondrial genes at inferring metazoan relationships relative to full mitogenome data.

Directory of Open Access Journals (Sweden)

Justin C Havird

Full Text Available Mitochondrial (mt genes are some of the most popular and widely-utilized genetic loci in phylogenetic studies of metazoan taxa. However, their linked nature has raised questions on whether using the entire mitogenome for phylogenetics is overkill (at best or pseudoreplication (at worst. Moreover, no studies have addressed the comparative phylogenetic utility of mitochondrial genes across individual lineages within the entire Metazoa. To comment on the phylogenetic utility of individual mt genes as well as concatenated subsets of genes, we analyzed mitogenomic data from 1865 metazoan taxa in 372 separate lineages spanning genera to subphyla. Specifically, phylogenies inferred from these datasets were statistically compared to ones generated from all 13 mt protein-coding (PC genes (i.e., the "supergene" set to determine which single genes performed "best" at, and the minimum number of genes required to, recover the "supergene" topology. Surprisingly, the popular marker COX1 performed poorest, while ND5, ND4, and ND2 were most likely to reproduce the "supergene" topology. Averaged across all lineages, the longest ∼2 mt PC genes were sufficient to recreate the "supergene" topology, although this average increased to ∼5 genes for datasets with 40 or more taxa. Furthermore, concatenation of the three "best" performing mt PC genes outperformed that of the three longest mt PC genes (i.e, ND5, COX1, and ND4. Taken together, while not all mt PC genes are equally interchangeable in phylogenetic studies of the metazoans, some subset can serve as a proxy for the 13 mt PC genes. However, the exact number and identity of these genes is specific to the lineage in question and cannot be applied indiscriminately across the Metazoa.

HYDRA: Revealing heterogeneity of imaging and genetic patterns through a multiple max-margin discriminative analysis framework.

Science.gov (United States)

Varol, Erdem; Sotiras, Aristeidis; Davatzikos, Christos

2017-01-15

Multivariate pattern analysis techniques have been increasingly used over the past decade to derive highly sensitive and specific biomarkers of diseases on an individual basis. The driving assumption behind the vast majority of the existing methodologies is that a single imaging pattern can distinguish between healthy and diseased populations, or between two subgroups of patients (e.g., progressors vs. non-progressors). This assumption effectively ignores the ample evidence for the heterogeneous nature of brain diseases. Neurodegenerative, neuropsychiatric and neurodevelopmental disorders are largely characterized by high clinical heterogeneity, which likely stems in part from underlying neuroanatomical heterogeneity of various pathologies. Detecting and characterizing heterogeneity may deepen our understanding of disease mechanisms and lead to patient-specific treatments. However, few approaches tackle disease subtype discovery in a principled machine learning framework. To address this challenge, we present a novel non-linear learning algorithm for simultaneous binary classification and subtype identification, termed HYDRA (Heterogeneity through Discriminative Analysis). Neuroanatomical subtypes are effectively captured by multiple linear hyperplanes, which form a convex polytope that separates two groups (e.g., healthy controls from pathologic samples); each face of this polytope effectively defines a disease subtype. We validated HYDRA on simulated and clinical data. In the latter case, we applied the proposed method independently to the imaging and genetic datasets of the Alzheimer's Disease Neuroimaging Initiative (ADNI 1) study. The imaging dataset consisted of T1-weighted volumetric magnetic resonance images of 123 AD patients and 177 controls. The genetic dataset consisted of single nucleotide polymorphism information of 103 AD patients and 139 controls. We identified 3 reproducible subtypes of atrophy in AD relative to controls: (1) diffuse and extensive

A Permian methane seep system as a paleoenvironmental analogue for the pre-metazoan carbonate platforms

Directory of Open Access Journals (Sweden)

Lucas Veríssimo Warren

Full Text Available ABSTRACT: Following the rise of metazoans, the beginning of bioclasticity and substrate competition, the saga of microbial mats was in a fluctuating decline in the end of the Neoproterozoic era. Increases in diversity during the Phanerozoic and punctual upturns in the microbial carbonate production occured after the events of global mass extinctions. Gradually along the Phanerozoic, the microbial colonies occupied isolated niches and grazers-free environments, characterized by physically and/or geochemically stressful conditions, such as those found in saline bays, alkaline lakes and hydrothermal or cold seep vents. Here we report one of the oldest occurrences of a vent camp coupled with cold seepage of methane in the geologic record, associated with well-preserved microbialites and elephant skin structures. During the seep activity, oxygen depletion and high salinity conditions are prohibitive for complex animal life, clearing the way to microbial colonies to flourish. Due to the co-occurrence of high adaptability and low competitiveness of microbial forms, they became highly specialized in stressful conditions. We argue that the sporadic microbial mat upturns in Earth’s history are not restricted to geological periods, following massive death of metazoan species; they also may occur in response to punctual paleoenvironmental conditions that enable microbial colonies to growth. Indeed, the Phanerozoic geological record is punctuated of these examples, in a kind of hide-and-seek game of Precambrian times.

Conservation and diversification of Msx protein in metazoan evolution.

Science.gov (United States)

Takahashi, Hirokazu; Kamiya, Akiko; Ishiguro, Akira; Suzuki, Atsushi C; Saitou, Naruya; Toyoda, Atsushi; Aruga, Jun

2008-01-01

Msx (/msh) family genes encode homeodomain (HD) proteins that control ontogeny in many animal species. We compared the structures of Msx genes from a wide range of Metazoa (Porifera, Cnidaria, Nematoda, Arthropoda, Tardigrada, Platyhelminthes, Mollusca, Brachiopoda, Annelida, Echiura, Echinodermata, Hemichordata, and Chordata) to gain an understanding of the role of these genes in phylogeny. Exon-intron boundary analysis suggested that the position of the intron located N-terminally to the HDs was widely conserved in all the genes examined, including those of cnidarians. Amino acid (aa) sequence comparison revealed 3 new evolutionarily conserved domains, as well as very strong conservation of the HDs. Two of the three domains were associated with Groucho-like protein binding in both a vertebrate and a cnidarian Msx homolog, suggesting that the interaction between Groucho-like proteins and Msx proteins was established in eumetazoan ancestors. Pairwise comparison among the collected HDs and their C-flanking aa sequences revealed that the degree of sequence conservation varied depending on the animal taxa from which the sequences were derived. Highly conserved Msx genes were identified in the Vertebrata, Cephalochordata, Hemichordata, Echinodermata, Mollusca, Brachiopoda, and Anthozoa. The wide distribution of the conserved sequences in the animal phylogenetic tree suggested that metazoan ancestors had already acquired a set of conserved domains of the current Msx family genes. Interestingly, although strongly conserved sequences were recovered from the Vertebrata, Cephalochordata, and Anthozoa, the sequences from the Urochordata and Hydrozoa showed weak conservation. Because the Vertebrata-Cephalochordata-Urochordata and Anthozoa-Hydrozoa represent sister groups in the Chordata and Cnidaria, respectively, Msx sequence diversification may have occurred differentially in the course of evolution. We speculate that selective loss of the conserved domains in Msx family

557 GHz Observations of Water Vapor Outflow from VY Canis Majoris and W Hydrae

Science.gov (United States)

Harwit, Martin; Bergin, Edwin A.

2002-02-01

We report the first detection of thermal water vapor emission in the 557 GHz, 110-101 ground-state transition of ortho-H2O toward VY Canis Majoris. In observations obtained with the Submillimeter Wave Astronomy Satellite, we measured a flux of ~450 Jy, in a spectrally resolved line centered on a velocity vLSR=25 km s-1 with an FWHM of ~35 km s-1, somewhat dependent on the assumed line shape. We analyze the line shape in the context of three different radial outflow models for which we provide analytical expressions. We also detected a weaker 557 GHz emission line from W Hydrae. We find that these and other H2O emission-line strengths scale as suggested by Zubko and Elitzur.

Reduction of low frequency error for SED36 and APS based HYDRA star trackers

Science.gov (United States)

Ouaknine, Julien; Blarre, Ludovic; Oddos-Marcel, Lionel; Montel, Johan; Julio, Jean-Marc

2017-11-01

In the frame of the CNES Pleiades satellite, a reduction of the star tracker low frequency error, which is the most penalizing error for the satellite attitude control, was performed. For that purpose, the SED36 star tracker was developed, with a design based on the flight qualified SED16/26. In this paper, the SED36 main features will be first presented. Then, the reduction process of the low frequency error will be developed, particularly the optimization of the optical distortion calibration. The result is an attitude low frequency error of 1.1" at 3 sigma along transverse axes. The implementation of these improvements to HYDRA, the new multi-head APS star tracker developed by SODERN, will finally be presented.

Cyclic [G(2′,5′)pA(3′,5′)p] Is the Metazoan Second Messenger Produced by DNA-Activated Cyclic GMP-AMP Synthase

OpenAIRE

Gao, Pu; Ascano, Manuel; Wu, Yang; Barchet, Winfried; Gaffney, Barbara L.; Zillinger, Thomas; Serganov, Artem A.; Liu, Yizhou; Jones, Roger A.; Hartmann, Gunther; Tuschl, Thomas; Patel, Dinshaw J.

2013-01-01

Recent studies identified cyclic GMP-AMP (cGAMP) as a metazoan second messenger triggering an interferon response. cGAMP is generated from GTP and ATP by cytoplasmic dsDNA sensor cGAMP synthase (cGAS). We combined structural, chemical, biochemical, and cellular assays to demonstrate that this second messenger contains G(2′,5′)pA and A(3′,5′)pG phosphodiester linkages, designated c[G(2′,5′) pA(3′,5′)p]. We show that, upon dsDNA binding, cGAS is activated through conformational transitions, res...

GTRF Calculations Using Hydra-TH (L3 Milestone THM.CFD.P5.05)

International Nuclear Information System (INIS)

Bakosi, Jozsef; Christon, Mark A.; Francois, Marianne M.; Lowrie, Robert B.; Nourgaliev, Robert

2012-01-01

This report describes the work carried out for completion of the Thermal Hydraulics Methods (THM) Level 3 Milestone THM.CFD.P5.05 for the Consortium for Advanced Simulation of Light Water Reactors (CASL). A series of body-fitted computational meshes have been generated by Numeca's Hexpress/Hybrid, a.k.a. 'Spider', meshing technology for the V5H 3 x 3 and 5 x 5 rod bundle geometries and subsequently used to compute the fluid dynamics of grid-to-rod fretting (GTRF). Spider is easy to use, fast, and automatically generates high-quality meshes for extremely complex geometries, required for the GTRF problem. Hydra-TH has been used to carry out large-eddy simulations on both 3 x 3 and 5 x 5 geometries, using different mesh resolutions. The results analyzed show good agreement with Star-CCM+ simulations and experimental data.

Hydra phantom applicability for carrying out tests of field uniformity in gamma cameras; Aplicabilidade do fantoma hydra para realizacao dos testes de uniformidade de campo em gama camaras

Energy Technology Data Exchange (ETDEWEB)

Aragao Filho, Geraldo L., E-mail: geraldo_lemos10@hotmail.com [Centro de Medicina Nuclear de Pernambuco (CEMUPE), Recife, PE (Brazil); Oliveira, Alex C.H., E-mail: oliveira_ach@yahoo.com [Universidade Federal de Pernambuco (DEN/UFPE), Recife, PE (Brazil). Dept. de Energia Nuclear; Lopes Filho, Ferdinand J.; Vieira, Jose W., E-mail: ferdinand.lopes@oi.com.br, E-mail: jose-wilson59@live.com [Instituto Federal de Pernambuco (IFPE), Recife, PE (Brazil)

2014-07-01

Nuclear Medicine is a medical modality that makes use of radioactive material 'in vivo' in humans, making them a temporary radioactive source. The radiation emitted by the patient's body is detected by a specific equipment, called a gamma camera, creates an image showing the spatial and temporal biodistribution of radioactive material administered to the patient. Therefore, it's of fundamental importance a number of specific measures to make sure that procedure be satisfactory, called quality control. To Nuclear Medicine, quality control of gamma camera has the purpose of ensuring accurate scintillographic imaging, truthful and reliable for the diagnosis, guaranteeing visibility and clarity of details of structures, and also to determine the frequency and the need for preventive maintenance of equipment. To ensure the quality control of the gamma camera it's necessary to use some simulators, called phantom, used in Nuclear Medicine to evaluate system performance, system calibration and simulation of injuries. The goal of this study was to validate a new simulator for nuclear medicine, the Hydra phantom. The phantom was initially built for construction of calibration curves used in radiotherapy planning and quality control in CT. It has similar characteristics to specific phantoms in nuclear medicine, containing inserts and water area. Those inserts are regionally sourced materials, many of them are already used in the literature and based on information about density and interaction of radiation with matter. To verify its efficiency in quality control in Nuclear Medicine, was performed a test for uniformity field, one of the main tests performed daily, so we can verify the ability of the gamma camera to reproduce a uniform distribution of the administered activity in the phantom, been analysed qualitatively, through the image, and quantitatively, through values established for Central Field Of View (CFOV) and Useful Field Of View (UFOV

Metazoan parasites of Plagioscion squamosissimus, an invasive species in the Tietê River, São Paulo, Brazil

Directory of Open Access Journals (Sweden)

Ivan Moura Lapera

Full Text Available Abstract This study focused on the characterization and analysis of communities and infra-communities of metazoan parasites of Plagioscion squamosissimus caught in Promissão Reservoir in the Tietê River in Borborema (21°39′58”S, 49°8′49”W, state of São Paulo, Brazil. Fifty adult specimens caught by professional fishermen in March 2015 were necropsied. The fish presented an average standard length of 25.2 ± 2.2 cm and average weight of 328.82 ± 89.03 g. A total of 5,227 specimens of metazoan parasites were collected: 2,880 (55.1% adult Diplectanum piscinarius (Monogenoidea: Diplectanidae and 2,347 (44.9% Austrodiplostomum compactum metacercariae (Digenea, Diplostomidae, both with 100% prevalence and mean abundance of 57.6 and 46.9, respectively. Parasite diversity was low (species richness = 2, with a Simpson index (D equal to 0.505, and low values of Brillouin (HB = 0.687 and Margalef diversity (I = 0.117 indices. Berger-Parker’s index of dominance (p = 0.551 indicated a slight dominance of the monogenean parasite D. piscinarius. There was a positive correlation, assessed by Pearson coefficient between parasite abundance of D. piscinarius and standard length (r = 0.43 and weight (r = 0.51 of hosts.

The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation.

Science.gov (United States)

Malik, Sohail; Roeder, Robert G

2010-11-01

The Mediator is an evolutionarily conserved, multiprotein complex that is a key regulator of protein-coding genes. In metazoan cells, multiple pathways that are responsible for homeostasis, cell growth and differentiation converge on the Mediator through transcriptional activators and repressors that target one or more of the almost 30 subunits of this complex. Besides interacting directly with RNA polymerase II, Mediator has multiple functions and can interact with and coordinate the action of numerous other co-activators and co-repressors, including those acting at the level of chromatin. These interactions ultimately allow the Mediator to deliver outputs that range from maximal activation of genes to modulation of basal transcription to long-term epigenetic silencing.

GTRF Calculations Using Hydra-TH (L3 Milestone THM.CFD.P5.05)

Energy Technology Data Exchange (ETDEWEB)

Bakosi, Jozsef [Los Alamos National Laboratory; Christon, Mark A. [Los Alamos National Laboratory; Francois, Marianne M. [Los Alamos National Laboratory; Lowrie, Robert B. [Los Alamos National Laboratory; Nourgaliev, Robert [Los Alamos National Laboratory

2012-09-05

This report describes the work carried out for completion of the Thermal Hydraulics Methods (THM) Level 3 Milestone THM.CFD.P5.05 for the Consortium for Advanced Simulation of Light Water Reactors (CASL). A series of body-fitted computational meshes have been generated by Numeca's Hexpress/Hybrid, a.k.a. 'Spider', meshing technology for the V5H 3 x 3 and 5 x 5 rod bundle geometries and subsequently used to compute the fluid dynamics of grid-to-rod fretting (GTRF). Spider is easy to use, fast, and automatically generates high-quality meshes for extremely complex geometries, required for the GTRF problem. Hydra-TH has been used to carry out large-eddy simulations on both 3 x 3 and 5 x 5 geometries, using different mesh resolutions. The results analyzed show good agreement with Star-CCM+ simulations and experimental data.

DISCOVERY OF A DISK GAP CANDIDATE AT 20 AU IN TW HYDRAE

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Akiyama, E.; Kusakabe, N.; Kandori, R. [National Astronomical Observatory of Japan, 2-21-1, Osawa, Mitaka, Tokyo 181-8588 (Japan); Muto, T. [Division of Liberal Arts, Kogakuin University, 1-24-2, Nishi-Shinjuku, Shinjuku-ku, Tokyo 163-8677 (Japan); Kataoka, A.; Kuzuhara, M. [Department of Earth and Planetary Sciences, Tokyo Institute of Technology, 2-12-1, Oklahoma, Ookayama, Meguro-ko, Tokyo 152-8551 (Japan); Hashimoto, J.; Wisniewski, J. [Department of Physics and Astronomy, The University of Oklahoma, 440 W. Brooks Street, Norman, OK 73019 (United States); Tsukagoshi, T. [College of Science, Ibaraki University, 2-1-1, Bunkyo, Mito, Ibaraki 310-8512 (Japan); Kwon, J. [Department of Astronomy, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Kudo, T.; Currie, T. [Subaru Telescope, National Astronomical Observatory of Japan, 650, North A' ohoku Place, Hilo, HI 96720 (United States); Grady, C. A. [Eureka Scientific, 2452 Delmer, Suite 100, Oakland, CA 96002 (United States); Takami, M. [Institute of Astronomy and Astrophysics, Academia Sinica, P.O. Box 23-141, Taipei 10617, Taiwan (China); Janson, M. [Department of Astronomy, Stockholm University, AlbaNova University Center, Stockholm, SE-106 91 (Sweden); Henning, T.; Carson, J. C. [Max Planck Institute for Astronomy, Königstuhl 17, D-69117 Heidelberg (Germany); Sitko, M. L. [Space Science Institute, 4750 Walnut Street, Suite 205, Boulder, CO 80301 (United States); Mayama, S. [The Center for the Promotion of Integrated Sciences, The Graduate University for Advance Studies, Shonan International Village, Hayama-cho, Miura-gun, Kanagawa 240-0115 (Japan); Thalmann, C., E-mail: eiji.akiyama@nao.ac.jp [Institute for Astronomy, ETH Zurich, Wolfgang-Pauli-Strasse 27, CH-8093 Zurich (Switzerland); and others

2015-04-01

We present a new Subaru/HiCIAO high-contrast H-band polarized intensity (PI) image of a nearby transitional disk associated with TW Hydrae. The scattered light from the disk was detected from 0.″ 2 to 1.″ 5 (11–81 AU) and the PI image shows a clear axisymmetric depression in PI at ∼0.″ 4 (∼20 AU) from the central star, similar to the ∼80 AU gap previously reported from Hubble Space Telescope images. The azimuthal PI profile also shows that the disk beyond 0.″ 2 is almost axisymmetric. We discuss two possible scenarios explaining the origin of the PI depression: (1) a gap structure may exist at ∼20 AU from the central star because of a shallow slope seen in the PI profile, and (2) grain growth may be occurring in the inner region of the disk. Multi-band observations at near-infrared and millimeter/submillimeter wavelengths play a complementary role in investigating dust opacity and may help reveal the origin of the gap more precisely.

Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes

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Sadhna Phanse

2016-03-01

Full Text Available Our analysis examines the conservation of multiprotein complexes among metazoa through use of high resolution biochemical fractionation and precision mass spectrometry applied to soluble cell extracts from 5 representative model organisms Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, Strongylocentrotus purpuratus, and Homo sapiens. The interaction network obtained from the data was validated globally in 4 distant species (Xenopus laevis, Nematostella vectensis, Dictyostelium discoideum, Saccharomyces cerevisiae and locally by targeted affinity-purification experiments. Here we provide details of our massive set of supporting biochemical fractionation data available via ProteomeXchange (http://www.ebi.ac.uk/pride/archive/projects/PXD002319-http://www.ebi.ac.uk/pride/archive/projects/PXD002328, PPIs via BioGRID (185267; and interaction network projections via (http://metazoa.med.utoronto.ca made fully accessible to allow further exploration. The datasets here are related to the research article on metazoan macromolecular complexes in Nature [1]. Keywords: Proteomics, Metazoa, Protein complexes, Biochemical, Fractionation

Cambrian archaeocyathan metazoans: revision of morphological characters and standardization of genus descriptions to establish an online identification tool

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Adeline Kerner

2011-11-01

Full Text Available Archaeocyatha represent the oldest calcified sponges and the first metazoans to build bioconstructions in association with calcimicrobes. They are a key group in biology, evolutionary studies, biostratigraphy, paleoecology and paleogeography of the early Cambrian times. The establishing of a new standardized terminology for archaeocyathans description has permitted the creation of the first knowledge base in English including descriptions of all archaeocyathan genera. This base, using the XPER² software package, is an integral part of the -Archaeocyatha- a knowledge base website, freely available at url http://www.infosyslab.fr/archaeocyatha. The website is composed of common information about Archaeocyatha, general remarks about the knowledge base, the description of the 307 genera recognized with images of type-specimens of type-species for each genus, as well as additional morphological data, an interactive free access key and its user guide.The automatic analysis and comparison of the digitized descriptions have identified some genera with highly similar morphology. These results are a great help for future taxonomic revisions and suggest a number of possible synonymies that require further study.

Metazoan parasite species richness in Neotropical fishes: hotspots and the geography of biodiversity.

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Luque, J L; Poulin, R

2007-06-01

Although research on parasite biodiversity has intensified recently, there are signs that parasites remain an underestimated component of total biodiversity in many regions of the planet. To identify geographical hotspots of parasite diversity, we performed qualitative and quantitative analyses of the parasite-host associations in fishes from Latin America and the Caribbean, a region that includes known hotspots of plant and animal biodiversity. The database included 10,904 metazoan parasite-host associations involving 1660 fish species. The number of host species with at least 1 parasite record was less than 10% of the total known fish species in the majority of countries. Associations involving adult endoparasites in actinopterygian fish hosts dominated the database. Across the whole region, no significant difference in parasite species richness was detected between marine and freshwater fishes. As a rule, host body size and study effort (number of studies per fish species) were good predictors of parasite species richness. Some interesting patterns emerged when we included only the regions with highest fish species biodiversity and study effort (Brazil, Mexico and the Caribbean Islands). Independently of differences in study effort or host body sizes, Mexico stands out as a hotspot of parasite diversity for freshwater fishes, as does Brasil for marine fishes. However, among 57 marine fish species common to all 3 regions, populations from the Caribbean consistently harboured more parasite species. These differences may reflect true biological patterns, or regional discrepancies in study effort and local priorities for fish parasitology research.

The Widespread Prevalence and Functional Significance of Silk-Like Structural Proteins in Metazoan Biological Materials.

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Carmel McDougall

Full Text Available In nature, numerous mechanisms have evolved by which organisms fabricate biological structures with an impressive array of physical characteristics. Some examples of metazoan biological materials include the highly elastic byssal threads by which bivalves attach themselves to rocks, biomineralized structures that form the skeletons of various animals, and spider silks that are renowned for their exceptional strength and elasticity. The remarkable properties of silks, which are perhaps the best studied biological materials, are the result of the highly repetitive, modular, and biased amino acid composition of the proteins that compose them. Interestingly, similar levels of modularity/repetitiveness and similar bias in amino acid compositions have been reported in proteins that are components of structural materials in other organisms, however the exact nature and extent of this similarity, and its functional and evolutionary relevance, is unknown. Here, we investigate this similarity and use sequence features common to silks and other known structural proteins to develop a bioinformatics-based method to identify similar proteins from large-scale transcriptome and whole-genome datasets. We show that a large number of proteins identified using this method have roles in biological material formation throughout the animal kingdom. Despite the similarity in sequence characteristics, most of the silk-like structural proteins (SLSPs identified in this study appear to have evolved independently and are restricted to a particular animal lineage. Although the exact function of many of these SLSPs is unknown, the apparent independent evolution of proteins with similar sequence characteristics in divergent lineages suggests that these features are important for the assembly of biological materials. The identification of these characteristics enable the generation of testable hypotheses regarding the mechanisms by which these proteins assemble and direct the

Hydra phantom applicability for carrying out tests of field uniformity in gamma cameras

International Nuclear Information System (INIS)

Aragao Filho, Geraldo L.; Oliveira, Alex C.H.

2014-01-01

Nuclear Medicine is a medical modality that makes use of radioactive material 'in vivo' in humans, making them a temporary radioactive source. The radiation emitted by the patient's body is detected by a specific equipment, called a gamma camera, creates an image showing the spatial and temporal biodistribution of radioactive material administered to the patient. Therefore, it's of fundamental importance a number of specific measures to make sure that procedure be satisfactory, called quality control. To Nuclear Medicine, quality control of gamma camera has the purpose of ensuring accurate scintillographic imaging, truthful and reliable for the diagnosis, guaranteeing visibility and clarity of details of structures, and also to determine the frequency and the need for preventive maintenance of equipment. To ensure the quality control of the gamma camera it's necessary to use some simulators, called phantom, used in Nuclear Medicine to evaluate system performance, system calibration and simulation of injuries. The goal of this study was to validate a new simulator for nuclear medicine, the Hydra phantom. The phantom was initially built for construction of calibration curves used in radiotherapy planning and quality control in CT. It has similar characteristics to specific phantoms in nuclear medicine, containing inserts and water area. Those inserts are regionally sourced materials, many of them are already used in the literature and based on information about density and interaction of radiation with matter. To verify its efficiency in quality control in Nuclear Medicine, was performed a test for uniformity field, one of the main tests performed daily, so we can verify the ability of the gamma camera to reproduce a uniform distribution of the administered activity in the phantom, been analysed qualitatively, through the image, and quantitatively, through values established for Central Field Of View (CFOV) and Useful Field Of View (UFOV). Also, was evaluated their

Structure and evolution of N-domains in AAA metalloproteases.

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Scharfenberg, Franka; Serek-Heuberger, Justyna; Coles, Murray; Hartmann, Marcus D; Habeck, Michael; Martin, Jörg; Lupas, Andrei N; Alva, Vikram

2015-02-27

Metalloproteases of the AAA (ATPases associated with various cellular activities) family play a crucial role in protein quality control within the cytoplasmic membrane of bacteria and the inner membrane of eukaryotic organelles. These membrane-anchored hexameric enzymes are composed of an N-terminal domain with one or two transmembrane helices, a central AAA ATPase module, and a C-terminal Zn(2+)-dependent protease. While the latter two domains have been well studied, so far, little is known about the N-terminal regions. Here, in an extensive bioinformatic and structural analysis, we identified three major, non-homologous groups of N-domains in AAA metalloproteases. By far, the largest one is the FtsH-like group of bacteria and eukaryotic organelles. The other two groups are specific to Yme1: one found in plants, fungi, and basal metazoans and the other one found exclusively in animals. Using NMR and crystallography, we determined the subunit structure and hexameric assembly of Escherichia coli FtsH-N, exhibiting an unusual α+β fold, and the conserved part of fungal Yme1-N from Saccharomyces cerevisiae, revealing a tetratricopeptide repeat fold. Our bioinformatic analysis showed that, uniquely among these proteins, the N-domain of Yme1 from the cnidarian Hydra vulgaris contains both the tetratricopeptide repeat region seen in basal metazoans and a region of homology to the N-domains of animals. Thus, it is a modern-day representative of an intermediate in the evolution of animal Yme1 from basal eukaryotic precursors. Copyright © 2015. Published by Elsevier Ltd.

Hierarchical partitioning of metazoan protein conservation profiles provides new functional insights.

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Jonathan Witztum

Full Text Available The availability of many complete, annotated proteomes enables the systematic study of the relationships between protein conservation and functionality. We explore this question based solely on the presence or absence of protein homologues (a.k.a. conservation profiles. We study 18 metazoans, from two distinct points of view: the human's and the fly's. Using the GOrilla gene ontology (GO analysis tool, we explore functional enrichment of the "universal proteins", those with homologues in all 17 other species, and of the "non-universal proteins". A large number of GO terms are strongly enriched in both human and fly universal proteins. Most of these functions are known to be essential. A smaller number of GO terms, exhibiting markedly different properties, are enriched in both human and fly non-universal proteins. We further explore the non-universal proteins, whose conservation profiles are consistent with the "tree of life" (TOL consistent, as well as the TOL inconsistent proteins. Finally, we applied Quantum Clustering to the conservation profiles of the TOL consistent proteins. Each cluster is strongly associated with one or a small number of specific monophyletic clades in the tree of life. The proteins in many of these clusters exhibit strong functional enrichment associated with the "life style" of the related clades. Most previous approaches for studying function and conservation are "bottom up", studying protein families one by one, and separately assessing the conservation of each. By way of contrast, our approach is "top down". We globally partition the set of all proteins hierarchically, as described above, and then identify protein families enriched within different subdivisions. While supporting previous findings, our approach also provides a tool for discovering novel relations between protein conservation profiles, functionality, and evolutionary history as represented by the tree of life.

Hydratools, a MATLAB® based data processing package for Sontek Hydra data

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Martini, M.; Lightsom, F.L.; Sherwood, C.R.; Xu, Jie; Lacy, J.R.; Ramsey, A.; Horwitz, R.

2005-01-01

The U.S. Geological Survey (USGS) has developed a set of MATLAB tools to process and convert data collected by Sontek Hydra instruments to netCDF, which is a format used by the USGS to process and archive oceanographic time-series data. The USGS makes high-resolution current measurements within 1.5 meters of the bottom. These data are used in combination with other instrument data from sediment transport studies to develop sediment transport models. Instrument manufacturers provide software which outputs unique binary data formats. Multiple data formats are cumbersome. The USGS solution is to translate data streams into a common data format: netCDF. The Hydratools toolbox is written to create netCDF format files following EPIC conventions, complete with embedded metadata. Data are accepted from both the ADV and the PCADP. The toolbox will detect and remove bad data, substitute other sources of heading and tilt measurements if necessary, apply ambiguity corrections, calculate statistics, return information about data quality, and organize metadata. Standardized processing and archiving makes these data more easily and routinely accessible locally and over the Internet. In addition, documentation of the techniques used in the toolbox provides a baseline reference for others utilizing the data.

M Stars in the TW Hydra Association: A Chandra Large Program Survey

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Punzi, Kristina; Kastner, Joel; Principe, David; Stelzer, Beate; Gorti, Uma; Pascucci, Illaria; Argiroffi, Costanza

2018-01-01

We have conducted a Cycle 18 Chandra Large Program survey of very cool members of the $\\sim$ 8 Myr-old TW Hydra Association (TWA) to extend our previous study of the potential connections between M star disks and X-rays (Kastner et al. 2016, AJ, 152, 3) to the extreme low-mass end of the stellar initial mass function. The spectral types of our targets extend down to the M/L borderline. Thus we can further investigate the potential connection between the intense X-ray emission from young, low-mass stars and the lifetimes of their circumstellar planet-forming discs, as well as better constrain the age at which coronal activity declines for stellar masses approaching the H-burning limit of $\\sim$ 0.08 M$_{\\odot}$. We present preliminary results from the Cycle 18 survey, including X-ray detection statistics and measurements of relative X-ray luminosities and coronal (X-ray) temperatures for those TWA stars detected by Chandra. This research is supported by SAO/CXC grant GO7-18002A and NASA Astrophysics Data Analysis program grants NNX12AH37G and NNX16AG13G to RIT.

Two-step evolution of endosymbiosis between hydra and algae.

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Ishikawa, Masakazu; Shimizu, Hiroshi; Nozawa, Masafumi; Ikeo, Kazuho; Gojobori, Takashi

2016-10-01

In the Hydra vulgaris group, only 2 of the 25 strains in the collection of the National Institute of Genetics in Japan currently show endosymbiosis with green algae. However, whether the other non-symbiotic strains also have the potential to harbor algae remains unknown. The endosymbiotic potential of non-symbiotic strains that can harbor algae may have been acquired before or during divergence of the strains. With the aim of understanding the evolutionary process of endosymbiosis in the H. vulgaris group, we examined the endosymbiotic potential of non-symbiotic strains of the H. vulgaris group by artificially introducing endosymbiotic algae. We found that 12 of the 23 non-symbiotic strains were able to harbor the algae until reaching the grand-offspring through the asexual reproduction by budding. Moreover, a phylogenetic analysis of mitochondrial genome sequences showed that all the strains with endosymbiotic potential grouped into a single cluster (cluster γ). This cluster contained two strains (J7 and J10) that currently harbor algae; however, these strains were not the closest relatives. These results suggest that evolution of endosymbiosis occurred in two steps; first, endosymbiotic potential was gained once in the ancestor of the cluster γ lineage; second, strains J7 and J10 obtained algae independently after the divergence of the strains. By demonstrating the evolution of the endosymbiotic potential in non-symbiotic H. vulgaris group strains, we have clearly distinguished two evolutionary steps. The step-by-step evolutionary process provides significant insight into the evolution of endosymbiosis in cnidarians. Copyright © 2016 Elsevier Inc. All rights reserved.

Two-Step Evolution of Endosymbiosis between Hydra and Algae

KAUST Repository

Ishikawa, Masakazu

2016-07-09

In the Hydra vulgaris group, only 2 of the 25 strains in the collection of the National Institute of Genetics in Japan currently show endosymbiosis with green algae. However, whether the other non-symbiotic strains also have the potential to harbor algae remains unknown. The endosymbiotic potential of non-symbiotic strains that can harbor algae may have been acquired before or during divergence of the strains. With the aim of understanding the evolutionary process of endosymbiosis in the H. vulgaris group, we examined the endosymbiotic potential of non-symbiotic strains of the H. vulgaris group by artificially introducing endosymbiotic algae. We found that 12 of the 23 non-symbiotic strains were able to harbor the algae until reaching the grand-offspring through the asexual reproduction by budding. Moreover, a phylogenetic analysis of mitochondrial genome sequences showed that all the strains with endosymbiotic potential grouped into a single cluster (cluster γ). This cluster contained two strains (J7 and J10) that currently harbor algae; however, these strains were not the closest relatives. These results suggest that evolution of endosymbiosis occurred in two steps; first, endosymbiotic potential was gained once in the ancestor of the cluster γ lineage; second, strains J7 and J10 obtained algae independently after the divergence of the strains. By demonstrating the evolution of the endosymbiotic potential in non-symbiotic H. vulgaris group strains, we have clearly distinguished two evolutionary steps. The step-by-step evolutionary process provides significant insight into the evolution of endosymbiosis in cnidarians.

Characterization of STIP, a multi-domain nuclear protein, highly conserved in metazoans, and essential for embryogenesis in Caenorhabditis elegans

International Nuclear Information System (INIS)

Ji Qiongmei; Huang, C.-H.; Peng Jianbin; Hashmi, Sarwar; Ye Tianzhang; Chen Ying

2007-01-01

We report here the identification and characterization of STIP, a multi-domain nuclear protein that contains a G-patch, a coiled-coil, and several short tryptophan-tryptophan repeats highly conserved in metazoan species. To analyze their functional role in vivo, we cloned nematode stip-1 genes and determined the spatiotemporal pattern of Caenorhabditis elegans STIP-1 protein. RNA analyses and Western blots revealed that stip-1 mRNA was produced via trans-splicing and translated as a 95-kDa protein. Using reporter constructs, we found STIP-1 to be expressed at all developmental stages and in many tissue/cell types including worm oocyte nuclei. We found that STIP-1 is targeted to the nucleus and forms large polymers with a rod-like shape when expressed in mammalian cells. Using deletion mutants, we mapped the regions of STIP-1 involved in nuclear import and polymer assembly. We further showed that knockdown of C. elegans stip-1 by RNA interference arrested development and resulted in morphologic abnormalities around the 16-cell stage followed by 100% lethality, suggesting its essential role in worm embryogenesis. Importantly, the embryonic lethal phenotype could be faithfully rescued with Drosophila and human genes via transgenic expression. Our data provide the first direct evidence that STIP have a conserved essential nuclear function across metazoans from worms to humans

A systematic computational analysis of the rRNA-3 ' UTR sequence complementarity suggests a regulatory mechanism influencing post-termination events in metazoan translation

Czech Academy of Sciences Publication Activity Database

Pánek, Josef; Kolář, Michal; Herrmannová, Anna; Valášek, Leoš Shivaya

2016-01-01

Roč. 22, č. 7 (2016), 957-967-957-967 ISSN 1355-8382 R&D Projects: GA ČR(CZ) GBP305/12/G034 Institutional support: RVO:61388971 ; RVO:68378050 Keywords : metazoan 18S rRNA-mRNA 3 ' UTRs complementarity * large-scale data set * statistics Subject RIV: EE - Microbiology, Virology Impact factor: 4.605, year: 2016

Not armour, but biomechanics, ecological opportunity and increased fecundity as keys to the origin and expansion of the mineralized benthic metazoan fauna

OpenAIRE

Cohen, B.L.

2005-01-01

This paper offers a new biotic interaction hypothesis for the Cambrian 'explosion' of mineralized, benthic, metazoan diversity. It proposes that organic-mineral composite structures (e.g. shells and muscle lever-arms) originated in Proterozoic lineages of primary larva-like, but reproductively competent, pelagic bilaterians because mineralization was both mechanically and energetically favourable, not because it provided armour against predation. Increased strength and rigidity of composite s...

Codon usage is associated with the evolutionary age of genes in metazoan genomes

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Linial Nathan

2009-12-01

Full Text Available Abstract Background Codon usage may vary significantly between different organisms and between genes within the same organism. Several evolutionary processes have been postulated to be the predominant determinants of codon usage: selection, mutation, and genetic drift. However, the relative contribution of each of these factors in different species remains debatable. The availability of complete genomes for tens of multicellular organisms provides an opportunity to inspect the relationship between codon usage and the evolutionary age of genes. Results We assign an evolutionary age to a gene based on the relative positions of its identified homologues in a standard phylogenetic tree. This yields a classification of all genes in a genome to several evolutionary age classes. The present study starts from the observation that each age class of genes has a unique codon usage and proceeds to provide a quantitative analysis of the codon usage in these classes. This observation is made for the genomes of Homo sapiens, Mus musculus, and Drosophila melanogaster. It is even more remarkable that the differences between codon usages in different age groups exhibit similar and consistent behavior in various organisms. While we find that GC content and gene length are also associated with the evolutionary age of genes, they can provide only a partial explanation for the observed codon usage. Conclusion While factors such as GC content, mutational bias, and selection shape the codon usage in a genome, the evolutionary history of an organism over hundreds of millions of years is an overlooked property that is strongly linked to GC content, protein length, and, even more significantly, to the codon usage of metazoan genomes.

Revisiting TW Hydrae in light of new astrometric data

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Teixeira, R.; Ducourant, C.; Galli, P. A. B.; Le Campion, J. F.; Zuckerman, B.; Krone-Martins, A. G. O.; Chauvin, G.; Song, I.

2014-10-01

Our efforts in the present work focused mainly on refining and improving the previous description and understanding of the stellar association TW Hydrae (TWA) including a very detailed membership analysis and its dynamical and evolutionary age.To achieve our objectives in a fully reliable way we take advantage of our own astrometric measurements (Ducourant et al. 2013) performed with NTT/EFOSC2 - ESO (La Silla - Chile) spread over three years (2007 - 2010) and of those published in the literature.A very detailed membership analysis based on the convergent point strategy as developed by our team (Galli et al. 2012, 2013) allowed us to define a consistent kinematic group containing 31 stars among the 44 proposed as TWA member in the literature. Assuming that our sample of stars may be contaminated by non-members and to get rid of the particular influence of each star we applied a Jacknife resampling technique generating 2000 random lists of 13 stars taken from our 16 stars and calculated for each the epoch of convergence when the radius is minimum. The mean of the epochs obtained and the dispersion about the mean give a dynamical age of 7.5± 0.7 Myr for the association that is in good agreement with the previous traceback age (De La Reza et al. 2006). We also estimated age for TWA moving group members from pre-main sequence evolutionary models (Siess et al. 2000) and find a mean age of 7.4± 1.2 Myr. These results show that the dynamical age of the association obtained via the traceback technique and the average age derived from theoretical evolutionary models are in good agreement.

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition.

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Alberti, Adriana; Poulain, Julie; Engelen, Stefan; Labadie, Karine; Romac, Sarah; Ferrera, Isabel; Albini, Guillaume; Aury, Jean-Marc; Belser, Caroline; Bertrand, Alexis; Cruaud, Corinne; Da Silva, Corinne; Dossat, Carole; Gavory, Frédérick; Gas, Shahinaz; Guy, Julie; Haquelle, Maud; Jacoby, E'krame; Jaillon, Olivier; Lemainque, Arnaud; Pelletier, Eric; Samson, Gaëlle; Wessner, Mark; Acinas, Silvia G; Royo-Llonch, Marta; Cornejo-Castillo, Francisco M; Logares, Ramiro; Fernández-Gómez, Beatriz; Bowler, Chris; Cochrane, Guy; Amid, Clara; Hoopen, Petra Ten; De Vargas, Colomban; Grimsley, Nigel; Desgranges, Elodie; Kandels-Lewis, Stefanie; Ogata, Hiroyuki; Poulton, Nicole; Sieracki, Michael E; Stepanauskas, Ramunas; Sullivan, Matthew B; Brum, Jennifer R; Duhaime, Melissa B; Poulos, Bonnie T; Hurwitz, Bonnie L; Pesant, Stéphane; Karsenti, Eric; Wincker, Patrick

2017-08-01

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems.

Fundamentals, current state of the development of, and prospects for further improvement of the new-generation thermal-hydraulic computational HYDRA-IBRAE/LM code for simulation of fast reactor systems

Science.gov (United States)

Alipchenkov, V. M.; Anfimov, A. M.; Afremov, D. A.; Gorbunov, V. S.; Zeigarnik, Yu. A.; Kudryavtsev, A. V.; Osipov, S. L.; Mosunova, N. A.; Strizhov, V. F.; Usov, E. V.

2016-02-01

The conceptual fundamentals of the development of the new-generation system thermal-hydraulic computational HYDRA-IBRAE/LM code are presented. The code is intended to simulate the thermalhydraulic processes that take place in the loops and the heat-exchange equipment of liquid-metal cooled fast reactor systems under normal operation and anticipated operational occurrences and during accidents. The paper provides a brief overview of Russian and foreign system thermal-hydraulic codes for modeling liquid-metal coolants and gives grounds for the necessity of development of a new-generation HYDRA-IBRAE/LM code. Considering the specific engineering features of the nuclear power plants (NPPs) equipped with the BN-1200 and the BREST-OD-300 reactors, the processes and the phenomena are singled out that require a detailed analysis and development of the models to be correctly described by the system thermal-hydraulic code in question. Information on the functionality of the computational code is provided, viz., the thermalhydraulic two-phase model, the properties of the sodium and the lead coolants, the closing equations for simulation of the heat-mass exchange processes, the models to describe the processes that take place during the steam-generator tube rupture, etc. The article gives a brief overview of the usability of the computational code, including a description of the support documentation and the supply package, as well as possibilities of taking advantages of the modern computer technologies, such as parallel computations. The paper shows the current state of verification and validation of the computational code; it also presents information on the principles of constructing of and populating the verification matrices for the BREST-OD-300 and the BN-1200 reactor systems. The prospects are outlined for further development of the HYDRA-IBRAE/LM code, introduction of new models into it, and enhancement of its usability. It is shown that the program of development and

Community ecology of the metazoan parasites of Atlantic Moonfish, Selene setapinnis (Osteichthyes: Carangidae from the coastal zone of the state of Rio de Janeiro, Brazil

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A. S. Cordeiro

Full Text Available Eighty-nine specimens of Selene setapinnis (Mitchill, 1815 collected from the coastal zone of the State of Rio de Janeiro (21-23ºS, 41-45ºW and 23º05'S, 44º30'W, Brazil, from August 2001 to May 2002, were necropsied to study their metazoan parasites. Eighty-one (91% specimens of S. setapinnis were parasitized by one or more metazoan species. Twenty-one species of parasites were collected: 8 digeneans, 3 monogeneans, 2 cestodes, 5 nematodes, and 3 copepods. The endoparasites (digeneans, cestodes, and nematodes were 74.1% of total number of parasite specimens collected. The monogenean Pseudomazocraes selene (Hargis, 1957 was the most dominant species with the highest prevalence in the parasite community of S. setapinnis. The metazoan parasites of this host species showed the typical aggregated pattern of distribution. Only one parasite species (Acanthocolpoides pauloi Travassos, Freitas & Buhrnheim, 1955 showed positive correlation between the host total length and parasite abundance in S. setapinnis. Caligus robustus Bassett-Smith, 1898, P. selene, and Terranova sp. demonstrated positive correlation between the host total length and prevalence. Larvae of Terranova sp. showed influence of the host sex on its prevalence. A pair of ectoparasite species, P. selene-C. robustus, exhibited positive covariation between their abundances. Two pairs of endoparasite species, L. microstomum-P. merus and A. pauloi-P. merus showed significant covariation among their abundances; and the pair Terranova sp.-Raphidascaris sp. had positive co-ocorrence and covariation in the infracommunities of S. setapinnis. Like the parasite communities of the other carangid fishes from Rio de Janeiro, the parasite community of S. setapinnis is apparently only a slightly ordered species complex, characterized by dominance of endoparasite species.

Poverty, violence, and family disorganization: Three "Hydras" and their role in children's street movement in Bangladesh.

Science.gov (United States)

Reza, Md Hasan

2016-05-01

The increasing number of children running away from home in Bangladesh is a major concern, and in need of critical attention. This yearlong study explores why children leave home with a sample of street children in Dhaka, Bangladesh. Purposive sampling from three locations in Dhaka yielded a sample of 75 homeless children aged 10-17. For each participant, a 60-90min in-depth qualitative interview was conducted multiple times. While the dominant explanations rely on poverty or abuse, the findings of this study reveal that the cause is actually three heads of a Hydra monster: poverty, abuse, and family disorganization and their interactions. It shows that the primary reasons for children breaking from their family are all interrelated. The findings from this study are likely to add knowledge regarding the issues and may lead to preventative interventions for street children and their families. Copyright © 2016 Elsevier Ltd. All rights reserved.

IDENTIFYING NEARBY, YOUNG, LATE-TYPE STARS BY MEANS OF THEIR CIRCUMSTELLAR DISKS

International Nuclear Information System (INIS)

Schneider, Adam; Song, Inseok; Melis, Carl; Zuckerman, B.; Bessell, Mike

2012-01-01

It has recently been shown that a significant fraction of late-type members of nearby, very young associations (age ∼<10 Myr) display excess emission at mid-IR wavelengths indicative of dusty circumstellar disks. We demonstrate that the detection of mid-IR excess emission can be utilized to identify new nearby, young, late-type stars including two definite new members ('TWA 33' and 'TWA 34') of the TW Hydrae Association (TWA). Both new TWA members display mid-IR excess emission in the Wide-field Infrared Survey Explorer catalog and they show proper motion and youthful spectroscopic characteristics—namely, Hα emission, strong lithium absorption, and low surface gravity features consistent with known TWA members. We also detect mid-IR excess—the first unambiguous evidence of a dusty circumstellar disk—around a previously identified UV-bright, young, accreting star (2M1337) that is a likely member of the Lower-Centaurus Crux region of the Scorpius-Centaurus Complex.

Incorporation of a horizontally transferred gene into an operon during cnidarian evolution.

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Catherine E Dana

Full Text Available Genome sequencing has revealed examples of horizontally transferred genes, but we still know little about how such genes are incorporated into their host genomes. We have previously reported the identification of a gene (flp that appears to have entered the Hydra genome through horizontal transfer. Here we provide additional evidence in support of our original hypothesis that the transfer was from a unicellular organism, and we show that the transfer occurred in an ancestor of two medusozoan cnidarian species. In addition we show that the gene is part of a bicistronic operon in the Hydra genome. These findings identify a new animal phylum in which trans-spliced leader addition has led to the formation of operons, and define the requirements for evolution of an operon in Hydra. The identification of operons in Hydra also provides a tool that can be exploited in the construction of transgenic Hydra strains.

Minicollagen-15, a novel minicollagen isolated from Hydra, forms tubule structures in nematocysts.

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Adamczyk, Patrizia; Meier, Sebastian; Gross, Thomas; Hobmayer, Bert; Grzesiek, Stephan; Bächinger, Hans Peter; Holstein, Thomas W; Ozbek, Suat

2008-02-29

Minicollagens constitute a family of unusually short collagen molecules isolated from cnidarians. They are restricted to the nematocyst, a cylindrical explosive organelle serving in defense and capture of prey. The nematocyst capsule contains a long tubule inside of its matrix, which is expelled and everted during an ultrafast discharge process. Here, we report the cloning and characterization of a novel minicollagen in Hydra, designated minicollagen-15 (NCol-15). NCol-15, like NCol-3 and NCol-4, shows deviations from the canonical cysteine pattern in its terminal cysteine-rich domains (CRDs). Minicollagens share common domain architectures with a central collagen sequence flanked by polyproline stretches and short N- and C-terminal CRDs. The CRDs are involved in the formation of a highly resistant cysteine network, which constitutes the basic structure of the nematocyst capsule. Unlike NCol-1, which is part of the capsule wall, NCol-15 is localized to tubules, arguing for a functional differentiation of minicollagens within the nematocyst architecture. NMR analysis of the altered C-terminal CRD of NCol-15 showed a novel disulfide-linked structure within the cysteine-containing region exhibiting similar folding kinetics and stability as the canonical CRDs. Our data provide evidence for evolutionary diversification among minicollagens, which probably facilitated alterations in the morphology of the nematocyst wall and tubule.

X-RAY DETERMINATION OF THE VARIABLE RATE OF MASS ACCRETION ONTO TW HYDRAE

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Brickhouse, N. S.; Cranmer, S. R.; Dupree, A. K.; Guenther, H. M.; Wolk, S. J. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Luna, G. J. M. [Current address: Instituto de Astronomia y Fisica del Espacio (IAFE), Buenos Aires (Argentina)

2012-12-01

Diagnostics of electron temperature (T{sub e} ), electron density (n{sub e} ), and hydrogen column density (N{sub H}) from the Chandra High Energy Transmission Grating spectrum of He-like Ne IX in TW Hydrae (TW Hya), in conjunction with a classical accretion model, allow us to infer the accretion rate onto the star directly from measurements of the accreting material. The new method introduces the use of the absorption of Ne IX lines as a measure of the column density of the intervening, accreting material. On average, the derived mass accretion rate for TW Hya is 1.5 Multiplication-Sign 10{sup -9} M{sub Sun} yr{sup -1}, for a stellar magnetic field strength of 600 G and a filling factor of 3.5%. Three individual Chandra exposures show statistically significant differences in the Ne IX line ratios, indicating changes in N{sub H}, T{sub e} , and n{sub e} by factors of 0.28, 1.6, and 1.3, respectively. In exposures separated by 2.7 days, the observations reported here suggest a five-fold reduction in the accretion rate. This powerful new technique promises to substantially improve our understanding of the accretion process in young stars.

Bringing ATLAS production to HPC resources. A case study with SuperMuc and Hydra

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Duckeck, Guenter; Walker, Rodney [LMU Muenchen (Germany); Kennedy, John; Mazzaferro, Luca [RZG Garching (Germany); Kluth, Stefan [Max-Planck-Institut fuer Physik, Muenchen (Germany); Collaboration: ATLAS-Collaboration

2015-07-01

The possible usage of Supercomputer systems or HPC resources by ATLAS is now becoming viable due to the changing nature of these systems and it is also very attractive due to the need for increasing amounts of simulated data. The ATLAS experiment at CERN will begin a period of high luminosity data taking in 2015. The corresponding need for simulated data might potentially exceed the capabilities of the current Grid infrastructure. ATLAS aims to address this need by opportunistically accessing resources such as cloud and HPC systems. This contribution presents the results of two projects undertaken by LMU/LRZ and MPP/RZG to use the supercomputer facilities SuperMuc (LRZ) and Hydra (RZG). Both are Linux based supercomputers in the 100 k CPU-core category. The integration of such HPC resources into the ATLAS production system poses many challenges. Firstly, established techniques and features of standard WLCG operation are prohibited or much restricted on HPC systems, e.g. Grid middleware, software installation, outside connectivity, etc. Secondly, efficient use of available resources requires massive multi-core jobs, back-fill submission and check-pointing. We discuss the customization of these components and the strategies for HPC usage as well as possibilities for future directions.

Functional chloroplasts in metazoan cells - a unique evolutionary strategy in animal life

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Krug Patrick J

2009-12-01

Full Text Available Abstract Background Among metazoans, retention of functional diet-derived chloroplasts (kleptoplasty is known only from the sea slug taxon Sacoglossa (Gastropoda: Opisthobranchia. Intracellular maintenance of plastids in the slug's digestive epithelium has long attracted interest given its implications for understanding the evolution of endosymbiosis. However, photosynthetic ability varies widely among sacoglossans; some species have no plastid retention while others survive for months solely on photosynthesis. We present a molecular phylogenetic hypothesis for the Sacoglossa and a survey of kleptoplasty from representatives of all major clades. We sought to quantify variation in photosynthetic ability among lineages, identify phylogenetic origins of plastid retention, and assess whether kleptoplasty was a key character in the radiation of the Sacoglossa. Results Three levels of photosynthetic activity were detected: (1 no functional retention; (2 short-term retention lasting about one week; and (3 long-term retention for over a month. Phylogenetic analysis of one nuclear and two mitochondrial loci revealed reciprocal monophyly of the shelled Oxynoacea and shell-less Plakobranchacea, the latter comprising a monophyletic Plakobranchoidea and paraphyletic Limapontioidea. Only species in the Plakobranchoidea expressed short- or long-term kleptoplasty, most belonging to a speciose clade of slugs bearing parapodia (lateral flaps covering the dorsum. Bayesian ancestral character state reconstructions indicated that functional short-term retention arose once in the last common ancestor of Plakobranchoidea, and independently evolved into long-term retention in four derived species. Conclusion We propose a sequential progression from short- to long-term kleptoplasty, with different adaptations involved in each step. Short-term kleptoplasty likely arose as a deficiency in plastid digestion, yielding additional energy via the release of fixed carbon

A TARGETED SEARCH FOR PECULIARLY RED L AND T DWARFS IN SDSS, 2MASS, AND WISE: DISCOVERY OF A POSSIBLE L7 MEMBER OF THE TW HYDRAE ASSOCIATION

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Kellogg, Kendra; Metchev, Stanimir [Western University, Centre for Planetary and Space Exploration, 1151 Richmond St, London, ON N6A 3K7 (Canada); Geißler, Kerstin; Hicks, Shannon [Stony Brook University, Stony Brook, NY 11790 (United States); Kirkpatrick, J. Davy [Infrared Processing and Analysis Center, Mail Code 100-22, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125 (United States); Kurtev, Radostin, E-mail: kkellogg@uwo.ca, E-mail: smetchev@uwo.ca [Instituto de Física y Astronomía, Facultad de Ciencias, Universidad de Valparaíso, Ave. Gran Bretaña 1111, Playa Ancha, Casilla 53, Valparaíso (Chile)

2015-12-15

We present the first results from a targeted search for brown dwarfs with unusual red colors indicative of peculiar atmospheric characteristics. These include objects with low surface gravities or with unusual dust content or cloud properties. From a positional cross-match of SDSS, 2MASS, and WISE, we have identified 40 candidate peculiar early-L to early-T dwarfs that are either new objects or have not been identified as peculiar through prior spectroscopy. Using low-resolution spectra, we confirm that 10 of the candidates are either peculiar or potential L/T binaries. With a J − K{sub s} color of 2.62 ± 0.15 mag, one of the new objects—the L7 dwarf 2MASS J11193254–1137466—is among the reddest field dwarfs currently known. Its proper motion and photometric parallax indicate that it is a possible member of the TW Hydrae moving group. If confirmed, it would be the lowest-mass (5–6 M{sub Jup}) free-floating member. We also report a new T dwarf, 2MASS J22153705+2110554, that was previously overlooked in the SDSS footprint. These new discoveries demonstrate that despite the considerable scrutiny already devoted to the SDSS and 2MASS surveys, our exploration of these data sets is not yet complete.

A TARGETED SEARCH FOR PECULIARLY RED L AND T DWARFS IN SDSS, 2MASS, AND WISE: DISCOVERY OF A POSSIBLE L7 MEMBER OF THE TW HYDRAE ASSOCIATION

International Nuclear Information System (INIS)

Kellogg, Kendra; Metchev, Stanimir; Geißler, Kerstin; Hicks, Shannon; Kirkpatrick, J. Davy; Kurtev, Radostin

2015-01-01

We present the first results from a targeted search for brown dwarfs with unusual red colors indicative of peculiar atmospheric characteristics. These include objects with low surface gravities or with unusual dust content or cloud properties. From a positional cross-match of SDSS, 2MASS, and WISE, we have identified 40 candidate peculiar early-L to early-T dwarfs that are either new objects or have not been identified as peculiar through prior spectroscopy. Using low-resolution spectra, we confirm that 10 of the candidates are either peculiar or potential L/T binaries. With a J − K s color of 2.62 ± 0.15 mag, one of the new objects—the L7 dwarf 2MASS J11193254–1137466—is among the reddest field dwarfs currently known. Its proper motion and photometric parallax indicate that it is a possible member of the TW Hydrae moving group. If confirmed, it would be the lowest-mass (5–6 M Jup ) free-floating member. We also report a new T dwarf, 2MASS J22153705+2110554, that was previously overlooked in the SDSS footprint. These new discoveries demonstrate that despite the considerable scrutiny already devoted to the SDSS and 2MASS surveys, our exploration of these data sets is not yet complete

Cell proliferation is necessary for the regeneration of oral structures in the anthozoan cnidarian Nematostella vectensis

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Passamaneck Yale J

2012-12-01

Full Text Available Abstract Background The contribution of cell proliferation to regeneration varies greatly between different metazoan models. Planarians rely on pluripotent neoblasts and amphibian limb regeneration depends upon formation of a proliferative blastema, while regeneration in Hydra can occur in the absence of cell proliferation. Recently, the cnidarian Nematostella vectensis has shown potential as a model for studies of regeneration because of the ability to conduct comparative studies of patterning during embryonic development, asexual reproduction, and regeneration. The present study investigates the pattern of cell proliferation during the regeneration of oral structures and the role of cell proliferation in this process. Results In intact polyps, cell proliferation is observed in both ectodermal and endodermal tissues throughout the entire oral-aboral axis, including in the tentacles and physa. Following bisection, there is initially little change in proliferation at the wound site of the aboral fragment, however, beginning 18 to 24 hours after amputation there is a dramatic increase in cell proliferation at the wound site in the aboral fragment. This elevated level of proliferation is maintained throughout the course or regeneration of oral structures, including the tentacles, the mouth, and the pharynx. Treatments with the cell proliferation inhibitors hydroxyurea and nocodazole demonstrate that cell proliferation is indispensable for the regeneration of oral structures. Although inhibition of regeneration by nocodazole was generally irreversible, secondary amputation reinitiates cell proliferation and regeneration. Conclusions The study has found that high levels of cell proliferation characterize the regeneration of oral structures in Nematostella, and that this cell proliferation is necessary for the proper progression of regeneration. Thus, while cell proliferation contributes to regeneration of oral structures in both Nematostella and

Metazoan meiofauna within the oxygen-minimum zone off Chile: Results of the 2001-PUCK expedition

Science.gov (United States)

Veit-Köhler, Gritta; Gerdes, Dieter; Quiroga, Eduardo; Hebbeln, Dierk; Sellanes, Javier

2009-07-01

A quantitative study of metazoan meiofauna was carried out at continental shelf and slope stations affected by the oxygen-minimum zone in the eastern South Pacific off Chile. Densities of meiobenthos at the investigated stations off Antofagasta (22°S), Concepción (36°S), and Chiloé (42°S) ranged from 1282.1 to 8847.8 ind 10 cm -2. Oxygen deficiency led only to average abundances, despite higher food availability and freshness at the corresponding sites. Sediment organic carbon, chlorophyll- a, and phaeopigment contents were used as measures of the input from water-column primary production, which accumulated at the oxygen-minimum zone stations. The highest abundances were found at a station with an oxygen content of 0.79 mL L -1, which was slightly elevated from what is defined as oxygen minimum (0.5 mL L -1). The most oxygenated site yielded the lowest densities. Meiofauna assemblages became more diverse with increasing bottom-water oxygenation, whereas nematodes were the most abundant taxon at every station, followed by annelids, copepods, and nauplii.

A complex small RNA repertoire is generated by a plant/fungal-like machinery and effected by a metazoan-like Argonaute in the single-cell human parasite Toxoplasma gondii.

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Laurence Braun

2010-05-01

Full Text Available In RNA silencing, small RNAs produced by the RNase-III Dicer guide Argonaute-like proteins as part of RNA-induced silencing complexes (RISC to regulate gene expression transcriptionally or post-transcriptionally. Here, we have characterized the RNA silencing machinery and exhaustive small RNAome of Toxoplasma gondii, member of the Apicomplexa, a phylum of animal- and human-infecting parasites that cause extensive health and economic damages to human populations worldwide. Remarkably, the small RNA-generating machinery of Toxoplasma is phylogenetically and functionally related to that of plants and fungi, and accounts for an exceptionally diverse array of small RNAs. This array includes conspicuous populations of repeat-associated small interfering RNA (siRNA, which, as in plants, likely generate and maintain heterochromatin at DNA repeats and satellites. Toxoplasma small RNAs also include many microRNAs with clear metazoan-like features whose accumulation is sometimes extremely high and dynamic, an unexpected finding given that Toxoplasma is a unicellular protist. Both plant-like heterochromatic small RNAs and metazoan-like microRNAs bind to a single Argonaute protein, Tg-AGO. Toxoplasma miRNAs co-sediment with polyribosomes, and thus, are likely to act as translational regulators, consistent with the lack of catalytic residues in Tg-AGO. Mass spectrometric analyses of the Tg-AGO protein complex revealed a common set of virtually all known RISC components so far characterized in human and Drosophila, as well as novel proteins involved in RNA metabolism. In agreement with its loading with heterochromatic small RNAs, Tg-AGO also associates substoichiometrically with components of known chromatin-repressing complexes. Thus, a puzzling patchwork of silencing processor and effector proteins from plant, fungal and metazoan origin accounts for the production and action of an unsuspected variety of small RNAs in the single-cell parasite Toxoplasma and

Conservation of complete trimethylation of lysine-43 in the rotor ring of c-subunits of metazoan adenosine triphosphate (ATP) synthases.

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Walpole, Thomas B; Palmer, David N; Jiang, Huibing; Ding, Shujing; Fearnley, Ian M; Walker, John E

2015-04-01

The rotors of ATP synthases turn about 100 times every second. One essential component of the rotor is a ring of hydrophobic c-subunits in the membrane domain of the enzyme. The rotation of these c-rings is driven by a transmembrane proton-motive force, and they turn against a surface provided by another membrane protein, known as subunit a. Together, the rotating c-ring and the static subunit a provide a pathway for protons through the membrane in which the c-ring and subunit a are embedded. Vertebrate and invertebrate c-subunits are well conserved. In the structure of the bovine F1-ATPase-c-ring subcomplex, the 75 amino acid c-subunit is folded into two transmembrane α-helices linked by a short loop. Each bovine rotor-ring consists of eight c-subunits with the N- and C-terminal α-helices forming concentric inner and outer rings, with the loop regions exposed to the phospholipid head-group region on the matrix side of the inner membrane. Lysine-43 is in the loop region and its ε-amino group is completely trimethylated. The role of this modification is unknown. If the trimethylated lysine-43 plays some important role in the functioning, assembly or degradation of the c-ring, it would be expected to persist throughout vertebrates and possibly invertebrates also. Therefore, we have carried out a proteomic analysis of c-subunits across representative species from different classes of vertebrates and from invertebrate phyla. In the twenty-nine metazoan species that have been examined, the complete methylation of lysine-43 is conserved, and it is likely to be conserved throughout the more than two million extant metazoan species. In unicellular eukaryotes and prokaryotes, when the lysine is conserved it is unmethylated, and the stoichiometries of c-subunits vary from 9-15. One possible role for the trimethylated residue is to provide a site for the specific binding of cardiolipin, an essential component of ATP synthases in mitochondria. © 2015 by The American

Patterns of oriented cell division during the steady-state morphogenesis of the body column in hydra.

Science.gov (United States)

Shimizu, H; Bode, P M; Bode, H R

1995-12-01

In an adult hydra, the tissue of the body column is in a dynamic state. The epithelial cells of both layers are constantly in the mitotic cycle. As the tissue expands, it is continuously displaced along the body axis in either an apical or basal direction, but not in a circumferential direction. Using a modified whole mount method we examined the orientation of mitotic spindles to determine what role the direction of cell division plays in axial displacement. Surprisingly, the direction of cell division was found to differ in the two epithelial layers. In the ectoderm it was somewhat biased in an axial direction. In the endoderm it was strongly biased in a circumferential direction. For both layers, the directional biases occurred throughout the length of the body column, with some regional variation in its extent. As buds developed into adults, the bias in each layer increased from an almost random distribution to the distinctly different orientations of the adult. Thus, to maintain the observed axial direction of tissue displacement, rearrangement of the epithelial cells of both layers must occur continuously in the adult as well as in developing animals. How the locomotory and contractile behavior of the muscle processes of the epithelial cells may effect changes in cell shape, and thereby influence the direction of cell division in each layer, is discussed.

Are the Immunocompetence and the Presence of Metazoan Parasites in Cyprinid Fish Affected by Reproductive Efforts of Cyprinid Fish?

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Karolína Rohlenová

2010-01-01

Full Text Available Each organism has the limited resources of energy that is distributed among important life traits. A trade-off between immune response and other physiological demands of organism especially costly reproduction is expected. Leuciscus cephalus, the cyprinid fish, was investigated during three periods varying in reproductive investment, that is, before-breeding, breeding, and after-breeding periods. We tested whether a potentially limited investment in immunity during the breeding is associated with higher susceptibility to the metazoan parasites. Following the immunocompetence handicap and sperm protection hypotheses, males expressing more elaborated sexual ornamentation should produce better quality sperm and be more parasitized. We found that reproductive investments in fish play an important role for energy allocation into somatic condition, immunity, and reproduction. The immune parameters including respiratory burst and leukocyte count were higher in breeding; however, parasite species richness and abundance appeared low. Males investing more in spawning tubercles reached high spermatocrite and were more parasitized by digeneans.

Precambrian supercontinents, glaciations, atmospheric oxygenation, metazoan evolution and an impact that may have changed the second half of Earth history

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Grant M. Young

2013-05-01

Full Text Available In more than 4 Ga of geological evolution, the Earth has twice gone through extreme climatic perturbations, when extensive glaciations occurred, together with alternating warm periods which were accompanied by atmospheric oxygenation. The younger of these two episodes of climatic oscillation preceded the Cambrian “explosion” of metazoan life forms, but similar extreme climatic conditions existed between about 2.4 and 2.2 Ga. Over long time periods, changing solar luminosity and mantle temperatures have played important roles in regulating Earth's climate but both periods of climatic upheaval are associated with supercontinents. Enhanced weathering on the orogenically and thermally buoyed supercontinents would have stripped CO2 from the atmosphere, initiating a cooling trend that resulted in continental glaciation. Ice cover prevented weathering so that CO2 built up once more, causing collapse of the ice sheets and ushering in a warm climatic episode. This negative feedback loop provides a plausible explanation for multiple glaciations of the Early and Late Proterozoic, and their intimate association with sedimentary rocks formed in warm climates. Between each glacial cycle nutrients were flushed into world oceans, stimulating photosynthetic activity and causing oxygenation of the atmosphere. Accommodation for many ancient glacial deposits was provided by rifting but escape from the climatic cycle was predicated on break-up of the supercontinent, when flooded continental margins had a moderating influence on weathering. The geochemistry of Neoproterozoic cap carbonates carries a strong hydrothermal signal, suggesting that they precipitated from deep sea waters, overturned and spilled onto continental shelves at the termination of glaciations. Paleoproterozoic (Huronian carbonates of the Espanola Formation were probably formed as a result of ponding and evaporation in a hydrothermally influenced, restricted rift setting. Why did metazoan

Metazoan parasite fauna of the bigeye flounder, Hippoglossina macrops, from Northern Chile. Influence of host age and sex

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González M Teresa

2001-01-01

Full Text Available The metazoan parasite fauna of Hippoglossina macrops (n = 123 from northern Chile (30°S is quantitatively described for the first time, and the role of host age and sex was evaluated. Twelve parasite species were recovered, including 5 ectoparasites (2 Monogenea, 2 Copepoda and 1 Piscicolidae and 7 endoparasites (1 Digenea, 3 Cestoda, 2 Acanthocephala, and 1 Nematoda. The copepod Holobomolochus chilensis, the monogenean Neoheterobothrium sp., the adult acanthocephalan Floridosentis sp. and the hirudinean, Gliptonobdella sp. are new geographical and host records. The most prevalent ectoparasitic species were the monogenean, Neoheterobothrium sp. and the copepod, H. chilensis. Among endoparasites, the acanthocephalans Floridosentis sp. and Corynosoma australe were most prevalent and abundant. Prevalence and mean intensity of infection for most parasitic species were not affected by host sex, however the prevalence of Floridosentis sp. was significantly greater in males. Intensity of infection was positively correlated with host age for Neoheterobothrium sp., and negatively correlated for Floridosentis sp. and H. chilensis. The helminth species richness of the host H. macrops was lower compared to related flatfishes from the Northern Hemisphere. The relationship of the helminth fauna of H. macrops, its feeding habits and ecological habitats are discussed.

Evolution of cyclin-dependent kinases (CDKs) and CDK-activating kinases (CAKs): differential conservation of CAKs in yeast and metazoa.

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Liu, J; Kipreos, E T

2000-07-01

Cyclin-dependent kinases (CDKs) function as central regulators of both the cell cycle and transcription. CDK activation depends on phosphorylation by a CDK-activating kinase (CAK). Different CAKs have been identified in budding yeast, fission yeast, and metazoans. All known CAKs belong to the extended CDK family. The sole budding yeast CAK, CAK1, and one of the two CAKs in fission yeast, csk1, have diverged considerably from other CDKs. Cell cycle regulatory components have been largely conserved in eukaryotes; however, orthologs of neither CAK1 nor csk1 have been identified in other species to date. To determine the evolutionary relationships of yeast and metazoan CAKs, we performed a phylogenetic analysis of the extended CDK family in budding yeast, fission yeast, humans, the fruit fly Drosophila melanogaster, and the nematode Caenorhabditis elegans. We observed that there were 10 clades for CDK-related genes, of which seven appeared ancestral, containing both yeast and metazoan genes. The four clades that contain CDKs that regulate transcription by phosphorylating the carboxyl-terminal domain (CTD) of RNA Polymerase II generally have only a single orthologous gene in each species of yeast and metazoans. In contrast, the ancestral cell cycle CDK (analogous to budding yeast CDC28) gave rise to a number of genes in metazoans, as did the ancestor of budding yeast PHO85. One ancestral clade is unique in that there are fission yeast and metazoan members, but there is no budding yeast ortholog, suggesting that it was lost subsequent to evolutionary divergence. Interestingly, CAK1 and csk1 branch together with high bootstrap support values. We used both the relative apparent synapomorphy analysis (RASA) method in combination with the S-F method of sampling reduced character sets and gamma-corrected distance methods to confirm that the CAK1/csk1 association was not an artifact of long-branch attraction. This result suggests that CAK1 and csk1 are orthologs and that a

Global isolation by distance despite strong regional phylogeography in a small metazoan

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Mills Scott

2007-11-01

Full Text Available Abstract Background Small vagile eukaryotic organisms, which comprise a large proportion of the Earth's biodiversity, have traditionally been thought to lack the extent of population structuring and geographic speciation observed in larger taxa. Here we investigate the patterns of genetic diversity, amongst populations of the salt lake microscopic metazoan Brachionus plicatilis s. s. (sensu stricto (Rotifera: Monogononta on a global scale. We examine the phylogenetic relationships of geographic isolates from four continents using a 603 bp fragment of the mitochondrial COI gene to investigate patterns of phylogeographic subdivision in this species. In addition we investigate the relationship between genetic and geographic distances on a global scale to try and reconcile the paradox between the high vagility of this species and the previously reported patterns of restricted gene flow, even over local spatial scales. Results Analysis of global sequence diversity of B. plicatilis s. s. reveals the presence of four allopatric genetic lineages: North American-Far East Asian, Western Mediterranean, Australian, and an Eastern Mediterranean lineage represented by a single isolate. Geographically orientated substructure is also apparent within the three best sampled lineages. Surprisingly, given this strong phylogeographic structure, B. plicatilis s. s. shows a significant correlation between geographic and genetic distance on a global scale ('isolation by distance' – IBD. Conclusion Despite its cosmopolitan distribution and potential for high gene flow, B. plicatilis s. s. is strongly structured at a global scale. IBD patterns have traditionally been interpreted to indicate migration-drift equilibrium, although in this system equilibrium conditions are incompatible with the observed genetic structure. Instead, we suggest the pattern may have arisen through persistent founder effects, acting in a similar fashion to geographic barriers for larger

Global isolation by distance despite strong regional phylogeography in a small metazoan

Science.gov (United States)

Mills, Scott; Lunt, David H; Gómez, Africa

2007-01-01

Background Small vagile eukaryotic organisms, which comprise a large proportion of the Earth's biodiversity, have traditionally been thought to lack the extent of population structuring and geographic speciation observed in larger taxa. Here we investigate the patterns of genetic diversity, amongst populations of the salt lake microscopic metazoan Brachionus plicatilis s. s. (sensu stricto) (Rotifera: Monogononta) on a global scale. We examine the phylogenetic relationships of geographic isolates from four continents using a 603 bp fragment of the mitochondrial COI gene to investigate patterns of phylogeographic subdivision in this species. In addition we investigate the relationship between genetic and geographic distances on a global scale to try and reconcile the paradox between the high vagility of this species and the previously reported patterns of restricted gene flow, even over local spatial scales. Results Analysis of global sequence diversity of B. plicatilis s. s. reveals the presence of four allopatric genetic lineages: North American-Far East Asian, Western Mediterranean, Australian, and an Eastern Mediterranean lineage represented by a single isolate. Geographically orientated substructure is also apparent within the three best sampled lineages. Surprisingly, given this strong phylogeographic structure, B. plicatilis s. s. shows a significant correlation between geographic and genetic distance on a global scale ('isolation by distance' – IBD). Conclusion Despite its cosmopolitan distribution and potential for high gene flow, B. plicatilis s. s. is strongly structured at a global scale. IBD patterns have traditionally been interpreted to indicate migration-drift equilibrium, although in this system equilibrium conditions are incompatible with the observed genetic structure. Instead, we suggest the pattern may have arisen through persistent founder effects, acting in a similar fashion to geographic barriers for larger organisms. Our data indicates

Space-based Coronagraphic Imaging Polarimetry of the TW Hydrae Disk: Shedding New Light on Self-shadowing Effects

Science.gov (United States)

Poteet, Charles A.; Chen, Christine H.; Hines, Dean C.; Perrin, Marshall D.; Debes, John H.; Pueyo, Laurent; Schneider, Glenn; Mazoyer, Johan; Kolokolova, Ludmilla

2018-06-01

We present Hubble Space Telescope Near-Infrared Camera and Multi-Object Spectrometer coronagraphic imaging polarimetry of the TW Hydrae protoplanetary disk. These observations simultaneously measure the total and polarized intensity, allowing direct measurement of the polarization fraction across the disk. In accord with the self-shadowing hypothesis recently proposed by Debes et al., we find that the total and polarized intensity of the disk exhibits strong azimuthal asymmetries at projected distances consistent with the previously reported bright and dark ring-shaped structures (∼45–99 au). The sinusoidal-like variations possess a maximum brightness at position angles near ∼268°–300° and are up to ∼28% stronger in total intensity. Furthermore, significant radial and azimuthal variations are also detected in the polarization fraction of the disk. In particular, we find that regions of lower polarization fraction are associated with annuli of increased surface brightness, suggesting that the relative proportion of multiple-to-single scattering is greater along the ring and gap structures. Moreover, we find strong (∼20%) azimuthal variation in the polarization fraction along the shadowed region of the disk. Further investigation reveals that the azimuthal variation is not the result of disk flaring effects, but is instead from a decrease in the relative contribution of multiple-to-single scattering within the shadowed region. Employing a two-layer scattering surface, we hypothesize that the diminished contribution in multiple scattering may result from shadowing by an inclined inner disk, which prevents direct stellar light from reaching the optically thick underlying surface component.

Comparative analysis of the metazoan parasite communities of leatherjackets, Oligoplites palometa, O. saurus, and O. saliens (Osteichthyes:Carangidae) from Sepetiba Bay, Rio de Janeiro, Brazil.

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Takemoto, R M; Amato, J F; Luque, J L

1996-11-01

One hundred and fifty-seven specimens of leatherjackets, 84 specimens of Oligoplites palometa (Cuvier), 37 specimens of O. saurus (Bloch & Schneider), and 36 specimens of O. saliens (Bloch) captured at the Sepetiba Bay, State of Rio de Janeiro, between March of 1991 and November of 1992, were necropsied to study their communities of metazoan parasites. All fishes studied were parasitized by one or more metazoan species. Eighteen parasite species were found in O. palometa and 13 parasite species were found in O. saurus and O. saliens, respectively. The digeneans were the majority of the parasite specimens collected, with 90.3%, 82.2%, and 87.7% in O. palometa, O. saurus, and O. saliens, respectively. The Simpson index was lower than 0.25 for the 3 host species, showing an absence of concentration for dominance. The similarity coefficients among the parasite communities of the 3 fish species was above 66%. The parasites of the 3 host species showed typical overdispersed pattern of distribution. Four cases of positive correlation between host's total length and prevalence and parasite intensity were found. The majority of the species did not show influence of host sex. The 3 host species had similar parasite diversity, which was not correlated with the host's total body length and there was no significant difference between male and female hosts. Oligoplites palometa and O. saurus each had one pair of ectoparasite species sharing a positive association and with a positive correlation between their intensities. No pairs of associated species were found in O. saliens. Parasites were found along the entire extension of the gastrointestinal tract of the 3 host species. The parasite communities of O. palometa, O. saurus, and O. saliens are defined as isolationists because there are few evidences of interspecific association or covariation. The presence of larval stages of cestodes and nematodes suggests that the three species of Oligoplites are at an intermediate level in

Exploring the HYDRAtion method for loading siRNA on liposomes: the interplay between stability and biological activity in human undiluted ascites fluid.

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Dakwar, George R; Braeckmans, Kevin; Ceelen, Wim; De Smedt, Stefaan C; Remaut, Katrien

2017-04-01

Delivery of small interfering RNA (siRNA) is recently gaining tremendous attention for the treatment of ovarian cancer. The present study investigated the potential of different liposomal formulations composed of (2,3-dioleoyloxy-propyl)-trimethylammonium (DOTAP) and 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) encapsulating siRNA (hydration method) for their ability to knockdown luciferase (Luc) activity in human ovarian cancer SKOV-3 cells. Fluorescence single particle tracking (fSPT) and fluorescence correlation spectroscopy (FCS) in human-undiluted ascites fluid obtained from a peritoneal carcinomatosis patient revealed that cationic hydra-lipoplexes (HYDRA-LPXs) and HYDRA-LPXs decorated with stable DSPE-PEG (DSPE HYDRA-LPXs) showed high stability during at least 24 h. HYDRA-LPXs decorated with sheddable C8 and C16 PEG-Ceramides (Cer HYDRA-LPXs) resulted in rapid and premature release of siRNA already in the first hours. Despite their role in preventing aggregation in vivo, liposomes decorated with stable PEG residues resulted in a poor transfection compared to the ones decorated with sheddable PEG residues in reduced serum conditions. Yet, the transfection efficiency of both Cer HYDRA-LPXs significantly decreased following 1 h of incubation in ascites fluid due to a drastic drop in the cellular uptake, while DSPE HYDRA-LPXs are still taken up by cells, but too stable to induce efficient gene silencing.

A genome-wide RNAi screen identifies regulators of cholesterol-modified hedgehog secretion in Drosophila.

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Reid Aikin

Full Text Available Hedgehog (Hh proteins are secreted molecules that function as organizers in animal development. In addition to being palmitoylated, Hh is the only metazoan protein known to possess a covalently-linked cholesterol moiety. The absence of either modification severely disrupts the organization of numerous tissues during development. It is currently not known how lipid-modified Hh is secreted and released from producing cells. We have performed a genome-wide RNAi screen in Drosophila melanogaster cells to identify regulators of Hh secretion. We found that cholesterol-modified Hh secretion is strongly dependent on coat protein complex I (COPI but not COPII vesicles, suggesting that cholesterol modification alters the movement of Hh through the early secretory pathway. We provide evidence that both proteolysis and cholesterol modification are necessary for the efficient trafficking of Hh through the ER and Golgi. Finally, we identified several putative regulators of protein secretion and demonstrate a role for some of these genes in Hh and Wingless (Wg morphogen secretion in vivo. These data open new perspectives for studying how morphogen secretion is regulated, as well as provide insight into regulation of lipid-modified protein secretion.

The evolutionary origin of the Runx/CBFbeta transcription factors – Studies of the most basal metazoans

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Groner Yoram

2008-08-01

Full Text Available Abstract Background Members of the Runx family of transcriptional regulators, which bind DNA as heterodimers with CBFβ, are known to play critical roles in embryonic development in many triploblastic animals such as mammals and insects. They are known to regulate basic developmental processes such as cell fate determination and cellular potency in multiple stem-cell types, including the sensory nerve cell progenitors of ganglia in mammals. Results In this study, we detect and characterize the hitherto unexplored Runx/CBFβ genes of cnidarians and sponges, two basal animal lineages that are well known for their extensive regenerative capacity. Comparative structural modeling indicates that the Runx-CBFβ-DNA complex from most cnidarians and sponges is highly similar to that found in humans, with changes in the residues involved in Runx-CBFβ dimerization in either of the proteins mirrored by compensatory changes in the binding partner. In situ hybridization studies reveal that Nematostella Runx and CBFβ are expressed predominantly in small isolated foci at the base of the ectoderm of the tentacles in adult animals, possibly representing neurons or their progenitors. Conclusion These results reveal that Runx and CBFβ likely functioned together to regulate transcription in the common ancestor of all metazoans, and the structure of the Runx-CBFβ-DNA complex has remained extremely conserved since the human-sponge divergence. The expression data suggest a hypothesis that these genes may have played a role in nerve cell differentiation or maintenance in the common ancestor of cnidarians and bilaterians.

Ecologia da comunidade de metazoários parasitos da anchova Pomatomus saltator (Linnaeus (Osteichthyes, Pomatomidae do litoral do estado do Rio de Janeiro, Brasil Community ecology of metazoan parasites of bluefish Pomatomus saltator (Linnaeus (Osteichthyes, Pomatomidae from the littoral of State of Rio de Janeiro, Brazil

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José Luis Luque

1999-01-01

Full Text Available Fifty-five specimens of bluefish, Pomatomus saltator (Linnaeus, 1766, collected at Cabo Frio (23ºS, 42ºW, State of Rio de Janeiro, Brazil, between March 1995 and November 1995, were necropsied to study their infracommunities of metazoan parasites. Sixteen species of metazoan parasites were collected. All fish were parasitized by one or more metazoan. The digeneans were the majority of the parasite specimens collected, with 44.2%, followed by the helminth larval stages (cestodes, acanthocephalans, and nematodes with 40.6%. The Simpson index for all parasite species was 0.097, indicating lack of dominance by any species in the parasite community. Microcotyle pomatomi Goto, 1899 showed the higher frequency of dominance and mean relative dominance. The parasite species of P. saltator showed the typical overdispersed pattern of distribution. The majority of parasite species showed positive correlation between the host's total body length and prevalence or parasite abundance. Two species, Brachyphallus parvus (Manter, 1947 and Phocanema sp. have differences in their prevalences and abundances in relation to sex of the hosts. The mean diversity in the infracommunities of P. saltator was H'=1.243±0.521, with correlation with the host's total length and without difference between male and female fish. The components of the parasite community of P. saltator showed overall positive association. All pairs confonned by ectoparasites and adult endoparasites species showed signiticant positive association or covariation between their abundances. Five pairs of endoparasites larval species showed positive association or covariation, and two pairs, showed negative association and covariation. The parasite community of P. saltator was dominated by species with high prevalence values, that composed a high number of associations, thus, is considered closer to the interactive type.

The origin and evolution of Basigin(BSG) gene: A comparative genomic and phylogenetic analysis.

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Zhu, Xinyan; Wang, Shenglan; Shao, Mingjie; Yan, Jie; Liu, Fei

2017-07-01

Basigin (BSG), also known as extracellular matrix metalloproteinase inducer (EMMPRIN) or cluster of differentiation 147 (CD147), plays various fundamental roles in the intercellular recognition involved in immunologic phenomena, differentiation, and development. In this study, we aimed to compare the similarities and differences of BSG among organisms and explore possible evolutionary relationships based on the comparison result. We used the extensive BLAST tool to search the metazoan genomes, N-glycosylation sites, the transmembrane region and other functional sites. We then identified BSG homologs from genomic sequences and analyzed their phylogenetic relationships. We identified that BSG genes exist not only in the vertebrate metazoans but also in the invertebrate metazoans such as Amphioxus B. floridae, D. melanogaster, A. mellifera, S. japonicum, C. gigas, and T. patagoniensis. After sequence analysis, we confirmed that only vertebrate metazoans and Cephalochordate (amphioxus B. floridae) have the classic structure (a signal peptide, two Ig-like domains (IgC2 and IgI), a transmembrane region, and an intracellular domain). The invertebrate metazoans (excluding amphioxus B. floridae) lack the N-terminal signal peptides and IgC2 domain. We then generated a phylogenetic tree, genome organization comparison, and chromosomal disposition analysis based on the biological information obtained from the NCBI and Ensembl databases. Finally, we established the possible evolutionary scenario of the BSG gene, which showed the restricted exon rearrangement that has occurred during evolution, forming the present-day BSG gene. Copyright © 2017 Elsevier Ltd. All rights reserved.

Hydraulic nuts (hydranuts) for critical bolted joints

International Nuclear Information System (INIS)

Greenwell, S.

2008-01-01

HydraNuts replace the original nut and torquing equipment, combining the two functions into one system. Designed for simple installation and operation, HydraNuts are fitted to the stud bolts. Once all HydraNuts are fitted to the application, flexible hydraulic hoses are connected, forming a closed loop hydraulic harness, allowing simultaneous pressurization of all HydraNuts. Hydraulic pressure is obtained by the use of a pumping unit and the resultant load generated is transferred to the studs and flange closure is obtained. Locking rings are rotated into place, supporting the tensioned load mechanically after hydraulic pressure is released. The hose harness is removed. (author)

Implications of duplicated cis-regulatory elements in the evolution of metazoans: the DDI model or how simplicity begets novelty.

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Jiménez-Delgado, Senda; Pascual-Anaya, Juan; Garcia-Fernàndez, Jordi

2009-07-01

The discovery that most regulatory genes were conserved among animals from distant phyla challenged the ideas that gene duplication and divergence of homologous coding sequences were the basis for major morphological changes in metazoan evolution. In recent years, however, the interest for the roles, conservation and changes of non-coding sequences grew-up in parallel with genome sequencing projects. Presently, many independent studies are highlighting the importance that subtle changes in cis-regulatory regions had in the evolution of morphology trough the Animal Kingdom. Here we will show and discuss some of these studies, and underscore the future of cis-Evo-Devo research. Nevertheless, we would also explore how gene duplication, which includes duplication of regulatory regions, may have been critical for spatial or temporal co-option of new regulatory networks, causing the deployment of new transcriptome scenarios, and how these induced morphological changes were critical for the evolution of new forms. Forty years after Susumu Ohno famous sentence 'natural selection merely modifies, while redundancy creates', we suggest the alternative: 'natural selection modifies, while redundancy of cis-regulatory elements innovates', and propose the Duplication-Degeneration-Innovation model to explain the increased evolvability of duplicated cis-regulatory regions. Paradoxically, making regulation simpler by subfunctionalization paved the path for future complexity or, in other words, 'to make it simple to make it complex'.

Nuclear Envelope Phosphatase 1-Regulatory Subunit 1 (Formerly TMEM188) Is the Metazoan Spo7p Ortholog and Functions in the Lipin Activation Pathway*

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Han, Sungwon; Bahmanyar, Shirin; Zhang, Peixiang; Grishin, Nick; Oegema, Karen; Crooke, Roseann; Graham, Mark; Reue, Karen; Dixon, Jack E.; Goodman, Joel M.

2012-01-01

Lipin-1 catalyzes the formation of diacylglycerol from phosphatidic acid. Lipin-1 mutations cause lipodystrophy in mice and acute myopathy in humans. It is heavily phosphorylated, and the yeast ortholog Pah1p becomes membrane-associated and active upon dephosphorylation by the Nem1p-Spo7p membrane complex. A mammalian ortholog of Nem1p is the C-terminal domain nuclear envelope phosphatase 1 (CTDNEP1, formerly “dullard”), but its Spo7p-like partner is unknown, and the need for its existence is debated. Here, we identify the metazoan ortholog of Spo7p, TMEM188, renamed nuclear envelope phosphatase 1-regulatory subunit 1 (NEP1-R1). CTDNEP1 and NEP1-R1 together complement a nem1Δspo7Δ strain to block endoplasmic reticulum proliferation and restore triacylglycerol levels and lipid droplet number. The two human orthologs are in a complex in cells, and the amount of CTDNEP1 is increased in the presence of NEP1-R1. In the Caenorhabditis elegans embryo, expression of nematode CTDNEP1 and NEP1-R1, as well as lipin-1, is required for normal nuclear membrane breakdown after zygote formation. The expression pattern of NEP1-R1 and CTDNEP1 in human and mouse tissues closely mirrors that of lipin-1. CTDNEP1 can dephosphorylate lipins-1a, -1b, and -2 in human cells only in the presence of NEP1-R1. The nuclear fraction of lipin-1b is increased when CTDNEP1 and NEP1-R1 are co-expressed. Therefore, NEP1-R1 is functionally conserved from yeast to humans and functions in the lipin activation pathway. PMID:22134922

Intermediate filament protein evolution and protists.

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Preisner, Harald; Habicht, Jörn; Garg, Sriram G; Gould, Sven B

2018-03-23

Metazoans evolved from a single protist lineage. While all eukaryotes share a conserved actin and tubulin-based cytoskeleton, it is commonly perceived that intermediate filaments (IFs), including lamin, vimentin or keratin among many others, are restricted to metazoans. Actin and tubulin proteins are conserved enough to be detectable across all eukaryotic genomes using standard phylogenetic methods, but IF proteins, in contrast, are notoriously difficult to identify by such means. Since the 1950s, dozens of cytoskeletal proteins in protists have been identified that seemingly do not belong to any of the IF families described for metazoans, yet, from a structural and functional perspective fit criteria that define metazoan IF proteins. Here, we briefly review IF protein discovery in metazoans and the implications this had for the definition of this protein family. We argue that the many cytoskeletal and filament-forming proteins of protists should be incorporated into a more comprehensive picture of IF evolution by aligning it with the recent identification of lamins across the phylogenetic diversity of eukaryotic supergroups. This then brings forth the question of how the diversity of IF proteins has unfolded. The evolution of IF proteins likely represents an example of convergent evolution, which, in combination with the speed with which these cytoskeletal proteins are evolving, generated their current diversity. IF proteins did not first emerge in metazoa, but in protists. Only the emergence of cytosolic IF proteins that appear to stem from a nuclear lamin is unique to animals and coincided with the emergence of true animal multicellularity. © 2018 Wiley Periodicals, Inc.

Evolution of selenoproteins in the metazoan

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Jiang Liang

2012-09-01

Full Text Available Abstract Background The selenocysteine (Sec containing proteins, selenoproteins, are an important group of proteins present throughout all 3 kingdoms of life. With the rapid progression of selenoprotein research in the post-genomic era, application of bioinformatics methods to the identification of selenoproteins in newly sequenced species has become increasingly important. Although selenoproteins in human and other vertebrates have been investigated, studies of primitive invertebrate selenoproteomes are rarely reported outside of insects and nematodes. Result A more integrated view of selenoprotein evolution was constructed using several representative species from different evolutionary eras. Using a SelGenAmic-based selenoprotein identification method, 178 selenoprotein genes were identified in 6 invertebrates: Amphimedon queenslandica, Trichoplax adhaerens, Nematostella vectensis, Lottia gigantean, Capitella teleta, and Branchiostoma floridae. Amphioxus was found to have the most abundant and variant selenoproteins of any animal currently characterized, including a special selenoprotein P (SelP possessing 3 repeated Trx-like domains and Sec residues in the N-terminal and 2 Sec residues in the C-terminal. This gene structure suggests the existence of two different strategies for extension of Sec numbers in SelP for the preservation and transportation of selenium. In addition, novel eukaryotic AphC-like selenoproteins were identified in sponges. Conclusion Comparison of various animal species suggests that even the most primitive animals possess a selenoproteome range and variety similar to humans. During evolutionary history, only a few new selenoproteins have emerged and few were lost. Furthermore, the massive loss of selenoproteins in nematodes and insects likely occurred independently in isolated partial evolutionary branches.

Metazoan meiofauna in deep-sea canyons and adjacent open slopes: A large-scale comparison with focus on the rare taxa

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Bianchelli, S.; Gambi, C.; Zeppilli, D.; Danovaro, R.

2010-03-01

Metazoan meiofaunal abundance, total biomass, nematode size and the richness of taxa were investigated along bathymetric gradients (from the shelf break down to ca. 5000-m depth) in six submarine canyons and on five adjacent open slopes of three deep-sea regions. The investigated areas were distributed along >2500 km, on the Portuguese to the Catalan and South Adriatic margins. The Portuguese and Catalan margins displayed the highest abundances, biomass and richness of taxa, while the lowest values were observed in the Central Mediterranean Sea. The comparison between canyons and the nearby open slopes showed the lack of significant differences in terms of meiofaunal abundance and biomass at any sampling depth. In most canyons and on most slopes, meiofaunal variables did not display consistent bathymetric patterns. Conversely, we found that the different topographic features were apparently responsible for significant differences in the abundance and distribution of the rare meiofaunal taxa (i.e. taxa accounting for Priapulida, Holothuroidea, Ascidiacea and Cnidaria, were encountered exclusively on open slopes, while others (including the Tanaidacea and Echinodea larvae) were found exclusively in canyons sediments. Results reported here indicate that, at large spatial scales, differences in deep-sea meiofaunal abundance and biomass are not only controlled by the available food sources, but also by the region or habitat specific topographic features, which apparently play a key role in the distribution of rare benthic taxa.

Design and Optimization of Multi-Pixel Transition-Edge Sensors for X-Ray Astronomy Applications

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Smith, Stephen J.; Adams, Joseph S.; Bandler, Simon R.; Chervenak, James A.; Datesman, Aaron Michael; Eckart, Megan E.; Ewin, Audrey J.; Finkbeiner, Fred M.; Kelley, Richard L.; Kilbourne, Caroline A.;

Temporal variation in the dispersion patterns of metazoan parasites of a coastal fish species from the Gulf of Mexico.

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Vidal-Martínez, V M; Pal, P; Aguirre-Macedo, M L; May-Tec, A L; Lewis, J W

2014-03-01

Global climate change (GCC) is expected to affect key environmental variables such as temperature and rainfall, which in turn influence the infection dynamics of metazoan parasites in tropical aquatic hosts. Thus, our aim was to determine how temporal patterns of temperature and rainfall influence the mean abundance and aggregation of three parasite species of the fish Cichlasoma urophthalmus from Yucatán, México. We calculated mean abundance and the aggregation parameter of the negative binomial distribution k for the larval digeneans Oligogonotylus manteri and Ascocotyle (Phagicola) nana and the ectoparasite Argulus yucatanus monthly from April 2005 to December 2010. Fourier analysis of time series and cross-correlations were used to determine potential associations between mean abundance and k for the three parasite species with water temperature and rainfall. Both O. manteri and A. (Ph.) nana exhibited their highest frequency peaks in mean abundance at 6 and 12 months, respectively, while their peak in k occurred every 24 months. For A. yucatanus the frequency peaks in mean abundance and k occurred every 12 months. We suggest that the level of aggregation at 24 months of O. manteri increases the likelihood of fish mortality. Such a scenario is less likely for A. (Ph.) nana and A. yucatanus, due to their low infection levels. Our findings suggest that under the conditions of GCC it would be reasonable to expect higher levels of parasite aggregation in tropical aquatic hosts, in turn leading to a potential increase in parasite-induced host mortality.

LncRNA, a new component of expanding RNA-protein regulatory network important for animal sperm development.

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Zhang, Chenwang; Gao, Liuze; Xu, Eugene Yujun

2016-11-01

Spermatogenesis is one of the fundamental processes of sexual reproduction, present in almost all metazoan animals. Like many other reproductive traits, developmental features and traits of spermatogenesis are under strong selective pressure to change, both at morphological and underlying molecular levels. Yet evidence suggests that some fundamental features of spermatogenesis may be ancient and conserved among metazoan species. Identifying the underlying conserved molecular mechanisms could reveal core components of metazoan spermatogenic machinery and provide novel insight into causes of human infertility. Conserved RNA-binding proteins and their interacting RNA network emerge to be a common theme important for animal sperm development. We review research on the recent addition to the RNA family - Long non-coding RNA (lncRNA) and its roles in spermatogenesis in the context of the expanding RNA-protein network. Copyright © 2016 Elsevier Ltd. All rights reserved.

Astronomers See First Stages of Planet-Building Around Nearby Star

Science.gov (United States)

2005-06-01

Interstellar travelers might want to detour around the star system TW Hydrae to avoid a messy planetary construction site. Astronomer David Wilner of the Harvard-Smithsonian Center for Astrophysics (CfA) and his colleagues have discovered that the gaseous protoplanetary disk surrounding TW Hydrae holds vast swaths of pebbles extending outward for at least 1 billion miles. These rocky chunks should continue to grow in size as they collide and stick together until they eventually form planets. Dust Disk Graphic Artist's Conception of Dusty Disk Around Young Star TW Hydrae CREDIT: Bill Saxton, NRAO/AUI/NSF (Click on image for larger version 1.8 MB) "We're seeing planet building happening right before our eyes," said Wilner. "The foundation has been laid and now the building materials are coming together to make a new solar system." Wilner used the National Science Foundation's Very Large Array to measure radio emissions from TW Hydrae. He detected radiation from a cold, extended dust disk suffused with centimeter-sized pebbles. Such pebbles are a prerequisite for planet formation, created as dust collects together into larger and larger clumps. Over millions of years, those clumps grow into planets. "We're seeing an important step on the path from interstellar dust particles to planets," said Mark Claussen (NRAO), a co-author on the paper announcing the discovery. "No one has seen this before." A dusty disk like that in TW Hydrae tends to emit radio waves with wavelengths similar to the size of the particles in the disk. Other effects can mask this, however. In TW Hydrae, the astronomers explained, both the relatively close distance of the system and the stage of the young star's evolution are just right to allow the relationship of particle size and wavelength to prevail. The scientists observed the young star's disk with the VLA at several centimeter-range wavelengths. "The strong emission at wavelengths of a few centimeters is convincing evidence that particles of

A Genome Wide Comparison to Identify Markers to Differentiate the Sex of Larval Stages of Schistosoma haematobium, Schistosoma bovis and their Respective Hybrids.

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Julien Kincaid-Smith

2016-11-01

Full Text Available For scientists working on gonochoric organisms, determining sex can be crucial for many biological questions and experimental studies, such as crossbreeding, but it can also be a challenging task, particularly when no sexual dimorphism is visible or cannot be directly observed. In metazoan parasites of the genus Schistosoma responsible for schistosomiasis, sex is genetically determined in the zygote with a female heterogametic ZW/ZZ system. Adult flukes have a pronounced sexual dimorphism, whereas the sexes of the larval stages are morphologically indistinguishable but can be distinguished uniquely by using molecular methods. Therefore, reliable methods are needed to identify the sex of larvae individuals. Here, we present an endpoint PCR-based assay using female-specific sequences identified using a genome-wide comparative analysis between males and females. This work allowed us to identify sex-markers for Schistosoma haematobium and Schistosoma bovis but also the hybrid between both species that has recently emerged in Corsica (France. Five molecular sex-markers were identified and are female-specific in S. haematobium and the hybrid parasite, whereas three of them are also female-specific in S. bovis. These molecular markers will be useful to conduct studies, such as experimental crosses on these disease-causing blood flukes, which are still largely neglected but no longer restricted to tropical areas.

Metazoan endoparasites of Serrasalmus marginatus (Characiformes: Serrasalminae in the Negro River, Pantanal, Brazil Metazoários endoparasitos de Serrasalmus marginatus (Characiformes: Serrasalminae no Rio Negro, Pantanal, Brasil

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Wagner Vicentin

2011-03-01

Full Text Available In order to inventory the metazoan endoparasites of Serrasalmus marginatus, 91 specimens were examined. They were captured in the Negro River in Pantanal wetland, State of Mato Grosso do Sul, Central-Western Brazil, from October 2007 to August 2008. Parasites of six taxa were recovered: Procamallanus (Spirocamallanus inopinatus, Contracaecum sp. (Nematoda, metacercarial type Diplostomulum (Digenea, Brevimulticaecum sp. (Nematoda and Sebekia oxycephala, Subtriquetra sp. 1 and Subtriquetra sp. 2 (Pentastomida. The latter five species are reported for the first time in S. marginatus.Com o objetivo de inventariar os metazoários endoparasitos em Serrasalmus marginatus, no Rio Negro, Pantanal, Mato Grosso do Sul, Brasil, foram examinados 91 espécimes capturados no período de outubro de 2007 a agosto de 2008. Foram registrados seis táxons parasitos: Procamallanus (Spirocamallanus inopinatus, Contracaecum sp. (Nematoda, metacercária do tipo Diplostomulum (Digenea; Brevimulticaecum sp. (Nematoda; e Sebekia oxycephala, Subtriquetra sp. 1 e Subtriquetra sp. 2 (Pentastomida. As últimas cinco espécies citadas são registradas pela primeira vez em S. marginatus.

Transcriptome analysis of the scleractinian coral Stylophora pistillata.

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Sarit Karako-Lampert

Full Text Available The principal architects of coral reefs are the scleractinian corals; these species are divided in two major clades referred to as "robust" and "complex" corals. Although the molecular diversity of the "complex" clade has received considerable attention, with several expressed sequence tag (EST libraries and a complete genome sequence having been constructed, the "robust" corals have received far less attention, despite the fact that robust corals have been prominent focal points for ecological and physiological studies. Filling this gap affords important opportunities to extend these studies and to improve our understanding of the differences between the two major clades. Here, we present an EST library from Stylophora pistillata (Esper 1797 and systematically analyze the assembled transcripts compared to putative homologs from the complete proteomes of six well-characterized metazoans: Nematostella vectensis, Hydra magnipapillata, Caenorhabditis elegans, Drosophila melanogaster, Strongylocentrotus purpuratus, Ciona intestinalis and Homo sapiens. Furthermore, comparative analyses of the Stylophora pistillata ESTs were performed against several Cnidaria from the Scleractinia, Actiniaria and Hydrozoa, as well as against other stony corals separately. Functional characterization of S. pistillata transcripts into KOG/COG categories and further description of Wnt and bone morphogenetic protein (BMP signaling pathways showed that the assembled EST library provides sufficient data and coverage. These features of this new library suggest considerable opportunities for extending our understanding of the molecular and physiological behavior of "robust" corals.

miRNA Repertoires of Demosponges Stylissa carteri and Xestospongia testudinaria

KAUST Repository

Liew, Yi Jin

2016-02-12

MicroRNAs (miRNAs) are small regulatory RNAs that are involved in many biological process in eukaryotes. They play a crucial role in modulating genetic expression of their targets, which makes them integral components of transcriptional regulatory networks. As sponges (phylum Porifera) are commonly considered the most basal metazoan, the in-depth capture of miRNAs from these organisms provides additional clues to the evolution of miRNA families in metazoans. Here, we identified the core proteins involved in the biogenesis of miRNAs, and obtained evidence for bona fide miRNA sequences for two marine sponges Stylissa carteri and Xestospongia testudinaria (11 and 19 respectively). Our analysis identified several miRNAs that are conserved amongst demosponges, and revealed that all of the novel miRNAs identified in these two species are specific to the class Demospongiae.

miRNA Repertoires of Demosponges Stylissa carteri and Xestospongia testudinaria

KAUST Repository

Liew, Yi Jin; Ryu, Tae Woo; Aranda, Manuel; Ravasi, Timothy

2016-01-01

MicroRNAs (miRNAs) are small regulatory RNAs that are involved in many biological process in eukaryotes. They play a crucial role in modulating genetic expression of their targets, which makes them integral components of transcriptional regulatory networks. As sponges (phylum Porifera) are commonly considered the most basal metazoan, the in-depth capture of miRNAs from these organisms provides additional clues to the evolution of miRNA families in metazoans. Here, we identified the core proteins involved in the biogenesis of miRNAs, and obtained evidence for bona fide miRNA sequences for two marine sponges Stylissa carteri and Xestospongia testudinaria (11 and 19 respectively). Our analysis identified several miRNAs that are conserved amongst demosponges, and revealed that all of the novel miRNAs identified in these two species are specific to the class Demospongiae.

Stealth proteins: in silico identification of a novel protein family rendering bacterial pathogens invisible to host immune defense.

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Peter Sperisen

2005-11-01

Full Text Available There are a variety of bacterial defense strategies to survive in a hostile environment. Generation of extracellular polysaccharides has proved to be a simple but effective strategy against the host's innate immune system. A comparative genomics approach led us to identify a new protein family termed Stealth, most likely involved in the synthesis of extracellular polysaccharides. This protein family is characterized by a series of domains conserved across phylogeny from bacteria to eukaryotes. In bacteria, Stealth (previously characterized as SacB, XcbA, or WefC is encoded by subsets of strains mainly colonizing multicellular organisms, with evidence for a protective effect against the host innate immune defense. More specifically, integrating all the available information about Stealth proteins in bacteria, we propose that Stealth is a D-hexose-1-phosphoryl transferase involved in the synthesis of polysaccharides. In the animal kingdom, Stealth is strongly conserved across evolution from social amoebas to simple and complex multicellular organisms, such as Dictyostelium discoideum, hydra, and human. Based on the occurrence of Stealth in most Eukaryotes and a subset of Prokaryotes together with its potential role in extracellular polysaccharide synthesis, we propose that metazoan Stealth functions to regulate the innate immune system. Moreover, there is good reason to speculate that the acquisition and spread of Stealth could be responsible for future epidemic outbreaks of infectious diseases caused by a large variety of eubacterial pathogens. Our in silico identification of a homologous protein in the human host will help to elucidate the causes of Stealth-dependent virulence. At a more basic level, the characterization of the molecular and cellular function of Stealth proteins may shed light on fundamental mechanisms of innate immune defense against microbial invasion.

Stealth Proteins: In Silico Identification of a Novel Protein Family Rendering Bacterial Pathogens Invisible to Host Immune Defense.

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2005-11-01

Full Text Available There are a variety of bacterial defense strategies to survive in a hostile environment. Generation of extracellular polysaccharides has proved to be a simple but effective strategy against the host's innate immune system. A comparative genomics approach led us to identify a new protein family termed Stealth, most likely involved in the synthesis of extracellular polysaccharides. This protein family is characterized by a series of domains conserved across phylogeny from bacteria to eukaryotes. In bacteria, Stealth (previously characterized as SacB, XcbA, or WefC is encoded by subsets of strains mainly colonizing multicellular organisms, with evidence for a protective effect against the host innate immune defense. More specifically, integrating all the available information about Stealth proteins in bacteria, we propose that Stealth is a D-hexose-1-phosphoryl transferase involved in the synthesis of polysaccharides. In the animal kingdom, Stealth is strongly conserved across evolution from social amoebas to simple and complex multicellular organisms, such as Dictyostelium discoideum, hydra, and human. Based on the occurrence of Stealth in most Eukaryotes and a subset of Prokaryotes together with its potential role in extracellular polysaccharide synthesis, we propose that metazoan Stealth functions to regulate the innate immune system. Moreover, there is good reason to speculate that the acquisition and spread of Stealth could be responsible for future epidemic outbreaks of infectious diseases caused by a large variety of eubacterial pathogens. Our in silico identification of a homologous protein in the human host will help to elucidate the causes of Stealth-dependent virulence. At a more basic level, the characterization of the molecular and cellular function of Stealth proteins may shed light on fundamental mechanisms of innate immune defense against microbial invasion.

Journal of Biosciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

The diploblastic Hydra is among the most primitive multicellular organisms. Using cross-hybridization with Xenopus probes, noggin-like transcripts were detected in the hypostome and basal disc of adult Hydra (Pelmatohydra oligactis), regions with properties similar to that of the amphibian organizer. This points to the ...

Gastrin/CCK-like immunoreactivity in the nervous system of coelenterates

DEFF Research Database (Denmark)

Grimmelikhuijzen, C J; Sundler, F; Rehfeld, J F

1980-01-01

Using immunocytochemistry, gastrin/CCK-like immunoreactivity is found in sensory nerve cells in the ectoderm of the mouth region of hydra and in nerve cells in the endoderm of all body regions of the sea anemone tealia. These results are corroborated by radioimmunoassay: One hydra contains at lea...

Evolutionary genomics of plant genes encoding N-terminal-TM-C2 domain proteins and the similar FAM62 genes and synaptotagmin genes of metazoans

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Craxton Molly

2007-07-01

Full Text Available Abstract Background Synaptotagmin genes are found in animal genomes and are known to function in the nervous system. Genes with a similar domain architecture as well as sequence similarity to synaptotagmin C2 domains have also been found in plant genomes. The plant genes share an additional region of sequence similarity with a group of animal genes named FAM62. FAM62 genes also have a similar domain architecture. Little is known about the functions of the plant genes and animal FAM62 genes. Indeed, many members of the large and diverse Syt gene family await functional characterization. Understanding the evolutionary relationships among these genes will help to realize the full implications of functional studies and lead to improved genome annotation. Results I collected and compared plant Syt-like sequences from the primary nucleotide sequence databases at NCBI. The collection comprises six groups of plant genes conserved in embryophytes: NTMC2Type1 to NTMC2Type6. I collected and compared metazoan FAM62 sequences and identified some similar sequences from other eukaryotic lineages. I found evidence of RNA editing and alternative splicing. I compared the intron patterns of Syt genes. I also compared Rabphilin and Doc2 genes. Conclusion Genes encoding proteins with N-terminal-transmembrane-C2 domain architectures resembling synaptotagmins, are widespread in eukaryotes. A collection of these genes is presented here. The collection provides a resource for studies of intron evolution. I have classified the collection into homologous gene families according to distinctive patterns of sequence conservation and intron position. The evolutionary histories of these gene families are traceable through the appearance of family members in different eukaryotic lineages. Assuming an intron-rich eukaryotic ancestor, the conserved intron patterns distinctive of individual gene families, indicate independent origins of Syt, FAM62 and NTMC2 genes. Resemblances

Metazoan parasites of Mandi-amarelo Pimelodus maculatus and of Jundiá Rhamdia quelen (Osteichthyes: Siluriformes) of Paraíba do Sul River, Volta Redonda, Rio de Janeiro.

Science.gov (United States)

Venancio, Aline Cristine Pinto; de Aguiar, Gesilene Ribeiro; Lopes, Patrícia da Silva; Alves, Dimitri Ramos

2010-01-01

Forty-one specimens of mandi-amarelo Pimelodus maculatus Lacépède, 1803 (Siluriformes: Pimelodidae) and 54 specimens of jundiá Rhamdia quelen (Quoy & Gaimard, 1824) (Siluriformes: Heptapteridae) were collected from the Paraíba do Sul River, Volta Redonda, State of Rio de Janeiro, Brazil between November 2007 and October 2008. These fish underwent necropsy so their infracommunities of metazoan parasites could be studied. The same three species of parasites were collected in the two fish species studied. These were one monogenean, one nematode, and one hirudinean. Cucullanus pinnai (Travassos, Artiga, and Pereira, 1928) (Nematoda: Cucullanidae) and Aphanoblastella sp. (Monogenea: Dactylogyridae) were the dominant species with the highest prevalence in P. maculatus and R. quelen. The parasite species of P. maculatus and R. quelen showed an atypical over-dispersed pattern of distribution. No parasite species showed significant correlation between the body total length of the siluriform hosts and their prevalence and abundance. The parasite species richness showed a mean value of 0.87 ± 0.67 (0-2) and 0.57 ± 0.56 (0-2) in P. maculatus and R. quelen, respectively, and no correlation with the body total length.

Human Cytomegalovirus Nuclear Egress Proteins Ectopically Expressed in the Heterologous Environment of Plant Cells are Strictly Targeted to the Nuclear Envelope.

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Lamm, Christian E; Link, Katrin; Wagner, Sabrina; Milbradt, Jens; Marschall, Manfred; Sonnewald, Uwe

2016-03-10

In all eukaryotic cells, the nucleus forms a prominent cellular compartment containing the cell's nuclear genome. Although structurally similar, animal and plant nuclei differ substantially in details of their architecture. One example is the nuclear lamina, a layer of tightly interconnected filament proteins (lamins) underlying the nuclear envelope of metazoans. So far no orthologous lamin genes could be detected in plant genomes and putative lamin-like proteins are only poorly described in plants. To probe for potentially conserved features of metazoan and plant nuclear envelopes, we ectopically expressed the core nuclear egress proteins of human cytomegalovirus pUL50 and pUL53 in plant cells. pUL50 localizes to the inner envelope of metazoan nuclei and recruits the nuclear localized pUL53 to it, forming heterodimers. Upon expression in plant cells, a very similar localization pattern of both proteins could be determined. Notably, pUL50 is specifically targeted to the plant nuclear envelope in a rim-like fashion, a location to which coexpressed pUL53 becomes strictly corecruited from its initial nucleoplasmic distribution. Using pUL50 as bait in a yeast two-hybrid screening, the cytoplasmic re-initiation supporting protein RISP could be identified. Interaction of pUL50 and RISP could be confirmed by coexpression and coimmunoprecipitation in mammalian cells and by confocal laser scanning microscopy in plant cells, demonstrating partial pUL50-RISP colocalization in areas of the nuclear rim and other intracellular compartments. Thus, our study provides strong evidence for conserved structural features of plant and metazoan nuclear envelops and identifies RISP as a potential pUL50-interacting plant protein.

Lack of Csk-mediated negative regulation in a unicellular SRC kinase.

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Schultheiss, Kira P; Suga, Hiroshi; Ruiz-Trillo, Iñaki; Miller, W Todd

2012-10-16

Phosphotyrosine-based signaling plays a vital role in cellular communication in multicellular organisms. Unexpectedly, unicellular choanoflagellates (the closest phylogenetic group to metazoans) possess numbers of tyrosine kinases that are comparable to those in complex metazoans. Here, we have characterized tyrosine kinases from the filasterean Capsaspora owczarzaki, a unicellular protist representing the sister group to choanoflagellates and metazoans. Two Src-like tyrosine kinases have been identified in C. owczarzaki (CoSrc1 and CoSrc2), both of which have the arrangement of SH3, SH2, and catalytic domains seen in mammalian Src kinases. In Capsaspora cells, CoSrc1 and CoSrc2 localize to punctate structures in filopodia that may represent primordial focal adhesions. We have cloned, expressed, and purified both enzymes. CoSrc1 and CoSrc2 are active tyrosine kinases. Mammalian Src kinases are normally regulated in a reciprocal fashion by autophosphorylation in the activation loop (which increases activity) and by Csk-mediated phosphorylation of the C-terminal tail (which inhibits activity). Similar to mammalian Src kinases, the enzymatic activities of CoSrc1 and CoSrc2 are increased by autophosphorylation in the activation loop. We have identified a Csk-like kinase (CoCsk) in the genome of C. owczarzaki. We cloned, expressed, and purified CoCsk and found that it has no measurable tyrosine kinase activity. Furthermore, CoCsk does not phosphorylate or regulate CoSrc1 or CoSrc2 in cells or in vitro, and CoSrc1 and CoSrc2 are active in Capsaspora cell lysates. Thus, the function of Csk as a negative regulator of Src family kinases appears to have arisen with the emergence of metazoans.

A New Metazoan Recombination Rate Record and Consistently High Recombination Rates in the Honey Bee Genus Apis Accompanied by Frequent Inversions but Not Translocations

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Kuster, Ryan; Miller, Katelyn; Fouks, Bertrand; Rubio Correa, Sara; Collazo, Juan; Phaincharoen, Mananya; Tingek, Salim; Koeniger, Nikolaus

2016-01-01

Abstract Western honey bees (Apis mellifera) far exceed the commonly observed 1–2 meiotic recombination events per chromosome and exhibit the highest Metazoan recombination rate (20 cM/Mb) described thus far. However, the reasons for this exceptional rate of recombination are not sufficiently understood. In a comparative study, we report on the newly constructed genomic linkage maps of Apis florea and Apis dorsata that represent the two honey bee lineages without recombination rate estimates so far. Each linkage map was generated de novo, based on SNP genotypes of haploid male offspring of a single female. The A. florea map spans 4,782 cM with 1,279 markers in 16 linkage groups. The A. dorsata map is 5,762 cM long and contains 1,189 markers in 16 linkage groups. Respectively, these map sizes result in average recombination rate estimates of 20.8 and 25.1 cM/Mb. Synteny analyses indicate that frequent intra-chromosomal rearrangements but no translocations among chromosomes accompany the high rates of recombination during the independent evolution of the three major honey bee lineages. Our results imply a common cause for the evolution of very high recombination rates in Apis. Our findings also suggest that frequent homologous recombination during meiosis might increase ectopic recombination and rearrangements within but not between chromosomes. It remains to be investigated whether the resulting inversions may have been important in the evolutionary differentiation between honey bee species. PMID:28173114

Metazoarios parásitos de Tlacuatzin canescens y Marmosa mexicana (Mammalia: Didelphimorphia de México Metazoan parasites of Tlacuatzin canescens and Marmosa mexicana (Mammalia: Didelphimorphia from Mexico

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Carmen Guzmán-Cornejo

2012-06-01

Full Text Available Como parte de un estudio sobre los metazoarios parásitos de mamíferos de México se recolectaron 4 ejemplares de ratones tlacuache: 2 de Tlacuatzin canescens (Allen, 1893 procedentes de Oaxaca y 2 de Marmosa mexicana Merriam, 1897 de Veracruz. Se presentan 5 registros nuevos de hospedero y localidad para ácaros de las especies Ixodes luciae Sénevet, 1940, Ixodes sinaloa Kohls y Clifford, 1966, las pulgas Plusaetis mathesoni (Traub 1950 y Polygenis martinezbaezi Vargas 1951, así como para el cestodo Hymenolepis sp. y por primera vez en México se registra el nematodo Hoineffia simplicispicula Navone, Suriano y Pujol, 1991.As a part of an ongoing project to inventory the metazoan parasites of Mexican mammals, 4 specimens of 2 species of mouse opossums (2 Tlacuatzin canescens [Allen, 1893] and 2 Marmosa mexicana Merriam, 1897, were collected from Oaxaca and Veracuz states, Mexico, respectively. Five new locality and host records are presented for the acari Ixodes luciae Sénevet, 1940, Ixodes sinaloa Kohls and Clifford, 1966, of fleas Plusaetis mathesoni (Traub 1950, and Polygenis martinezbaezi Vargas 1951, as well as the cestode Hymenolepis sp., while the nematode Hoineffia simplicispicula Navone, Suriano and Pujol, 1991, is recorded for the first time in Mexico.

A trophic framework for animal origins

DEFF Research Database (Denmark)

Mills, D. B.; Canfield, D. E.

2017-01-01

Metazoans emerged in a microbial world and play a unique role in the biosphere as the only complex multicellular eukaryotes capable of phagocytosis. While the bodyplan and feeding mode of the last common metazoan ancestor remain unresolved, the earliest multicellular stem-metazoans likely subsist...

CEPF Western Ghats Special Series: Metazoan community composition in tree hole aquatic habitats of Silent Valley National Park and New Amarambalam Reserve Forest of the Western Ghats, India

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K.A. Nishadh

2012-11-01

Full Text Available In a study of the metazoan community composition in tree hole aquatic habitat of a tropical rainforest, Silent Valley National Park, and the adjacent moist deciduous forest, New Amarambalam Reserve Forest, of the Western Ghats, 28 different species were recorded from 150 tree hole aquatic habitats with an average of 3-5 species per tree hole. Most of the recorded organisms (96.8% belong to Odonata (dragonflies and damselflies, Heteroptera (bugs, Diptera (flies, Coleoptera (beetles and Trichoptera (caddisflies. The study reports the first record of toe-winged beetle larvae (Ptilodactylidae in a tree hole aquatic habitat. The most significant observation is the prolific occurrence of trichopteran larvae as the second most abundant taxa in tree holes of Silent Valley National Park, and this stands as the first comprehensive record of the entire order in the habitat studied. The study upholds the importance of less explored microhabitats in the Western Ghats region in terms of sustaining unique community composition in the most delicate and extreme habitat conditions. It also puts forward important ecological research questions on biodiversity ecosystem functionality which could impart important lessons for managing and conserving the diminishing tropical evergreen forests which are significant for these unique habitats.

Flies selected for longevity retain a young gene expression profile

DEFF Research Database (Denmark)

Sarup, Pernille Merete; Sørensen, Peter; Loeschcke, Volker

2011-01-01

  We investigated correlated responses in the transcriptomes of longevity-selected lines of Drosophila melanogaster to identify pathways that affect life span in metazoan systems. We evaluated the gene expression profile in young, middle-aged, and old male flies, finding that 530 genes were...

A “Rosetta Stone” for metazoan zooplankton: DNA barcode analysis of species diversity of the Sargasso Sea (Northwest Atlantic Ocean)

Science.gov (United States)

Bucklin, Ann; Ortman, Brian D.; Jennings, Robert M.; Nigro, Lisa M.; Sweetman, Christopher J.; Copley, Nancy J.; Sutton, Tracey; Wiebe, Peter H.

2010-12-01

Species diversity of the metazoan holozooplankton assemblage of the Sargasso Sea, Northwest Atlantic Ocean, was examined through coordinated morphological taxonomic identification of species and DNA sequencing of a ˜650 base-pair region of mitochondrial cytochrome oxidase I (mtCOI) as a DNA barcode (i.e., short sequence for species recognition and discrimination). Zooplankton collections were made from the surface to 5,000 meters during April, 2006 on the R/V R.H. Brown. Samples were examined by a ship-board team of morphological taxonomists; DNA barcoding was carried out in both ship-board and land-based DNA sequencing laboratories. DNA barcodes were determined for a total of 297 individuals of 175 holozooplankton species in four phyla, including: Cnidaria (Hydromedusae, 4 species; Siphonophora, 47); Arthropoda (Amphipoda, 10; Copepoda, 34; Decapoda, 9; Euphausiacea, 10; Mysidacea, 1; Ostracoda, 27); and Mollusca (Cephalopoda, 8; Heteropoda, 6; Pteropoda, 15); and Chaetognatha (4). Thirty species of fish (Teleostei) were also barcoded. For all seven zooplankton groups for which sufficient data were available, Kimura-2-Parameter genetic distances were significantly lower between individuals of the same species (mean=0.0114; S.D. 0.0117) than between individuals of different species within the same group (mean=0.3166; S.D. 0.0378). This difference, known as the barcode gap, ensures that mtCOI sequences are reliable characters for species identification for the oceanic holozooplankton assemblage. In addition, DNA barcodes allow recognition of new or undescribed species, reveal cryptic species within known taxa, and inform phylogeographic and population genetic studies of geographic variation. The growing database of "gold standard" DNA barcodes serves as a Rosetta Stone for marine zooplankton, providing the key for decoding species diversity by linking species names, morphology, and DNA sequence variation. In light of the pivotal position of zooplankton in ocean

Diffusible iodine-based contrast-enhanced computed tomography (diceCT): an emerging tool for rapid, high-resolution, 3-D imaging of metazoan soft tissues.

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Gignac, Paul M; Kley, Nathan J; Clarke, Julia A; Colbert, Matthew W; Morhardt, Ashley C; Cerio, Donald; Cost, Ian N; Cox, Philip G; Daza, Juan D; Early, Catherine M; Echols, M Scott; Henkelman, R Mark; Herdina, A Nele; Holliday, Casey M; Li, Zhiheng; Mahlow, Kristin; Merchant, Samer; Müller, Johannes; Orsbon, Courtney P; Paluh, Daniel J; Thies, Monte L; Tsai, Henry P; Witmer, Lawrence M

2016-06-01

Morphologists have historically had to rely on destructive procedures to visualize the three-dimensional (3-D) anatomy of animals. More recently, however, non-destructive techniques have come to the forefront. These include X-ray computed tomography (CT), which has been used most commonly to examine the mineralized, hard-tissue anatomy of living and fossil metazoans. One relatively new and potentially transformative aspect of current CT-based research is the use of chemical agents to render visible, and differentiate between, soft-tissue structures in X-ray images. Specifically, iodine has emerged as one of the most widely used of these contrast agents among animal morphologists due to its ease of handling, cost effectiveness, and differential affinities for major types of soft tissues. The rapid adoption of iodine-based contrast agents has resulted in a proliferation of distinct specimen preparations and scanning parameter choices, as well as an increasing variety of imaging hardware and software preferences. Here we provide a critical review of the recent contributions to iodine-based, contrast-enhanced CT research to enable researchers just beginning to employ contrast enhancement to make sense of this complex new landscape of methodologies. We provide a detailed summary of recent case studies, assess factors that govern success at each step of the specimen storage, preparation, and imaging processes, and make recommendations for standardizing both techniques and reporting practices. Finally, we discuss potential cutting-edge applications of diffusible iodine-based contrast-enhanced computed tomography (diceCT) and the issues that must still be overcome to facilitate the broader adoption of diceCT going forward. © 2016 The Authors. Journal of Anatomy published by John Wiley & Sons Ltd on behalf of Anatomical Society.

Use of an activated beta-catenin to identify Wnt pathway target genes in caenorhabditis elegans, including a subset of collagen genes expressed in late larval development.

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Jackson, Belinda M; Abete-Luzi, Patricia; Krause, Michael W; Eisenmann, David M

2014-04-16

The Wnt signaling pathway plays a fundamental role during metazoan development, where it regulates diverse processes, including cell fate specification, cell migration, and stem cell renewal. Activation of the beta-catenin-dependent/canonical Wnt pathway up-regulates expression of Wnt target genes to mediate a cellular response. In the nematode Caenorhabditis elegans, a canonical Wnt signaling pathway regulates several processes during larval development; however, few target genes of this pathway have been identified. To address this deficit, we used a novel approach of conditionally activated Wnt signaling during a defined stage of larval life by overexpressing an activated beta-catenin protein, then used microarray analysis to identify genes showing altered expression compared with control animals. We identified 166 differentially expressed genes, of which 104 were up-regulated. A subset of the up-regulated genes was shown to have altered expression in mutants with decreased or increased Wnt signaling; we consider these genes to be bona fide C. elegans Wnt pathway targets. Among these was a group of six genes, including the cuticular collagen genes, bli-1 col-38, col-49, and col-71. These genes show a peak of expression in the mid L4 stage during normal development, suggesting a role in adult cuticle formation. Consistent with this finding, reduction of function for several of the genes causes phenotypes suggestive of defects in cuticle function or integrity. Therefore, this work has identified a large number of putative Wnt pathway target genes during larval life, including a small subset of Wnt-regulated collagen genes that may function in synthesis of the adult cuticle.

First Description of Sulphur-Oxidizing Bacterial Symbiosis in a Cnidarian (Medusozoa Living in Sulphidic Shallow-Water Environments.

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Sylvie Abouna

Full Text Available Since the discovery of thioautotrophic bacterial symbiosis in the giant tubeworm Riftia pachyptila, there has been great impetus to investigate such partnerships in other invertebrates. In this study, we present the occurrence of a sulphur-oxidizing symbiosis in a metazoan belonging to the phylum Cnidaria in which this event has never been described previously.Scanning Electron Microscope (SEM, Transmission Electron Microscope (TEM observations and Energy-dispersive X-ray spectroscopy (EDXs analysis, were employed to unveil the presence of prokaryotes population bearing elemental sulphur granules, growing on the body surface of the metazoan. Phylogenetic assessments were also undertaken to identify this invertebrate and microorganisms in thiotrophic symbiosis. Our results showed the occurrence of a thiotrophic symbiosis in a cnidarian identified as Cladonema sp.This is the first report describing the occurrence of a sulphur-oxidizing symbiosis in a cnidarian. Furthermore, of the two adult morphologies, the polyp and medusa, this mutualistic association was found restricted to the polyp form of Cladonema sp.

First Description of Sulphur-Oxidizing Bacterial Symbiosis in a Cnidarian (Medusozoa) Living in Sulphidic Shallow-Water Environments.

Science.gov (United States)

Abouna, Sylvie; Gonzalez-Rizzo, Silvina; Grimonprez, Adrien; Gros, Olivier

2015-01-01

Since the discovery of thioautotrophic bacterial symbiosis in the giant tubeworm Riftia pachyptila, there has been great impetus to investigate such partnerships in other invertebrates. In this study, we present the occurrence of a sulphur-oxidizing symbiosis in a metazoan belonging to the phylum Cnidaria in which this event has never been described previously. Scanning Electron Microscope (SEM), Transmission Electron Microscope (TEM) observations and Energy-dispersive X-ray spectroscopy (EDXs) analysis, were employed to unveil the presence of prokaryotes population bearing elemental sulphur granules, growing on the body surface of the metazoan. Phylogenetic assessments were also undertaken to identify this invertebrate and microorganisms in thiotrophic symbiosis. Our results showed the occurrence of a thiotrophic symbiosis in a cnidarian identified as Cladonema sp. This is the first report describing the occurrence of a sulphur-oxidizing symbiosis in a cnidarian. Furthermore, of the two adult morphologies, the polyp and medusa, this mutualistic association was found restricted to the polyp form of Cladonema sp.

Ecologia da comunidade de metazoários parasitos da Maria-Luiza, Paralonchurus brasiliensis (Osteichthyes: Sciaenidae do litoral do Estado do Rio de Janeiro, Brasil - DOI: 10.4025/actascibiolsci.v25i2.2009 Community ecology of the metazoan parasites of Banded Croaker, Paralonchurus brasiliensis (Osteichthyes: Sciaenidae, from the coastal zone of the State of Rio de Janeiro, Brazil- DOI: 10.4025/actascibiolsci.v25i2.2009

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Renata da Silva Ribeiro

2003-04-01

Full Text Available Foram examinados 93 espécimes de Paralonchurus brasiliensis (Steindachner, 1875, provenientes da Pedra de Guaratiba (23º01’S, 43º38’W litoral do Estado do Rio de Janeiro, Brasil. No período de setembro de 2001 até março de 2002, sendo necropsiados para estudo da sua comunidade de metazoários parasitos. Quinze espécies de parasitos foram coletadas. Paralonchurus brasiliensis é um novo registro de hospedeiro para 13 espécies de parasitos. Contracaecum sp. foi a espécie dominante, com os maiores índices de prevalência e abundância parasitária. Os componentes da comunidade parasitária de P. brasiliensis apresentaram o típico padrão de distribuição superdispersa. A abundância e a prevalência de Procamallanus (Spirocamallus pereirai apresentaram correlação positiva com o comprimento total do hospedeiro. A abundância de Contracaecum sp. apresentou correlação positiva com o comprimento total do hospedeiro. Um par de endoparasitos adultos (Aponurus laguncula - Procamallanus (S. pereirai apresentou covariação negativa e um par de estágios larvais de endoparasitos apresentou covariação positiva entres as abundâncias. Paralonchurus brasiliensis apresentou uma comunidade de metazoários parasitos composta de espécies generalistas, pouco ordenadas e com poucas evidências de associações interespecíficas. Este padrão está em concordância com os estudos realizados com comunidades parasitárias de siaenídeos da região neotropicalNinety-three specimens of banded croaker, Paralonchurus brasiliensis (Steindachner, 1875, collected from Pedra de Guaratiba (23º01’S, 43º38’W, coastal zone, State of Rio de Janeiro, Brazil, between September 2001 and March 2002, were necropsied to study their infracommunities of metazoan parasites. Fifteen species of metazoan parasites were collected. Paralonchurus brasiliensis is a new host record for 13 parasite species. The majority of fishes were parasitized by one or more metazoan

Investigation of metal toxicity to tropical biota. Recommendations for revision of Australian water quality guidelines

International Nuclear Information System (INIS)

Marchich, S.

1997-01-01

The specific objectives of this study were to: review available data on the toxicity of metals to aquatic biota in tropical Australia; identify metals considered to be priority toxicants to aquatic biota in tropical Australia; and employ previously developed toxicity testing protocols for two tropical freshwater species to obtain preliminary toxicity data for two priority metals. From the literature review, it was concluded that insufficient metal toxicity data exist for Australian tropical species. Data were absent for a range of metals (eg Ag, As, Al, Cr, Hg, Ni, Sb and Se) listed in the current Australian water quality guidelines. Aluminium, Cd, Co, Cu, Ni, Mn, Pb, U, V and Zn were identified as priority metals of potential ecotoxicological concern in aquatic ecosystems of tropical Australia, largely as a consequence of mining activities, but also from urban impacts. Instead of testing the toxicity of the priority metals for which data do not currently exist (ie Al, Co, Ni and V), it was deemed more important to conduct further experimental work on Cu and U, in the context of elucidating the relatively high variability in the toxic response of these two metals. As a result, Cu and U were selected and toxicity tests conducted using two tropical freshwater species (green hydra (Hydra viridissima) and gudgeon fish (Mogurnda mogurnda)) from the Australian wet/dry tropics using test protocols designed to maximise the greatest sensitivity of metal response in the shortest period of time. Hydra viridissima was about eight times more sensitive to Cu than U, whereas M. mogurnda was about twenty times more sensitive. Once differences between the sublethal and lethal endpoints of the two organisms were corrected by statistical extrapolation, H. viridissima was approximately seven times more sensitive than M. mogurnda to U, but only about three times more sensitive to Cu. Both species were more sensitive to Cu than U. These results are generally consistent with those from

An open source web interface for linking models to infrastructure system databases

Science.gov (United States)

Knox, S.; Mohamed, K.; Harou, J. J.; Rheinheimer, D. E.; Medellin-Azuara, J.; Meier, P.; Tilmant, A.; Rosenberg, D. E.

2016-12-01

Models of networked engineered resource systems such as water or energy systems are often built collaboratively with developers from different domains working at different locations. These models can be linked to large scale real world databases, and they are constantly being improved and extended. As the development and application of these models becomes more sophisticated, and the computing power required for simulations and/or optimisations increases, so has the need for online services and tools which enable the efficient development and deployment of these models. Hydra Platform is an open source, web-based data management system, which allows modellers of network-based models to remotely store network topology and associated data in a generalised manner, allowing it to serve multiple disciplines. Hydra Platform uses a web API using JSON to allow external programs (referred to as `Apps') to interact with its stored networks and perform actions such as importing data, running models, or exporting the networks to different formats. Hydra Platform supports multiple users accessing the same network and has a suite of functions for managing users and data. We present ongoing development in Hydra Platform, the Hydra Web User Interface, through which users can collaboratively manage network data and models in a web browser. The web interface allows multiple users to graphically access, edit and share their networks, run apps and view results. Through apps, which are located on the server, the web interface can give users access to external data sources and models without the need to install or configure any software. This also ensures model results can be reproduced by removing platform or version dependence. Managing data and deploying models via the web interface provides a way for multiple modellers to collaboratively manage data, deploy and monitor model runs and analyse results.

A rolling circle replication mechanism produces multimeric lariats of mitochondrial DNA in Caenorhabditis elegans.

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Samantha C Lewis

2015-02-01

Full Text Available Mitochondrial DNA (mtDNA encodes respiratory complex subunits essential to almost all eukaryotes; hence respiratory competence requires faithful duplication of this molecule. However, the mechanism(s of its synthesis remain hotly debated. Here we have developed Caenorhabditis elegans as a convenient animal model for the study of metazoan mtDNA synthesis. We demonstrate that C. elegans mtDNA replicates exclusively by a phage-like mechanism, in which multimeric molecules are synthesized from a circular template. In contrast to previous mammalian studies, we found that mtDNA synthesis in the C. elegans gonad produces branched-circular lariat structures with multimeric DNA tails; we were able to detect multimers up to four mtDNA genome unit lengths. Further, we did not detect elongation from a displacement-loop or analogue of 7S DNA, suggesting a clear difference from human mtDNA in regard to the site(s of replication initiation. We also identified cruciform mtDNA species that are sensitive to cleavage by the resolvase RusA; we suggest these four-way junctions may have a role in concatemer-to-monomer resolution. Overall these results indicate that mtDNA synthesis in C. elegans does not conform to any previously documented metazoan mtDNA replication mechanism, but instead are strongly suggestive of rolling circle replication, as employed by bacteriophages. As several components of the metazoan mitochondrial DNA replisome are likely phage-derived, these findings raise the possibility that the rolling circle mtDNA replication mechanism may be ancestral among metazoans.

Metazoários parasitos de seis espécies de peixes do Reservatório de Lajes, Estado do Rio de Janeiro, Brasil Metazoan parasites of six fishes species from Lajes Reservoir in the State of Rio de Janeiro, Brazil

Directory of Open Access Journals (Sweden)

Aline R. Paraguassú

2007-09-01

Full Text Available Entre abril de 2002 e julho de 2003, foram necropsiados 231 espécimes de peixes: 39 Astyanax bimaculatus (Linnaeus, 1758, 79 A. fasciatus (Cuvier, 1819, 23 Hypostomus affinis (Steindachner, 1877, 26 Hoplias malabaricus (Bloch, 1794, 30 Loricariichthys castaneus (Castelnau, 1855 e 34 Trachelyopterus striatulus (Steindachner, 1876 provenientes do Reservatório de Lajes (22º42' - 22º50'S, 43º53' 44º05'O, Estado do Rio de Janeiro, Brasil, para estudo das suas comunidades parasitárias. A maioria dos espécimes de H. affinis (95,6% e H. malabaricus (84,6% estavam parasitados por pelo menos uma espécie de metazoário. Em A. bimaculatus, A. fasciatus, L. castaneus e T. striatulus 41%, 39,2%, 56,7% e 14,7% dos espécimes estavam parasitados, respectivamente. Foram coletadas oito diferentes espécies de metazoários parasitos: 2 em A. bimaculatus, 3 em A. fasciatus, 3 em H. affinis, 4 em H. malabaricus, 4 em L. castaneus e 1 em T. striatulus. As comunidades de metazoários parasitos das seis espécies de peixes estudadas apresentaram típico padrão de distribuição agregada. Foram observados dois casos de correlação negativa entre a abundância e a prevalência parasitárias e o comprimento total dos hospedeiros. A comunidade parasitária de L. castaneus apresentou os maiores valores de intensidade média, índice de dispersão e diversidade. As comunidades parasitárias dos peixes estudados apresentaram escassez de correlação entre a abundância, riqueza parasitária e diversidade com o comprimento total dos hospedeiros. Os baixos valores de riqueza e diversidade das comuni-dades parasitárias podem ser atribuídos as características oligotróficas do Reservatório de Lajes.From April 2002 to July 2003, 231 freshwater fishes from Lajes Reservoir in the State of Rio de Janeiro, Brazil (22º42' - 22º50'S, 43º53' - 44º05'W were necropsied to study their community metazoan parasites: 39 Astyanax bimaculatus (Linnaeus, 1758, 79 A. fasciatus

The Capsaspora genome reveals a complex unicellular prehistory of animals.

Science.gov (United States)

Suga, Hiroshi; Chen, Zehua; de Mendoza, Alex; Sebé-Pedrós, Arnau; Brown, Matthew W; Kramer, Eric; Carr, Martin; Kerner, Pierre; Vervoort, Michel; Sánchez-Pons, Núria; Torruella, Guifré; Derelle, Romain; Manning, Gerard; Lang, B Franz; Russ, Carsten; Haas, Brian J; Roger, Andrew J; Nusbaum, Chad; Ruiz-Trillo, Iñaki

2013-01-01

To reconstruct the evolutionary origin of multicellular animals from their unicellular ancestors, the genome sequences of diverse unicellular relatives are essential. However, only the genome of the choanoflagellate Monosiga brevicollis has been reported to date. Here we completely sequence the genome of the filasterean Capsaspora owczarzaki, the closest known unicellular relative of metazoans besides choanoflagellates. Analyses of this genome alter our understanding of the molecular complexity of metazoans' unicellular ancestors showing that they had a richer repertoire of proteins involved in cell adhesion and transcriptional regulation than previously inferred only with the choanoflagellate genome. Some of these proteins were secondarily lost in choanoflagellates. In contrast, most intercellular signalling systems controlling development evolved later concomitant with the emergence of the first metazoans. We propose that the acquisition of these metazoan-specific developmental systems and the co-option of pre-existing genes drove the evolutionary transition from unicellular protists to metazoans.

Seasonal patterns in metazoan parasite community of the "Fat Sleeper" Dormitator latifrons (Pisces: Eleotridae from Tres Palos Lagoon, Guerrero, Mexico

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Juan Violante-González

2008-09-01

Full Text Available Dormitator is among the most important fish genera in the Mexican Pacific coastal lagoon systems. In Tres Palos Lagoon, the Fat Sleeper Dormitator latifrons is one of the most significant species based on catch volume, although it is only consumed locally. Very little information exists on this species’ parasitofauna. Composition and temporal variation in the metazoan parasite community structure of Dormitator latifrons from Tres Palos Lagoon (99º47’ W, 16º48’ N, Guerrero, Mexico, were determined using seasonal samples taken between April 2000 and June 2002. Ten parasite species (55 817 individuals were recovered from 219 examined hosts. These species included eight helminths (Ascocotyle (Phagicola longa, Echinochasmus leopoldinae, Clinostomum complanatum, Pseudoacanthostomum panamense, Saccocoelioides lamothei, Parvitaenia cochlearii, Contracaecum sp. and Neoechinorhynchus golvani and two crustaceans (Argulus sp. and Ergasilus sp.. Five of the helminth species exhibited seasonal variation in their infection dynamics associated with environmental changes during the dry and rainy seasons. The variations in the infection dynamics generated changes in the community structure over time. Rev. Biol. Trop. 56 (3: 1419-1427. Epub 2008 September 30.Entre abril del 2000 y junio del 2002 se efectuó un estudio para determinar la composición y la variación temporal en la estructura de la comunidad de parásitos metazoarios del popoyote Dormitator latifrons en la laguna de Tres Palos, Guerrero, México, a partir de muestras temporales. Se recuperaron diez especies de parásitos (55 817 individuos de 219 hospederos examinados. Estas especies incluyeron ocho helmintos (Ascocotyle (Phagicola longa, Echinochasmus leopoldinae, Clinostomum complanatum, Pseudoacanthostomum panamense, Saccocoelioides lamothei, Parvitaenia cochlearii, Contracaecum sp. y Neoechinorhynchus golvani y dos crustáceos (Argulus sp. y Ergasilus sp.. Cinco de las especies de

Hohlraum designs for high velocity implosions on NIF

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Meezan Nathan B.

2013-11-01

Full Text Available In this paper, we compare experimental shock and capsule trajectories to design calculations using the radiation-hydrodynamics code hydra. The measured trajectories from surrogate ignition targets are consistent with reducing the x-ray flux on the capsule by about 85%. A new method of extracting the radiation temperature from x-ray data shows that about half of the apparent 15% flux deficit in the data with respect to the simulations can be explained by hydra overestimating the x-ray flux on the capsule.

Evaluation and network of EC-decision support systems in the field of hydrological dispersion models and of aquatic radioecological research: assessment of environmental models and software

Energy Technology Data Exchange (ETDEWEB)

Monte, Luigi [ENEA, Roma (Italy). Centro Ricerche Casaccia, Unita Tecnico Scientifica, Protezione e Sviluppo dell' Ambiente e del Territorio, Tecnologie Ambientali; Hofman, Dmitry [Studsvik Radwaste AB, Nykoeping (Sweden); Brittain, John [Oslo Univ., Oslo (Norway)

2006-02-15

The present report describes the results of an assessment of state-of-the-art computerised Decision Support Systems based on environmental models for the management of fresh water ecosystems contaminated by radioactive substances. The models are examined and compared to identify their main features, the application domains, the performances, etc., for a rationale of the entire sector in view of the needs of potential users. A similar assessment was performed for the software products implementing the Decision Support Systems. This work was carried out in the frame of the network EVANET-HYDRA financed by the European Commission. [Italian] II presente rapporto descrive i risultati della valutazione dello stato dell'arte di Decision Support Systems sviluppati a livello internazionale per il management degli ecosistemi acquatici contaminati da sostanze radioattive. I modelli sono stati esaminati e confrontati per individuarne le caratteristiche, le funzionalita, i domini di applicazione, ecc. per la sistematizzazione razionale dell'intero settore in vista delle esigenze di degli utenti. Una simile analisi e stata effettuata per i prodotti software che implementano i Decision Support Systems. Il presente lavoro e stato svolto nell'ambito del network EVANET-HYDRA finanziato dalla Commissione Europea.

Finding the smoking gun: protein tyrosine phosphatases as tools and targets of unicellular microorganisms and viruses.

Science.gov (United States)

Heneberg, P

2012-01-01

Protein tyrosine phosphatases (PTPs) are increasingly recognized as important effectors of host-pathogen interactions. Since Guan and Dixon reported in 1990 that phosphatase YopH serves as an essential virulence determinant of Yersinia, the field shifted significantly forward, and dozens of PTPs were identified in various microorganisms and even in viruses. The discovery of extensive tyrosine signaling networks in non-metazoan organisms refuted the moth-eaten paradigm claiming that these organisms rely exclusively on phosphoserine/phosphothreonine signaling. Similarly to humans, phosphotyrosine signaling is thought to comprise a small fraction of total protein phosphorylation, but plays a disproportionately important role in cell-cycle control, differentiation, and invasiveness. Here we summarize the state-of-art knowledge on PTPs of important non-metazoan pathogens (Listeria monocytogenes, Staphylococcus aureus, Porphyromonas gingivalis, Caulobacter crescentus, Yersinia, Synechocystis, Leishmania, Plasmodium falciparum, Entamoeba histolytica, etc.), and focus also at the microbial proteins affecting directly or indirectly the PTPs of the host (Mycobacterium tuberculosis MTSA-10, Bacillus anthracis anthrax toxin, streptococcal β protein, Helicobacter pylori CagA and VacA, Leishmania GP63 and EF-1α, Plasmodium hemozoin, etc.). This is the first review summarizing the knowledge on biological activity and pharmacological inhibition of non-metazoan PTPs, with the emphasis of those important in host-pathogen interactions. Targeting of numerous non-metazoan PTPs is simplified by the fact that they act either as ectophosphatases or are secreted outside of the pathogen. Interfering with tyrosine phosphorylation represents a powerful pharmacologic approach, and even though the PTP inhibitors are difficult to develop, lifting the fog of phosphatase inhibition is of the great market potential and further clinical impact.

The evolution of the dystroglycan complex, a major mediator of muscle integrity

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Josephine C. Adams

2015-09-01

Full Text Available Basement membrane (BM extracellular matrices are crucial for the coordination of different tissue layers. A matrix adhesion receptor that is important for BM function and stability in many mammalian tissues is the dystroglycan (DG complex. This comprises the non-covalently-associated extracellular α-DG, that interacts with laminin in the BM, and the transmembrane β-DG, that interacts principally with dystrophin to connect to the actin cytoskeleton. Mutations in dystrophin, DG, or several enzymes that glycosylate α-DG underlie severe forms of human muscular dystrophy. Nonwithstanding the pathophysiological importance of the DG complex and its fundamental interest as a non-integrin system of cell-ECM adhesion, the evolution of DG and its interacting proteins is not understood. We analysed the phylogenetic distribution of DG, its proximal binding partners and key processing enzymes in extant metazoan and relevant outgroups. We identify that DG originated after the divergence of ctenophores from porifera and eumetazoa. The C-terminal half of the DG core protein is highly-conserved, yet the N-terminal region, that includes the laminin-binding region, has undergone major lineage-specific divergences. Phylogenetic analysis based on the C-terminal IG2_MAT_NU region identified three distinct clades corresponding to deuterostomes, arthropods, and mollusks/early-diverging metazoans. Whereas the glycosyltransferases that modify α-DG are also present in choanoflagellates, the DG-binding proteins dystrophin and laminin originated at the base of the metazoa, and DG-associated sarcoglycan is restricted to cnidarians and bilaterians. These findings implicate extensive functional diversification of DG within invertebrate lineages and identify the laminin-DG-dystrophin axis as a conserved adhesion system that evolved subsequent to integrin-ECM adhesion, likely to enhance the functional complexity of cell-BM interactions in early metazoans.

ANOTHER LOOK AT THE EASTERN BANDED STRUCTURE: A STELLAR DEBRIS STREAM AND A POSSIBLE PROGENITOR

International Nuclear Information System (INIS)

Grillmair, C. J.

2011-01-01

Using the Sloan Digital Sky Survey Data Release 7, we re-examine the Eastern Banded Structure (EBS), a stellar debris stream first discovered in Data Release 5 and more recently detected in velocity space by Schlaufman et al. The visible portion of the stream is 18 0 long, lying roughly in the Galactic Anticenter direction and extending from Hydra to Cancer. At an estimated distance of 9.7 kpc, the stream is ∼170 pc across on the sky. The curvature of the stream implies a fairly eccentric box orbit that passes close to both the Galactic center and to the Sun, making it dynamically distinct from the nearby Monoceros, Anticenter, and GD-1 streams. Within the stream is a relatively strong, 2 0 -wide concentration of stars with a very similar color-magnitude distribution that we designate Hydra I. Given its prominence within the stream and its unusual morphology, we suggest that Hydra I is the last vestige of EBS's progenitor, possibly already unbound or in the final throes of tidal dissolution. Though both Hydra I and the EBS have a relatively high-velocity dispersion, given the comparatively narrow width of the stream and the high frequency of encounters with the bulge and massive constituents of the disk that such an eccentric orbit would entail, we suggest that the progenitor was likely a globular cluster and that both it and the stream have undergone significant heating over time.

Microarray glycan profiling reveals algal fucoidan epitopes in diverse marine metazoans

DEFF Research Database (Denmark)

Asunción Salmeán, Armando; Hervé, Cécile; Jørgensen, Bodil

2017-01-01

Despite the biological importance and pharmacological potential of glycans from marine organisms, there are many unanswered questions regarding their distribution, function, and evolution. Here we describe microarray-based glycan profiling of a diverse selection of marine animals using antibodies...... raised against fucoidan isolated from a brown alga. We demonstrate the presence of two fucoidan epitopes in six animals belonging to three phyla including Porifera, Molusca, and Chordata. We studied the spatial distribution of these epitopes in Cliona celata ("boring sponge") and identified...

Focusing experiments with light ion diodes

International Nuclear Information System (INIS)

Johnson, D.L.

1978-01-01

A review of recent experimental and theoretical work at Sandia Laboratories on magnetically insulated single stage ion diodes for inertial confinement fusion experiments is presented. The production, focusing, and numerical simulation of a 0.5 TW annular proton beam using the Proto I dual transmission line generator is described. The modular magnetically insulated ion diode for the Hydra generator is also described along with recent experimental results. A brief description of how an array of modular diodes similar to the Hydra magnetically insulated diode could be used on the EBFA I generator for breakeven fusion experiments is presented

The carbohydrate sequence markup language (CabosML): an XML description of carbohydrate structures.

Science.gov (United States)

Kikuchi, Norihiro; Kameyama, Akihiko; Nakaya, Shuuichi; Ito, Hiromi; Sato, Takashi; Shikanai, Toshihide; Takahashi, Yoriko; Narimatsu, Hisashi

2005-04-15

Bioinformatics resources for glycomics are very poor as compared with those for genomics and proteomics. The complexity of carbohydrate sequences makes it difficult to define a common language to represent them, and the development of bioinformatics tools for glycomics has not progressed. In this study, we developed a carbohydrate sequence markup language (CabosML), an XML description of carbohydrate structures. The language definition (XML Schema) and an experimental database of carbohydrate structures using an XML database management system are available at http://www.phoenix.hydra.mki.co.jp/CabosDemo.html kikuchi@hydra.mki.co.jp.

Metazoan parasites from odontocetes off New Zealand: new records.

Science.gov (United States)

Lehnert, Kristina; Randhawa, Haseeb; Poulin, Robert

2017-10-01

Information about the parasite fauna of spectacled porpoises and cetaceans from New Zealand waters in general is scarce. This study takes advantage of material archived in collections of the Otago Museum in Dunedin and Massey University in Auckland, sampled from cetacean species found stranded along the New Zealand coastline between 2007 and 2014. Parasites from seven species of cetaceans (spectacled porpoise, Phocoena dioptrica (n = 2 individuals examined); pygmy sperm whale (n = 1); long-finned pilot whale, Globicephala melas (n = 1); Risso's dolphin, Grampus griseus (n = 1); short-beaked common dolphin, Delphinus delphis (n = 7); striped dolphin, Stenella coeruleoalba (n = 3) and dusky dolphin, Lagenorhynchus obscurus (n = 2)) from the respiratory and gastro-intestinal tract, cranial sinus, liver, urogenital and mammary tract, fascia and blubber were investigated. Ten parasite species were identified, belonging to the Nematoda (Stenurus minor, Stenurus globicephalae, Halocercus sp. (Pseudaliidae), Anisakis sp. (Anisakidae), Crassicauda sp. (Crassicaudidae)), Cestoda (Phyllobothrium delphini and Monorygma grimaldii (Phyllobothriidae)), Trematoda (Brachicladium palliata and Brachicladium delphini (Brachicladiidae)) and Crustacea (Scutocyamus antipodensis (Cyamidae)). Some of the parasite species encountered comprises new records for their host. Although the material was not sampled within a systematic parasitological survey, the findings contain valuable new information about the parasite fauna of rare, vagile and vulnerable marine wildlife from a remote oceanic environment.

Elaeophora in the meninges of a Malayan sambar (Rusa unicolor equina).

Science.gov (United States)

Bernard, Jennifer; Grunenwald, Caroline; Stalis, Ilse H; Varney, Megan; Zuba, Jeff; Gerhold, Richard

2016-11-01

An adult nematode was grossly identified in the meninges of a Malayan sambar (Rusa unicolor equina), with numerous microfilariae associated with encephalitis and vasculitis on histopathology. The nematode was confirmed to be Elaeophora schneideri by sequencing a portion of the 18S rRNA gene. Our report highlights the potential for aberrant migration of E. schneideri in exotic deer species and the use of advanced testing to specifically identify this metazoan parasite, avoiding misidentification of Parelaphostrongylus tenuis. © 2016 The Author(s).

The Water Security Hydra

Science.gov (United States)

Lall, U.

2017-12-01

As the editor of a new journal on water security, I have been pondering what it can mean theoretically and practically. At one level, it is pretty aobvious that it refers to the ability to affordably and reliably access water of appropriate quality, and to be protected from the water related ravages of nature, such as floods, droughts and water borne disease. The concept of water security can apply to a family, a company, a state or globally. Of course, since we value the environment, water security embraces the needs of the environment. Where, we consider economic development or energy production, water security also emerges as a critical factor. So, in short it touches almost all things about water that pertain to our lives. New stresses are created by a changing climate, growing populations and an ever changing society, economic activity and environment. Thus, if assuring water security is a goal at any of the scales of interest, many factors need to be considered, and what can really be assured, where and for how long emerges as an interesting question. Local (place, time, individuals, politics) as well as global (climate, economics, hydrology) factors interact to determine outcomes, not all of which are readily mapped in our mathematical or cognitive models to a functional notion of what constitutes security in the face of changing conditions and actors. Further, assurance implies going beyond characterization to developing actions, responses to stressors and risk mitigation strategies. How these perform in the short and long run, and what are the outcomes and strategies for impact mitigation in the event of failure then determines water security. Recognizing that providing assurance of water security has always been the goal of water management, regulation and development, perhaps the challenge is to understand what this means from the perspective of not just the "water managers" but the individuals who are the unwitting beneficiaries, or the instruments for the approval of the strategies that are implemented. In this talk, I will strive to lay out a cognitive framework for how performance evaluation of water security, and instrument design for assurance can be approached from a multi-stress and multi-user perspective. Selected examples will be used to lillustrate the idea in the context of America's Water.

Identification and activity of a lower eukaryotic serine proteinase inhibitor (serpin) from Cyanea capillata: analysis of a jellyfish serpin, jellypin.

Science.gov (United States)

Cole, Elisabeth B; Miller, David; Rometo, David; Greenberg, Robert M; Brömme, Dieter; Cataltepe, Sule; Pak, Stephen C; Mills, David R; Silverman, Gary A; Luke, Cliff J

2004-09-21

Delineating the phylogenetic relationships among members of a protein family can provide a high degree of insight into the evolution of domain structure and function relationships. To identify an early metazoan member of the high molecular weight serine proteinase inhibitor (serpin) superfamily, we initiated a cDNA library screen of the cnidarian, Cyanea capillata. We identified one serpin cDNA encoding for a full-length serpin, jellypin. Phylogenetic analysis using the deduced amino acid sequence showed that jellypin was most similar to the platyhelminthe Echinococcus multiocularis serpin and the clade P serpins, suggesting that this serpin evolved approximately 1000 million years ago (MYA). Modeling of jellypin showed that it contained all the functional elements of an inhibitory serpin. In vitro biochemical analysis confirmed that jellypin was an inhibitor of the S1 clan SA family of serine proteinases. Analysis of the interactions between the human serine proteinases, chymotrypsin, cathepsin G, and elastase, showed that jellypin inhibited these enzymes in the classical serpin manner, forming a SDS stable enzyme/inhibitor complex. These data suggest that the coevolution of serpin structure and inhibitory function date back to at least early metazoan evolution, approximately 1000 MYA.

The Amphimedon queenslandica genome and the evolution of animal complexity

Energy Technology Data Exchange (ETDEWEB)

Srivastava, Mansi; Simakov, Oleg; Chapman, Jarrod; Fahey, Bryony; Gauthier, Marie E.A.; Mitros, Therese; Richards, Gemma S.; Conaco, Cecilia; Dacre, Michael; Hellsten, Uffe; Larroux, Claire; Putnam, Nicholas H.; Stanke, Mario; Adamska, Maja; Darling, Aaron; Degnan, Sandie M.; Oakley, Todd H.; Plachetzki, David C.; Zhai, Yufeng; Adamski, Marcin; Calcino, Andrew; Cummins, Scott F.; Goodstein, David M.; Harris, Christina; Jackson, Daniel J.; Leys, Sally P.; Shu, Shengqiang; Woodcroft, Ben J.; Vervoort, Michel; Kosik, Kenneth S.; Manning, Gerard; Degnan, Bernard M.; Rokhsar, Daniel S.

2010-07-01

Sponges are an ancient group of animals that diverged from other metazoans over 600 million years ago. Here we present the draft genome sequence of Amphimedon queenslandica, a demosponge from the Great Barrier Reef, and show that it is remarkably similar to other animal genomes in content, structure and organization. Comparative analysis enabled by the sponge sequence reveals genomic events linked to the origin and early evolution of animals, including the appearance, expansion, and diversification of pan-metazoan transcription factor, signaling pathway, and structural genes. This diverse 'toolkit' of genes correlates with critical aspects of all metazoan body plans, and comprises cell cycle control and growth, development, somatic and germ cell specification, cell adhesion, innate immunity, and allorecognition. Notably, many of the genes associated with the emergence of animals are also implicated in cancer, which arises from defects in basic processes associated with metazoan multicellularity.

Fighting the Hydra: America’s Southern Border and National Security

Science.gov (United States)

2011-03-23

Mexican migrant workers from continuing to work within the United States outside of the Bracero Program and without the limited protection it provided...identify and deport illegal immigrants from the Bracero Program who had remained in the United States after their contract expired.18 The number of...Prohibition Act was the major commodity being transported illegally. 16 Fred L. Koestler, “ Bracero Program ,” Handbook of Texas Online, http://www.tshaonline

Functional studies on the role of Notch signaling in Hydractinia development.

Science.gov (United States)

Gahan, James M; Schnitzler, Christine E; DuBuc, Timothy Q; Doonan, Liam B; Kanska, Justyna; Gornik, Sebastian G; Barreira, Sofia; Thompson, Kerry; Schiffer, Philipp; Baxevanis, Andreas D; Frank, Uri

2017-08-01

The function of Notch signaling was previously studied in two cnidarians, Hydra and Nematostella, representing the lineages Hydrozoa and Anthozoa, respectively. Using pharmacological inhibition in Hydra and a combination of pharmacological and genetic approaches in Nematostella, it was shown in both animals that Notch is required for tentacle morphogenesis and for late stages of stinging cell maturation. Surprisingly, a role for Notch in neural development, which is well documented in bilaterians, was evident in embryonic Nematostella but not in adult Hydra. Adult neurogenesis in the latter seemed to be unaffected by DAPT, a drug that inhibits Notch signaling. To address this apparent discrepancy, we studied the role of Notch in Hydractinia echinata, an additional hydrozoan, in all life stages. Using CRISPR-Cas9 mediated mutagenesis, transgenesis, and pharmacological interference we show that Notch is dispensable for Hydractinia normal neurogenesis in all life stages but is required for the maturation of stinging cells and for tentacle morphogenesis. Our results are consistent with a conserved role for Notch in morphogenesis and nematogenesis across Cnidaria, and a lineage-specific loss of Notch dependence in neurogenesis in hydrozoans. Copyright © 2017 Elsevier Inc. All rights reserved.

Hércules contra la Hidra y la muerte del Internet

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Eduardo Piza Volio

2011-04-01

Full Text Available Hercules killed the Hydra of Lerna in a bloody battle—the second of the labor tasks imposed upon him in atonement for his hideous crimes. The Hydra was a horrible, aggressive mythological monster with many heads and poisonous blood, whose heads multiplied each time one of them was severed. This article explores some mathematical methods about this interesting epic battle. A generalization of the original Kirby & Paris model is proposed. We also study the connection of this model with Goodstein ultra-growing and recursive sequences. As an interesting application, we next analyze the inevitable death of another huge monster of our modern era: the Internet.

Biochemical diversification through foreign gene expression in bdelloid rotifers.

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Chiara Boschetti

Full Text Available Bdelloid rotifers are microinvertebrates with unique characteristics: they have survived tens of millions of years without sexual reproduction; they withstand extreme desiccation by undergoing anhydrobiosis; and they tolerate very high levels of ionizing radiation. Recent evidence suggests that subtelomeric regions of the bdelloid genome contain sequences originating from other organisms by horizontal gene transfer (HGT, of which some are known to be transcribed. However, the extent to which foreign gene expression plays a role in bdelloid physiology is unknown. We address this in the first large scale analysis of the transcriptome of the bdelloid Adineta ricciae: cDNA libraries from hydrated and desiccated bdelloids were subjected to massively parallel sequencing and assembled transcripts compared against the UniProtKB database by blastx to identify their putative products. Of ~29,000 matched transcripts, ~10% were inferred from blastx matches to be horizontally acquired, mainly from eubacteria but also from fungi, protists, and algae. After allowing for possible sources of error, the rate of HGT is at least 8%-9%, a level significantly higher than other invertebrates. We verified their foreign nature by phylogenetic analysis and by demonstrating linkage of foreign genes with metazoan genes in the bdelloid genome. Approximately 80% of horizontally acquired genes expressed in bdelloids code for enzymes, and these represent 39% of enzymes in identified pathways. Many enzymes encoded by foreign genes enhance biochemistry in bdelloids compared to other metazoans, for example, by potentiating toxin degradation or generation of antioxidants and key metabolites. They also supplement, and occasionally potentially replace, existing metazoan functions. Bdelloid rotifers therefore express horizontally acquired genes on a scale unprecedented in animals, and foreign genes make a profound contribution to their metabolism. This represents a potential

Variación entre años de las infracomunidades de parásitos metazoos de la corvina Cilus gilberti (Pisces: Sciaenidae en Chile Between-years variation in infracommunities of metazoan parasites of the croaker Cilus gilberti (Pisces: Sciaenidae from Chile

Directory of Open Access Journals (Sweden)

FÉLIX GARCÍAS

2001-12-01

Full Text Available Se comparan la composición, riqueza, diversidad, abundancia y dominancia en las infracomunidades de parásitos metazoos de 86 ejemplares de corvina Cilus gilberti (Abbott 1889, recolectados en dos muestras tomadas con 15 años de diferencia en la zona de Talcahuano, VIII región, Chile. Se pretende averiguar si estas características comunitarias se modifican o no sustantivamente entre años. Se recolectaron un total de 26 taxa, a los que se les determinó la prevalencia, aunque sólo a 22 se les determinó la abundancia. El 69 % de los 26 taxa ocurría en ambos años, sin embargo, al comparar la composición infracomunitaria entre años, sólo se consideró a aquellos 13 taxa que estaban en al menos 10 corvinas del total de 86 examinadas, y a hospedadores de similar longitud corporal. Hay variaciones significativas entre años en la composición de las infracomunidades de parásitos pero no en la riqueza, abundancia, diversidad y dominancia. Aunque los antecedentes son escasos, la observada relativamente alta variabilidad composicional y baja variabilidad agregada es similar a lo encontrado en infracomunidades de parásitos, tanto de peces como de mamíferos. Se discute la medida en que estos resultados representan compensación o estasis comunitaria, entre cuyas causas podrían estar las interacciones biológicasThe composition, richness, diversity, abundance and dominance in infracommunities of metazoan parasites found in 86 croaker Cilus gilberti (Abbott 1889 are compared between two samples taken off Talcahuano, Chile, with 15 years of difference. All hosts harboured parasites, and 26 taxa were collected. The prevalence of all taxa, and the abundance of 22 taxa were recorded. Most (69 % taxa were found in both years. However, to compare between years, we just considered those 13 taxa occurring in at least 10 host individuals. Significant variations in composition but not in richness, abundance, diversity and dominance were found when

Conservation of the human integrin-type beta-propeller domain in bacteria.

Directory of Open Access Journals (Sweden)

Bhanupratap Chouhan

Full Text Available Integrins are heterodimeric cell-surface receptors with key functions in cell-cell and cell-matrix adhesion. Integrin α and β subunits are present throughout the metazoans, but it is unclear whether the subunits predate the origin of multicellular organisms. Several component domains have been detected in bacteria, one of which, a specific 7-bladed β-propeller domain, is a unique feature of the integrin α subunits. Here, we describe a structure-derived motif, which incorporates key features of each blade from the X-ray structures of human αIIbβ3 and αVβ3, includes elements of the FG-GAP/Cage and Ca(2+-binding motifs, and is specific only for the metazoan integrin domains. Separately, we searched for the metazoan integrin type β-propeller domains among all available sequences from bacteria and unicellular eukaryotic organisms, which must incorporate seven repeats, corresponding to the seven blades of the β-propeller domain, and so that the newly found structure-derived motif would exist in every repeat. As the result, among 47 available genomes of unicellular eukaryotes we could not find a single instance of seven repeats with the motif. Several sequences contained three repeats, a predicted transmembrane segment, and a short cytoplasmic motif associated with some integrins, but otherwise differ from the metazoan integrin α subunits. Among the available bacterial sequences, we found five examples containing seven sequential metazoan integrin-specific motifs within the seven repeats. The motifs differ in having one Ca(2+-binding site per repeat, whereas metazoan integrins have three or four sites. The bacterial sequences are more conserved in terms of motif conservation and loop length, suggesting that the structure is more regular and compact than those example structures from human integrins. Although the bacterial examples are not full-length integrins, the full-length metazoan-type 7-bladed β-propeller domains are present, and

Evaluation and network of EC-decision support systems in the field of hydrological dispersion models and of aquatic radioecological research: assessment of environmental models and software

International Nuclear Information System (INIS)

Monte, Luigi; Brittain, John

2006-02-01

The present report describes the results of an assessment of state-of-the-art computerised Decision Support Systems based on environmental models for the management of fresh water ecosystems contaminated by radioactive substances. The models are examined and compared to identify their main features, the application domains, the performances, etc., for a rationale of the entire sector in view of the needs of potential users. A similar assessment was performed for the software products implementing the Decision Support Systems. This work was carried out in the frame of the network EVANET-HYDRA financed by the European Commission [it

HIF VNL Progress Report to DOE, April 22, 2005

International Nuclear Information System (INIS)

Barnard, J

2005-01-01

We have made progress in learning to use the code Hydra to do detailed modeling of targets for Accelerator Driven High Energy Density Physics. Hydra is a state-of-the-art 3D, radiative transfer hydrodynamics modeling code developed at LLNL. In particular, we have carried out two-dimensional simulations of a 23 MeV, 1 mm radius Neon beam striking a 48 micron thick Aluminum foil at 10% solid density, and observed the heating of the foil by the beam. The Bragg peak was chosen to fall near the center of the foil, and as expected, rarefaction waves propagated symmetrically inward (at a speed of order the sound speed), as the heated material flowed outward and cooled. Foams allow relatively high temperatures to be attained over longer timescales, and the foils behaved, at least qualitatively, as predicted by previous analysis. Design of a number of configurations, ion species, and material compositions will be carried out using this code. Further, calculations by our collaborators at Tech-X corporation have compared results from the SRIM code (a code for understanding detailed energy deposition and scattering of ions in a cold solid) with cold dEdX curves published by Northcliffe and Schilling in 1970. The latter publication was used for making previous analytic estimates of ion energies and foil widths for experiments in which relatively large regions of uniform temperature are reached in the foil. The two sources agreed well, giving some confidence to our analytic estimates, and allowing us to rule out dE/dx discrepancies in early runs of the Hydra code that gave anomalous results. The anomalies were later found to arise from improperly set parameters in the input deck for Hydra

SPARQL-enabled identifier conversion with Identifiers.org.

Science.gov (United States)

Wimalaratne, Sarala M; Bolleman, Jerven; Juty, Nick; Katayama, Toshiaki; Dumontier, Michel; Redaschi, Nicole; Le Novère, Nicolas; Hermjakob, Henning; Laibe, Camille

2015-06-01

On the semantic web, in life sciences in particular, data is often distributed via multiple resources. Each of these sources is likely to use their own International Resource Identifier for conceptually the same resource or database record. The lack of correspondence between identifiers introduces a barrier when executing federated SPARQL queries across life science data. We introduce a novel SPARQL-based service to enable on-the-fly integration of life science data. This service uses the identifier patterns defined in the Identifiers.org Registry to generate a plurality of identifier variants, which can then be used to match source identifiers with target identifiers. We demonstrate the utility of this identifier integration approach by answering queries across major producers of life science Linked Data. The SPARQL-based identifier conversion service is available without restriction at http://identifiers.org/services/sparql. © The Author 2015. Published by Oxford University Press.

SPARQL-enabled identifier conversion with Identifiers.org

Science.gov (United States)

Wimalaratne, Sarala M.; Bolleman, Jerven; Juty, Nick; Katayama, Toshiaki; Dumontier, Michel; Redaschi, Nicole; Le Novère, Nicolas; Hermjakob, Henning; Laibe, Camille

2015-01-01

Motivation: On the semantic web, in life sciences in particular, data is often distributed via multiple resources. Each of these sources is likely to use their own International Resource Identifier for conceptually the same resource or database record. The lack of correspondence between identifiers introduces a barrier when executing federated SPARQL queries across life science data. Results: We introduce a novel SPARQL-based service to enable on-the-fly integration of life science data. This service uses the identifier patterns defined in the Identifiers.org Registry to generate a plurality of identifier variants, which can then be used to match source identifiers with target identifiers. We demonstrate the utility of this identifier integration approach by answering queries across major producers of life science Linked Data. Availability and implementation: The SPARQL-based identifier conversion service is available without restriction at http://identifiers.org/services/sparql. Contact: sarala@ebi.ac.uk PMID:25638809

Eye Development in Sepia officinalis Embryo: What the Uncommon Gene Expression Profiles Tell Us about Eye Evolution.

Science.gov (United States)

Imarazene, Boudjema; Andouche, Aude; Bassaglia, Yann; Lopez, Pascal-Jean; Bonnaud-Ponticelli, Laure

2017-01-01

In metazoans, there is a remarkable diversity of photosensitive structures; their shapes, physiology, optical properties, and development are different. To approach the evolution of photosensitive structures and visual function, cephalopods are particularly interesting organisms due to their most highly centralized nervous system and their camerular eyes which constitute a convergence with those of vertebrates. The eye morphogenesis in numerous metazoans is controlled mainly by a conserved Retinal Determination Gene Network (RDGN) including pax, six, eya , and dac playing also key developmental roles in non-retinal structures and tissues of vertebrates and Drosophila . Here we have identified and explored the role of Sof-dac, Sof-six1/2, Sof-eya in eye morphogenesis, and nervous structures controlling the visual function in Sepia officinalis . We compare that with the already shown expressions in eye development of Sof-otx and Sof-pax genes. Rhodopsin is the pigment responsible for light sensitivity in metazoan, which correlate to correlate visual function and eye development. We studied Sof-rhodopsin expression during retina differentiation. By in situ hybridization, we show that (1) all of the RDGN genes, including Sof-pax6 , are expressed in the eye area during the early developmental stages but they are not expressed in the retina, unlike Sof-otx , which could have a role in retina differentiation; (2) Sof-rhodopsin is expressed in the retina just before vision gets functional, from stage 23 to hatching. Our results evidence a role of Sof-six1/2, Sof-eya , and Sof-dac in eye development. However, the gene network involved in the retinal photoreceptor differentiation remains to be determined. Moreover, for the first time, Sof-rhodopsin expression is shown in the embryonic retina of cuttlefish suggesting the evolutionary conservation of the role of rhodopsin in visual phototransduction within metazoans. These findings are correlated with the physiological and

Eye Development in Sepia officinalis Embryo: What the Uncommon Gene Expression Profiles Tell Us about Eye Evolution

Directory of Open Access Journals (Sweden)

Boudjema Imarazene

2017-08-01

Full Text Available In metazoans, there is a remarkable diversity of photosensitive structures; their shapes, physiology, optical properties, and development are different. To approach the evolution of photosensitive structures and visual function, cephalopods are particularly interesting organisms due to their most highly centralized nervous system and their camerular eyes which constitute a convergence with those of vertebrates. The eye morphogenesis in numerous metazoans is controlled mainly by a conserved Retinal Determination Gene Network (RDGN including pax, six, eya, and dac playing also key developmental roles in non-retinal structures and tissues of vertebrates and Drosophila. Here we have identified and explored the role of Sof-dac, Sof-six1/2, Sof-eya in eye morphogenesis, and nervous structures controlling the visual function in Sepia officinalis. We compare that with the already shown expressions in eye development of Sof-otx and Sof-pax genes. Rhodopsin is the pigment responsible for light sensitivity in metazoan, which correlate to correlate visual function and eye development. We studied Sof-rhodopsin expression during retina differentiation. By in situ hybridization, we show that (1 all of the RDGN genes, including Sof-pax6, are expressed in the eye area during the early developmental stages but they are not expressed in the retina, unlike Sof-otx, which could have a role in retina differentiation; (2 Sof-rhodopsin is expressed in the retina just before vision gets functional, from stage 23 to hatching. Our results evidence a role of Sof-six1/2, Sof-eya, and Sof-dac in eye development. However, the gene network involved in the retinal photoreceptor differentiation remains to be determined. Moreover, for the first time, Sof-rhodopsin expression is shown in the embryonic retina of cuttlefish suggesting the evolutionary conservation of the role of rhodopsin in visual phototransduction within metazoans. These findings are correlated with the

A conserved SREBP-1/phosphatidylcholine feedback circuit regulates lipogenesis in metazoans.

Science.gov (United States)

Walker, Amy K; Jacobs, René L; Watts, Jennifer L; Rottiers, Veerle; Jiang, Karen; Finnegan, Deirdre M; Shioda, Toshi; Hansen, Malene; Yang, Fajun; Niebergall, Lorissa J; Vance, Dennis E; Tzoneva, Monika; Hart, Anne C; Näär, Anders M

2011-11-11

Sterol regulatory element-binding proteins (SREBPs) activate genes involved in the synthesis and trafficking of cholesterol and other lipids and are critical for maintaining lipid homeostasis. Aberrant SREBP activity, however, can contribute to obesity, fatty liver disease, and insulin resistance, hallmarks of metabolic syndrome. Our studies identify a conserved regulatory circuit in which SREBP-1 controls genes in the one-carbon cycle, which produces the methyl donor S-adenosylmethionine (SAMe). Methylation is critical for the synthesis of phosphatidylcholine (PC), a major membrane component, and we find that blocking SAMe or PC synthesis in C. elegans, mouse liver, and human cells causes elevated SREBP-1-dependent transcription and lipid droplet accumulation. Distinct from negative regulation of SREBP-2 by cholesterol, our data suggest a feedback mechanism whereby maturation of nuclear, transcriptionally active SREBP-1 is controlled by levels of PC. Thus, nutritional or genetic conditions limiting SAMe or PC production may activate SREBP-1, contributing to human metabolic disorders. Copyright © 2011 Elsevier Inc. All rights reserved.

Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa.

Science.gov (United States)

Borowiec, Marek L; Lee, Ernest K; Chiu, Joanna C; Plachetzki, David C

2015-11-23

Understanding the phylogenetic relationships among major lineages of multicellular animals (the Metazoa) is a prerequisite for studying the evolution of complex traits such as nervous systems, muscle tissue, or sensory organs. Transcriptome-based phylogenies have dramatically improved our understanding of metazoan relationships in recent years, although several important questions remain. The branching order near the base of the tree, in particular the placement of the poriferan (sponges, phylum Porifera) and ctenophore (comb jellies, phylum Ctenophora) lineages is one outstanding issue. Recent analyses have suggested that the comb jellies are sister to all remaining metazoan phyla including sponges. This finding is surprising because it suggests that neurons and other complex traits, present in ctenophores and eumetazoans but absent in sponges or placozoans, either evolved twice in Metazoa or were independently, secondarily lost in the lineages leading to sponges and placozoans. To address the question of basal metazoan relationships we assembled a novel dataset comprised of 1080 orthologous loci derived from 36 publicly available genomes representing major lineages of animals. From this large dataset we procured an optimized set of partitions with high phylogenetic signal for resolving metazoan relationships. This optimized data set is amenable to the most appropriate and computationally intensive analyses using site-heterogeneous models of sequence evolution. We also employed several strategies to examine the potential for long-branch attraction to bias our inferences. Our analyses strongly support the Ctenophora as the sister lineage to other Metazoa. We find no support for the traditional view uniting the ctenophores and Cnidaria. Our findings are supported by Bayesian comparisons of topological hypotheses and we find no evidence that they are biased by long-branch attraction. Our study further clarifies relationships among early branching metazoan lineages

Discordance between morphological and molecular species boundaries among Caribbean species of the reef sponge Callyspongia

OpenAIRE

DeBiasse, Melissa B; Hellberg, Michael E

2015-01-01

Sponges are among the most species-rich and ecologically important taxa on coral reefs, yet documenting their diversity is difficult due to the simplicity and plasticity of their morphological characters. Genetic attempts to identify species are hampered by the slow rate of mitochondrial sequence evolution characteristic of sponges and some other basal metazoans. Here we determine species boundaries of the Caribbean coral reef sponge genus Callyspongia using a multilocus, model-based approach...

OBSERVAÇÕES SOBRE DEGENERESCÊNCIA E COMPORTAMENTO EM DIFERENTES ÉPOCAS DE PLANTIO DE QUATRO VARIEDADES DE BATATA (Solanum Tuberosum L. COMMENTS ON DEGENERATION AND BEHAVIOR AT DIFFERENT PLANTING DATES OF FOUR POTATO (Solanum tuberosum L. VARIETIES

Directory of Open Access Journals (Sweden)

Peter E. Sonnenberg

2007-09-01

Full Text Available

As variedades de batata DELTA-A, HANSA, HYDRA e TONDRA foram plantadas em duas gerações, a primeira na seca e a segunda, nas águas de 1971, em Goiânia. Para o primeiro plantio, usaram-se batatas-sementes importadas, para o segundo, as filhas destas. HANSA, HYDRA e TONDRA produziram mais na segunda geração do que na primeira, devido às melhores condições da época chuvosa. A produção da DELTA-A praticamente não variou nas duas épocas. HANSA foi significantemente superior às outras, em produção total, nas duas épocas e em produção de tubérculos comerciáveis (acima de 33 mm, na época chuvosa. Neste período, seus tubérculos grandes, (acima de 40 mm apresentaram-se com superdesenvolvimento de lenticelas e manchados internamente, ficando comercialmente desvalorizados. A variedade HYDRA destacou-se das demais pela produção de batatas grandes, principalmente na seca. Mostrou-se, porém, muito suscetível à sarna comum, cujo ataque inutilizou grande parte de seus tubérculos. TONDRA foi a variedade que melhor se adaptou ao período chuvoso. Produziu duas vezes mais tubérculos comerciáveis e quase três vezes mais tubérculos grandes, que na seca.

The four potato varieties DELTA-A, HANSA, HYDRA and TONDRA were tested in the dry and in the rainy season of 1971, in Goiânia. Imported certified seed potatoes were used for the first planting and the harvested tubers, for the second. All varieties, except DELTA-A, yielded more in the rainy than in the dry season. This difference was found to be caused by the better water supply during the rainy season. There was no significant influence of the season on the production of DELTA-A. HANSA produced in both seasons significantly more in total weight than the other varieties and more marketable potatoes (over 33 mm in the rainy season. But the large

Metazoan Scc4 homologs link sister chromatid cohesion to cell and axon migration guidance

NARCIS (Netherlands)

V.C. Seitan (Vlad); P.A. Banks (Peter); S. Laval (Steve); N.A. Majid (Nazia); D. Dorsett (Dale); A. Rana (Amer); J. Smith (Jeremy); A. Bateman (Alex); S. Krpic (Sanja); A. Hostert (Arnd); S.M. Rollins; H. Erdjument-Bromage (Hediye); P. Tempst (Paul); C.Y. Benard (Claire); S. Hekimi (Siegfried); S.F. Newbury (Sarah); T. Strachan (Tom)

2006-01-01

textabstractSaccharomyces cerevisiae Scc2 binds Scc4 to form an essential complex that loads cohesin onto chromosomes. The prevalence of Scc2 orthologs in eukaryotes emphasizes a conserved role in regulating sister chromatid cohesion, but homologs of Scc4 have not hitherto been identified outside

Replicating centromeric chromatin: Spatial and temporal control of CENP-A assembly

International Nuclear Information System (INIS)

Nechemia-Arbely, Yael; Fachinetti, Daniele; Cleveland, Don W.

2012-01-01

The centromere is the fundamental unit for insuring chromosome inheritance. This complex region has a distinct type of chromatin in which histone H3 is replaced by a structurally different homologue identified in humans as CENP-A. In metazoans, specific DNA sequences are neither required nor sufficient for centromere identity. Rather, an epigenetic mark comprised of CENP-A containing chromatin is thought to be the major determinant of centromere identity. In this view, CENP-A deposition and chromatin assembly are fundamental processes for the maintenance of centromeric identity across mitotic and meiotic divisions. Several lines of evidence support CENP-A deposition in metazoans occurring at only one time in the cell cycle. Such cell cycle-dependent loading of CENP-A is found in divergent species from human to fission yeast, albeit with differences in the cell cycle point at which CENP-A is assembled. Cell cycle dependent CENP-A deposition requires multiple assembly factors for its deposition and maintenance. This review discusses the regulation of new CENP-A deposition and its relevance to centromere identity and inheritance.

The diversification of the LIM superclass at the base of the metazoa increased subcellular complexity and promoted multicellular specialization.

Directory of Open Access Journals (Sweden)

Bernard J Koch

Full Text Available Throughout evolution, the LIM domain has been deployed in many different domain configurations, which has led to the formation of a large and distinct group of proteins. LIM proteins are involved in relaying stimuli received at the cell surface to the nucleus in order to regulate cell structure, motility, and division. Despite their fundamental roles in cellular processes and human disease, little is known about the evolution of the LIM superclass.We have identified and characterized all known LIM domain-containing proteins in six metazoans and three non-metazoans. In addition, we performed a phylogenetic analysis on all LIM domains and, in the process, have identified a number of novel non-LIM domains and motifs in each of these proteins. Based on these results, we have formalized a classification system for LIM proteins, provided reasonable timing for class and family origin events; and identified lineage-specific loss events. Our analysis is the first detailed description of the full set of LIM proteins from the non-bilaterian species examined in this study.Six of the 14 LIM classes originated in the stem lineage of the Metazoa. The expansion of the LIM superclass at the base of the Metazoa undoubtedly contributed to the increase in subcellular complexity required for the transition from a unicellular to multicellular lifestyle and, as such, was a critically important event in the history of animal multicellularity.

Nuclear power - the Hydra's head

Energy Technology Data Exchange (ETDEWEB)

Bunyard, P

1986-01-01

Following the accident at Chernobyl, the nuclear policies of many governments have been reconsidered and restated. Those in favour of nuclear power are those with highly centralised state bureaucracies, such as France and the USSR, where public opinion is disregarded. In more democratic countries, where referenda are held, such as Austria and Sweden, the people have chosen to do away with nuclear power. Indeed, the author states that nuclear power represents the State against the people, the State against democracy. Reference is made to the IAEA Reactor Safety Conference held in September, 1986, in Vienna, and the declaration sent to it by AntiAtom International. This called for the United Nations to promote the phasing out of nuclear power facilities throughout the world. It also called on the IAEA to support the phasing out of nuclear power and promote benign energy forms instead.

Nuclear power - the Hydra's head

International Nuclear Information System (INIS)

Bunyard, Peter.

1986-01-01

Following the accident at Chernobyl, the nuclear policies of many governments have been reconsidered and restated. Those in favour of nuclear power are those with highly centralised state bureaucracies, such as France and the USSR, where public opinion is disregarded. In more democratic countries, where referenda are held, such as Austria and Sweden, the people have chosen to do away with nuclear power. Indeed, the author states that nuclear power represents the State against the people, the State against democracy. Reference is made to the IAEA Reactor Safety Conference held in September, 1986, in Vienna, and the declaration sent to it by AntiAtom International. This called for the United Nations to promote the phasing out of nuclear power facilities throughout the world. It also called on the IAEA to support the phasing out of nuclear power and promote benign energy forms instead. (UK)

N-termini of fungal CSL transcription factors are disordered, enriched in regulatory motifs and inhibit DNA binding in fission yeast.

Directory of Open Access Journals (Sweden)

Martin Převorovský

Full Text Available CSL (CBF1/RBP-Jκ/Suppressor of Hairless/LAG-1 transcription factors are the effector components of the Notch receptor signalling pathway, which is critical for metazoan development. The metazoan CSL proteins (class M can also function in a Notch-independent manner. Recently, two novel classes of CSL proteins, designated F1 and F2, have been identified in fungi. The role of the fungal CSL proteins is unclear, because the Notch pathway is not present in fungi. In fission yeast, the Cbf11 and Cbf12 CSL paralogs play antagonistic roles in cell adhesion and the coordination of cell and nuclear division. Unusually long N-terminal extensions are typical for fungal and invertebrate CSL family members. In this study, we investigate the functional significance of these extended N-termini of CSL proteins.We identify 15 novel CSL family members from 7 fungal species and conduct bioinformatic analyses of a combined dataset containing 34 fungal and 11 metazoan CSL protein sequences. We show that the long, non-conserved N-terminal tails of fungal CSL proteins are likely disordered and enriched in phosphorylation sites and PEST motifs. In a case study of Cbf12 (class F2, we provide experimental evidence that the protein is proteolytically processed and that the N-terminus inhibits the Cbf12-dependent DNA binding activity in an electrophoretic mobility shift assay.This study provides insight into the characteristics of the long N-terminal tails of fungal CSL proteins that may be crucial for controlling DNA-binding and CSL function. We propose that the regulation of DNA binding by Cbf12 via its N-terminal region represents an important means by which fission yeast strikes a balance between the class F1 and class F2 paralog activities. This mode of regulation might be shared with other CSL-positive fungi, some of which are relevant to human disease and biotechnology.

Open Software Tools Applied to Jordan's National Multi-Agent Water Management Model

Science.gov (United States)

Knox, Stephen; Meier, Philipp; Harou, Julien; Yoon, Jim; Selby, Philip; Lachaut, Thibaut; Klassert, Christian; Avisse, Nicolas; Khadem, Majed; Tilmant, Amaury; Gorelick, Steven

2016-04-01

Jordan is the fourth most water scarce country in the world, where demand exceeds supply in a politically and demographically unstable context. The Jordan Water Project (JWP) aims to perform policy evaluation by modelling the hydrology, economics, and governance of Jordan's water resource system. The multidisciplinary nature of the project requires a modelling software system capable of integrating submodels from multiple disciplines into a single decision making process and communicating results to stakeholders. This requires a tool for building an integrated model and a system where diverse data sets can be managed and visualised. The integrated Jordan model is built using Pynsim, an open-source multi-agent simulation framework implemented in Python. Pynsim operates on network structures of nodes and links and supports institutional hierarchies, where an institution represents a grouping of nodes, links or other institutions. At each time step, code within each node, link and institution can executed independently, allowing for their fully autonomous behaviour. Additionally, engines (sub-models) perform actions over the entire network or on a subset of the network, such as taking a decision on a set of nodes. Pynsim is modular in design, allowing distinct modules to be modified easily without affecting others. Data management and visualisation is performed using Hydra (www.hydraplatform.org), an open software platform allowing users to manage network structure and data. The Hydra data manager connects to Pynsim, providing necessary input parameters for the integrated model. By providing a high-level portal to the model, Hydra removes a barrier between the users of the model (researchers, stakeholders, planners etc) and the model itself, allowing them to manage data, run the model and visualise results all through a single user interface. Pynsim's ability to represent institutional hierarchies, inter-network communication and the separation of node, link and

Drug: D06895 [KEGG MEDICUS

Lifescience Database Archive (English)

Full Text Available D06895 Crude ... Drug Aluminum silicate hydrate with silicon dioxide (JP17); Hydra...21] ... Same as: E00192 Therapeutic category: 5100 ... Clay mineral comprised of natural hydrated aluminium silicate and silico

Combined Effects of JP-8 Fuel and Ceramic Thermal Barrier Coatings on the Performance and Emissions of a DI Diesel Engine

National Research Council Canada - National Science Library

Klett, David

1999-01-01

.... The experiments were conducted on a Ricardo Hydra single-cylinder DI diesel engine. Thin ceramic thermal barrier coatings were applied to various combustion chamber surfaces including the piston crown, cylinder head, and cylinder liner...

Nigerian

African Journals Online (AJOL)

USER

2016-11-08

Nov 8, 2016 ... Ethiopian Journal of Environmental Studies & Management 9(6): 769 ... Nigerian Building and Road Research Institute, Abuja, Nigeria .... solid waste had posed a hydra-headed ... further divided into five clusters made up.

The Influence of deep-sea bed CO₂ sequestration on small metazoan (meiofaunal) community structure and function

Energy Technology Data Exchange (ETDEWEB)

Carman, Kevin R. [Louisiana State Univ., Baton Rouge, LA (United States); Fleeger, John W. [Louisiana State Univ., Baton Rouge, LA (United States); Thistle, David [Florida State Univ., Tallahassee, FL (United States)

2013-02-17

reduction in pH to about 7.0 after 30 days were as great as an extreme pH reduction (5.4), suggesting that moderate CO₂2metazoans (nematodes and copepods). While we found evidence for negative impacts on deep-sea benthos, we also observed that small-scale experiments with CO₂22222

Expanded functional diversity of shaker K(+ channels in cnidarians is driven by gene expansion.

Directory of Open Access Journals (Sweden)

Timothy Jegla

Full Text Available The genome of the cnidarian Nematostella vectensis (starlet sea anemone provides a molecular genetic view into the first nervous systems, which appeared in a late common ancestor of cnidarians and bilaterians. Nematostella has a surprisingly large and diverse set of neuronal signaling genes including paralogs of most neuronal signaling molecules found in higher metazoans. Several ion channel gene families are highly expanded in the sea anemone, including three subfamilies of the Shaker K(+ channel gene family: Shaker (Kv1, Shaw (Kv3 and Shal (Kv4. In order to better understand the physiological significance of these voltage-gated K(+ channel expansions, we analyzed the function of 18 members of the 20 gene Shaker subfamily in Nematostella. Six of the Nematostella Shaker genes express functional homotetrameric K(+ channels in vitro. These include functional orthologs of bilaterian Shakers and channels with an unusually high threshold for voltage activation. We identified 11 Nematostella Shaker genes with a distinct "silent" or "regulatory" phenotype; these encode subunits that function only in heteromeric channels and serve to further diversify Nematostella Shaker channel gating properties. Subunits with the regulatory phenotype have not previously been found in the Shaker subfamily, but have evolved independently in the Shab (Kv2 family in vertebrates and the Shal family in a cnidarian. Phylogenetic analysis indicates that regulatory subunits were present in ancestral cnidarians, but have continued to diversity at a high rate after the split between anthozoans and hydrozoans. Comparison of Shaker family gene complements from diverse metazoan species reveals frequent, large scale duplication has produced highly unique sets of Shaker channels in the major metazoan lineages.

Broad Phylogenetic Occurrence of the Oxygen-Binding Hemerythrins in Bilaterians.

Science.gov (United States)

Costa-Paiva, Elisa M; Schrago, Carlos G; Halanych, Kenneth M

2017-10-01

Animal tissues need to be properly oxygenated for carrying out catabolic respiration and, as such, natural selection has presumably favored special molecules that can reversibly bind and transport oxygen. Hemoglobins, hemocyanins, and hemerythrins (Hrs) fulfill this role, with Hrs being the least studied. Knowledge of oxygen-binding proteins is crucial for understanding animal physiology. Hr genes are present in the three domains of life, Archaea, Bacteria, and Eukaryota; however, within Animalia, Hrs has been reported only in marine species in six phyla (Annelida, Brachiopoda, Priapulida, Bryozoa, Cnidaria, and Arthropoda). Given this observed Hr distribution, whether all metazoan Hrs share a common origin is circumspect. We investigated Hr diversity and evolution in metazoans, by employing in silico approaches to survey for Hrs from of 120 metazoan transcriptomes and genomes. We found 58 candidate Hr genes actively transcribed in 36 species distributed in 11 animal phyla, with new records in Echinodermata, Hemichordata, Mollusca, Nemertea, Phoronida, and Platyhelminthes. Moreover, we found that "Hrs" reported from Cnidaria and Arthropoda were not consistent with that of other metazoan Hrs. Contrary to previous suggestions that Hr genes were absent in deuterostomes, we find Hr genes present in deuterostomes and were likely present in early bilaterians, but not in nonbilaterian animal lineages. As expected, the Hr gene tree did not mirror metazoan phylogeny, suggesting that Hrs evolutionary history was complex and besides the oxygen carrying capacity, the drivers of Hr evolution may also consist of secondary functional specializations of the proteins, like immunological functions. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

The evolution and expression of panarthropod frizzled genes

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Ralf eJanssen

2015-08-01

Full Text Available Wnt signaling regulates many important processes during metazoan development. It has been shown that Wnt ligands represent an ancient and diverse family of proteins that likely function in complex signaling landscapes to induce target cells via receptors including those of the Frizzled (Fz family. The four subfamilies of Fz receptors also evolved early in metazoan evolution. To date, Fz receptors have been characterised mainly in mammals, the nematode Caenorhabditis elegans and insects such as Drosophila melanogaster. To compare these findings with other metazoans, we explored the repertoire of fz genes in three panarthropod species: Parasteatoda tepidariorum, Glomeris marginata and Euperipatoides kanangrensis, representing the Chelicerata, Myriapoda and Onychophora respectively. We found that these three diverse panarthropods each have four fz genes, with representatives of all four metazoan fz subfamilies found in Glomeris and Euperipatoides, while Parasteatoda does not have a fz3 gene, but has two fz4 paralogues. Furthermore we characterized the expression patterns of all the fz genes among these animals. Our results exemplify the evolutionary diversity of Fz receptors and reveals conserved and divergent aspects of their protein sequences and expression patterns among panarthropods; thus providing new insights into the evolution of Wnt signaling more generally.

The SH2 Domain–Containing Proteins in 21 Species Establish the Provenance and Scope of Phosphotyrosine Signaling in Eukaryotes

Science.gov (United States)

Liu, Bernard A.; Shah, Eshana; Jablonowski, Karl; Stergachis, Andrew; Engelmann, Brett; Nash, Piers D.

2014-01-01

The Src homology 2 (SH2) domains are participants in metazoan signal transduction, acting as primary mediators for regulated protein-protein interactions with tyrosine-phosphorylated substrates. Here, we describe the origin and evolution of SH2 domain proteins by means of sequence analysis from 21 eukaryotic organisms from the basal unicellular eukaryotes, where SH2 domains first appeared, through the multicellular animals and increasingly complex metazoans. On the basis of our results, SH2 domains and phosphotyrosine signaling emerged in the early Unikonta, and the numbers of SH2 domains expanded in the choanoflagellate and metazoan lineages with the development of tyrosine kinases, leading to rapid elaboration of phosphotyrosine signaling in early multicellular animals. Our results also indicated that SH2 domains coevolved and the number of the domains expanded alongside protein tyrosine kinases and tyrosine phosphatases, thereby coupling phosphotyrosine signaling to downstream signaling networks. Gene duplication combined with domain gain or loss produced novel SH2-containing proteins that function within phosphotyrosine signaling, which likely have contributed to diversity and complexity in metazoans. We found that intra- and intermolecular interactions within and between SH2 domain proteins increased in prevalence along with organismal complexity and may function to generate more highly connected and robust phosphotyrosine signaling networks. PMID:22155787

Gluconeogenesis: An ancient biochemical pathway with a new twist

OpenAIRE

Miyamoto, Tetsuya; Amrein, Hubert

2017-01-01

Synthesis of sugars from simple carbon sources is critical for survival of animals under limited nutrient availability. Thus, sugar-synthesizing enzymes should be present across the entire metazoan spectrum. Here, we explore the evolution of glucose and trehalose synthesis using a phylogenetic analysis of enzymes specific for the two pathways. Our analysis reveals that the production of trehalose is the more ancestral biochemical process, found in single cell organisms and primitive metazoans...

Time-resolved soft x-ray spectra from laser-produced Cu plasma

International Nuclear Information System (INIS)

Cone, K.V.; Dunn, J.; Baldis, H.A.; May, M.J.; Purvis, M.A.; Scott, H.A.; Schneider, M.B.

2012-01-01

The volumetric heating of a thin copper target has been studied with time resolved x-ray spectroscopy. The copper target was heated from a plasma produced using the Lawrence Livermore National Laboratory's Compact Multipulse Terrawatt (COMET) laser. A variable spaced grating spectrometer coupled to an x-ray streak camera measured soft x-ray emission (800-1550 eV) from the back of the copper target to characterize the bulk heating of the target. Radiation hydrodynamic simulations were modeled in 2-dimensions using the HYDRA code. The target conditions calculated by HYDRA were post-processed with the atomic kinetics code CRETIN to generate synthetic emission spectra. A comparison between the experimental and simulated spectra indicates the presence of specific ionization states of copper and the corresponding electron temperatures and ion densities throughout the laser-heated copper target.

Constitutive Activity in an Ancestral Form of Abl Tyrosine Kinase.

Directory of Open Access Journals (Sweden)

Saadat U Aleem

Full Text Available The c-abl proto-oncogene encodes a nonreceptor tyrosine kinase that is found in all metazoans, and is ubiquitously expressed in mammalian tissues. The Abl tyrosine kinase plays important roles in the regulation of mammalian cell physiology. Abl-like kinases have been identified in the genomes of unicellular choanoflagellates, the closest relatives to the Metazoa, and in related unicellular organisms. Here, we have carried out the first characterization of a premetazoan Abl kinase, MbAbl2, from the choanoflagellate Monosiga brevicollis. The enzyme possesses SH3, SH2, and kinase domains in a similar arrangement to its mammalian counterparts, and is an active tyrosine kinase. MbAbl2 lacks the N-terminal myristoylation and cap sequences that are critical regulators of mammalian Abl kinase activity, and we show that MbAbl2 is constitutively active. When expressed in mammalian cells, MbAbl2 strongly phosphorylates cellular proteins on tyrosine, and transforms cells much more potently than mammalian Abl kinase. Thus, MbAbl2 appears to lack the autoinhibitory mechanism that tightly constrains the activity of mammalian Abl kinases, suggesting that this regulatory apparatus arose more recently in metazoan evolution.

The role of exon shuffling in shaping protein-protein interaction networks

Directory of Open Access Journals (Sweden)

França Gustavo S

2010-12-01

Full Text Available Abstract Background Physical protein-protein interaction (PPI is a critical phenomenon for the function of most proteins in living organisms and a significant fraction of PPIs are the result of domain-domain interactions. Exon shuffling, intron-mediated recombination of exons from existing genes, is known to have been a major mechanism of domain shuffling in metazoans. Thus, we hypothesized that exon shuffling could have a significant influence in shaping the topology of PPI networks. Results We tested our hypothesis by compiling exon shuffling and PPI data from six eukaryotic species: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Cryptococcus neoformans and Arabidopsis thaliana. For all four metazoan species, genes enriched in exon shuffling events presented on average higher vertex degree (number of interacting partners in PPI networks. Furthermore, we verified that a set of protein domains that are simultaneously promiscuous (known to interact to multiple types of other domains, self-interacting (able to interact with another copy of themselves and abundant in the genomes presents a stronger signal for exon shuffling. Conclusions Exon shuffling appears to have been a recurrent mechanism for the emergence of new PPIs along metazoan evolution. In metazoan genomes, exon shuffling also promoted the expansion of some protein domains. We speculate that their promiscuous and self-interacting properties may have been decisive for that expansion.

Widespread presence of human BOULE homologs among animals and conservation of their ancient reproductive function.

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Chirag Shah

2010-07-01

Full Text Available Sex-specific traits that lead to the production of dimorphic gametes, sperm in males and eggs in females, are fundamental for sexual reproduction and accordingly widespread among animals. Yet the sex-biased genes that underlie these sex-specific traits are under strong selective pressure, and as a result of adaptive evolution they often become divergent. Indeed out of hundreds of male or female fertility genes identified in diverse organisms, only a very small number of them are implicated specifically in reproduction in more than one lineage. Few genes have exhibited a sex-biased, reproductive-specific requirement beyond a given phylum, raising the question of whether any sex-specific gametogenesis factors could be conserved and whether gametogenesis might have evolved multiple times. Here we describe a metazoan origin of a conserved human reproductive protein, BOULE, and its prevalence from primitive basal metazoans to chordates. We found that BOULE homologs are present in the genomes of representative species of each of the major lineages of metazoans and exhibit reproductive-specific expression in all species examined, with a preponderance of male-biased expression. Examination of Boule evolution within insect and mammalian lineages revealed little evidence for accelerated evolution, unlike most reproductive genes. Instead, purifying selection was the major force behind Boule evolution. Furthermore, loss of function of mammalian Boule resulted in male-specific infertility and a global arrest of sperm development remarkably similar to the phenotype in an insect boule mutation. This work demonstrates the conservation of a reproductive protein throughout eumetazoa, its predominant testis-biased expression in diverse bilaterian species, and conservation of a male gametogenic requirement in mice. This shows an ancient gametogenesis requirement for Boule among Bilateria and supports a model of a common origin of spermatogenesis.

Evolution of disorder in Mediator complex and its functional relevance.

Science.gov (United States)

Nagulapalli, Malini; Maji, Sourobh; Dwivedi, Nidhi; Dahiya, Pradeep; Thakur, Jitendra K

2016-02-29

Mediator, an important component of eukaryotic transcriptional machinery, is a huge multisubunit complex. Though the complex is known to be conserved across all the eukaryotic kingdoms, the evolutionary topology of its subunits has never been studied. In this study, we profiled disorder in the Mediator subunits of 146 eukaryotes belonging to three kingdoms viz., metazoans, plants and fungi, and attempted to find correlation between the evolution of Mediator complex and its disorder. Our analysis suggests that disorder in Mediator complex have played a crucial role in the evolutionary diversification of complexity of eukaryotic organisms. Conserved intrinsic disordered regions (IDRs) were identified in only six subunits in the three kingdoms whereas unique patterns of IDRs were identified in other Mediator subunits. Acquisition of novel molecular recognition features (MoRFs) through evolution of new subunits or through elongation of the existing subunits was evident in metazoans and plants. A new concept of 'junction-MoRF' has been introduced. Evolutionary link between CBP and Med15 has been provided which explain the evolution of extended-IDR in CBP from Med15 KIX-IDR junction-MoRF suggesting role of junction-MoRF in evolution and modulation of protein-protein interaction repertoire. This study can be informative and helpful in understanding the conserved and flexible nature of Mediator complex across eukaryotic kingdoms. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Parasites as Biological Tags for Stock Discrimination of Beaked Redfish (Sebastes mentella: Parasite Infra-Communities vs. Limited Resolution of Cytochrome Markers.

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Regina Klapper

Full Text Available The use of parasites as biological tags for discrimination of fish stocks has become a commonly used approach in fisheries management. Metazoan parasite community analysis and anisakid nematode population genetics based on a mitochondrial cytochrome marker were applied in order to assess the usefulness of the two parasitological methods for stock discrimination of beaked redfish Sebastes mentella of three fishing grounds in the North East Atlantic. Multivariate, model-based approaches demonstrated that the metazoan parasite fauna of beaked redfish from East Greenland differed from Tampen, northern North Sea, and Bear Island, Barents Sea. A joint model (latent variable model was used to estimate the effects of covariates on parasite species and identified four parasite species as main source of differences among fishing grounds; namely Chondracanthus nodosus, Anisakis simplex s.s., Hysterothylacium aduncum, and Bothriocephalus scorpii. Due to its high abundance and differences between fishing grounds, Anisakis simplex s.s. was considered as a major biological tag for host stock differentiation. Whilst the sole examination of Anisakis simplex s.s. on a population genetic level is only of limited use, anisakid nematodes (in particular, A. simplex s.s. can serve as biological tags on a parasite community level. This study confirmed the use of multivariate analyses as a tool to evaluate parasite infra-communities and to identify parasite species that might serve as biological tags. The present study suggests that S. mentella in the northern North Sea and Barents Sea is not sub-structured.

Journal of Biosciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Journal of Biosciences. Surendra Ghaskadbi. Articles written in Journal of Biosciences. Volume 26 Issue 2 June 2001 pp 153-155 Articles. Hydra constitutively expresses transcripts involved in vertebrate neural differentiation · Sandipan Chatterjee Shweta Lahudkar N N Godbole Surendra Ghaskadbi.

A spiral-like chain from a hydrogen-bonded cyclic dichloride contain ...

Indian Academy of Sciences (India)

TECS

in the form of small hydrogen bonded clusters. The results of a ... cules,4 have been recently published.5,6 Studies on water clusters are of current research interest7 as evidenced by the .... bromide dihydrate.38 The IR spectrum of the hydra-.

A technique of the structural-tectonic elevations prediction using Earth remote sensing data

Science.gov (United States)

Tishaev, I. V.; Zatserkovnyi, V. I.; Yagorlytska, K. P.

2016-12-01

We consider an approach of using methods of Earth remote sensing data (RSD) classification for solving tasks of exploration geology and geophysics. Information obtained from the remote sensing data gives a possibility to clarify the structure of investigated areas and to determine neotectonic elevations, which act as certain indicators of promising areas with hydra-carbons contents. Reasonability of using such methods of RSD classification is based on connection between deep structure of surface resources (structural-tectonic setting) with current landscape, character of hydrologic network, geo-morphological, geo-botanical and other features. The advantage of Bayes classificator is not only in determination of object belonging to certain class, but also in calculation of probability of such belonging. For the formulated task this lets to forecast a presence of structural-tectonic elevations, which are potentially promising areas for hydra-carbons contents, using a formali! zed quantitative criterion. contents.

Hospital closure: Phoenix, Hydra or Titanic?

Science.gov (United States)

Dunne, T; Davis, S

1996-01-01

Very little has been published about the effects of hospital closure in terms of the service, financial or management issues of the process. Attempts through a case-study format to redress the balance and as such represents the reflections of practitioners who have recently undergone the experience of hospital closure and the often neglected issues arising both during and after the process.

One ring to rule them all: trafficking of heme and heme synthesis intermediates in the metazoans.

Science.gov (United States)

Hamza, Iqbal; Dailey, Harry A

2012-09-01

The appearance of heme, an organic ring surrounding an iron atom, in evolution forever changed the efficiency with which organisms were able to generate energy, utilize gasses and catalyze numerous reactions. Because of this, heme has become a near ubiquitous compound among living organisms. In this review we have attempted to assess the current state of heme synthesis and trafficking with a goal of identifying crucial missing information, and propose hypotheses related to trafficking that may generate discussion and research. The possibilities of spatially organized supramolecular enzyme complexes and organelle structures that facilitate efficient heme synthesis and subsequent trafficking are discussed and evaluated. Recently identified players in heme transport and trafficking are reviewed and placed in an organismal context. Additionally, older, well established data are reexamined in light of more recent studies on cellular organization and data available from newer model organisms. This article is part of a Special Issue entitled: Cell Biology of Metals. Copyright © 2012 Elsevier B.V. All rights reserved.

NGC 3312: A victim of ram pressure sweeping

International Nuclear Information System (INIS)

Mcmahon, P.M.; Richter, O.G.; Vangorkom, J.H.; Ferguson, H.C.

1990-01-01

Researchers are undertaking a volume limited survey of the Hydra I cluster in neutral hydrogen using the National Radio Astronomy Observatory's Very Large Array (VLA). The main purpose is to study the effects of a dense environment on the gaseous component of the galaxies. Observational evidence has been accumulating recently that ram pressure sweeping does occur in the centers of clusters, but it is possible that tidal interactions play a role as well. Results of high resolution HI imaging of NGC 3312, the large peculiar spiral near the cluster center are presented. Hydra I (= A1060) is the nearest rich cluster beyond Virgo and, as such, presents a unique opportunity to do a complete survey of a cluster. It is similar to the Virgo cluster in many of its general physical characteristics, such as size, x ray luminosity, velocity dispersion, and galaxy content (high spiral fraction). However, Hydra I appears to be more regular and relaxed. This is evident in the x ray distribution in its central region, which is radially symmetric and centered on the dominant galaxy, NGC 3311, a cD-like elliptical. The observed x ray luminosity implies a central gas density of 4.5 x 10 to the 3rd power cm(-3). Gallagher (1978) argued from optical images of NGC 3312 that this galaxy might be an ideal candidate to directly study effects of the ram pressure process; it might currently be undergoing stripping of its interstellar medium. The researchers' data are consistent with this suggestion, but other origins of the peculiar appearance cannot yet be ruled out

Outside The Box: Building a Digital Asset Management Ecosystem for Preservation and Access

Directory of Open Access Journals (Sweden)

Andrew Weidner

2017-04-01

Full Text Available The University of Houston (UH Libraries made an institutional commitment in late 2015 to migrate the data for its digitized cultural heritage collections to open source systems for preservation and access: Hydra-in-a-Box, Archivematica, and ArchivesSpace. This article describes the work that the UH Libraries implementation team has completed to date, including open source tools for streamlining digital curation workflows, minting and resolving identifiers, and managing SKOS vocabularies. These systems, workflows, and tools, collectively known as the Bayou City Digital Asset Management System (BCDAMS, represent a novel effort to solve common issues in the digital curation lifecycle and may serve as a model for other institutions seeking to implement flexible and comprehensive systems for digital preservation and access.

Field performance of three real-time moisture sensors in sandy loam and clay loam soils

Science.gov (United States)

The study was conducted to evaluate HydraProbe (HyP), Campbell Time Domain Reflectometry (TDR) and Watermarks (WM) moisture sensors for their ability to estimate water content based on calibrated neutron probe measurements. The three sensors were in-situ tested under natural weather conditions over ...

Comparative myoanatomy of cycliophoran life cycle stages

DEFF Research Database (Denmark)

Neves, Ricardo C.; Cunha, Maria R.; Funch, Peter

2010-01-01

The metazoan phylum Cycliophora includes small cryptic epibionts that live attached to the mouthparts of clawed lobsters. The life cycle is complex, with alternating sexual and asexual generations, and involves several sessile and free-living stages. So far, the morphological and genetic characte......The metazoan phylum Cycliophora includes small cryptic epibionts that live attached to the mouthparts of clawed lobsters. The life cycle is complex, with alternating sexual and asexual generations, and involves several sessile and free-living stages. So far, the morphological and genetic...

Gene prediction and RFX transcriptional regulation analysis using comparative genomics

OpenAIRE

Chu, Jeffrey Shih Chieh

2011-01-01

Regulatory Factor X (RFX) is a family of transcription factors (TF) that is conserved in all metazoans, in some fungi, and in only a few single-cellular organisms. Seven members are found in mammals, nine in fishes, three in fruit flies, and a single member in nematodes and fungi. RFX is involved in many different roles in humans, but a particular function that is conserved in many metazoans is its regulation of ciliogenesis. Probing over 150 genomes for the presence of RFX and ciliary genes ...

A broad but restricted requirement for TAF-5 (human TAFII100) for embryonic transcription in Caenorhabditis elegans.

Science.gov (United States)

Walker, Amy K; Blackwell, T Keith

2003-02-21

As conserved components of the transcription factor (TF) IID- and TFTC/SAGA-related complexes, TATA-binding protein-associated factors (TAF(II)s) are important for eukaryotic mRNA transcription. In yeast, genetic analyses suggest that, although some individual TAF(II)s are required for transcription of most genes, others have highly specialized functions. Much less is known about the functions of TAF(II)s in metazoans, which have more complex genomes that include many tissue-specific genes. TAF-5 (human (h) TAF(II)100) is of particular interest because it is predicted to have an important structural role. Here we describe the first genetics-based analysis of TAF-5 in a metazoan. By performing RNA interference in Caenorhabditis elegans embryos, which can survive for several cell generations without transcription, we found that taf-5 is important for a significant fraction of transcription. However, TAF-5 is apparently not essential for the expression of multiple developmental and other metazoan-specific genes. This phenotype remarkably resembles the previously described effects of similarly depleting two C. elegans histone fold TAF(II)s, TAF-9 (hTAF(II)31/32) and TAF-10 (hTAF(II)30), but is distinct from the widespread transcription block caused by TAF-4 (hTAF(II)130) depletion. Our findings suggest that TAF-5, TAF-9, and TAF-10 are part of a functional module of TFIID- and TFTC/SAGA-related complexes that can be bypassed in many metazoan-specific genes.

Metazoan parasites of dogs in Sabah, Malaysia.

Science.gov (United States)

MacAdam, I; Gudan, D; Timbs, D V; Urquhart, H R; Sewell, M M

1984-02-01

The parasites which occurred most frequently in 175 owned or stray dogs in Sabah were Ancylostoma spp. present in 68% of the animals. Dirofilaria immitis occurred in 70% of the adult dogs but neither D. immitis nor Spirocerca lupi were present in puppies under four months of age. The latter attained a prevalence of 30% in the adults. In contrast Toxocara canis occurred in 81% of the puppies but infrequently in older dogs. Dipylidium caninum was moderately prevalent (15 to 25%) in dogs of all ages. Ticks were the most common arthropod parasite being present on 26% of the dogs and were mainly Rhipicephalus sanguineus. Demodectic and sarcoptic mange were confirmed and fleas and lice were also recovered.

Marine microalgae attack and feed on metazoans

DEFF Research Database (Denmark)

Berge, Terje; Poulsen, Louise K.; Moldrup, Morten

2012-01-01

Free-living microalgae from the dinoflagellate genus Karlodinium are known to formmassive blooms in eutrophic coastal waters worldwide and are often associated with fish kills. Natural bloom populations, recently shown to consist of the two mixotrophic and toxic species Karlodinium armiger...... and Karlodinium veneficum have caused fast paralysis and mortality of finfish and copepods in the laboratory, and have been associated with reduced metazooplankton biomass in-situ. Here we show that a strain of K. armiger (K-0688) immobilises the common marine copepod Acartia tonsa in a densitydependent manner...... and collectively ingests the grazer to promote its own growth rate. In contrast, four strains of K. veneficum did not attack or affect the motility and survival of the copepods. Copepod immobilisation by the K. armiger strain was fast (within 15min) and caused by attacks of swarming cells, likely through...

A Viral (Arc)hive for Metazoan Memory.

Science.gov (United States)

Parrish, Nicholas F; Tomonaga, Keizo

2018-01-11

Arc, a master regulator of synaptic plasticity, contains sequence elements that are evolutionarily related to retrotransposon Gag genes. Two related papers in this issue of Cell show that Arc retains retroviral-like capsid-forming ability and can transmit mRNA between cells in the nervous system, a process that may be important for synaptic function. Copyright © 2017 Elsevier Inc. All rights reserved.

Managing examination malpractice in Nigerian University system ...

African Journals Online (AJOL)

Examination malpractice is as old as examination itself. However, the rate at which examination malpractices occurs in the Nigerian educational system is highly disturbing. The challenge therefore needs prompt attention. The phenomenon which has both moral and legal dimensions is considered as a hydra-headed ...

Thoughts on identifiers

CERN Multimedia

CERN. Geneva

2005-01-01

As business processes and information transactions have become an inextricably intertwined with the Web, the importance of assignment, registration, discovery, and maintenance of identifiers has increased. In spite of this, integrated frameworks for managing identifiers have been slow to emerge. Instead, identification systems arise (quite naturally) from immediate business needs without consideration for how they fit into larger information architectures. In addition, many legacy identifier systems further complicate the landscape, making it difficult for content managers to select and deploy identifier systems that meet both the business case and long term information management objectives. This presentation will outline a model for evaluating identifier applications and the functional requirements of the systems necessary to support them. The model is based on a layered analysis of the characteristics of identifier systems, including: * Functional characteristics * Technology * Policy * Business * Social T...

Achieving Standard in Secondary Education through the Eradication ...

African Journals Online (AJOL)

Examination malpractice had been and is still a serious canker-worm toNigerian education system. This hydra-headed monster has eaten deep intothe bone marrows of Nigerians even from primary school levels to tertiaryinstitutions. No wonder, the researchers sought to find out the opinions ofprincipals, teachers and ...

Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships.

Science.gov (United States)

Pick, K S; Philippe, H; Schreiber, F; Erpenbeck, D; Jackson, D J; Wrede, P; Wiens, M; Alié, A; Morgenstern, B; Manuel, M; Wörheide, G

2010-09-01

Despite expanding data sets and advances in phylogenomic methods, deep-level metazoan relationships remain highly controversial. Recent phylogenomic analyses depart from classical concepts in recovering ctenophores as the earliest branching metazoan taxon and propose a sister-group relationship between sponges and cnidarians (e.g., Dunn CW, Hejnol A, Matus DQ, et al. (18 co-authors). 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452:745-749). Here, we argue that these results are artifacts stemming from insufficient taxon sampling and long-branch attraction (LBA). By increasing taxon sampling from previously unsampled nonbilaterians and using an identical gene set to that reported by Dunn et al., we recover monophyletic Porifera as the sister group to all other Metazoa. This suggests that the basal position of the fast-evolving Ctenophora proposed by Dunn et al. was due to LBA and that broad taxon sampling is of fundamental importance to metazoan phylogenomic analyses. Additionally, saturation in the Dunn et al. character set is comparatively high, possibly contributing to the poor support for some nonbilaterian nodes.

Interorgan Communication Pathways in Physiology: Focus on Drosophila.

Science.gov (United States)

Droujinine, Ilia A; Perrimon, Norbert

2016-11-23

Studies in mammals and Drosophila have demonstrated the existence and significance of secreted factors involved in communication between distal organs. In this review, primarily focusing on Drosophila, we examine the known interorgan communication factors and their functions, physiological inducers, and integration in regulating physiology. Moreover, we describe how organ-sensing screens in Drosophila can systematically identify novel conserved interorgan communication factors. Finally, we discuss how interorgan communication enabled and evolved as a result of specialization of organs. Together, we anticipate that future studies will establish a model for metazoan interorgan communication network (ICN) and how it is deregulated in disease.

Molecular Gut Content Profiling to Investigate the In Situ Grazing and Selectivity of Dolioletta gegenbauri in Summer Continental Shelf Intrusion Waters of the South Atlantic Bight, USA

Science.gov (United States)

Walters, T. L.; Frazier, L.; Gibson, D. M.; Paffenhofer, G. A.; Frischer, M. E.

2016-02-01

Gelatinous metazooplankton play a crucial role in marine planktonic food webs and it has been suggested that they may become increasingly important in the Future Ocean. However, largely due to methodological challenges and reliance on laboratory cultivation approaches, the in situ diet of zooplankton with complex life histories and diverse prey choices remains poorly investigated. This is particularly true for the gelatinous zooplankton including the pelagic tunicate, Dolioletta gegenbauri that form large blooms in productive subtropical continental shelf environments. To investigate the diet of D. gegenbauri we developed a molecular gut profiling approach based on the use of a Peptide Nucleic Acid (PNA) PCR blocker. Using a doliolid-specific PNA blocker, it was possible to enrich the amplification of prey and parasite DNA from whole animal DNA extracts of doliolids. Gut contents from the water column, wild and captive-fed doliolids were profiled after PNA-PCR by denaturing HPLC (dHPLC), clone library and next generation sequencing (NGS) approaches. Studies were conducted during 5 summer cruises in the mid-shelf of the South Atlantic Bight. Comparison of gut profiles to available prey in the water column revealed evidence of prey selection towards larger prey species, including diatoms, dinoflagelletes and also metazoan prey that were likely captured as larvae and eggs. Wild-caught doliolids contained significantly more metazoan sequences than did the captive-fed doliolids. Ingestion of metazoan prey suggests that metazoans may contribute both the nutrition of doliolids and the potential role of doliolids as trophic cascade agents in continental shelf pelagic food webs.

USHIE ET AL, INJODEMAR 3

African Journals Online (AJOL)

user

It was in complete realization of these hydra-headed problems that the military leaders that ... addition, the moral fortitude of the Nigerian public servant was badly shaken by the ..... Harvard Business Review. March April, 60. 72. th. Mamoria, C. B. (1993) Personnel Management: Management of Human Resource (12 ed.) ...

Chandra Adds to Story of the Way We Were

Science.gov (United States)

2003-05-01

Data from NASA's Chandra X-ray Observatory have enabled astronomers to use a new way to determine if a young star is surrounded by a planet-forming disk like our early Sun. These results suggest that disks around young stars can evolve rapidly to form planets, or they can be disrupted by close encounters with other stars. Chandra observed two young star systems, TW Hydrae and HD 98800, both of which are in the TW Hydrae Association, a loose cluster of 10 million-year-old stars. Observations at infrared and other wavelengths have shown that several stars in the TW Hydrae Association are surrounded by disks of dust and gas. At a distance of about 180 light years from Earth, these systems are among the nearest analogs to the early solar nebula from which Earth formed. "X-rays give us an excellent new way to probe the disks around stars," said Joel Kastner of the Rochester Institute of Technology in Rochester, NY during a press conference today in Nashville, Tenn. at a meeting of the American Astronomical Society. "They can tell us whether a disk is very near to its parent star and dumping matter onto it, or whether such activity has ceased to be important. In the latter case, presumably the disk has been assimilated into larger bodies - perhaps planets--or disrupted." TW Hydrae and HD 98800A Chandra 0th Order Image of HD98800 Kastner and his colleagues found examples of each type of behavior in their study. One star, TW Hydrae, namesake of the TW Hydrae Association, exhibited features in its X-ray spectrum that provide strong, new evidence that matter is accreting onto the star from a circumstellar disk. They concluded that matter is guided by the star's magnetic field onto one or more hot spots on the surface of the star. In contrast, Chandra observations of the young multiple star system HD 98800 revealed that its brightest star, HD 98800A, is producing X-rays much as the Sun does, from a hot upper atmosphere or corona. HD 98800 is a complex multiple-star system

Metazoan parasites of Geophagus brasiliensis (Perciformes: Cichlidae in Patos lagoon, extreme south of Brazil

Directory of Open Access Journals (Sweden)

Gabriela Lopes Rassier

Full Text Available Abstract This study has evaluated the parasitic fauna of 79 pearl cichlids (Geophagus brasiliensis from the estuary of Patos Lagoon (31° 57' S and 52° 06' W, Rio Grande do Sul, Brazil, during the months of May and June in 2011 and 2012. All the hosts analyzed were infected with at least one species of parasite. A total of eleven metazoa were identified in 459 specimens collected. The trematode Austrodiplostomum compactum (34.2% and ergasilids Ergasilus lizae (32.9% and Gauchergasilus lizae (32.9% were the most prevalent species. The trematodes Thometrema overstreeti and Posthodiplostomum sp. had significantly higher prevalence in fish longer than 20 cm. The sex of the host had no effect on parasite prevalence and abundance. Pearl cichlids are registered as a new host for the trematodes Lobatostoma sp., Homalometron pseudopallidum and Thometrema overstreeti, for the ergasilids Ergasilus lizae and Gauchergasilus euripedesi and for the argulid Argulus spinolosus. The crustacean E. lizae is recorded in Rio Grande do Sul for the first time.

Sponge non-metastatic Group I Nme gene/protein - structure and function is conserved from sponges to humans

Science.gov (United States)

2011-01-01

Background Nucleoside diphosphate kinases NDPK are evolutionarily conserved enzymes present in Bacteria, Archaea and Eukarya, with human Nme1 the most studied representative of the family and the first identified metastasis suppressor. Sponges (Porifera) are simple metazoans without tissues, closest to the common ancestor of all animals. They changed little during evolution and probably provide the best insight into the metazoan ancestor's genomic features. Recent studies show that sponges have a wide repertoire of genes many of which are involved in diseases in more complex metazoans. The original function of those genes and the way it has evolved in the animal lineage is largely unknown. Here we report new results on the metastasis suppressor gene/protein homolog from the marine sponge Suberites domuncula, NmeGp1Sd. The purpose of this study was to investigate the properties of the sponge Group I Nme gene and protein, and compare it to its human homolog in order to elucidate the evolution of the structure and function of Nme. Results We found that sponge genes coding for Group I Nme protein are intron-rich. Furthermore, we discovered that the sponge NmeGp1Sd protein has a similar level of kinase activity as its human homolog Nme1, does not cleave negatively supercoiled DNA and shows nonspecific DNA-binding activity. The sponge NmeGp1Sd forms a hexamer, like human Nme1, and all other eukaryotic Nme proteins. NmeGp1Sd interacts with human Nme1 in human cells and exhibits the same subcellular localization. Stable clones expressing sponge NmeGp1Sd inhibited the migratory potential of CAL 27 cells, as already reported for human Nme1, which suggests that Nme's function in migratory processes was engaged long before the composition of true tissues. Conclusions This study suggests that the ancestor of all animals possessed a NmeGp1 protein with properties and functions similar to evolutionarily recent versions of the protein, even before the appearance of true tissues

NET-COMPUTER: Internet Computer Architecture and its Application in E-Commerce

Directory of Open Access Journals (Sweden)

P. O. Umenne

2012-12-01

Full Text Available Research in Intelligent Agents has yielded interesting results, some of which have been translated into commer­cial ventures. Intelligent Agents are executable software components that represent the user, perform tasks on behalf of the user and when the task terminates, the Agents send the result to the user. Intelligent Agents are best suited for the Internet: a collection of computers connected together in a world-wide computer network. Swarm and HYDRA computer architectures for Agents’ execution were developed at the University of Surrey, UK in the 90s. The objective of the research was to develop a software-based computer architecture on which Agents execution could be explored. The combination of Intelligent Agents and HYDRA computer architecture gave rise to a new computer concept: the NET-Computer in which the comput­ing resources reside on the Internet. The Internet computers form the hardware and software resources, and the user is provided with a simple interface to access the Internet and run user tasks. The Agents autonomously roam the Internet (NET-Computer executing the tasks. A growing segment of the Internet is E-Commerce for online shopping for products and services. The Internet computing resources provide a marketplace for product suppliers and consumers alike. Consumers are looking for suppliers selling products and services, while suppliers are looking for buyers. Searching the vast amount of information available on the Internet causes a great deal of problems for both consumers and suppliers. Intelligent Agents executing on the NET-Computer can surf through the Internet and select specific information of interest to the user. The simulation results show that Intelligent Agents executing HYDRA computer architecture could be applied in E-Commerce.

CD4 T-Lymphocytes cell counts in adults with human ...

African Journals Online (AJOL)

2010-02-08

Feb 8, 2010 ... on one hand and Nigeria on the other hand to bring down this Hydra-headed monster called HIV/AIDS. Keywords: CD4+ T-lymphocyte cell count, HIV/AIDS infections, Tertiary health .... stigma toward HIV-infected persons and the fear of suffering discrimination in the society. Also, the hospital was recently ...

Ekspress Grupp jahib viit Eesti internetiportaali / Gert D. Hankewitz

Index Scriptorium Estoniae

Hankewitz, Gert D.

2006-01-01

Kuigi pakkumisi eestimaiste Internetiportaalide kv.ee, osta.ee, hydra.ee, cvkeskus.ee ja autod24.ee ostmiseks on LHV-le esitanud viis firmat, peetakse tõsisemaid läbirääkimisi siiski vaid Ekspress Grupi ja Soome päritolu Sanoma WSOY-ga. Lisa: Portaalidega müügis ka neid haldavad firmad

Interferometric Studies of Red Giants with MAPPIT

Science.gov (United States)

Ireland, Michael J.

2002-06-01

Powerful new tools for the analysis of wavelength-dispersed aperture masking data are presented, as applied to the MAPPIT instrument of the 3.9 m Anglo-Australia Telescope. By using both baseline and wavelength bootstrapping simultaneously, solutions were found for the phase of wavefronts degraded by atmospheric and instrumental effects. This allowed coherent processing of many data sets, greatly improving signal-to-noise both at the longest baselines for well resolved objects, and at all baselines in for data in TiO absorption bands. Using this new techniques, as well as power spectrum-based techniques, wavelength-dependent diameters are found in the range 650-950 nm for the following stars: R Carinae, R Leonis, omicron Ceti, R Hydrae, W Hydrae, R Doradus, L2 Puppis, alpha Orionis, gamma Crucis, eta Carinae and VY Canis Majoris. All the Mira-like stars showed greater than 50% variation in diameter over the available wavelength range. L2 Puppis, a semi-regular variable resolved for the first time, showed a variation in diameter consistent with scattering by a recently ejected shell of dust.

The first metazoa living in permanently anoxic conditions

Directory of Open Access Journals (Sweden)

Heiner Iben

2010-04-01

Full Text Available Abstract Background Several unicellular organisms (prokaryotes and protozoa can live under permanently anoxic conditions. Although a few metazoans can survive temporarily in the absence of oxygen, it is believed that multi-cellular organisms cannot spend their entire life cycle without free oxygen. Deep seas include some of the most extreme ecosystems on Earth, such as the deep hypersaline anoxic basins of the Mediterranean Sea. These are permanently anoxic systems inhabited by a huge and partly unexplored microbial biodiversity. Results During the last ten years three oceanographic expeditions were conducted to search for the presence of living fauna in the sediments of the deep anoxic hypersaline L'Atalante basin (Mediterranean Sea. We report here that the sediments of the L'Atalante basin are inhabited by three species of the animal phylum Loricifera (Spinoloricus nov. sp., Rugiloricus nov. sp. and Pliciloricus nov. sp. new to science. Using radioactive tracers, biochemical analyses, quantitative X-ray microanalysis and infrared spectroscopy, scanning and transmission electron microscopy observations on ultra-sections, we provide evidence that these organisms are metabolically active and show specific adaptations to the extreme conditions of the deep basin, such as the lack of mitochondria, and a large number of hydrogenosome-like organelles, associated with endosymbiotic prokaryotes. Conclusions This is the first evidence of a metazoan life cycle that is spent entirely in permanently anoxic sediments. Our findings allow us also to conclude that these metazoans live under anoxic conditions through an obligate anaerobic metabolism that is similar to that demonstrated so far only for unicellular eukaryotes. The discovery of these life forms opens new perspectives for the study of metazoan life in habitats lacking molecular oxygen.

Zooplankton diversity across three Red Sea reefs using pyrosequencing

KAUST Repository

Pearman, John K.

2014-07-30

Coral reefs are considered among the most diverse ecosystems on Earth, yet little is known about the diversity of plankton in the surrounding water column. Moreover, few studies have utilized genomic methods to investigate zooplankton diversity in any habitat. This study investigated the diversity of taxa by sampling 45 stations around three reef systems in the central/southern Red Sea. The diversity of metazoan plankton was investigated by targeting the 18S rRNA gene and clustering OTUs at 97% sequence similarity. A total of 754 and 854 metazoan OTUs were observed in the data set for the 1380F and 1389F primer sets respectively. The phylum Arthropoda dominated both primer sets accounting for ~60% of reads followed by Cnidaria (~20%). Only about 20% of OTUs were shared between all three reef systems and the relation between geographic distance and Jaccard Similarity measures was not significant. Cluster analysis showed that there was no distinct split between reefs and stations from different reefs clustered together both for metazoans as a whole and for the phyla Arthropoda, Cnidaria and Chordata separately. This suggests that distance may not be a determining factor in the taxonomic composition of stations.

ATAD3 proteins: brokers of a mitochondria-endoplasmic reticulum connection in mammalian cells.

Science.gov (United States)

Baudier, Jacques

2018-05-01

In yeast, a sequence of physical and genetic interactions termed the endoplasmic reticulum (ER)-mitochondria organizing network (ERMIONE) controls mitochondria-ER interactions and mitochondrial biogenesis. Several functions that characterize ERMIONE complexes are conserved in mammalian cells, suggesting that a similar tethering complex must exist in metazoans. Recent studies have identified a new family of nuclear-encoded ATPases associated with diverse cellular activities (AAA+-ATPase) mitochondrial membrane proteins specific to multicellular eukaryotes, called the ATPase family AAA domain-containing protein 3 (ATAD3) proteins (ATAD3A and ATAD3B). These proteins are crucial for normal mitochondrial-ER interactions and lie at the heart of processes underlying mitochondrial biogenesis. ATAD3A orthologues have been studied in flies, worms, and mammals, highlighting the widespread importance of this gene during embryonic development and in adulthood. ATAD3A is a downstream effector of target of rapamycin (TOR) signalling in Drosophila and exhibits typical features of proteins from the ERMIONE-like complex in metazoans. In humans, mutations in the ATAD3A gene represent a new link between altered mitochondrial-ER interaction and recognizable neurological syndromes. The primate-specific ATAD3B protein is a biomarker of pluripotent embryonic stem cells. Through negative regulation of ATAD3A function, ATAD3B supports mitochondrial stemness properties. © 2017 Cambridge Philosophical Society.

Massively Parallel RNA Sequencing Identifies a Complex Immune Gene Repertoire in the lophotrochozoan Mytilus edulis

Science.gov (United States)

Philipp, Eva E. R.; Kraemer, Lars; Melzner, Frank; Poustka, Albert J.; Thieme, Sebastian; Findeisen, Ulrike; Schreiber, Stefan; Rosenstiel, Philip

2012-01-01

The marine mussel Mytilus edulis and its closely related sister species are distributed world-wide and play an important role in coastal ecology and economy. The diversification in different species and their hybrids, broad ecological distribution, as well as the filter feeding mode of life has made this genus an attractive model to investigate physiological and molecular adaptations and responses to various biotic and abiotic environmental factors. In the present study we investigated the immune system of Mytilus, which may contribute to the ecological plasticity of this species. We generated a large Mytilus transcriptome database from different tissues of immune challenged and stress treated individuals from the Baltic Sea using 454 pyrosequencing. Phylogenetic comparison of orthologous groups of 23 species demonstrated the basal position of lophotrochozoans within protostomes. The investigation of immune related transcripts revealed a complex repertoire of innate recognition receptors and downstream pathway members including transcripts for 27 toll-like receptors and 524 C1q domain containing transcripts. NOD-like receptors on the other hand were absent. We also found evidence for sophisticated TNF, autophagy and apoptosis systems as well as for cytokines. Gill tissue and hemocytes showed highest expression of putative immune related contigs and are promising tissues for further functional studies. Our results partly contrast with findings of a less complex immune repertoire in ecdysozoan and other lophotrochozoan protostomes. We show that bivalves are interesting candidates to investigate the evolution of the immune system from basal metazoans to deuterostomes and protostomes and provide a basis for future molecular work directed to immune system functioning in Mytilus. PMID:22448234

A multipartite mitochondrial genome in the potato cyst nematode Globodera pallida.

Science.gov (United States)

Armstrong, M R; Blok, V C; Phillips, M S

2000-01-01

The mitochondrial genome (mtDNA) of the plant parasitic nematode Globodera pallida exists as a population of small, circular DNAs that, taken individually, are of insufficient length to encode the typical metazoan mitochondrial gene complement. As far as we are aware, this unusual structural organization is unique among higher metazoans, although interesting comparisons can be made with the multipartite mitochondrial genome organizations of plants and fungi. The variation in frequency between populations displayed by some components of the mtDNA is likely to have major implications for the way in which mtDNA can be used in population and evolutionary genetic studies of G. pallida.

Mitochondrial apoptotic pathways induced by Drosophila programmed cell death regulators

International Nuclear Information System (INIS)

Claveria, Cristina; Torres, Miguel

2003-01-01

Multicellular organisms eliminate unwanted or damaged cells by cell death, a process essential to the maintenance of tissue homeostasis. Cell death is a tightly regulated event, whose alteration by excess or defect is involved in the pathogenesis of many diseases such as cancer, autoimmune syndromes, and neurodegenerative processes. Studies in model organisms, especially in the nematode Caenorhabditis elegans, have been crucial in identifying the key molecules implicated in the regulation and execution of programmed cell death. In contrast, the study of cell death in Drosophila melanogaster, often an excellent model organism, has identified regulators and mechanisms not obviously conserved in other metazoans. Recent molecular and cellular analyses suggest, however, that the mechanisms of action of the main programmed cell death regulators in Drosophila include a canonical mitochondrial pathway

Large-scale discovery of promoter motifs in Drosophila melanogaster.

Directory of Open Access Journals (Sweden)

Thomas A Down

2007-01-01

Full Text Available A key step in understanding gene regulation is to identify the repertoire of transcription factor binding motifs (TFBMs that form the building blocks of promoters and other regulatory elements. Identifying these experimentally is very laborious, and the number of TFBMs discovered remains relatively small, especially when compared with the hundreds of transcription factor genes predicted in metazoan genomes. We have used a recently developed statistical motif discovery approach, NestedMICA, to detect candidate TFBMs from a large set of Drosophila melanogaster promoter regions. Of the 120 motifs inferred in our initial analysis, 25 were statistically significant matches to previously reported motifs, while 87 appeared to be novel. Analysis of sequence conservation and motif positioning suggested that the great majority of these discovered motifs are predictive of functional elements in the genome. Many motifs showed associations with specific patterns of gene expression in the D. melanogaster embryo, and we were able to obtain confident annotation of expression patterns for 25 of our motifs, including eight of the novel motifs. The motifs are available through Tiffin, a new database of DNA sequence motifs. We have discovered many new motifs that are overrepresented in D. melanogaster promoter regions, and offer several independent lines of evidence that these are novel TFBMs. Our motif dictionary provides a solid foundation for further investigation of regulatory elements in Drosophila, and demonstrates techniques that should be applicable in other species. We suggest that further improvements in computational motif discovery should narrow the gap between the set of known motifs and the total number of transcription factors in metazoan genomes.

Nematode and arthropod genomes provide new insights into the evolution of class 2 B1 GPCRs.

Science.gov (United States)

Cardoso, João C R; Félix, Rute C; Power, Deborah M

2014-01-01

Nematodes and arthropods are the most speciose animal groups and possess Class 2 B1 G-protein coupled receptors (GPCRs). Existing models of invertebrate Class 2 B1 GPCR evolution are mainly centered on Caenorhabditis elegans and Drosophila melanogaster and a few other nematode and arthropod representatives. The present study reevaluates the evolution of metazoan Class 2 B1 GPCRs and orthologues by exploring the receptors in several nematode and arthropod genomes and comparing them to the human receptors. Three novel receptor phylogenetic clusters were identified and designated cluster A, cluster B and PDF-R-related cluster. Clusters A and B were identified in several nematode and arthropod genomes but were absent from D. melanogaster and Culicidae genomes, whereas the majority of the members of the PDF-R-related cluster were from nematodes. Cluster A receptors were nematode and arthropod-specific but shared a conserved gene environment with human receptor loci. Cluster B members were orthologous to human GCGR, PTHR and Secretin members with which they probably shared a common origin. PDF-R and PDF-R related clusters were present in representatives of both nematodes and arthropods. The results of comparative analysis of GPCR evolution and diversity in protostomes confirm previous notions that C. elegans and D. melanogaster genomes are not good representatives of nematode and arthropod phyla. We hypothesize that at least four ancestral Class 2 B1 genes emerged early in the metazoan radiation, which after the protostome-deuterostome split underwent distinct selective pressures that resulted in duplication and deletion events that originated the current Class 2 B1 GPCRs in nematode and arthropod genomes.

The dynamically evolving nematocyst content of an anthozoan, a scyphozoan, and a hydrozoan.

Science.gov (United States)

Rachamim, Tamar; Morgenstern, David; Aharonovich, Dikla; Brekhman, Vera; Lotan, Tamar; Sher, Daniel

2015-03-01

Nematocytes, the stinging cells of cnidarians, are the most evolutionarily ancient venom apparatus. These nanosyringe-like weaponry systems reach pressures of approximately 150 atmospheres before discharging and punching through the outer layer of the prey or predator at accelerations of more than 5 million g, making them one of the fastest biomechanical events known. To gain better understanding of the function of the complex, phylum-specific nematocyst organelle, and its venom payload, we compared the soluble nematocyst's proteome from the sea anemone Anemonia viridis, the jellyfish Aurelia aurita, and the hydrozoan Hydra magnipapillata, each belonging to one of the three basal cnidarian lineages which diverged over 600 Ma. Although the basic morphological and functional characteristics of the nematocysts of the three organisms are similar, out of hundreds of proteins identified in each organism, only six are shared. These include structural proteins, a chaperone which may help maintain venon activity over extended periods, and dickkopf, an enigmatic Wnt ligand which may also serve as a toxin. Nevertheless, many protein domains are shared between the three organisms' nematocyst content suggesting common proteome functionalities. The venoms of Hydra and Aurelia appear to be functionally similar and composed mainly of cytotoxins and enzymes, whereas the venom of the Anemonia is markedly unique and based on peptide neurotoxins. Cnidarian venoms show evidence for functional recruitment, yet evidence for diversification through positive selection, common to other venoms, is lacking. The final injected nematocyst payload comprises a mixture of dynamically evolving proteins involved in the development, maturation, maintenance, and discharge of the nematocysts, which is unique to each organism and potentially to each nematocyst type. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved

NEW MEMBERS OF THE SCORPIUS-CENTAURUS COMPLEX AND AGES OF ITS SUB-REGIONS

Energy Technology Data Exchange (ETDEWEB)

Song, Inseok [Department of Physics and Astronomy, The University of Georgia, Athens, GA 30602-2451 (United States); Zuckerman, B. [Department of Physics and Astronomy, University of California, Los Angeles, 475 Portola Plaza, Los Angeles, CA 90095-1547 (United States); Bessell, M. S. [Research School of Astronomy and Astrophysics, Institute of Advanced Studies, The Australian National University, ACT 2611 (Australia)

2012-07-15

We have spectroscopically identified {approx}100 G-, K-, and M-type members of the Scorpius-Centaurus complex. To deduce the age of these young stars we compare their Li {lambda}6708 absorption line strengths against those of stars in the TW Hydrae association and {beta} Pictoris moving group. These line strengths indicate that Sco-Cen stars are younger than {beta} Pic stars whose ages of {approx}12 Myr have previously been derived from a kinematic traceback analysis. Our derived age, {approx}10 Myr, for stars in the Lower Centaurus Crux and Upper Centaurus Lupus subgroups of ScoCen is younger than previously published ages based on the moving cluster method and upper main-sequence fitting. The discrepant ages are likely due to an incorrect (or lack of) cross-calibration between model-dependent and model-independent age-dating methods.

Ultraviolet irradiation initiates ectopic foot formation in regenerating ...

Indian Academy of Sciences (India)

If the head or base piece of a bisected hydra is irradiated and recombined with the unirradiated missing part, regeneration proceeds normally indicating that exposure of a body part with either an intact head or foot to UVC does not influence pattern formation. Most significantly, in the middle piece, but not in the head or the ...

Research and Development. Annual Report 2000

Energy Technology Data Exchange (ETDEWEB)

NONE

2001-07-01

This report discusses the research and development activities in which NVE has been involved in 2000. These activities fall into three categories: watercourse research, hydrological research and energy related research. The HYDRA research programme, which studied flooding and human intervention, is discussed in particular. The report includes a list of research and development reports that were published in 2000.

Does the inherence heuristic take us to psychological essentialism?

Science.gov (United States)

Marmodoro, Anna; Murphy, Robin A; Baker, A G

2014-10-01

We argue that the claim that essence-based causal explanations emerge, hydra-like, from an inherence heuristic is incomplete. No plausible mechanism for the transition from concrete properties, or cues, to essences is provided. Moreover, the fundamental shotgun and storytelling mechanisms of the inherence heuristic are not clearly enough specified to distinguish them, developmentally, from associative or causal networks.

Spliceosomal small nuclear RNAs of Tetrahymena thermophila and some possible snRNA-snRNA base-pairing interactions

DEFF Research Database (Denmark)

Orum, H; Nielsen, Henrik; Engberg, J

1991-01-01

We have identified and characterized the full set of spliceosomal small nuclear RNAs (snRNAs; U1, U2, U4, U5 and U6) from the ciliated protozoan Tetrahymena thermophila. With the exception of U4 snRNA, the sizes of the T. thermophila snRNAs are closely similar to their metazoan homologues. The T....... thermophila snRNAs all have unique 5' ends, which start with an adenine residue. In contrast, with the exception of U6, their 3' ends show some size heterogeneity. The primary sequences of the T. thermophila snRNAs contain the sequence motifs shown, or proposed, to be of functional importance in other...

The mitochondrial genome of the sipunculid Phascolopsis gouldii supports its association with Annelida rather than Mollusca

Energy Technology Data Exchange (ETDEWEB)

Boore, Jeffrey L.; Staton, Joseph

2001-09-01

We have determined the sequence of about half (7470 nts) of the mitochondrial genome of the sipunculid Phascolopsis gouldii, the first representative of this phylum to be so studied. All of the 19 identified genes are transcribed from the same DNA strand. The arrangement of these genes is remarkably similar to that of the oligochaete annelid Lumbricus terrestris. Comparison of both the inferred amino acid sequences and the gene arrangements of a variety of diverse metazoan taxa reveals that the phylum Sipuncula is more closely related to Annelida than to Mollusca. This requires reinterpretation of the homology of several embryological features and of patterns of animal body plan evolution.

On the way to identify microorganisms in drinking water distribution networks via DNA analysis of the gut content of freshwater isopods.

Science.gov (United States)

Mayer, Michael; Keller, Adrian; Szewzyk, Ulrich; Warnecke, Hans-Joachim

2015-05-10

Pure drinking water is the basis for a healthy society. In Germany the drinking water regulations demand for analysis of water via detection of certain microbiological parameters by cultivation only. However, not all prokaryotes can be detected by these standard methods. How to gain more and better information about the bacteria present in drinking water and its distribution systems? The biofilms in drinking water distribution systems are built by bacteria and therefore represent a valuable source of information about the species present. Unfortunately, these biofilms are badly accessible. We thus exploited the circumstance that a lot of metazoans graze the biofilms, so that the content of their guts partly reflects the respective biofilm biocenosis. Therefore, we collected omnivorous isopods, prepared their guts and examined and characterized their contents based on 16S und 18S rDNA analysis. These molecularbiological investigations provide a profound basis for the characterization of the biocenosis and thereby biologically assess the drinking water ecosystems. Combined with a thorough identification of the species and the knowledge of their habitats, this approach can provide useful indications for the assessment of drinking-water quality and the early detection of problems in the distribution system. Copyright © 2015 Elsevier B.V. All rights reserved.

Why bacteria matter in animal development and evolution.

Science.gov (United States)

Fraune, Sebastian; Bosch, Thomas C G

2010-07-01

While largely studied because of their harmful effects on human health, there is growing appreciation that bacteria are important partners for invertebrates and vertebrates, including man. Epithelia in metazoans do not only select their microbiota; a coevolved consortium of microbes enables both invertebrates and vertebrates to expand the range of diet supply, to shape the complex immune system and to control pathogenic bacteria. Microbes in zebrafish and mice regulate gut epithelial homeostasis. In a squid, microbes control the development of the symbiotic light organ. These discoveries point to a key role for bacteria in any metazoan existence, and imply that beneficial bacteria-host interactions should be considered an integral part of development and evolution.

Sequence finishing and mapping of Drosophila melanogasterheterochromatin

Energy Technology Data Exchange (ETDEWEB)

Hoskins, Roger A.; Carlson, Joseph W.; Kennedy, Cameron; Acevedo,David; Evans-Holm, Martha; Frise, Erwin; Wan, Kenneth H.; Park, Soo; Mendez-Lago, Maria; Rossi, Fabrizio; Villasante, Alfredo; Dimitri,Patrizio; Karpen, Gary H.; Celniker, Susan E.

2007-06-15

Genome sequences for most metazoans are incomplete due tothe presence of repeated DNA in the pericentromeric heterochromatin. Theheterochromatic regions of D. melanogaster contain 20 Mb of sequenceamenable to mapping, sequence assembly and finishing. Here we describethe generation of 15 Mb of finished or improved heterochromatic sequenceusing available clone resources and assembly and mapping methods. We alsoconstructed a BAC-based physical map that spans approximately 13 Mb ofthe pericentromeric heterochromatin, and a cytogenetic map that positionsapproximately 11 Mb of BAC contigs and sequence scaffolds in specificchromosomal locations. The integrated sequence assembly and maps greatlyimprove our understanding of the structure and composition of this poorlyunderstood fraction of a metazoan genome and provide a framework forfunctional analyses.

Operation and maintenance manual for diode performance analysis program DIODE0

International Nuclear Information System (INIS)

Boyer, W.B.

1977-03-01

This program computes diode performance parameters for the e beam fusion accelerators HYDRA, PROTO I and PROTO II. The program works in conjunction with other programs in the data acquisition facility library. It reads the input data produced by the Tekronix R7012 Transient Digitizers off the disc. It then computes and plots the diode corrected voltages, impedances, powers, and energies

Identifiability in stochastic models

CERN Document Server

1992-01-01

The problem of identifiability is basic to all statistical methods and data analysis, occurring in such diverse areas as Reliability Theory, Survival Analysis, and Econometrics, where stochastic modeling is widely used. Mathematics dealing with identifiability per se is closely related to the so-called branch of ""characterization problems"" in Probability Theory. This book brings together relevant material on identifiability as it occurs in these diverse fields.

Improved crystallization and diffraction of caffeine-induced death suppressor protein 1 (Cid1)

Energy Technology Data Exchange (ETDEWEB)

Yates, Luke A., E-mail: luke@strubi.ox.ac.uk; Durrant, Benjamin P.; Barber, Michael; Harlos, Karl [University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Fleurdépine, Sophie; Norbury, Chris J. [University of Oxford, South Parks Road, Oxford OX1 3RE (United Kingdom); Gilbert, Robert J. C., E-mail: luke@strubi.ox.ac.uk [University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom)

2015-02-21

The use of truncation and RNA-binding mutations of caffeine induced death suppressor protein 1 (Cid1) as a means to enhance crystallogenesis leading to an improvement of X-ray diffraction resolution by 1.5 Å is reported. The post-transcriptional addition of uridines to the 3′-end of RNAs is an important regulatory process that is critical for coding and noncoding RNA stability. In fission yeast and metazoans this untemplated 3′-uridylylation is catalysed by a single family of terminal uridylyltransferases (TUTs) whose members are adapted to specific RNA targets. In Schizosaccharomyces pombe the TUT Cid1 is responsible for the uridylylation of polyadenylated mRNAs, targeting them for destruction. In metazoans, the Cid1 orthologues ZCCHC6 and ZCCHC11 uridylate histone mRNAs, targeting them for degradation, but also uridylate microRNAs, altering their maturation. Cid1 has been studied as a model TUT that has provided insights into the larger and more complex metazoan enzyme system. In this paper, two strategies are described that led to improvements both in the crystallogenesis of Cid1 and in the resolution of diffraction by ∼1.5 Å. These advances have allowed high-resolution crystallo@@graphic studies of this TUT system to be initiated.

Genome-Wide Identification and Characterization of Tyrosine Kinases in the Silkworm, Bombyx mori

Directory of Open Access Journals (Sweden)

Songzhen He

2018-03-01

Full Text Available The tyrosine kinases (TKs are important parts of metazoan signaling pathways and play significant roles in cell growth, development, apoptosis and disease. Genome-wide characterization of TKs has been conducted in many metazoans, however, systematic information about this family in Lepidoptera is still lacking. We retrieved 33 TK-encoding genes in silkworm and classified them into 25 subfamilies by sequence analysis, without members in AXL, FRK, PDGFR, STYK1 and TIE subfamilies. Although domain sequences in each subfamily are conserved, TKs in vertebrates tend to be remarkably conserved and stable. Our results of phylogenetic analysis supported the previous conclusion for the second major expansion of TK family. Gene-Ontology (GO analysis revealed that a higher proportion of BmTKs played roles in binding, catalysis, signal transduction, metabolism, biological regulation and response to stimulus, compared to all silkworm genes annotated in GO. Moreover, the expression profile analysis of BmTKs among multiple tissues and developmental stages demonstrated that many genes exhibited stage-specific and/or sex-related expression during embryogenesis, molting and metamorphosis, and that 8 BmTKs presented tissue-specific high expression. Our study provides systematic description of silkworm tyrosine kinases, and may also provide further insights into metazoan TKs and assist future studies addressing their functions.

Improved crystallization and diffraction of caffeine-induced death suppressor protein 1 (Cid1)

International Nuclear Information System (INIS)

Yates, Luke A.; Durrant, Benjamin P.; Barber, Michael; Harlos, Karl; Fleurdépine, Sophie; Norbury, Chris J.; Gilbert, Robert J. C.

2015-01-01

The use of truncation and RNA-binding mutations of caffeine induced death suppressor protein 1 (Cid1) as a means to enhance crystallogenesis leading to an improvement of X-ray diffraction resolution by 1.5 Å is reported. The post-transcriptional addition of uridines to the 3′-end of RNAs is an important regulatory process that is critical for coding and noncoding RNA stability. In fission yeast and metazoans this untemplated 3′-uridylylation is catalysed by a single family of terminal uridylyltransferases (TUTs) whose members are adapted to specific RNA targets. In Schizosaccharomyces pombe the TUT Cid1 is responsible for the uridylylation of polyadenylated mRNAs, targeting them for destruction. In metazoans, the Cid1 orthologues ZCCHC6 and ZCCHC11 uridylate histone mRNAs, targeting them for degradation, but also uridylate microRNAs, altering their maturation. Cid1 has been studied as a model TUT that has provided insights into the larger and more complex metazoan enzyme system. In this paper, two strategies are described that led to improvements both in the crystallogenesis of Cid1 and in the resolution of diffraction by ∼1.5 Å. These advances have allowed high-resolution crystallo@@graphic studies of this TUT system to be initiated

The PP2C Alphabet is a negative regulator of stress-activated protein kinase signaling in Drosophila.

Science.gov (United States)

Baril, Caroline; Sahmi, Malha; Ashton-Beaucage, Dariel; Stronach, Beth; Therrien, Marc

2009-02-01

The Jun N-terminal kinase and p38 pathways, also known as stress-activated protein kinase (SAPK) pathways, are signaling conduits reiteratively used throughout the development and adult life of metazoans where they play central roles in the control of apoptosis, immune function, and environmental stress responses. We recently identified a Drosophila Ser/Thr phosphatase of the PP2C family, named Alphabet (Alph), which acts as a negative regulator of the Ras/ERK pathway. Here we show that Alph also plays an inhibitory role with respect to Drosophila SAPK signaling during development as well as under stress conditions such as oxidative or genotoxic stresses. Epistasis experiments suggest that Alph acts at a step upstream of the MAPKKs Hep and Lic. Consistent with this interpretation, biochemical experiments identify the upstream MAPKKKs Slpr, Tak1, and Wnd as putative substrates. Together with previous findings, this work identifies Alph as a general attenuator of MAPK signaling in Drosophila.

Strabismus-mediated primary archenteron invagination is uncoupled from Wnt/β-catenin-dependent endoderm cell fate specification in Nematostella vectensis (Anthozoa, Cnidaria: Implications for the evolution of gastrulation

Directory of Open Access Journals (Sweden)

Kumburegama Shalika

2011-01-01

Full Text Available Abstract Background Gastrulation is a uniquely metazoan character, and its genesis was arguably the key step that enabled the remarkable diversification within this clade. The process of gastrulation involves two tightly coupled events during embryogenesis of most metazoans. Morphogenesis produces a distinct internal epithelial layer in the embryo, and this epithelium becomes segregated as an endoderm/endomesodermal germ layer through the activation of a specific gene regulatory program. The developmental mechanisms that induced archenteron formation and led to the segregation of germ layers during metazoan evolution are unknown. But an increased understanding of development in early diverging taxa at the base of the metazoan tree may provide insights into the origins of these developmental mechanisms. Results In the anthozoan cnidarian Nematostella vectensis, initial archenteron formation begins with bottle cell-induced buckling of the blastula epithelium at the animal pole. Here, we show that bottle cell formation and initial gut invagination in Nematostella requires NvStrabismus (NvStbm, a maternally-expressed core component of the Wnt/Planar Cell Polarity (PCP pathway. The NvStbm protein is localized to the animal pole of the zygote, remains asymmetrically expressed through the cleavage stages, and becomes restricted to the apical side of invaginating bottle cells at the blastopore. Antisense morpholino-mediated NvStbm-knockdown blocks bottle cell formation and initial archenteron invagination, but it has no effect on Wnt/ß-catenin signaling-mediated endoderm cell fate specification. Conversely, selectively blocking Wnt/ß-catenin signaling inhibits endoderm cell fate specification but does not affect bottle cell formation and initial archenteron invagination. Conclusions Our results demonstrate that Wnt/PCP-mediated initial archenteron invagination can be uncoupled from Wnt/ß-catenin-mediated endoderm cell fate specification in

Assessment of Flagellate Diversity at Deep-Sea Hydrothermal Vents Using the Combined Approach of Culture-Dependent and Culture-Independent Methods

National Research Council Canada - National Science Library

Atkins, Michael

2000-01-01

.... Molecular and ultrastructural evidence point to one of the isolates. Ancyromonas, as a plausible candidate for the closest relative to the common ancestor of Metazoans, Fungi, and Choanoglagellates...

Identifying Knowledge and Communication

Directory of Open Access Journals (Sweden)

Eduardo Coutinho Lourenço de Lima

2006-12-01

Full Text Available In this paper, I discuss how the principle of identifying knowledge which Strawson advances in ‘Singular Terms and Predication’ (1961, and in ‘Identifying Reference and Truth-Values’ (1964 turns out to constrain communication. The principle states that a speaker’s use of a referring expression should invoke identifying knowledge on the part of the hearer, if the hearer is to understand what the speaker is saying, and also that, in so referring, speakers are attentive to hearers’ epistemic states. In contrasting it with Russell’s Principle (Evans 1982, as well as with the principle of identifying descriptions (Donnellan 1970, I try to show that the principle of identifying knowledge, ultimately a condition for understanding, makes sense only in a situation of conversation. This allows me to conclude that the cooperative feature of communication (Grice 1975 and reference (Clark andWilkes-Gibbs 1986 holds also at the understanding level. Finally, I discuss where Strawson’s views seem to be unsatisfactory, and suggest how they might be improved.

The Evolution of the Secreted Regulatory Protein Progranulin.

Science.gov (United States)

Palfree, Roger G E; Bennett, Hugh P J; Bateman, Andrew

2015-01-01

Progranulin is a secreted growth factor that is active in tumorigenesis, wound repair, and inflammation. Haploinsufficiency of the human progranulin gene, GRN, causes frontotemporal dementia. Progranulins are composed of chains of cysteine-rich granulin modules. Modules may be released from progranulin by proteolysis as 6kDa granulin polypeptides. Both intact progranulin and some of the granulin polypeptides are biologically active. The granulin module occurs in certain plant proteases and progranulins are present in early diverging metazoan clades such as the sponges, indicating their ancient evolutionary origin. There is only one Grn gene in mammalian genomes. More gene-rich Grn families occur in teleost fish with between 3 and 6 members per species including short-form Grns that have no tetrapod counterparts. Our goals are to elucidate progranulin and granulin module evolution by investigating (i): the origins of metazoan progranulins (ii): the evolutionary relationships between the single Grn of tetrapods and the multiple Grn genes of fish (iii): the evolution of granulin module architectures of vertebrate progranulins (iv): the conservation of mammalian granulin polypeptide sequences and how the conserved granulin amino acid sequences map to the known three dimensional structures of granulin modules. We report that progranulin-like proteins are present in unicellular eukaryotes that are closely related to metazoa suggesting that progranulin is among the earliest extracellular regulatory proteins still employed by multicellular animals. From the genomes of the elephant shark and coelacanth we identified contemporary representatives of a precursor for short-from Grn genes of ray-finned fish that is lost in tetrapods. In vertebrate Grns pathways of exon duplication resulted in a conserved module architecture at the amino-terminus that is frequently accompanied by an unusual pattern of tandem nearly identical module repeats near the carboxyl-terminus. Polypeptide

Contribuciones al conocimiento del género Phragmotheca Cuatr. (Bombacaceae-Quararibeae

Directory of Open Access Journals (Sweden)

Fernández Alonso José Luis

1996-11-01

Full Text Available The systematic position of Phragmotheca in the tribe quararibeae is discussed and a key for the Bombacaceae with simple or unifoliolate leaves occurring in northern South America is included. The diagnostic utility of some characters in the segregation of species in Phragmotheca, is reviewed and a diagnostic key is presented. Four new species and two new infraspecific taxa are described and illustrated: P.rubriflora, P.lemniscata, P.hydra, P.siderosa subsp. megacarpa and P. amazonica varo leticiana from Colombia and P.sidereotricha from Perú.Se comenta la posición sistemática de Phragmotheca en relación con la tribu Quararibeae y se incluye una clave para la separación de los géneros de bombacáceas de hoja entera o unifoliolada del norte de Suramérica. Se revisa la utilidad de algunos caracteres en la separación de las especies y se presenta una clave diagnóstica. Se describen e ilustran 4 nuevas especies y dos taxones infraespecíficos P. rubriflora, P. lemniscata, P. hydra, P. siderosa subsp. megacarpa, P. amazonica varo leticiana de Colombia y P. sidereotricha de Perú.

EVOLUTION OF A RING AROUND THE PLUTO–CHARON BINARY

Energy Technology Data Exchange (ETDEWEB)

Bromley, Benjamin C. [Department of Physics and Astronomy, University of Utah, 115 S 1400 E, Rm 201, Salt Lake City, UT 84112 (United States); Kenyon, Scott J., E-mail: bromley@physics.utah.edu, E-mail: skenyon@cfa.harvard.edu [Smithsonian Astrophysical Observatory, 60 Garden St., Cambridge, MA 02138 (United States)

2015-08-10

We consider the formation of satellites around the Pluto–Charon binary. An early collision between the two partners likely produced the binary and a narrow ring of debris, out of which arose the moons Styx, Nix, Kerberos, and Hydra. How the satellites emerged from the compact ring is uncertain. Here we show that a particle ring spreads from physical collisions and collective gravitational scattering, similar to migration. Around a binary, these processes take place in the reference frames of “most circular” orbits, akin to circular ones in a Keplerian potential. Ring particles damp to these orbits and avoid destructive collisions. Damping and diffusion also help particles survive dynamical instabilities driven by resonances with the binary. In some situations, particles become trapped near resonances that sweep outward with the tidal evolution of the Pluto–Charon binary. With simple models and numerical experiments, we show how the Pluto–Charon impact ring may have expanded into a broad disk, out of which grew the circumbinary moons. In some scenarios, the ring can spread well beyond the orbit of Hydra, the most distant moon, to form a handful of smaller satellites. If these small moons exist, New Horizons will find them.

De-identifying an EHR Database

DEFF Research Database (Denmark)

Lauesen, Søren; Pantazos, Kostas; Lippert, Søren

2011-01-01

-identified a Danish EHR database with 437,164 patients. The goal was to generate a version with real medical records, but related to artificial persons. We developed a de-identification algorithm that uses lists of named entities, simple language analysis, and special rules. Our algorithm consists of 3 steps: collect...... lists of identifiers from the database and external resources, define a replacement for each identifier, and replace identifiers in structured data and free text. Some patient records could not be safely de-identified, so the de-identified database has 323,122 patient records with an acceptable degree...... of anonymity, readability and correctness (F-measure of 95%). The algorithm has to be adjusted for each culture, language and database....

Evolution of glycosaminoglycans and their glycosyltransferases: Implications for the extracellular matrices of animals and the capsules of pathogenic bacteria.

Science.gov (United States)

DeAngelis, Paul L

2002-11-01

Glycosaminoglycans (linear polysaccharides with a repeating disaccharide backbone containing an amino sugar) are essential components of extracellular matrices of animals. These complex molecules play important structural, adhesion, and signaling roles in mammals. Direct detection of glycosaminoglycans has been reported in a variety of organisms, but perhaps more definitive tests for the glycosyltransferase genes should be utilized to clarify the distribution of glycosaminoglycans in metazoans. Recently, glycosyltransferases that form the hyaluronan, heparin/heparan, or chondroitin backbone were identified at the molecular level. The three types of glycosyltransferases appear to have evolved independently based on sequence comparisons and other characteristics. All metazoans appear to possess heparin/heparan. Chondroitin is found in some worms, arthropods, and higher animals. Hyaluronan is found only in two of the three main branches of chordates. The presence of several types of glycosaminoglycans in the body allows multiple communication channels and adhesion systems to operate simultaneously. Certain pathogenic bacteria produce extracellular coatings, called capsules, which are composed of glycosaminoglycans that increase their virulence during infection. The capsule helps shield the microbe from the host defenses and/or modulates host physiology. The bacterial and animal polysaccharides are chemically identical or at least very similar. Therefore, no immune response is generated, in contrast to the vast majority of capsular polymers from other bacteria. In microbial systems, it appears that in most cases functional convergent evolution of glycosaminoglycan glycosyltransferases occurred, rather than direct horizontal gene transfer from their vertebrate hosts. Copyright 2002 Wiley-Liss, Inc.

Sponge budding is a spatiotemporal morphological patterning process: Insights from synchrotron radiation-based x-ray microtomography into the asexual reproduction of Tethya wilhelma

Directory of Open Access Journals (Sweden)

Nickel Michael

2009-09-01

Full Text Available Abstract Background Primary agametic-asexual reproduction mechanisms such as budding and fission are present in all non-bilaterian and many bilaterian animal taxa and are likely to be metazoan ground pattern characters. Cnidarians display highly organized and regulated budding processes. In contrast, budding in poriferans was thought to be less specific and related to the general ability of this group to reorganize their tissues. Here we test the hypothesis of morphological pattern formation during sponge budding. Results We investigated the budding process in Tethya wilhelma (Demospongiae by applying 3D morphometrics to high resolution synchrotron radiation-based x-ray microtomography (SR-μCT image data. We followed the morphogenesis of characteristic body structures and identified distinct morphological states which indeed reveal characteristic spatiotemporal morphological patterns in sponge bud development. We discovered the distribution of skeletal elements, canal system and sponge tissue to be based on a sequential series of distinct morphological states. Based on morphometric data we defined four typical bud stages. Once they have reached the final stage buds are released as fully functional juvenile sponges which are morphologically and functionally equivalent to adult specimens. Conclusion Our results demonstrate that budding in demosponges is considerably more highly organized and regulated than previously assumed. Morphological pattern formation in asexual reproduction with underlying genetic regulation seems to have evolved early in metazoans and was likely part of the developmental program of the last common ancestor of all Metazoa (LCAM.

Sponge budding is a spatiotemporal morphological patterning process: Insights from synchrotron radiation-based x-ray microtomography into the asexual reproduction of Tethya wilhelma.

Science.gov (United States)

Hammel, Jörg U; Herzen, Julia; Beckmann, Felix; Nickel, Michael

2009-09-08

Primary agametic-asexual reproduction mechanisms such as budding and fission are present in all non-bilaterian and many bilaterian animal taxa and are likely to be metazoan ground pattern characters. Cnidarians display highly organized and regulated budding processes. In contrast, budding in poriferans was thought to be less specific and related to the general ability of this group to reorganize their tissues. Here we test the hypothesis of morphological pattern formation during sponge budding. We investigated the budding process in Tethya wilhelma (Demospongiae) by applying 3D morphometrics to high resolution synchrotron radiation-based x-ray microtomography (SR-muCT) image data. We followed the morphogenesis of characteristic body structures and identified distinct morphological states which indeed reveal characteristic spatiotemporal morphological patterns in sponge bud development. We discovered the distribution of skeletal elements, canal system and sponge tissue to be based on a sequential series of distinct morphological states. Based on morphometric data we defined four typical bud stages. Once they have reached the final stage buds are released as fully functional juvenile sponges which are morphologically and functionally equivalent to adult specimens. Our results demonstrate that budding in demosponges is considerably more highly organized and regulated than previously assumed. Morphological pattern formation in asexual reproduction with underlying genetic regulation seems to have evolved early in metazoans and was likely part of the developmental program of the last common ancestor of all Metazoa (LCAM).

Phylogenetic analysis of the SINA/SIAH ubiquitin E3 ligase family in Metazoa.

Science.gov (United States)

Pepper, Ian J; Van Sciver, Robert E; Tang, Amy H

2017-08-07

The RAS signaling pathway is a pivotal developmental pathway that controls many fundamental biological processes including cell proliferation, differentiation, movement and apoptosis. Drosophila Seven-IN-Absentia (SINA) is a ubiquitin E3 ligase that is the most downstream signaling "gatekeeper" whose biological activity is essential for proper RAS signal transduction. Vertebrate SINA homologs (SIAHs) share a high degree of amino acid identity with that of Drosophila SINA. SINA/SIAH is the most conserved signaling component in the canonical EGFR/RAS/RAF/MAPK signal transduction pathway. Vertebrate SIAH1, 2, and 3 are the three orthologs to invertebrate SINA protein. SINA and SIAH1 orthologs are found in all major taxa of metazoans. These proteins have four conserved functional domains, known as RING (Really Interesting New Gene), SZF (SIAH-type zinc finger), SBS (substrate binding site) and DIMER (Dimerization). In addition to the siah1 gene, most vertebrates encode two additional siah genes (siah2 and siah3) in their genomes. Vertebrate SIAH2 has a highly divergent and extended N-terminal sequence, while its RING, SZF, SBS and DIMER domains maintain high amino acid identity/similarity to that of SIAH1. But unlike vertebrate SIAH1 and SIAH2, SIAH3 lacks a functional RING domain, suggesting that SIAH3 may be an inactive E3 ligase. The SIAH3 subtree exhibits a high degree of amino acid divergence when compared to the SIAH1 and SIAH2 subtrees. We find that SIAH1 and SIAH2 are expressed in all human epithelial cell lines examined thus far, while SIAH3 is only expressed in a limited subset of cancer cell lines. Through phylogenetic analyses of metazoan SINA and SIAH E3 ligases, we identified many invariant and divergent amino acid residues, as well as the evolutionarily conserved functional motifs in this medically relevant gene family. Our phylomedicinal study of this unique metazoan SINA/SIAH protein family has provided invaluable evolution-based support towards future

The scavenger receptor repertoire in six cnidarian species and its putative role in cnidarian-dinoflagellate symbiosis

Directory of Open Access Journals (Sweden)

Emilie F. Neubauer

2016-11-01

Full Text Available Many cnidarians engage in a mutualism with endosymbiotic photosynthetic dinoflagellates that forms the basis of the coral reef ecosystem. Interpartner interaction and regulation includes involvement of the host innate immune system. Basal metazoans, including cnidarians have diverse and complex innate immune repertoires that are just beginning to be described. Scavenger receptors (SR are a diverse superfamily of innate immunity genes that recognize a broad array of microbial ligands and participate in phagocytosis of invading microbes. The superfamily includes subclades named SR-A through SR-I that are categorized based on the arrangement of sequence domains including the scavenger receptor cysteine rich (SRCR, the C-type lectin (CTLD and the CD36 domains. Previous functional and gene expression studies on cnidarian-dinoflagellate symbiosis have implicated SR-like proteins in interpartner communication and regulation. In this study, we characterized the SR repertoire from a combination of genomic and transcriptomic resources from six cnidarian species in the Class Anthozoa. We combined these bioinformatic analyses with functional experiments using the SR inhibitor fucoidan to explore a role for SRs in cnidarian symbiosis and immunity. Bioinformatic searches revealed a large diversity of SR-like genes that resembled SR-As, SR-Bs, SR-Es and SR-Is. SRCRs, CTLDs and CD36 domains were identified in multiple sequences in combinations that were highly homologous to vertebrate SRs as well as in proteins with novel domain combinations. Phylogenetic analyses of CD36 domains of the SR-B-like sequences from a diversity of metazoans grouped cnidarian with bilaterian sequences separate from other basal metazoans. All cnidarian sequences grouped together with moderate support in a subclade separately from bilaterian sequences. Functional experiments were carried out on the sea anemone Aiptasia pallida that engages in a symbiosis with Symbiodinium minutum

Cancer

Science.gov (United States)

Murdin, P.

2000-11-01

(the Crab; abbrev. Cnc, genitive Cancri; area 506 sq. deg.) A northern zodiacal constellation which lies between Gemini and Leo, and culminates at midnight in late January. It represents the crab that, in Greek mythology, Hercules crushed underfoot during his fight with the multi-headed Hydra. The name of α Cancri, its brightest star, is Acubens, which comes from the Arabic word meaning `the claw...

Environmental Studies of Macrozoobenthos, Aquatic Macrophytes, and Juvenile Fishes in the St. Clair-Detroit River System, 1983-1984

Science.gov (United States)

1986-02-01

during the same month in successive years, and differences in densities between years were usually less than 30%. Hydra, Oligochaeta, Manayunkia...FCTFCEIIV -4 q.5CC7 1 .4461 4. .6645 .7 (15 3 C.C414I13 C.IC c.I;csv 2 c.(4eti2n3 (.IC (.%(57 ANALYSIS OF VARIANCE TABLES - - -- 11EP5 IkEA PCDPLS PECCECLPE

Floating attenuator wave energy device. Wavegen HYDRA project

Energy Technology Data Exchange (ETDEWEB)

NONE

2004-07-01

The Wavegen Project which set out to develop a floating externally tensioned articulated wave-energy generator based on work carried out at RMCS Shrivenham in the 1980s has been abandoned until further notice. The computer modelling carried out in the early days indicated much promise, but the promise turned to disappointment when difficulties cropped-up in attempting to put the design into practice. A particular problem arose in matching the external tension to an equivalent beam stiffness to tune the natural bending frequency of the raft to that of the driving waves. A further eleven practical problems encountered are discussed.

Policing Families. The Many-Headed Hydra of Surveillance

Czech Academy of Sciences Publication Activity Database

Mechthild, Nagel

2018-01-01

Roč. 17, č. 2 (2018), s. 2-11 ISSN 2155-9708 R&D Projects: GA ČR(CZ) GJ16-00994Y Institutional support: RVO:67985955 Keywords : social performance * performativity of Child Protective Services * elitism * racism * parenting Subject RIV: AA - Philosophy ; Religion OBOR OECD: Philosophy, History and Philosophy of science and technology https://cdn.ymaws.com/www.apaonline.org/resource/collection/D03EBDAB-82D7-4B28-B897-C050FDC1ACB4/ Feminism V17n2.pdf

Discovery of a Free-Floating Double Planet?

Science.gov (United States)

Kohler, Susanna

2017-07-01

An object previously identified as a free-floating, large Jupiter analogturns out to be two objects each with the mass of a few Jupiters. This system is the lowest-mass binary weve ever discovered.Tracking Down Ages2MASS J111932541137466 is thought to be a member of the TW Hydrae Association, a group of roughly two dozen young stars moving together in the solar neighborhood. [University of Western Ontario/Carnegie Institution of Washington DTM/David Rodriguez]Brown dwarfs represent the bottom end of the stellar mass spectrum, with masses too low to fuse hydrogen (typically below 75-80 Jupiter masses). Observing these objects provides us a unique opportunity to learn about stellar evolution and atmospheric models but to properly understand these observations, we need to determine the dwarfs masses and ages.This is surprisingly difficult, however. Brown dwarfs cool continuously as they age, which creates an observational degeneracy: dwarfs of different masses and ages can have the same luminosity, making it difficult to infer their physical properties from observations.We can solve this problem with an independent measurement of the dwarfs masses. One approach is to find brown dwarfs that are members of nearby stellar associations called moving groups. The stars within the association share the same approximate age, so a brown dwarfs age can be estimated based on the easier-to-identify ages of other stars in the group.An Unusual BinaryRecently, a team of scientists led by William Best (Institute for Astronomy, University of Hawaii) were following up on such an object: the extremely red, low-gravity L7 dwarf 2MASS J111932541137466, possibly a member of the TW Hydrae Association. With the help of the powerful adaptive optics on the Keck II telescope in Hawaii, however, the team discovered that this Jupiter-like objectwas hiding something: its actually two objects of equal flux orbiting each other.Keck images of 2MASS J111932541137466 reveal that this object is actually

Evolutionary hierarchy of vertebrate-like heterotrimeric G protein families.

Science.gov (United States)

Krishnan, Arunkumar; Mustafa, Arshi; Almén, Markus Sällman; Fredriksson, Robert; Williams, Michael J; Schiöth, Helgi B

2015-10-01

Heterotrimeric G proteins perform a crucial role as molecular switches controlling various cellular responses mediated by G protein-coupled receptor (GPCR) signaling pathway. Recent data have shown that the vertebrate-like G protein families are found across metazoans and their closest unicellular relatives. However, an overall evolutionary hierarchy of vertebrate-like G proteins, including gene family annotations and in particular mapping individual gene gain/loss events across diverse holozoan lineages is still incomplete. Here, with more expanded invertebrate taxon sampling, we have reconstructed phylogenetic trees for each of the G protein classes/families and provide a robust classification and hierarchy of vertebrate-like heterotrimeric G proteins. Our results further extend the evidence that the common ancestor (CA) of holozoans had at least five ancestral Gα genes corresponding to all major vertebrate Gα classes and contain a total of eight genes including two Gβ and one Gγ. Our results also indicate that the GNAI/O-like gene likely duplicated in the last CA of metazoans to give rise to GNAI- and GNAO-like genes, which are conserved across invertebrates. Moreover, homologs of GNB1-4 paralogon- and GNB5 family-like genes are found in most metazoans and that the unicellular holozoans encode two ancestral Gβ genes. Similarly, most bilaterian invertebrates encode two Gγ genes which include a representative of the GNG gene cluster and a putative homolog of GNG13. Interestingly, our results also revealed key evolutionary events such as the Drosophila melanogaster eye specific Gβ subunit that is found conserved in most arthropods and several previously unidentified species specific expansions within Gαi/o, Gαs, Gαq, Gα12/13 classes and the GNB1-4 paralogon. Also, we provide an overall proposed evolutionary scenario on the expansions of all G protein families in vertebrate tetraploidizations. Our robust classification/hierarchy is essential to further

Insights into metazoan evolution from alvinella pompejana cDNAs

Directory of Open Access Journals (Sweden)

Thierry Jean-Claude

2010-11-01

Full Text Available Abstract Background Alvinella pompejana is a representative of Annelids, a key phylum for evo-devo studies that is still poorly studied at the sequence level. A. pompejana inhabits deep-sea hydrothermal vents and is currently known as one of the most thermotolerant Eukaryotes in marine environments, withstanding the largest known chemical and thermal ranges (from 5 to 105°C. This tube-dwelling worm forms dense colonies on the surface of hydrothermal chimneys and can withstand long periods of hypo/anoxia and long phases of exposure to hydrogen sulphides. A. pompejana specifically inhabits chimney walls of hydrothermal vents on the East Pacific Rise. To survive, Alvinella has developed numerous adaptations at the physiological and molecular levels, such as an increase in the thermostability of proteins and protein complexes. It represents an outstanding model organism for studying adaptation to harsh physicochemical conditions and for isolating stable macromolecules resistant to high temperatures. Results We have constructed four full length enriched cDNA libraries to investigate the biology and evolution of this intriguing animal. Analysis of more than 75,000 high quality reads led to the identification of 15,858 transcripts and 9,221 putative protein sequences. Our annotation reveals a good coverage of most animal pathways and networks with a prevalence of transcripts involved in oxidative stress resistance, detoxification, anti-bacterial defence, and heat shock protection. Alvinella proteins seem to show a slow evolutionary rate and a higher similarity with proteins from Vertebrates compared to proteins from Arthropods or Nematodes. Their composition shows enrichment in positively charged amino acids that might contribute to their thermostability. The gene content of Alvinella reveals that an important pool of genes previously considered to be specific to Deuterostomes were in fact already present in the last common ancestor of the Bilaterian animals, but have been secondarily lost in model invertebrates. This pool is enriched in glycoproteins that play a key role in intercellular communication, hormonal regulation and immunity. Conclusions Our study starts to unravel the gene content and sequence evolution of a deep-sea annelid, revealing key features in eukaryote adaptation to extreme environmental conditions and highlighting the proximity of Annelids and Vertebrates.

Community ecology of the metazoan parasites of snoek Thyrsites ...

African Journals Online (AJOL)

The stability and randomness in parasite acquisition, as indicated by the lack of nestedness of the parasite assemblage, can be ascribed to the opportunistic feeding behaviour and nomadic movement of T. atun in the southern Benguela. The homogeneity of the community structure of long-lived endoparasites suggests that ...

Methods for the development of large computer codes under LTSS

International Nuclear Information System (INIS)

Sicilian, J.M.

1977-06-01

TRAC is a large computer code being developed by Group Q-6 for the analysis of the transient thermal hydraulic behavior of light-water nuclear reactors. A system designed to assist the development of TRAC is described. The system consists of a central HYDRA dataset, R6LIB, containing files used in the development of TRAC, and a file maintenance program, HORSE, which facilitates the use of this dataset

A theory of biological pattern formation

OpenAIRE

Gierer, Alfred; Meinhardt, H.

2006-01-01

The paper addresses the formation of striking patterns within originally near-homogenous tissue, the process prototypical for embryology, and represented in particularly puristic form by cut sections of hydra regenerating a complete animal with head and foot. Essential requirements are autocatalytic, self-enhancing activation, combined with inhibitory or depletion effects of wider range - “lateral inhibition”. Not only de-novo-pattern formation, but also well known, striking features of devel...

Comparative Analysis of Hydraulic Fracturing Wastewater Practices in Unconventional Shale Development: Newspaper Coverage of Stakeholder Concerns and Social License to Operate

OpenAIRE

Joel Gehman; Dara Y. Thompson; Daniel S. Alessi; Diana M. Allen; Greg G. Goss

2016-01-01

In this article we review prior literature regarding the concept of social license to operate, and related concepts, including corporate social responsibility, sustainable development, stakeholder management and cumulative effects. Informed by these concepts, we search for newspaper articles published in North American provinces and states where the Barnett, Duvernay, Marcellus and Montney shale plays are located. Using these data, we tabulate coverage of stakeholder concerns related to hydra...

Identifying Breast Cancer Oncogenes

Science.gov (United States)

2011-10-01

cells we observed that it promoted transformation of HMLE cells, suggesting a tumor suppressive role of Merlin in breast cancer (Figure 4B). A...08-1-0767 TITLE: Identifying Breast Cancer Oncogenes PRINCIPAL INVESTIGATOR: Yashaswi Shrestha...Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std. Z39.18 W81XWH-08-1-0767 Identifying Breast Cancer Oncogenes Yashaswi Shrestha Dana-Farber

In situ exposures using caged organisms: a multi-compartment approach to detect aquatic toxicity and bioaccumulation

International Nuclear Information System (INIS)

Burton, G. Allen; Greenberg, Marc S.; Rowland, Carolyn D.; Irvine, Cameron A.; Lavoie, Daniel R.; Brooker, John A.; Moore, Laurie; Raymer, Delia F.N.; McWilliam, Ruth A.

2005-01-01

An in situ toxicity and bioaccumulation assessment approach is described to assess stressor exposure and effects in surface waters (low and high flow), the sediment-water interface, surficial sediments and pore waters (including groundwater upwellings). This approach can be used for exposing species, representing major functional and taxonomic groups. Pimephales promelas, Daphnia magna, Ceriodaphnia dubia, Hyalella azteca, Hyalella sp., Chironomus tentans, Lumbriculus variegatus, Hydra attenuatta, Hexagenia sp. and Baetis tibialis were successfully used to measure effects on survival, growth, feeding, and/or uptake. Stressors identified included chemical toxicants, suspended solids, photo-induced toxicity, indigenous predators, and flow. Responses varied between laboratory and in situ exposures in many cases and were attributed to differing exposure dynamics and sample-processing artifacts. These in situ exposure approaches provide unique assessment information that is complementary to traditional laboratory-based toxicity and bioaccumulation testing and reduce the uncertainties of extrapolating from the laboratory to field responses. - In situ exposures provide unique information that is complementary to traditional lab-based toxicity results

Eric Davidson and deep time.

Science.gov (United States)

Erwin, Douglas H

2017-10-13

Eric Davidson had a deep and abiding interest in the role developmental mechanisms played in generating evolutionary patterns documented in deep time, from the origin of the euechinoids to the processes responsible for the morphological architectures of major animal clades. Although not an evolutionary biologist, Davidson's interests long preceded the current excitement over comparative evolutionary developmental biology. Here I discuss three aspects at the intersection between his research and evolutionary patterns in deep time: First, understanding the mechanisms of body plan formation, particularly those associated with the early diversification of major metazoan clades. Second, a critique of early claims about ancestral metazoans based on the discoveries of highly conserved genes across bilaterian animals. Third, Davidson's own involvement in paleontology through a collaborative study of the fossil embryos from the Ediacaran Doushantuo Formation in south China.

Young Stars with SALT

Energy Technology Data Exchange (ETDEWEB)

Riedel, Adric R. [Department of Astronomy, California Institute of Technology, Pasadena, CA 91125 (United States); Alam, Munazza K.; Rice, Emily L.; Cruz, Kelle L. [Department of Astrophysics, The American Museum of Natural History, New York, NY 10024 (United States); Henry, Todd J., E-mail: arr@caltech.edu [RECONS Institute, Chambersburg, PA (United States)

2017-05-10

We present a spectroscopic and kinematic analysis of 79 nearby M dwarfs in 77 systems. All of these dwarfs are low-proper-motion southern hemisphere objects and were identified in a nearby star survey with a demonstrated sensitivity to young stars. Using low-resolution optical spectroscopy from the Red Side Spectrograph on the South African Large Telescope, we have determined radial velocities, H-alpha, lithium 6708 Å, and potassium 7699 Å equivalent widths linked to age and activity, and spectral types for all of our targets. Combined with astrometric information from literature sources, we identify 44 young stars. Eighteen are previously known members of moving groups within 100 pc of the Sun. Twelve are new members, including one member of the TW Hydra moving group, one member of the 32 Orionis moving group, 9 members of Tucana-Horologium, one member of Argus, and two new members of AB Doradus. We also find 14 young star systems that are not members of any known groups. The remaining 33 star systems do not appear to be young. This appears to be evidence of a new population of nearby young stars not related to the known nearby young moving groups.

The NOAA Dataset Identifier Project

Science.gov (United States)

de la Beaujardiere, J.; Mccullough, H.; Casey, K. S.

2013-12-01

The US National Oceanic and Atmospheric Administration (NOAA) initiated a project in 2013 to assign persistent identifiers to datasets archived at NOAA and to create informational landing pages about those datasets. The goals of this project are to enable the citation of datasets used in products and results in order to help provide credit to data producers, to support traceability and reproducibility, and to enable tracking of data usage and impact. A secondary goal is to encourage the submission of datasets for long-term preservation, because only archived datasets will be eligible for a NOAA-issued identifier. A team was formed with representatives from the National Geophysical, Oceanographic, and Climatic Data Centers (NGDC, NODC, NCDC) to resolve questions including which identifier scheme to use (answer: Digital Object Identifier - DOI), whether or not to embed semantics in identifiers (no), the level of granularity at which to assign identifiers (as coarsely as reasonable), how to handle ongoing time-series data (do not break into chunks), creation mechanism for the landing page (stylesheet from formal metadata record preferred), and others. Decisions made and implementation experience gained will inform the writing of a Data Citation Procedural Directive to be issued by the Environmental Data Management Committee in 2014. Several identifiers have been issued as of July 2013, with more on the way. NOAA is now reporting the number as a metric to federal Open Government initiatives. This paper will provide further details and status of the project.

Oceanographic profile Zooplankton biomass measurements collected using net in the Antarctic during 1989 (NODC Accession 0000971)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Composition of the metazoan plankton was studied during R.V. "Dmitry Mendeleev" cruise 43 (February to April, 1989) in the Atlantic sector of the Southern Ocean....

Parameter identifiability and redundancy: theoretical considerations.

Directory of Open Access Journals (Sweden)

Mark P Little

Full Text Available BACKGROUND: Models for complex biological systems may involve a large number of parameters. It may well be that some of these parameters cannot be derived from observed data via regression techniques. Such parameters are said to be unidentifiable, the remaining parameters being identifiable. Closely related to this idea is that of redundancy, that a set of parameters can be expressed in terms of some smaller set. Before data is analysed it is critical to determine which model parameters are identifiable or redundant to avoid ill-defined and poorly convergent regression. METHODOLOGY/PRINCIPAL FINDINGS: In this paper we outline general considerations on parameter identifiability, and introduce the notion of weak local identifiability and gradient weak local identifiability. These are based on local properties of the likelihood, in particular the rank of the Hessian matrix. We relate these to the notions of parameter identifiability and redundancy previously introduced by Rothenberg (Econometrica 39 (1971 577-591 and Catchpole and Morgan (Biometrika 84 (1997 187-196. Within the widely used exponential family, parameter irredundancy, local identifiability, gradient weak local identifiability and weak local identifiability are shown to be largely equivalent. We consider applications to a recently developed class of cancer models of Little and Wright (Math Biosciences 183 (2003 111-134 and Little et al. (J Theoret Biol 254 (2008 229-238 that generalize a large number of other recently used quasi-biological cancer models. CONCLUSIONS/SIGNIFICANCE: We have shown that the previously developed concepts of parameter local identifiability and redundancy are closely related to the apparently weaker properties of weak local identifiability and gradient weak local identifiability--within the widely used exponential family these concepts largely coincide.

Early evolution of the LIM homeobox gene family

Energy Technology Data Exchange (ETDEWEB)

Srivastava, Mansi; Larroux, Claire; Lu, Daniel R; Mohanty, Kareshma; Chapman, Jarrod; Degnan, Bernard M; Rokhsar, Daniel S

2010-01-01

LIM homeobox (Lhx) transcription factors are unique to the animal lineage and have patterning roles during embryonic development in flies, nematodes and vertebrates, with a conserved role in specifying neuronal identity. Though genes of this family have been reported in a sponge and a cnidarian, the expression patterns and functions of the Lhx family during development in non-bilaterian phyla are not known. We identified Lhx genes in two cnidarians and a placozoan and report the expression of Lhx genes during embryonic development in Nematostella and the demosponge Amphimedon. Members of the six major LIM homeobox subfamilies are represented in the genomes of the starlet sea anemone, Nematostella vectensis, and the placozoan Trichoplax adhaerens. The hydrozoan cnidarian, Hydra magnipapillata, has retained four of the six Lhx subfamilies, but apparently lost two others. Only three subfamilies are represented in the haplosclerid demosponge Amphimedon queenslandica. A tandem cluster of three Lhx genes of different subfamilies and a gene containing two LIM domains in the genome of T. adhaerens (an animal without any neurons) indicates that Lhx subfamilies were generated by tandem duplication. This tandem cluster in Trichoplax is likely a remnant of the original chromosomal context in which Lhx subfamilies first appeared. Three of the six Trichoplax Lhx genes are expressed in animals in laboratory culture, as are all Lhx genes in Hydra. Expression patterns of Nematostella Lhx genes correlate with neural territories in larval and juvenile polyp stages. In the aneural demosponge, A. queenslandica, the three Lhx genes are expressed widely during development, including in cells that are associated with the larval photosensory ring. The Lhx family expanded and diversified early in animal evolution, with all six subfamilies already diverged prior to the cnidarian-placozoan-bilaterian last common ancestor. In Nematostella, Lhx gene expression is correlated with neural

Early evolution of the LIM homeobox gene family

Directory of Open Access Journals (Sweden)

Degnan Bernard M

2010-01-01

Full Text Available Abstract Background LIM homeobox (Lhx transcription factors are unique to the animal lineage and have patterning roles during embryonic development in flies, nematodes and vertebrates, with a conserved role in specifying neuronal identity. Though genes of this family have been reported in a sponge and a cnidarian, the expression patterns and functions of the Lhx family during development in non-bilaterian phyla are not known. Results We identified Lhx genes in two cnidarians and a placozoan and report the expression of Lhx genes during embryonic development in Nematostella and the demosponge Amphimedon. Members of the six major LIM homeobox subfamilies are represented in the genomes of the starlet sea anemone, Nematostella vectensis, and the placozoan Trichoplax adhaerens. The hydrozoan cnidarian, Hydra magnipapillata, has retained four of the six Lhx subfamilies, but apparently lost two others. Only three subfamilies are represented in the haplosclerid demosponge Amphimedon queenslandica. A tandem cluster of three Lhx genes of different subfamilies and a gene containing two LIM domains in the genome of T. adhaerens (an animal without any neurons indicates that Lhx subfamilies were generated by tandem duplication. This tandem cluster in Trichoplax is likely a remnant of the original chromosomal context in which Lhx subfamilies first appeared. Three of the six Trichoplax Lhx genes are expressed in animals in laboratory culture, as are all Lhx genes in Hydra. Expression patterns of Nematostella Lhx genes correlate with neural territories in larval and juvenile polyp stages. In the aneural demosponge, A. queenslandica, the three Lhx genes are expressed widely during development, including in cells that are associated with the larval photosensory ring. Conclusions The Lhx family expanded and diversified early in animal evolution, with all six subfamilies already diverged prior to the cnidarian-placozoan-bilaterian last common ancestor. In

Impact of Amorphous Silica Nanoparticles on a Living Organism: Morphological, Behavioural and Molecular Biology Implications.

Directory of Open Access Journals (Sweden)

Alfredo eAmbrosone

2014-09-01

Full Text Available It is generally accepted that silica (SiO2 is not toxic. But the increasing use of silica nanoparticles (SiO2NPs in many different industrial fields has prompted the careful investigation of its toxicity in biological systems. In this report, we describe the effects elicited by SiO2NPs on animal and cell physiology. Stable and monodisperse amorphous silica nanoparticles 25nm in diameter, were administered to living Hydra vulgaris (Cnidaria. The dose-related effects were defined by morphological and behavioural assays. The results revealed an all-or-nothing lethal toxicity with a rather high threshold (35nM NPs and a LT50 of 38h. At sub lethal doses the morpho-physiological effects included: animal morphology alterations, paralysis of the gastric region, disorganization and depletion of tentacle specialized cells, increase of apoptotic and collapsed cells and reduction of the epithelial cell proliferation rate. Transcriptome analysis (RNAseq revealed 45 differentially expressed genes, mostly involved in stress response and cuticle renovation. Our results show that Hydra reacts to SiO2NPs, is able to rebalance the animal homeostasis up to a relatively high doses of SiO2NPs and that the physiological modifications are transduced to gene expression modulation.

Impact of Amorphous SiO{sub 2} Nanoparticles on a Living Organism: Morphological, Behavioral, and Molecular Biology Implications

Energy Technology Data Exchange (ETDEWEB)

Ambrosone, Alfredo; Scotto di Vettimo, Maria Rosaria [Istituto di Cibernetica “Eduardo Caianiello”, Consiglio Nazionale delle Ricerche, Pozzuoli (Italy); Malvindi, Maria Ada [Center for Biomolecular Nanotechnologies@UNILE, Istituto Italiano di Tecnologia, Arnesano (Italy); Roopin, Modi; Levy, Oren [The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan (Israel); Marchesano, Valentina [Istituto di Cibernetica “Eduardo Caianiello”, Consiglio Nazionale delle Ricerche, Pozzuoli (Italy); Pompa, Pier Paolo [Center for Biomolecular Nanotechnologies@UNILE, Istituto Italiano di Tecnologia, Arnesano (Italy); Tortiglione, Claudia; Tino, Angela, E-mail: a.tino@cib.na.cnr.it [Istituto di Cibernetica “Eduardo Caianiello”, Consiglio Nazionale delle Ricerche, Pozzuoli (Italy)

2014-09-29

It is generally accepted that silica (SiO{sub 2}) is not toxic. But the increasing use of silica nanoparticles (SiO{sub 2}NPs) in many different industrial fields has prompted the careful investigation of their toxicity in biological systems. In this report, we describe the effects elicited by SiO{sub 2}NPs on animal and cell physiology. Stable and monodisperse amorphous silica nanoparticles, 25 nM in diameter, were administered to living Hydra vulgaris (Cnidaria). The dose-related effects were defined by morphological and behavioral assays. The results revealed an all-or-nothing lethal toxicity with a rather high threshold (35 nM NPs) and a LT50 of 38 h. At sub lethal doses, the morphophysiological effects included: animal morphology alterations, paralysis of the gastric region, disorganization and depletion of tentacle specialized cells, increase of apoptotic and collapsed cells, and reduction of the epithelial cell proliferation rate. Transcriptome analysis (RNAseq) revealed 45 differentially expressed genes, mostly involved in stress response and cuticle renovation. Our results show that Hydra reacts to SiO{sub 2}NPs, is able to rebalance the animal homeostasis up to a relatively high doses of SiO{sub 2}NPs, and that the physiological modifications are transduced to gene expression modulation.

Conservation and divergence of chemical defense system in the tunicate Oikopleura dioica revealed by genome wide response to two xenobiotics

Directory of Open Access Journals (Sweden)

Yadetie Fekadu

2012-02-01

Full Text Available Abstract Background Animals have developed extensive mechanisms of response to xenobiotic chemical attacks. Although recent genome surveys have suggested a broad conservation of the chemical defensome across metazoans, global gene expression responses to xenobiotics have not been well investigated in most invertebrates. Here, we performed genome survey for key defensome genes in Oikopleura dioica genome, and explored genome-wide gene expression using high density tiling arrays with over 2 million probes, in response to two model xenobiotic chemicals - the carcinogenic polycyclic aromatic hydrocarbon benzo[a]pyrene (BaP the pharmaceutical compound Clofibrate (Clo. Results Oikopleura genome surveys for key genes of the chemical defensome suggested a reduced repertoire. Not more than 23 cytochrome P450 (CYP genes could be identified, and neither CYP1 family genes nor their transcriptional activator AhR was detected. These two genes were present in deuterostome ancestors. As in vertebrates, the genotoxic compound BaP induced xenobiotic biotransformation and oxidative stress responsive genes. Notable exceptions were genes of the aryl hydrocarbon receptor (AhR signaling pathway. Clo also affected the expression of many biotransformation genes and markedly repressed genes involved in energy metabolism and muscle contraction pathways. Conclusions Oikopleura has the smallest number of CYP genes among sequenced animal genomes and lacks the AhR signaling pathway. However it appears to have basic xenobiotic inducible biotransformation genes such as a conserved genotoxic stress response gene set. Our genome survey and expression study does not support a role of AhR signaling pathway in the chemical defense of metazoans prior to the emergence of vertebrates.

Parasites and malignancies, a review, with emphasis on digestive cancer induced by Cryptosporidium parvum (Alveolata: Apicomplexa).

Science.gov (United States)

Benamrouz, S; Conseil, V; Creusy, C; Calderon, E; Dei-Cas, E; Certad, G

2012-05-01

The International Agency for Research on Cancer (IARC) identifies ten infectious agents (viruses, bacteria, parasites) able to induce cancer disease in humans. Among parasites, a carcinogenic role is currently recognized to the digenetic trematodes Schistosoma haematobium, leading to bladder cancer, and to Clonorchis sinensis or Opisthorchis viverrini, which cause cholangiocarcinoma. Furthermore, several reports suspected the potential association of other parasitic infections (due to Protozoan or Metazoan parasites) with the development of neoplastic changes in the host tissues. The present work shortly reviewed available data on the involvement of parasites in neoplastic processes in humans or animals, and especially focused on the carcinogenic power of Cryptosporidium parvum infection. On the whole, infection seems to play a crucial role in the etiology of cancer.

Lessons from "lower" organisms: what worms, flies, and zebrafish can teach us about human energy metabolism.

Directory of Open Access Journals (Sweden)

Amnon Schlegel

2007-11-01

Full Text Available A pandemic of metabolic diseases (atherosclerosis, diabetes mellitus, and obesity, unleashed by multiple social and economic factors beyond the control of most individuals, threatens to diminish human life span for the first time in the modern era. Given the redundancy and inherent complexity of processes regulating the uptake, transport, catabolism, and synthesis of nutrients, magic bullets to target these diseases will be hard to find. Recent studies using the worm Caenorhabditis elegans, the fly Drosophila melanogaster, and the zebrafish Danio rerio indicate that these "lower" metazoans possess unique attributes that should help in identifying, investigating, and even validating new pharmaceutical targets for these diseases. We summarize findings in these organisms that shed light on highly conserved pathways of energy homeostasis.

Parasites and malignancies, a review, with emphasis on digestive cancer induced by Cryptosporidium parvum (Alveolata: Apicomplexa

Directory of Open Access Journals (Sweden)

Benamrouz S.

2012-05-01

Full Text Available The International Agency for Research on Cancer (IARC identifies ten infectious agents (viruses, bacteria, parasites able to induce cancer disease in humans. Among parasites, a carcinogenic role is currently recognized to the digenetic trematodes Schistosoma haematobium, leading to bladder cancer, and to Clonorchis sinensis or Opisthorchis viverrini, which cause cholangiocarcinoma. Furthermore, several reports suspected the potential association of other parasitic infections (due to Protozoan or Metazoan parasites with the development of neoplastic changes in the host tissues. The present work shortly reviewed available data on the involvement of parasites in neoplastic processes in humans or animals, and especially focused on the carcinogenic power of Cryptosporidium parvum infection. On the whole, infection seems to play a crucial role in the etiology of cancer.

The Protein Identifier Cross-Referencing (PICR service: reconciling protein identifiers across multiple source databases

Directory of Open Access Journals (Sweden)

Leinonen Rasko

2007-10-01

Full Text Available Abstract Background Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs. Results We have created the Protein Identifier Cross-Reference (PICR service, a web application that provides interactive and programmatic (SOAP and REST access to a mapping algorithm that uses the UniProt Archive (UniParc as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV or Microsoft Excel (XLS files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface. Conclusion We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR

Near Identifiability of Dynamical Systems

Science.gov (United States)

Hadaegh, F. Y.; Bekey, G. A.

1987-01-01

Concepts regarding approximate mathematical models treated rigorously. Paper presents new results in analysis of structural identifiability, equivalence, and near equivalence between mathematical models and physical processes they represent. Helps establish rigorous mathematical basis for concepts related to structural identifiability and equivalence revealing fundamental requirements, tacit assumptions, and sources of error. "Structural identifiability," as used by workers in this field, loosely translates as meaning ability to specify unique mathematical model and set of model parameters that accurately predict behavior of corresponding physical system.

Ecobiological studies of the freshwater lakes at Schirmacher Oasis, Antarctica

Digital Repository Service at National Institute of Oceanography (India)

Verlecar, X.N.; Dhargalkar, V.K.; Matondkar, S.G.P.

, Turbillaria, Tardigrades and Rotifers were dominant faunal groups. Bacteria and yeasts were predominant in soils and lake sediments. Detritus and associated bacteria form an important source of food for the opportunistic feeders such as metazoans. Long term...

The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes

KAUST Repository

Bracken-Grissom, Heather; Collins, Allen G.; Collins, Timothy; Crandall, Keith; Distel, Daniel; Dunn, Casey; Giribet, Gonzalo; Haddock, Steven; Knowlton, Nancy; Martindale, Mark; Medina, Monica; Messing, Charles; O'Brien, Stephen J.; Paulay, Gustav; Putnam, Nicolas; Ravasi, Timothy; Rouse, Greg W.; Ryan, Joseph F.; Schulze, Anja; Worheide, Gert; Adamska, Maja; Bailly, Xavier; Breinholt, Jesse; Browne, William E.; Diaz, M. Christina; Evans, Nathaniel; Flot, Jean-Francois; Fogarty, Nicole; Johnston, Matthew; Kamel, Bishoy; Kawahara, Akito Y.; Laberge, Tammy; Lavrov, Dennis; Michonneau, Francois; Moroz, Leonid L.; Oakley, Todd; Osborne, Karen; Pomponi, Shirley A.; Rhodes, Adelaide; Rodriguez-Lanetty, Mauricio; Santos, Scott R.; Satoh, Nori; Thacker, Robert W.; Van de Peer, Yves; Voolstra, Christian R.; Welch, David Mark; Winston, Judith; Zhou, Xin

2013-01-01

Over 95% of all metazoan (animal) species comprise the invertebrates, but very few genomes from these organisms have been sequenced. We have, therefore, formed a Global Invertebrate Genomics Alliance (GIGA). Our intent is to build a collaborative

Automatic calibration and signal switching system for the particle beam fusion research data acquisition facility

Energy Technology Data Exchange (ETDEWEB)

Boyer, W.B.

1979-09-01

This report describes both the hardware and software components of an automatic calibration and signal system (Autocal) for the data acquisition system for the Sandia particle beam fusion research accelerators Hydra, Proto I, and Proto II. The Autocal hardware consists of off-the-shelf commercial equipment. The various hardware components, special modifications and overall system configuration are described. Special software has been developed to support the Autocal hardware. Software operation and maintenance are described.

NASA safety standard for lifting devices and equipment

Science.gov (United States)

1990-09-01

NASA's minimum safety requirements are established for the design, testing, inspection, maintenance, certification, and use of overhead and gantry cranes (including top running monorail, underhung, and jib cranes), mobile cranes, derrick hoists, and special hoist supported personnel lifting devices (these do not include elevators, ground supported personnel lifts, or powered platforms). Minimum requirements are also addressed for the testing, inspection, and use of Hydra-sets, hooks, and slings. Safety standards are thoroughly detailed.

Corvus

Science.gov (United States)

Murdin, P.

2000-11-01

(the Crow; abbrev. Crv, gen. Corvi; area 184 sq. deg.) A southern constellation which lies between Virgo and Hydra, and culminates at midnight in late March. It represents the crow that in Greek mythology was sent by the god Apollo with a cup for water but loitered at a fig tree until the fruit became ripe and then returned, having eaten its fill, with a water-snake which it blamed for delaying i...

Neurotoxin localization to ectodermal gland cells uncovers an alternative mechanism of venom delivery in sea anemones

OpenAIRE

Moran, Yehu; Genikhovich, Grigory; Gordon, Dalia; Wienkoop, Stefanie; Zenkert, Claudia; Özbek, Suat; Technau, Ulrich; Gurevitz, Michael

2011-01-01

Jellyfish, hydras, corals and sea anemones (phylum Cnidaria) are known for their venomous stinging cells, nematocytes, used for prey and defence. Here we show, however, that the potent Type I neurotoxin of the sea anemone Nematostella vectensis, Nv1, is confined to ectodermal gland cells rather than nematocytes. We demonstrate massive Nv1 secretion upon encounter with a crustacean prey. Concomitant discharge of nematocysts probably pierces the prey, expediting toxin penetration. Toxin efficie...

Automatic calibration and signal switching system for the particle beam fusion research data acquisition facility

International Nuclear Information System (INIS)

Boyer, W.B.

1979-09-01

This report describes both the hardware and software components of an automatic calibration and signal system (Autocal) for the data acquisition system for the Sandia particle beam fusion research accelerators Hydra, Proto I, and Proto II. The Autocal hardware consists of off-the-shelf commercial equipment. The various hardware components, special modifications and overall system configuration are described. Special software has been developed to support the Autocal hardware. Software operation and maintenance are described

The energy aware smart home

OpenAIRE

Jahn, M.; Jentsch, M.; Prause, C.R.; Pramudianto, F.; Al-Akkad, A.; Reiners, R.

2010-01-01

In this paper, we present a novel smart home system integrating energy efficiency features. The smart home application is built on top of Hydra, a middleware framework that facilitates the intelligent communication of heterogeneous embedded devices through an overlay P2P network. We interconnect common devices available in private households and integrate wireless power metering plugs to gain access to energy consumption data. These data are used for monitoring and analyzing consumed energy o...

Wnt signaling in limb organogenesis

OpenAIRE

Geetha-Loganathan, Poongodi; Nimmagadda, Suresh; Scaal, Martin

2008-01-01

Secreted signaling molecules of the Wnt family have been found to play a central role in controlling embryonic development of a wide range of taxa from Hydra to humans. The most extensively studied Wnt signaling pathway is the canonical Wnt pathway, which controls gene expression by stabilizing β-catenin, and regulates a multitude of developmental processes. More recently, noncanonical Wnt pathways, which are β-catenin-independent, have been found to be important developmental regulators. Und...

Making the cut

Energy Technology Data Exchange (ETDEWEB)

Mcshannon, G. [Hydra Mining Tools International Ltd. (United Kingdom)

2006-04-15

The paper explains how coal mines around the world can benefit from the use of cowless, radial shearer drums. Hydra Mining has designed and manufactured a range of shearer drums to combat problems ranging from dust, frictional ignitions, geological problems or low production rates. This allows the mine operator to maximise production efficiency. The company tailor-makes shearer drums for each longwall face to optimise the cutting performance of every installation. 8 figs.

Comparative biology of the pentraxin protein family: evolutionarily conserved component of innate immune system.

Science.gov (United States)

Armstrong, Peter B

2015-01-01

The immune system is based on the actions of the collection of specialized immune defense cells and their secreted proteins and peptides that defend the host against infection by parasites. Parasites are organisms that live part or all of their lives in close physical association with the host and extract nutrients from the host and, by releasing toxins and virulence factors, cause disease with the potential for injury and premature death of that host. Parasites of the metazoa can be viruses, eubacteria, fungi, protozoans, and other metazoans. The immune system operates to kill or eliminate parasites and eliminate or detoxify their toxins and virulence factors. Although some of the elements of immune systems are specific to a particular phylum of metazoans, others show extensive evolutionary conservation, being present in several or all major phyla of the metazoa. The pentraxins display this latter character in their roles in immune defense. Pentraxins have been documented in vertebrates, nonvertebrate chordates, arthropods, and mollusks and may be present in other taxa of metazoans. Presumably the pentraxins appeared early in the evolution of metazoa, prior to their evolutionary divergence in the Precambrian epoch into many phyla present today, and have been preserved for the 542 million years since that explosive evolutionary radiation. The fidelity with which these phyla have preserved the pentraxins suggests that the functions of these proteins are important for survival of the members of these diverse taxa of animals. Copyright © 2015 Elsevier Inc. All rights reserved.

Fulltext PDF

Indian Academy of Sciences (India)

environment we talked about last time, that metazoans have created for efficient ... and have been working on ... which adopt this niche successfully have to work out ways to .... arsenal such that bugs which are normally safe suddenly discover.

Spatial variation in meiofaunal abundance of some coralline beaches of Mauritius

Digital Repository Service at National Institute of Oceanography (India)

Ingole, B.S.; Ansari, Z.A.; Parulekar, A.H.

Abundance of metazoan meiofauna was examined at 12 coralline sandy beaches of Mauritius island during September-October, 1987. Beach sediment comprised of moderately well sorted sand particles (Mz=0.53-2.80 phi ; x=1.70). Population density...

Microcystins do not provide anti-herbivore defence against mixotrophic flagellates

NARCIS (Netherlands)

Wilken, S.; Wiezer, S.M.H.; Huisman, J.; Van Donk, E.

2010-01-01

While most experiments investigating zooplankton grazing on harmful cyanobacteria have been carried out with metazoan plankton, several protozoa can also feed efficiently on cyanobacteria. We investigated grazing by the mixotrophic flagellate Ochromonas sp. on the toxic cyanobacterium Microcystis

Motif enrichment tool.

Science.gov (United States)

Blatti, Charles; Sinha, Saurabh

2014-07-01

The Motif Enrichment Tool (MET) provides an online interface that enables users to find major transcriptional regulators of their gene sets of interest. MET searches the appropriate regulatory region around each gene and identifies which transcription factor DNA-binding specificities (motifs) are statistically overrepresented. Motif enrichment analysis is currently available for many metazoan species including human, mouse, fruit fly, planaria and flowering plants. MET also leverages high-throughput experimental data such as ChIP-seq and DNase-seq from ENCODE and ModENCODE to identify the regulatory targets of a transcription factor with greater precision. The results from MET are produced in real time and are linked to a genome browser for easy follow-up analysis. Use of the web tool is free and open to all, and there is no login requirement. ADDRESS: http://veda.cs.uiuc.edu/MET/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Apicobasal domain identities of expanding tubular membranes depend on glycosphingolipid biosynthesis.

Science.gov (United States)

Zhang, Hongjie; Abraham, Nessy; Khan, Liakot A; Hall, David H; Fleming, John T; Göbel, Verena

2011-09-18

Metazoan internal organs are assembled from polarized tubular epithelia that must set aside an apical membrane domain as a lumenal surface. In a global Caenorhabditis elegans tubulogenesis screen, interference with several distinct fatty-acid-biosynthetic enzymes transformed a contiguous central intestinal lumen into multiple ectopic lumens. We show that multiple-lumen formation is caused by apicobasal polarity conversion, and demonstrate that in situ modulation of lipid biosynthesis is sufficient to reversibly switch apical domain identities on growing membranes of single post-mitotic cells, shifting lumen positions. Follow-on targeted lipid-biosynthesis pathway screens and functional genetic assays were designed to identify a putative single causative lipid species. They demonstrate that fatty-acid biosynthesis affects polarity through sphingolipid synthesis, and reveal ceramide glucosyltransferases (CGTs) as end-point biosynthetic enzymes in this pathway. Our findings identify glycosphingolipids, CGT products and obligate membrane lipids, as critical determinants of in vivo polarity and indicate that they sort new components to the expanding apical membrane.

The carnegie protein trap library: a versatile tool for Drosophila developmental studies.

Science.gov (United States)

Buszczak, Michael; Paterno, Shelley; Lighthouse, Daniel; Bachman, Julia; Planck, Jamie; Owen, Stephenie; Skora, Andrew D; Nystul, Todd G; Ohlstein, Benjamin; Allen, Anna; Wilhelm, James E; Murphy, Terence D; Levis, Robert W; Matunis, Erika; Srivali, Nahathai; Hoskins, Roger A; Spradling, Allan C

2007-03-01

Metazoan physiology depends on intricate patterns of gene expression that remain poorly known. Using transposon mutagenesis in Drosophila, we constructed a library of 7404 protein trap and enhancer trap lines, the Carnegie collection, to facilitate gene expression mapping at single-cell resolution. By sequencing the genomic insertion sites, determining splicing patterns downstream of the enhanced green fluorescent protein (EGFP) exon, and analyzing expression patterns in the ovary and salivary gland, we found that 600-900 different genes are trapped in our collection. A core set of 244 lines trapped different identifiable protein isoforms, while insertions likely to act as GFP-enhancer traps were found in 256 additional genes. At least 8 novel genes were also identified. Our results demonstrate that the Carnegie collection will be useful as a discovery tool in diverse areas of cell and developmental biology and suggest new strategies for greatly increasing the coverage of the Drosophila proteome with protein trap insertions.

Conserved domains and SINE diversity during animal evolution.

Science.gov (United States)

Luchetti, Andrea; Mantovani, Barbara

2013-10-01

Eukaryotic genomes harbour a number of mobile genetic elements (MGEs); moving from one genomic location to another, they are known to impact on the host genome. Short interspersed elements (SINEs) are well-represented, non-autonomous retroelements and they are likely the most diversified MGEs. In some instances, sequence domains conserved across unrelated SINEs have been identified; remarkably, one of these, called Nin, has been conserved since the Radiata-Bilateria splitting. Here we report on two new domains: Inv, derived from Nin, identified in insects and in deuterostomes, and Pln, restricted to polyneopteran insects. The identification of Inv and Pln sequences allowed us to retrieve new SINEs, two in insects and one in a hemichordate. The diverse structural combination of the different domains in different SINE families, during metazoan evolution, offers a clearer view of SINE diversity and their frequent de novo emergence through module exchange, possibly underlying the high evolutionary success of SINEs. © 2013 Elsevier Inc. All rights reserved.

Genetic mapping uncovers cis-regulatory landscape of RNA editing.

Science.gov (United States)

Ramaswami, Gokul; Deng, Patricia; Zhang, Rui; Anna Carbone, Mary; Mackay, Trudy F C; Li, Jin Billy

2015-09-16

Adenosine-to-inosine (A-to-I) RNA editing, catalysed by ADAR enzymes conserved in metazoans, plays an important role in neurological functions. Although the fine-tuning mechanism provided by A-to-I RNA editing is important, the underlying rules governing ADAR substrate recognition are not well understood. We apply a quantitative trait loci (QTL) mapping approach to identify genetic variants associated with variability in RNA editing. With very accurate measurement of RNA editing levels at 789 sites in 131 Drosophila melanogaster strains, here we identify 545 editing QTLs (edQTLs) associated with differences in RNA editing. We demonstrate that many edQTLs can act through changes in the local secondary structure for edited dsRNAs. Furthermore, we find that edQTLs located outside of the edited dsRNA duplex are enriched in secondary structure, suggesting that distal dsRNA structure beyond the editing site duplex affects RNA editing efficiency. Our work will facilitate the understanding of the cis-regulatory code of RNA editing.

Comparative metabolomics reveals endogenous ligands of DAF-12, a nuclear hormone receptor regulating C. elegans development and lifespan

Science.gov (United States)

Mahanti, Parag; Bose, Neelanjan; Bethke, Axel; Judkins, Joshua C.; Wollam, Joshua; Dumas, Kathleen J.; Zimmerman, Anna M.; Campbell, Sydney L.; Hu, Patrick J.; Antebi, Adam; Schroeder, Frank C.

2014-01-01

SUMMARY Small-molecule ligands of nuclear hormone receptors (NHRs) govern the transcriptional regulation of metazoan development, cell differentiation, and metabolism. However, the physiological ligands of many NHRs remain poorly characterized primarily due to lack of robust analytical techniques. Using comparative metabolomics, we identified endogenous steroids that act as ligands of the C. elegans NHR, DAF-12, a vitamin-D and liver-X receptor homolog regulating larval development, fat metabolism, and lifespan. The identified molecules feature unexpected chemical modifications and include only one of two DAF-12 ligands reported earlier, necessitating a revision of previously proposed ligand biosynthetic pathways. We further show that ligand profiles are regulated by a complex enzymatic network including the Rieske oxygenase DAF-36, the short-chain dehydrogenase DHS-16, and the hydroxysteroid dehydrogenase, HSD-1. Our results demonstrate the advantages of comparative metabolomics over traditional candidate-based approaches and provide a blueprint for the identification of ligands for other C. elegans and mammalian NHRs. PMID:24411940

The biogeochemistry of anchialine caves: Progress and possibilities

Science.gov (United States)

Pohlman, John W.

2011-01-01

Recent investigations of anchialine caves and sinkholes have identified complex food webs dependent on detrital and, in some cases, chemosynthetically produced organic matter. Chemosynthetic microbes in anchialine systems obtain energy from reduced compounds produced during organic matter degradation (e.g., sulfide, ammonium, and methane), similar to what occurs in deep ocean cold seeps and mud volcanoes, but distinct from dominant processes operating at hydrothermal vents and sulfurous mineral caves where the primary energy source is mantle derived. This review includes case studies from both anchialine and non-anchialine habitats, where evidence for in situ chemosynthetic production of organic matter and its subsequent transfer to higher trophic level metazoans is documented. The energy sources and pathways identified are synthesized to develop conceptual models for elemental cycles and energy cascades that occur within oligotrophic and eutrophic anchialine caves. Strategies and techniques for testing the hypothesis of chemosynthesis as an active process in anchialine caves are also suggested.

Mixed metazoan and bacterial infection of the gas bladder of the lined seahorse-a case report.

Science.gov (United States)

Anderson, Paul A; Petty, Barbara D

2013-03-01

Five wild-caught Lined Seahorses Hippocampus erectus from an aquarium system presented with altered buoyancy and distended upper trunks. Radiography of one specimen revealed a reduced air volume in the gas bladder. Pneumocystocentesis revealed a brown exudate of numerous leukocytes, parasite ova, and Gram- and acid-fast-positive bacilli under wet mounts and stains. Necropsies revealed enlarged, friable kidneys and distended gas bladders containing copious purulent exudate, necrotic tissue, and adult digeneans Dictysarca virens. Bacterial isolates from exudate cultures grown on Lowenstein-Jensen medium were identified as Gordonia sp. and Mycobacterium poriferae by high-performance liquid chromatography and 16S ribosomal DNA sequencing. Histopathology demonstrated a histiocytic response in kidney and gas bladder exudate, inflammation of the gas bladder wall, and infection of the gas bladder lumen with parasite ova and acid-fast-positive and Gomori's methenamine silver-positive bacilli. Praziquantel is prescribed for digenean infections but dissolves incompletely in seawater and is toxic to this host. Eradication of intermediate host vectors is a management option. Treatment of Gordonia infection has not been addressed in nonhuman animals, and there is no known effective treatment for Mycobacterium spp. infection in fishes. This is the first case report of digenean infection of the gas bladder in a syngnathid, Gordonia sp. infection in a nonhuman animal, and M. poriferae infection in a fish.

Autophagy in unicellular eukaryotes

NARCIS (Netherlands)

Kiel, J.A.K.W.

2010-01-01

Cells need a constant supply of precursors to enable the production of macromolecules to sustain growth and survival. Unlike metazoans, unicellular eukaryotes depend exclusively on the extracellular medium for this supply. When environmental nutrients become depleted, existing cytoplasmic components

The ctenophore genome and the evolutionary origins of neural systems

NARCIS (Netherlands)

Moroz, Leonid L.; Kocot, Kevin M.; Citarella, Mathew R.; Dosung, Sohn; Norekian, Tigran P.; Povolotskaya, Inna S.; Grigorenko, Anastasia P.; Dailey, Christopher; Berezikov, Eugene; Buckley, Katherine M.; Ptitsyn, Andrey; Reshetov, Denis; Mukherjee, Krishanu; Moroz, Tatiana P.; Bobkova, Yelena; Yu, Fahong; Kapitonov, Vladimir V.; Jurka, Jerzy; Bobkov, Yuri V.; Swore, Joshua J.; Girardo, David O.; Fodor, Alexander; Gusev, Fedor; Sanford, Rachel; Bruders, Rebecca; Kittler, Ellen; Mills, Claudia E.; Rast, Jonathan P.; Derelle, Romain; Solovyev, Victor V.; Kondrashov, Fyodor A.; Swalla, Billie J.; Sweedler, Jonathan V.; Rogaev, Evgeny I.; Halanych, Kenneth M.; Kohn, Andrea B.

2014-01-01

The origins of neural systems remain unresolved. In contrast to other basal metazoans, ctenophores (comb jellies) have both complex nervous and mesoderm-derived muscular systems. These holoplanktonic predators also have sophisticated ciliated locomotion, behaviour and distinct development. Here we

Comunidad de parásitos metazoarios de la charra Cichlasoma trimaculatum en la laguna de Tres Palos, Guerrero, México Metazoan parasite community in the three-spot cichlid Cichlasoma trimaculatum from Tres Palos Lagoon, Guerrero, Mexico

Directory of Open Access Journals (Sweden)

Juan Violante-González

2008-12-01

Full Text Available Entre abril de 2000 y noviembre de 2002 se examinó la composición de la comunidad de parásitos metazoarios de la charra, Cichlasoma trimaculatum a partir de muestras temporales. Fueron recuperadas 12 especies de parásitos (40 969 individuos de 231 hospederos examinados; 10 helmintos: Ascocotyle (Phagicola longa, Austrodiplostomum compactum, Cladocystis trifolium, Clinostomum complanatum, Crassicutis cichlasomae, Posthodiplostomum minimum, Pseudoacanthostomum panamense, Neoechinorhynchus golvani, Southwellina hispida y Contracaecum sp., y 2 crustáceos: Argulus sp. y Ergasilus sp. La comunidad se caracterizó por un número mayor de parásitos generalistas y pocos especialistas de cíclidos, además por ser pobre en especies. De las 5 especies comunes dentro de la comunidad, 4 presentaron variación temporal en su dinámica de infección a lo largo del tiempo, la cual fue asociada con cambios ambientales generados durante las temporadas de secas y lluvias. La variación en la dinámica de infección de las especies comunes fue capaz de generar cambios en la estructura, tanto en el nivel de componente como en el de infracomunidad; sin embargo, no se observó un patrón claro, lo que indica que la comunidad puede ser poco predecible, como se sugiere para otras comunidades de parásitos de peces dulceacuícolas.We analyzed metazoan parasite community composition in the three-spot cichlid Cichlasoma trimaculatum using seasonal samples taken between April 2000 and November 2002 from the Tres Palos Lagoon, Guerrero, Mexico. A total of 231 hosts were examined. Of the 12 parasite species recovered (40,969 individuals, 10 were helminths: Ascocotyle (Phagicola longa, Austrodiplostomum compactum, Cladocystis trifolium, Clinostomum complanatum, Crassicutis cichlasomae, Posthodiplostomum minimum, Pseudoacanthostomum panamense, Neoechinorhynchus golvani, Southwellina hispida, and Contracaecum sp. The remaining 2 were the crustaceans Argulus sp. and

The evolutionary diversification of LSF and Grainyhead transcription factors preceded the radiation of basal animal lineages

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Kaufman Les

2010-04-01

Full Text Available Abstract Background The transcription factors of the LSF/Grainyhead (GRH family are characterized by the possession of a distinctive DNA-binding domain that bears no clear relationship to other known DNA-binding domains, with the possible exception of the p53 core domain. In triploblastic animals, the LSF and GRH subfamilies have diverged extensively with respect to their biological roles, general expression patterns, and mechanism of DNA binding. For example, Grainyhead (GRH homologs are expressed primarily in the epidermis, and they appear to play an ancient role in maintaining the epidermal barrier. By contrast, LSF homologs are more widely expressed, and they regulate general cellular functions such as cell cycle progression and survival in addition to cell-lineage specific gene expression. Results To illuminate the early evolution of this family and reconstruct the functional divergence of LSF and GRH, we compared homologs from 18 phylogenetically diverse taxa, including four basal animals (Nematostella vectensis, Vallicula multiformis, Trichoplax adhaerens, and Amphimedon queenslandica, a choanoflagellate (Monosiga brevicollis and several fungi. Phylogenetic and bioinformatic analyses of these sequences indicate that (1 the LSF/GRH gene family originated prior to the animal-fungal divergence, and (2 the functional diversification of the LSF and GRH subfamilies occurred prior to the divergence between sponges and eumetazoans. Aspects of the domain architecture of LSF/GRH proteins are well conserved between fungi, choanoflagellates, and metazoans, though within the Metazoa, the LSF and GRH families are clearly distinct. We failed to identify a convincing LSF/GRH homolog in the sequenced genomes of the algae Volvox carteri and Chlamydomonas reinhardtii or the amoebozoan Dictyostelium purpureum. Interestingly, the ancestral GRH locus has become split into two separate loci in the sea anemone Nematostella, with one locus encoding a DNA binding

The phylogeny of Arthrotardigrada

DEFF Research Database (Denmark)

Hansen, Jesper Guldberg

2011-01-01

The order Arthrotardigrada, or water bears, constitutes a small group of 160 species of marine, microscopical invertebrates, within the phylum Tardigrada. Although the position of tardigrades in the Animal Kingdom has received much attention focusing on the metazoan phylogeny, the phylogenetic...

Is Echinococcus intermedius a valid species?

Science.gov (United States)

Medical and veterinary sciences require scientific names to discriminate pathogenic organisms in our living environment. Various species concepts have been proposed for metazoan animals. There are, however, constant controversies over their validity because of lack of a common criterion to define ...

Pathogen-mediated selection for MHC variability in wild zebrafish

Czech Academy of Sciences Publication Activity Database

Smith, C.; Ondračková, Markéta; Spence, R.; Adams, S.; Betts, D. S.; Mallon, E.

2011-01-01

Roč. 13, č. 6 (2011), s. 589-605 ISSN 1522-0613 Institutional support: RVO:68081766 Keywords : digenean * frequency-dependent selection * heterozygote advantage * major histocompatibility complex * metazoan parasite * pathogen-driven selection Subject RIV: EG - Zoology Impact factor: 1.029, year: 2011

Surface enhanced raman scattering on tardigrada - Towards monitoring and imaging molecular structures in live cryptobiotic organisms

DEFF Research Database (Denmark)

Kneipp, Harald; Møbjerg, Nadja; Jørgensen, Aslak

2013-01-01

Tardigrades are microscopic metazoans which are able to survive extreme physical and chemical conditions by entering a stress tolerant state called cryptobiosis. At present, the molecular mechanisms behind cryptobiosis are still poorly understood. We show that surface enhanced Raman scattering su...

SIMPLE METHOD FOR THE EXTRACTION OF PHOTOPIGMENTS AND MYCOSPORINE-LIKE AMINO ACIDS (MAAS) FROM SYMBIODINIUM SPP.

Science.gov (United States)

Numerous extraction methods have been developed and used in the quantitation of both photopigments and mycosporine amino acids (MAAs) found in Symbiodinium sp. and zooanthellate metazoans. We have development of a simple, mild extraction procedure using methanol, which when coupl...

Novel interactions between vertebrate Hox genes

NARCIS (Netherlands)

Hooiveld, MHW; Morgan, R; Rieden, PID; Houtzager, E; Pannese, M; Damen, K; Boncinelli, E; Durston, AJ

1999-01-01

Understanding why metazoan Hox/HOM-C genes are expressed in spatiotemporal sequences showing colinearity with their genomic sequence is a central challenge in developmental biology. Here, we studied the consequences of ectopically expressing Hox genes to investigate whether Hox-Hox interactions

Receptor tyrosine kinase signaling: a view from quantitative proteomics

DEFF Research Database (Denmark)

Dengjel, Joern; Kratchmarova, Irina; Blagoev, Blagoy

2009-01-01

Growth factor receptor signaling via receptor tyrosine kinases (RTKs) is one of the basic cellular communication principals found in all metazoans. Extracellular signals are transferred via membrane spanning receptors into the cytoplasm, reversible tyrosine phosphorylation being the hallmark of all...

Gene regulation by MAP kinase cascades

DEFF Research Database (Denmark)

Fiil, Berthe Katrine; Petersen, Klaus; Petersen, Morten

2009-01-01

Mitogen-activated protein kinase (MAPK) cascades are signaling modules that transduce extracellular stimuli to a range of cellular responses. Research in yeast and metazoans has shown that MAPK-mediated phosphorylation directly or indirectly regulates the activity of transcription factors. Plant ...

Characterization of Small HSPs from Anemonia viridis Reveals Insights into Molecular Evolution of Alpha Crystallin Genes among Cnidarians

OpenAIRE

Nicosia, Aldo; Maggio, Teresa; Mazzola, Salvatore; Gianguzza, Fabrizio; Cuttitta, Angela; Costa, Salvatore

2014-01-01

Gene family encoding small Heat-Shock Proteins (sHSPs containing α-crystallin domain) are found both in prokaryotic and eukaryotic organisms; however, there is limited knowledge of their evolution. In this study, two small HSP genes termed AvHSP28.6 and AvHSP27, both organized in one intron and two exons, were characterised in the Mediterranean snakelocks anemone Anemonia viridis. The release of the genome sequence of Hydra magnipapillata and Nematostella vectensis enabled a comprehensive stu...

Old Books Bring New Life to the Brick and Mortar Library

Science.gov (United States)

2012-08-01

Beijing 108   constellations, centering primarily on the Greek and Roman mythology surrounding the constellations. As with star atlases that would...obscure Greek myths. So who was Hydra and why is he always shown with a crow and a cup in a laurel tree? The Greek myth says Apollo asked the crow to... Greek letters to the brighter starts, with alpha being the brightest. These letters were placed on the charts themselves. So just a few years before

NET-COMPUTER: Internet Computer Architecture and its Application in E-Commerce

OpenAIRE

P. O. Umenne; M. O. Odhiambo

2012-01-01

Research in Intelligent Agents has yielded interesting results, some of which have been translated into commer­cial ventures. Intelligent Agents are executable software components that represent the user, perform tasks on behalf of the user and when the task terminates, the Agents send the result to the user. Intelligent Agents are best suited for the Internet: a collection of computers connected together in a world-wide computer network. Swarm and HYDRA computer architectures for Agents’ ex...

Noise Budget for the X-Ray Microcalorimeter Spectrometer (XMS) Core Array

Science.gov (United States)

Kilbourne, Caroline Anne

2010-01-01

The purpose of this document is to present and archive the noise budget for the XMS detector, in order, at this stage in mission planning, to learn the scale of the requirements placed on the other instrument subsystems. This document mainly concerns the core array, specifically the baseline version that emerged from the trade studies associated with the ESA Phase A study report. Qualitative extension to the Hydra approach to the outer array is included at the end.

Performance Evaluation at the Hardware Architecture Level and the Operating System Kernel Design Level.

Science.gov (United States)

1977-12-01

program utilizing kernel semaphores for synchronization . The Hydra kernel instructions were sampled at random using the hardware monitor. The changes in...thatf r~i~h olvrAt- 1,o;lil armcrl han itf,. own sell of primitive func ions; and c onparinoms acrosns dif fc’rnt opt ratieg ; .emsf is riot possiblc...kcrnel dcsign level is complicated by the fact that each operating system kernel ha. its own set of primitive functions and compari!ons across

Who gets caught for corruption when corruption is pervasive? Evidence from China's anti-bribery blacklist

OpenAIRE

Zhou, Liming; Jin, Zhangfeng; Wang, Zheng

2016-01-01

Original Open Access Repository: https://hydra.hull.ac.uk/resources/hull:13057 This article empirically investigates why in a corruption-pervasive country only a minority of the firms get caught for bribery while the majority get away with it. By matching manufacturing firms to a blacklist of bribers in the healthcare sector of a province in China, we show that the government-led blacklisting is selective: while economically more visible firms are slightly more likely to be blacklisted, st...

Chattahoochee River Water Quality Analysis.

Science.gov (United States)

1978-04-01

runoff coeffi- cient (CPERV) and the impervious area runoff coefficient ( CIMP ) for each basin so that the computed runoff most nearly matched the...observed runoff. The values of CPERV and CIMP for the research watersheds were used for those basins in the study which had comparable land use patterns... CIMP is applied to the input hydra- graphs to arrive at the runoff rate from the impervious areas. The runoff rate from the impervious areas is used

The BAH domain of ORC1 links H4K20me2 to DNA replication licensing and Meier-Gorlin syndrome

Energy Technology Data Exchange (ETDEWEB)

Kuo, Alex J; Song, Jikui; Cheung, Peggie; Ishibe-Murakami, Satoko; Yamazoe, Sayumi; Chen, James K; Patel, Dinshaw J; Gozani, Or [Stanford; (MSKCC); (Stanford-MED)

2012-07-11

The recognition of distinctly modified histones by specialized 'effector' proteins constitutes a key mechanism for transducing molecular events at chromatin to biological outcomes. Effector proteins influence DNA-templated processes, including transcription, DNA recombination and DNA repair; however, no effector functions have yet been identified within the mammalian machinery that regulate DNA replication. Here we show that ORC1 - a component of ORC (origin of replication complex), which mediates pre-DNA replication licensing - contains a bromo adjacent homology (BAH) domain that specifically recognizes histone H4 dimethylated at lysine 20 (H4K20me2). Recognition of H4K20me2 is a property common to BAH domains present within diverse metazoan ORC1 proteins. Structural studies reveal that the specificity of the BAH domain for H4K20me2 is mediated by a dynamic aromatic dimethyl-lysine-binding cage and multiple intermolecular contacts involving the bound peptide. H4K20me2 is enriched at replication origins, and abrogating ORC1 recognition of H4K20me2 in cells impairs ORC1 occupancy at replication origins, ORC chromatin loading and cell-cycle progression. Mutation of the ORC1 BAH domain has been implicated in the aetiology of Meier-Gorlin syndrome (MGS), a form of primordial dwarfism, and ORC1 depletion in zebrafish results in an MGS-like phenotype. We find that wild-type human ORC1, but not ORC1-H4K20me2-binding mutants, rescues the growth retardation of orc1 morphants. Moreover, zebrafish depleted of H4K20me2 have diminished body size, mirroring the phenotype of orc1 morphants. Together, our results identify the BAH domain as a novel methyl-lysine-binding module, thereby establishing the first direct link between histone methylation and the metazoan DNA replication machinery, and defining a pivotal aetiological role for the canonical H4K20me2 mark, via ORC1, in primordial dwarfism.

The Evolution of the Secreted Regulatory Protein Progranulin.

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Roger G E Palfree

Full Text Available Progranulin is a secreted growth factor that is active in tumorigenesis, wound repair, and inflammation. Haploinsufficiency of the human progranulin gene, GRN, causes frontotemporal dementia. Progranulins are composed of chains of cysteine-rich granulin modules. Modules may be released from progranulin by proteolysis as 6kDa granulin polypeptides. Both intact progranulin and some of the granulin polypeptides are biologically active. The granulin module occurs in certain plant proteases and progranulins are present in early diverging metazoan clades such as the sponges, indicating their ancient evolutionary origin. There is only one Grn gene in mammalian genomes. More gene-rich Grn families occur in teleost fish with between 3 and 6 members per species including short-form Grns that have no tetrapod counterparts. Our goals are to elucidate progranulin and granulin module evolution by investigating (i: the origins of metazoan progranulins (ii: the evolutionary relationships between the single Grn of tetrapods and the multiple Grn genes of fish (iii: the evolution of granulin module architectures of vertebrate progranulins (iv: the conservation of mammalian granulin polypeptide sequences and how the conserved granulin amino acid sequences map to the known three dimensional structures of granulin modules. We report that progranulin-like proteins are present in unicellular eukaryotes that are closely related to metazoa suggesting that progranulin is among the earliest extracellular regulatory proteins still employed by multicellular animals. From the genomes of the elephant shark and coelacanth we identified contemporary representatives of a precursor for short-from Grn genes of ray-finned fish that is lost in tetrapods. In vertebrate Grns pathways of exon duplication resulted in a conserved module architecture at the amino-terminus that is frequently accompanied by an unusual pattern of tandem nearly identical module repeats near the carboxyl

Unveiling the Biodiversity of Deep-Sea Nematodes through Metabarcoding: Are We Ready to Bypass the Classical Taxonomy?

Science.gov (United States)

Dell'Anno, Antonio; Carugati, Laura; Corinaldesi, Cinzia; Riccioni, Giulia; Danovaro, Roberto

2015-01-01

Nematodes inhabiting benthic deep-sea ecosystems account for >90% of the total metazoan abundances and they have been hypothesised to be hyper-diverse, but their biodiversity is still largely unknown. Metabarcoding could facilitate the census of biodiversity, especially for those tiny metazoans for which morphological identification is difficult. We compared, for the first time, different DNA extraction procedures based on the use of two commercial kits and a previously published laboratory protocol and tested their suitability for sequencing analyses of 18S rDNA of marine nematodes. We also investigated the reliability of Roche 454 sequencing analyses for assessing the biodiversity of deep-sea nematode assemblages previously morphologically identified. Finally, intra-genomic variation in 18S rRNA gene repeats was investigated by Illumina MiSeq in different deep-sea nematode morphospecies to assess the influence of polymorphisms on nematode biodiversity estimates. Our results indicate that the two commercial kits should be preferred for the molecular analysis of biodiversity of deep-sea nematodes since they consistently provide amplifiable DNA suitable for sequencing. We report that the morphological identification of deep-sea nematodes matches the results obtained by metabarcoding analysis only at the order-family level and that a large portion of Operational Clustered Taxonomic Units (OCTUs) was not assigned. We also show that independently from the cut-off criteria and bioinformatic pipelines used, the number of OCTUs largely exceeds the number of individuals and that 18S rRNA gene of different morpho-species of nematodes displayed intra-genomic polymorphisms. Our results indicate that metabarcoding is an important tool to explore the diversity of deep-sea nematodes, but still fails in identifying most of the species due to limited number of sequences deposited in the public databases, and in providing quantitative data on the species encountered. These aspects

cisMEP: an integrated repository of genomic epigenetic profiles and cis-regulatory modules in Drosophila.

Science.gov (United States)

Yang, Tzu-Hsien; Wang, Chung-Ching; Hung, Po-Cheng; Wu, Wei-Sheng

2014-01-01

Cis-regulatory modules (CRMs), or the DNA sequences required for regulating gene expression, play the central role in biological researches on transcriptional regulation in metazoan species. Nowadays, the systematic understanding of CRMs still mainly resorts to computational methods due to the time-consuming and small-scale nature of experimental methods. But the accuracy and reliability of different CRM prediction tools are still unclear. Without comparative cross-analysis of the results and combinatorial consideration with extra experimental information, there is no easy way to assess the confidence of the predicted CRMs. This limits the genome-wide understanding of CRMs. It is known that transcription factor binding and epigenetic profiles tend to determine functions of CRMs in gene transcriptional regulation. Thus integration of the genome-wide epigenetic profiles with systematically predicted CRMs can greatly help researchers evaluate and decipher the prediction confidence and possible transcriptional regulatory functions of these potential CRMs. However, these data are still fragmentary in the literatures. Here we performed the computational genome-wide screening for potential CRMs using different prediction tools and constructed the pioneer database, cisMEP (cis-regulatory module epigenetic profile database), to integrate these computationally identified CRMs with genomic epigenetic profile data. cisMEP collects the literature-curated TFBS location data and nine genres of epigenetic data for assessing the confidence of these potential CRMs and deciphering the possible CRM functionality. cisMEP aims to provide a user-friendly interface for researchers to assess the confidence of different potential CRMs and to understand the functions of CRMs through experimentally-identified epigenetic profiles. The deposited potential CRMs and experimental epigenetic profiles for confidence assessment provide experimentally testable hypotheses for the molecular mechanisms

A voltage-gated H+ channel underlying pH homeostasis in calcifying coccolithophores.

Directory of Open Access Journals (Sweden)

Alison R Taylor

2011-06-01

Full Text Available Marine coccolithophorid phytoplankton are major producers of biogenic calcite, playing a significant role in the global carbon cycle. Predicting the impacts of ocean acidification on coccolithophore calcification has received much recent attention and requires improved knowledge of cellular calcification mechanisms. Uniquely amongst calcifying organisms, coccolithophores produce calcified scales (coccoliths in an intracellular compartment and secrete them to the cell surface, requiring large transcellular ionic fluxes to support calcification. In particular, intracellular calcite precipitation using HCO₃⁻ as the substrate generates equimolar quantities of H+ that must be rapidly removed to prevent cytoplasmic acidification. We have used electrophysiological approaches to identify a plasma membrane voltage-gated H+ conductance in Coccolithus pelagicus ssp braarudii with remarkably similar biophysical and functional properties to those found in metazoans. We show that both C. pelagicus and Emiliania huxleyi possess homologues of metazoan H(v1 H+ channels, which function as voltage-gated H+ channels when expressed in heterologous systems. Homologues of the coccolithophore H+ channels were also identified in a diversity of eukaryotes, suggesting a wide range of cellular roles for the H(v1 class of proteins. Using single cell imaging, we demonstrate that the coccolithophore H+ conductance mediates rapid H+ efflux and plays an important role in pH homeostasis in calcifying cells. The results demonstrate a novel cellular role for voltage gated H+ channels and provide mechanistic insight into biomineralisation by establishing a direct link between pH homeostasis and calcification. As the coccolithophore H+ conductance is dependent on the trans-membrane H+ electrochemical gradient, this mechanism will be directly impacted by, and may underlie adaptation to, ocean acidification. The presence of this H+ efflux pathway suggests that there is no obligate

Wrestling the Hydra: Exploiting Organizational Evolution in Terrorist Groups

Science.gov (United States)

2013-05-02

outside that come from the competition for scarce resources.28 25 Aldrich, 22. The 26...forced to rebuild following the employment of over 250,000 Turkish troops and security forces.39 The Zapatitstas sit on the other end of the spectrum...consistency has and will continue to be tested. Al-Qaeda and its franchises fall far short of presenting a monolithic front. In fact, if this look at

The molecular evolution of the p120-catenin subfamily and its functional associations.

Directory of Open Access Journals (Sweden)

Robert H Carnahan

2010-12-01

Full Text Available p120-catenin (p120 is the prototypical member of a subclass of armadillo-related proteins that includes δ-catenin/NPRAP, ARVCF, p0071, and the more distantly related plakophilins 1-3. In vertebrates, p120 is essential in regulating surface expression and stability of all classical cadherins, and directly interacts with Kaiso, a BTB/ZF family transcription factor.To clarify functional relationships between these proteins and how they relate to the classical cadherins, we have examined the proteomes of 14 diverse vertebrate and metazoan species. The data reveal a single ancient δ-catenin-like p120 family member present in the earliest metazoans and conserved throughout metazoan evolution. This single p120 family protein is present in all protostomes, and in certain early-branching chordate lineages. Phylogenetic analyses suggest that gene duplication and functional diversification into "p120-like" and "δ-catenin-like" proteins occurred in the urochordate-vertebrate ancestor. Additional gene duplications during early vertebrate evolution gave rise to the seven vertebrate p120 family members. Kaiso family members (i.e., Kaiso, ZBTB38 and ZBTB4 are found only in vertebrates, their origin following that of the p120-like gene lineage and coinciding with the evolution of vertebrate-specific mechanisms of epigenetic gene regulation by CpG island methylation.The p120 protein family evolved from a common δ-catenin-like ancestor present in all metazoans. Through several rounds of gene duplication and diversification, however, p120 evolved in vertebrates into an essential, ubiquitously expressed protein, whereas loss of the more selectively expressed δ-catenin, p0071 and ARVCF are tolerated in most species. Together with phylogenetic studies of the vertebrate cadherins, our data suggest that the p120-like and δ-catenin-like genes co-evolved separately with non-neural (E- and P-cadherin and neural (N- and R-cadherin cadherin lineages, respectively. The

African Zoology - Vol 45, No 2 (2010)

African Journals Online (AJOL)

Ecology of metazoan parasites of Clarias gariepinus (Osteichthyes: Clariidae) from the Nwanedi-Luphephe Dams of the Limpopo River System, South Africa · EMAIL ... Towards a standardized and optimized protocol for rapid biodiversity assessments: spider species richness and assemblage composition in two savanna ...

Trait-mediated diversification in nematode predator–prey systems

NARCIS (Netherlands)

Mulder, C.; Helder, J.; Vervoort, M.T.W.; Vonk, J.A.

2011-01-01

Nematodes are presumably the most numerous Metazoans in terrestrial habitats. They are represented at all trophic levels and are known to respond to nutrient limitation, prey availability, and microbial resources. Predatory nematodes reside at the highest trophic level, and as such their feeding

Rather than by direct acquisition via lateral gene transfer, GHF5 cellulases were passed on from early Pratylenchidae to root-knot and cyst nematodes

NARCIS (Netherlands)

Rybarczyk-Mydlowska, K.D.; Maboreke, H.R.; Megen, van H.H.B.; Elsen, van den S.J.J.; Mooijman, P.J.W.; Smant, G.; Bakker, J.; Helder, J.

2012-01-01

Background: Plant parasitic nematodes are unusual Metazoans as they are equipped with genes that allow for symbiont-independent degradation of plant cell walls. Among the cell wall-degrading enzymes, glycoside hydrolase family 5 (GHF5) cellulases are relatively well characterized, especially for

Sex is a ubiquitous, ancient, and inherent attribute of eukaryotic life

NARCIS (Netherlands)

Speijer, Dave; Lukeš, Julius; Eliáš, Marek

2015-01-01

Sexual reproduction and clonality in eukaryotes are mostly seen as exclusive, the latter being rather exceptional. This view might be biased by focusing almost exclusively on metazoans. We analyze and discuss reproduction in the context of extant eukaryotic diversity, paying special attention to

Global biogeography and evolution of Cuvierina pteropods

NARCIS (Netherlands)

Burridge, A.K.; Goetze, E.; Raes, N.; Huisman, J.; Peijnenburg, K.T.C.A.

2015-01-01

Background: helled pteropods are planktonic gastropods that are potentially good indicators of the effects of ocean acidification. They also have high potential for the study of zooplankton evolution because they are metazoan plankton with a good fossil record. We investigated phenotypic and genetic

Devonian rise in atmospheric oxygen correlated to the radiations of terrestrial plants and large predatory fish

DEFF Research Database (Denmark)

Dahl, Tais Wittchen; Hammarlund, Emma; Anbar, Ariel D.

2010-01-01

after the initial rise of animals and, therefore, suggesting that early metazoans evolved in a relatively low oxygen environment. This later oxygenation correlates with the diversification of vascular plants, which likely contributed to increased oxygenation through the enhanced burial of organic carbon...

Mixed messages: Re-initiation factors regulate translation of animal mRNAs

OpenAIRE

Obermayer, Benedikt; Rajewsky, Nikolaus

2014-01-01

When ribosomes encounter upstream open reading frames (uORFs) during scanning of the 5' untranslated region (5' UTR), translation of the downstream ORF requires re-initiation. In a recent paper in Nature, Schleich et al. describe metazoan factors which specifically promote re-initiation.

Tyrosine phosphorylation of the BRI1 receptor kinase occurs via a posttranslational modification and is activated by the juxtamembrane domain

Science.gov (United States)

In metazoans, receptor kinases control many essential processes related to growth and development and response to the environment. The receptor kinases in plants and animals are structurally similar but evolutionarily distinct from one another, and thus while most animal receptor kinases are tyrosin...

The Conserved RNA Exonuclease Rexo5 Is Required for 3′ End Maturation of 28S rRNA, 5S rRNA, and snoRNAs

Directory of Open Access Journals (Sweden)

Stefanie Gerstberger

2017-10-01

Full Text Available Non-coding RNA biogenesis in higher eukaryotes has not been fully characterized. Here, we studied the Drosophila melanogaster Rexo5 (CG8368 protein, a metazoan-specific member of the DEDDh 3′-5′ single-stranded RNA exonucleases, by genetic, biochemical, and RNA-sequencing approaches. Rexo5 is required for small nucleolar RNA (snoRNA and rRNA biogenesis and is essential in D. melanogaster. Loss-of-function mutants accumulate improperly 3′ end-trimmed 28S rRNA, 5S rRNA, and snoRNA precursors in vivo. Rexo5 is ubiquitously expressed at low levels in somatic metazoan cells but extremely elevated in male and female germ cells. Loss of Rexo5 leads to increased nucleolar size, genomic instability, defective ribosome subunit export, and larval death. Loss of germline expression compromises gonadal growth and meiotic entry during germline development.

Earth history. Low mid-Proterozoic atmospheric oxygen levels and the delayed rise of animals.

Science.gov (United States)

Planavsky, Noah J; Reinhard, Christopher T; Wang, Xiangli; Thomson, Danielle; McGoldrick, Peter; Rainbird, Robert H; Johnson, Thomas; Fischer, Woodward W; Lyons, Timothy W

2014-10-31

The oxygenation of Earth's surface fundamentally altered global biogeochemical cycles and ultimately paved the way for the rise of metazoans at the end of the Proterozoic. However, current estimates for atmospheric oxygen (O2) levels during the billion years leading up to this time vary widely. On the basis of chromium (Cr) isotope data from a suite of Proterozoic sediments from China, Australia, and North America, interpreted in the context of data from similar depositional environments from Phanerozoic time, we find evidence for inhibited oxidation of Cr at Earth's surface in the mid-Proterozoic (1.8 to 0.8 billion years ago). These data suggest that atmospheric O2 levels were at most 0.1% of present atmospheric levels. Direct evidence for such low O2 concentrations in the Proterozoic helps explain the late emergence and diversification of metazoans. Copyright © 2014, American Association for the Advancement of Science.

Gluconeogenesis: An ancient biochemical pathway with a new twist.

Science.gov (United States)

Miyamoto, Tetsuya; Amrein, Hubert

2017-07-03

Synthesis of sugars from simple carbon sources is critical for survival of animals under limited nutrient availability. Thus, sugar-synthesizing enzymes should be present across the entire metazoan spectrum. Here, we explore the evolution of glucose and trehalose synthesis using a phylogenetic analysis of enzymes specific for the two pathways. Our analysis reveals that the production of trehalose is the more ancestral biochemical process, found in single cell organisms and primitive metazoans, but also in insects. The gluconeogenic-specific enzyme glucose-6-phosphatase (G6Pase) first appears in Cnidaria, but is also present in Echinodermata, Mollusca and Vertebrata. Intriguingly, some species of nematodes and arthropods possess the genes for both pathways. Moreover, expression data from Drosophila suggests that G6Pase and, hence, gluconeogenesis, initially had a neuronal function. We speculate that in insects-and possibly in some vertebrates-gluconeogenesis may be used as a means of neuronal signaling.

Evolution and integration of innate immune systems from fruit flies to man: lessons and questions.

Science.gov (United States)

Martinelli, Cosimo; Reichhart, Jean-Marc

2005-01-01

Despite broad differences in morphology, ecology and behavior, the fruit fly Drosophila melanogaster and humans show a remarkably high degree of conservation for many molecular, cellular, and developmental aspects of their biology. During the last decade, similarities have also been discovered in some of the mechanisms regulating their innate immune system. These parallels regard mainly the Toll-like receptor family and the intracellular signaling pathways involved in the control of the immune response. However, if the overall similarities are important, the detailed pathogen recognition mechanisms differ significantly between fly and humans, highlighting a complicated evolutionary history of the metazoan innate defenses. In this review, we will discuss the main similarities and differences between the two types of organisms. We hope that this current knowledge will be used as a starting point for a more comprehensive view of innate immunity within the broad variety of metazoan phyla.

Identifying tier one key suppliers.

Science.gov (United States)

Wicks, Steve

2013-01-01

In today's global marketplace, businesses are becoming increasingly reliant on suppliers for the provision of key processes, activities, products and services in support of their strategic business goals. The result is that now, more than ever, the failure of a key supplier has potential to damage reputation, productivity, compliance and financial performance seriously. Yet despite this, there is no recognised standard or guidance for identifying a tier one key supplier base and, up to now, there has been little or no research on how to do so effectively. This paper outlines the key findings of a BCI-sponsored research project to investigate good practice in identifying tier one key suppliers, and suggests a scalable framework process model and risk matrix tool to help businesses effectively identify their tier one key supplier base.

Investigating the Effects of Land Cover Change on the Hydrology of the Mississippi River Basin

Science.gov (United States)

Twine, T. E.; Coe, M. T.; Lenters, J. D.; Kucharik, C. J.; Donner, S.; Foley, J. A.

2001-12-01

Humans have greatly altered the Earth's landscape since the beginning of sedentary agriculture. Through the conversion of forests and grasslands to croplands and pasture, human land use activities have changed biogeochemical cycles including the water cycle. Using IBIS, a global land surface model with 0.5-degree resolution (Foley et al., 1996; Kucharik et al., 2000), and HYDRA, a runoff-routing algorithm with 5-minute resolution (Coe, 2000), we have studied how land cover change may affect the hydrology of the Mississippi River Basin. The IBIS model describes physical, physiological, and ecological processes occurring in vegetative canopies and soils. Through forcing from climate data and vegetation and soil properties, IBIS simulates energy, water, and biogeochemical cycles at small time-steps (30-60 minutes). Lenters et al. (2000) have validated the IBIS-modeled water budget over the Mississippi River Basin at several scales and HYDRA-modeled discharge has been compared favorably to United States Geological Survey stream gauge data (Donner et al., 2001). This work extends those studies through use of an improved version of IBIS. The IBIS model has been calibrated for use over the continental United States through an improved phenology routine and the inclusion of corn and soybeans as land cover types. Results from a comparison of a control run of natural vegetation with experimental runs of corn and soybean cover will be shown.

PLANETARY NEBULAE IN FACE-ON SPIRAL GALAXIES. II. PLANETARY NEBULA SPECTROSCOPY

International Nuclear Information System (INIS)

Herrmann, Kimberly A.; Ciardullo, Robin

2009-01-01

As the second step in our investigation of the mass-to-light ratio of spiral disks, we present the results of a spectroscopic survey of planetary nebulae (PNe) in five nearby, low-inclination galaxies: IC 342, M74 (NGC 628), M83 (NGC 5236), M94 (NGC 4736), and M101 (NGC 5457). Using 50 setups of the WIYN/Hydra and Blanco/Hydra spectrographs, and 25 observations with the Hobby-Eberly Telescope's Medium Resolution Spectrograph, we determine the radial velocities of 99, 102, 162, 127, and 48 PNe, respectively, to a precision better than 15 km s -1 . Although the main purpose of this data set is to facilitate dynamical mass measurements throughout the inner and outer disks of large spiral galaxies, our spectroscopy has other uses as well. Here, we co-add these spectra to show that, to first order, the [O III] and Balmer line ratios of PNe vary little over the top ∼1.5 mag of the PN luminosity function. The only obvious spectral change occurs with [N II], which increases in strength as one proceeds down the luminosity function. We also show that typical [O III]-bright planetaries have E(B - V) ∼ 0.2 of circumstellar extinction, and that this value is virtually independent of [O III] luminosity. We discuss the implications this has for understanding the population of PN progenitors.

Fragmentation of the large subunit ribosomal RNA gene in oyster mitochondrial genomes

Directory of Open Access Journals (Sweden)

Milbury Coren A

2010-09-01

Full Text Available Abstract Background Discontinuous genes have been observed in bacteria, archaea, and eukaryotic nuclei, mitochondria and chloroplasts. Gene discontinuity occurs in multiple forms: the two most frequent forms result from introns that are spliced out of the RNA and the resulting exons are spliced together to form a single transcript, and fragmented gene transcripts that are not covalently attached post-transcriptionally. Within the past few years, fragmented ribosomal RNA (rRNA genes have been discovered in bilateral metazoan mitochondria, all within a group of related oysters. Results In this study, we have characterized this fragmentation with comparative analysis and experimentation. We present secondary structures, modeled using comparative sequence analysis of the discontinuous mitochondrial large subunit rRNA genes of the cupped oysters C. virginica, C. gigas, and C. hongkongensis. Comparative structure models for the large subunit rRNA in each of the three oyster species are generally similar to those for other bilateral metazoans. We also used RT-PCR and analyzed ESTs to determine if the two fragmented LSU rRNAs are spliced together. The two segments are transcribed separately, and not spliced together although they still form functional rRNAs and ribosomes. Conclusions Although many examples of discontinuous ribosomal genes have been documented in bacteria and archaea, as well as the nuclei, chloroplasts, and mitochondria of eukaryotes, oysters are some of the first characterized examples of fragmented bilateral animal mitochondrial rRNA genes. The secondary structures of the oyster LSU rRNA fragments have been predicted on the basis of previous comparative metazoan mitochondrial LSU rRNA structure models.

Simulation study on effects of signaling network structure on the developmental increase in complexity

Energy Technology Data Exchange (ETDEWEB)

Keranen, Soile V.E.

2003-04-02

The developmental increase in structural complexity in multicellular life forms depends on local, often non-periodic differences in gene expression. These depend on a network of gene-gene interactions coded within the organismal genome. To better understand how genomic information generates complex expression patterns, I have modeled the pattern forming behavior of small artificial genomes in virtual blastoderm embryos. I varied several basic properties of these genomic signaling networks, such as the number of genes, the distributions of positive (inductive) and negative (repressive) interactions, and the strengths of gene-gene interactions, and analyzed their effects on developmental pattern formation. The results show how even simple genomes can generate complex non-periodic patterns under suitable conditions. They also show how the frequency of complex patterns depended on the numbers and relative arrangements of positive and negative interactions. For example, negative co-regulation of signaling pathway components increased the likelihood of (complex) patterns relative to differential negative regulation of the pathway components. Interestingly, neither quantitative differences either in strengths of signaling interactions nor multiple response thresholds to signal concentration (as in morphogen gradients) were essential for formation of multiple, spatially unique cell types. Thus, with combinatorial code of gene regulation and hierarchical signaling interactions, it is theoretically possible to organize metazoan embryogenesis with just a small fraction of the metazoan genome. Because even small networks can generate complex patterns when they contain a suitable set of connections, evolution of metazoan complexity may have depended more on selection for favourable configurations of signaling interactions than on the increase in numbers of regulatory genes.

Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa.

Science.gov (United States)

Geisen, S; Laros, I; Vizcaíno, A; Bonkowski, M; de Groot, G A

2015-09-01

Protists, the most diverse eukaryotes, are largely considered to be free-living bacterivores, but vast numbers of taxa are known to parasitize plants or animals. High-throughput sequencing (HTS) approaches now commonly replace cultivation-based approaches in studying soil protists, but insights into common biases associated with this method are limited to aquatic taxa and samples. We created a mock community of common free-living soil protists (amoebae, flagellates, ciliates), extracted DNA and amplified it in the presence of metazoan DNA using 454 HTS. We aimed at evaluating whether HTS quantitatively reveals true relative abundances of soil protists and at investigating whether the expected protist community structure is altered by the co-amplification of metazoan-associated protist taxa. Indeed, HTS revealed fundamentally different protist communities from those expected. Ciliate sequences were highly over-represented, while those of most amoebae and flagellates were under-represented or totally absent. These results underpin the biases introduced by HTS that prevent reliable quantitative estimations of free-living protist communities. Furthermore, we detected a wide range of nonadded protist taxa probably introduced along with metazoan DNA, which altered the protist community structure. Among those, 20 taxa most closely resembled parasitic, often pathogenic taxa. Therewith, we provide the first HTS data in support of classical observational studies that showed that potential protist parasites are hosted by soil metazoa. Taken together, profound differences in amplification success between protist taxa and an inevitable co-extraction of protist taxa parasitizing soil metazoa obscure the true diversity of free-living soil protist communities. © 2015 John Wiley & Sons Ltd.

Earth’s oxygen cycle and the evolution of animal life

Science.gov (United States)

Reinhard, Christopher T.; Planavsky, Noah J.; Olson, Stephanie L.; Lyons, Timothy W.; Erwin, Douglas H.

2016-01-01

The emergence and expansion of complex eukaryotic life on Earth is linked at a basic level to the secular evolution of surface oxygen levels. However, the role that planetary redox evolution has played in controlling the timing of metazoan (animal) emergence and diversification, if any, has been intensely debated. Discussion has gravitated toward threshold levels of environmental free oxygen (O2) necessary for early evolving animals to survive under controlled conditions. However, defining such thresholds in practice is not straightforward, and environmental O2 levels can potentially constrain animal life in ways distinct from threshold O2 tolerance. Herein, we quantitatively explore one aspect of the evolutionary coupling between animal life and Earth’s oxygen cycle—the influence of spatial and temporal variability in surface ocean O2 levels on the ecology of early metazoan organisms. Through the application of a series of quantitative biogeochemical models, we find that large spatiotemporal variations in surface ocean O2 levels and pervasive benthic anoxia are expected in a world with much lower atmospheric pO2 than at present, resulting in severe ecological constraints and a challenging evolutionary landscape for early metazoan life. We argue that these effects, when considered in the light of synergistic interactions with other environmental parameters and variable O2 demand throughout an organism’s life history, would have resulted in long-term evolutionary and ecological inhibition of animal life on Earth for much of Middle Proterozoic time (∼1.8–0.8 billion years ago). PMID:27457943

Vertical gradients in species richness and community composition across the twilight zone in the North Pacific Subtropical Gyre.

Science.gov (United States)

Sommer, Stephanie A; Van Woudenberg, Lauren; Lenz, Petra H; Cepeda, Georgina; Goetze, Erica

2017-11-01

Although metazoan animals in the mesopelagic zone play critical roles in deep pelagic food webs and in the attenuation of carbon in midwaters, the diversity of these assemblages is not fully known. A metabarcoding survey of mesozooplankton diversity across the epipelagic, mesopelagic and upper bathypelagic zones (0-1500 m) in the North Pacific Subtropical Gyre revealed far higher estimates of species richness than expected given prior morphology-based studies in the region (4,024 OTUs, 10-fold increase), despite conservative bioinformatic processing. Operational taxonomic unit (OTU) richness of the full assemblage peaked at lower epipelagic-upper mesopelagic depths (100-300 m), with slight shoaling of maximal richness at night due to diel vertical migration, in contrast to expectations of a deep mesopelagic diversity maximum as reported for several plankton groups in early systematic and zoogeographic studies. Four distinct depth-stratified species assemblages were identified, with faunal transitions occurring at 100 m, 300 m and 500 m. Highest diversity occurred in the smallest zooplankton size fractions (0.2-0.5 mm), which had significantly lower % OTUs classified due to poor representation in reference databases, suggesting a deep reservoir of poorly understood diversity in the smallest metazoan animals. A diverse meroplankton assemblage also was detected (350 OTUs), including larvae of both shallow and deep living benthic species. Our results provide some of the first insights into the hidden diversity present in zooplankton assemblages in midwaters, and a molecular reappraisal of vertical gradients in species richness, depth distributions and community composition for the full zooplankton assemblage across the epipelagic, mesopelagic and upper bathypelagic zones. © 2017 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Marine Invertebrate Larvae Associated with Symbiodinium: A Mutualism from the Start?

Directory of Open Access Journals (Sweden)

Miguel Mies

2017-05-01

Full Text Available Symbiodinium are dinoflagellate photosynthetic algae that associate with a diverse array of marine invertebrates, and these relationships are comprehensively documented for adult animal hosts. Conversely, comparatively little is known about the associations during larval development of animal hosts, although four different metazoan phyla (Porifera, Cnidaria, Acoelomorpha, and Mollusca produce larvae associated with Symbiodinium. These phyla represent considerable diversities in larval forms, manner of symbiont acquisition, and requirements on the presence of symbionts for successful metamorphosis. Importantly, the different requirements are conveyed by specific symbiont types that are selected by the host animal larvae. Nevertheless, it remains to be determined whether these associations during larval stages already represent mutualistic interactions, as evident from the relationship of Symbiodinium with their adult animal hosts. For instance, molecular studies suggest that the host larval transcriptome is nearly unaltered after symbiont acquisition. Even so, a symbiosis-specific gene has been identified in Symbiodinium that is expressed in larval host stages, and similar genes are currently being described for host organisms. However, some reports suggest that the metabolic exchange between host larvae and Symbiodinium may not cover the energetic requirements of the host. Here, we review current studies to summarize what is known about the association between metazoan larvae and Symbiodinium. In particular, our aim was to gather in how far the mutualistic relationship present between adult animals hosts and Symbiodinium is already laid out at the time of symbiont acquisition by host larvae. We conclude that the mutualistic relationship between animal hosts and algal symbionts in many cases is not set up during larval development. Furthermore, symbiont identity may influence whether a mutualism can be established during host larval stages.

Marine Invertebrate Larvae Associated with Symbiodinium: A Mutualism from the Start?

KAUST Repository

Mies, Miguel

2017-05-30

Symbiodinium are dinoflagellate photosynthetic algae that associate with a diverse array of marine invertebrates, and these relationships are comprehensively documented for adult animal hosts. Conversely, comparatively little is known about the associations during larval development of animal hosts, although four different metazoan phyla (Porifera, Cnidaria, Acoelomorpha, and Mollusca) produce larvae associated with Symbiodinium. These phyla represent considerable diversities in larval forms, manner of symbiont acquisition, and requirements on the presence of symbionts for successful metamorphosis. Importantly, the different requirements are conveyed by specific symbiont types that are selected by the host animal larvae. Nevertheless, it remains to be determined whether these associations during larval stages already represent mutualistic interactions, as evident from the relationship of Symbiodinium with their adult animal hosts. For instance, molecular studies suggest that the host larval transcriptome is nearly unaltered after symbiont acquisition. Even so, a symbiosis-specific gene has been identified in Symbiodinium that is expressed in larval host stages, and similar genes are currently being described for host organisms. However, some reports suggest that the metabolic exchange between host larvae and Symbiodinium may not cover the energetic requirements of the host. Here, we review current studies to summarize what is known about the association between metazoan larvae and Symbiodinium. In particular, our aim was to gather in how far the mutualistic relationship present between adult animals hosts and Symbiodinium is already laid out at the time of symbiont acquisition by host larvae. We conclude that the mutualistic relationship between animal hosts and algal symbionts in many cases is not set up during larval development. Furthermore, symbiont identity may influence whether a mutualism can be established during host larval stages.

Loss of sexual reproduction and dwarfing in a small metazoan.

Directory of Open Access Journals (Sweden)

Claus-Peter Stelzer

2010-09-01

Full Text Available Asexuality has major theoretical advantages over sexual reproduction, yet newly formed asexual lineages rarely endure. The success, or failure, of such lineages is affected by their mechanism of origin, because it determines their initial genetic makeup and variability. Most previously described mechanisms imply that asexual lineages are randomly frozen subsamples of a sexual population.We found that transitions to obligate parthenogenesis (OP in the rotifer Brachionus calyciflorus, a small freshwater invertebrate which normally reproduces by cyclical parthenogenesis, were controlled by a simple Mendelian inheritance. Pedigree analysis suggested that obligate parthenogens were homozygous for a recessive allele, which caused inability to respond to the chemical signals that normally induce sexual reproduction in this species. Alternative mechanisms, such as ploidy changes, could be ruled out on the basis of flow cytometric measurements and genetic marker analysis. Interestingly, obligate parthenogens were also dwarfs (approximately 50% smaller than cyclical parthenogens, indicating pleiotropy or linkage with genes that strongly affect body size. We found no adverse effects of OP on survival or fecundity.This mechanism of inheritance implies that genes causing OP may evolve within sexual populations and remain undetected in the heterozygous state long before they get frequent enough to actually cause a transition to asexual reproduction. In this process, genetic variation at other loci might become linked to OP genes, leading to non-random associations between asexuality and other phenotypic traits.

Economic costs of protistan and metazoan parasites to global mariculture.

Science.gov (United States)

Shinn, A P; Pratoomyot, J; Bron, J E; Paladini, G; Brooker, E E; Brooker, A J

2015-01-01

Parasites have a major impact on global finfish and shellfish aquaculture, having significant effects on farm production, sustainability and economic viability. Parasite infections and impacts can, according to pathogen and context, be considered to be either unpredictable/sporadic or predictable/regular. Although both types of infection may result in the loss of stock and incur costs associated with the control and management of infection, predictable infections can also lead to costs associated with prophylaxis and related activities. The estimation of the economic cost of a parasite event is frequently complicated by the complex interplay of numerous factors associated with a specific incident, which may range from direct production losses to downstream socio-economic impacts on livelihoods and satellite industries associated with the primary producer. In this study, we examine the world's major marine and brackish water aquaculture production industries and provide estimates of the potential economic costs attributable to a range of key parasite pathogens using 498 specific events for the purposes of illustration and estimation of costs. This study provides a baseline resource for risk assessment and the development of more robust biosecurity practices, which can in turn help mitigate against and/or minimise the potential impacts of parasite-mediated disease in aquaculture.

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

NARCIS (Netherlands)

Abad, P.; Gouzy, J.; Aury, J.M.; Tytgat, T.O.G.; Smant, G.

2008-01-01

Plant-parasitic nematodes are major agricultural pests worldwide and novel approaches to control them are sorely needed. We report the draft genome sequence of the root-knot nematode Meloidogyne incognita, a biotrophic parasite of many crops, including tomato, cotton and coffee. Most of the

A map of directional genetic interactions in a metazoan cell.

Science.gov (United States)

Fischer, Bernd; Sandmann, Thomas; Horn, Thomas; Billmann, Maximilian; Chaudhary, Varun; Huber, Wolfgang; Boutros, Michael

2015-03-06

Gene-gene interactions shape complex phenotypes and modify the effects of mutations during development and disease. The effects of statistical gene-gene interactions on phenotypes have been used to assign genes to functional modules. However, directional, epistatic interactions, which reflect regulatory relationships between genes, have been challenging to map at large-scale. Here, we used combinatorial RNA interference and automated single-cell phenotyping to generate a large genetic interaction map for 21 phenotypic features of Drosophila cells. We devised a method that combines genetic interactions on multiple phenotypes to reveal directional relationships. This network reconstructed the sequence of protein activities in mitosis. Moreover, it revealed that the Ras pathway interacts with the SWI/SNF chromatin-remodelling complex, an interaction that we show is conserved in human cancer cells. Our study presents a powerful approach for reconstructing directional regulatory networks and provides a resource for the interpretation of functional consequences of genetic alterations.

Identifying Strategic Scientific Opportunities

Science.gov (United States)

As NCI's central scientific strategy office, CRS collaborates with the institute's divisions, offices, and centers to identify research opportunities to advance NCI's vision for the future of cancer research.

SOCIODEMOGRAPHIC DATA USED FOR IDENTIFYING ...

Science.gov (United States)

Due to unique social and demographic characteristics, various segments of the population may experience exposures different from those of the general population, which, in many cases, may be greater. When risk assessments do not characterize subsets of the general population, the populations that may experience the greatest risk remain unidentified. When such populations are not identified, the social and demographic data relevant to these populations is not considered when preparing exposure estimates, which can underestimate exposure and risk estimates for at-risk populations. Thus, it is necessary for risk or exposure assessors characterizing a diverse population, to first identify and then enumerate certain groups within the general population who are at risk for greater contaminant exposures. The document entitled Sociodemographic Data Used for Identifying Potentially Highly Exposed Populations (also referred to as the Highly Exposed Populations document), assists assessors in identifying and enumerating potentially highly exposed populations. This document presents data relating to factors which potentially impact an individual or group's exposure to environmental contaminants based on activity patterns (how time is spent), microenvironments (locations where time is spent), and other socio-demographic data such as age, gender, race and economic status. Populations potentially more exposed to various chemicals of concern, relative to the general population

Does interspecies hybridization affect the host specificity of parasites in cyprinid fish?

Czech Academy of Sciences Publication Activity Database

Šimková, A.; Dávidová, M.; Papoušek, Ivo; Vetešník, Lukáš

2013-01-01

Roč. 6, č. 95 (2013), s. 95 ISSN 1756-3305 R&D Projects: GA ČR GAP505/12/0375 Institutional support: RVO:68081766 Keywords : Cyprinid fish * Interspecies hybridization * Metazoan parasites * Monogenea * Host specificity Subject RIV: EG - Zoology Impact factor: 3.251, year: 2013

Next Generation sequencing of the Trichinella murrelli mitochondrial genome allows comprehensive comparison of its divergence from the principal agent of human trichinellosis, Trichinella spiralis

Science.gov (United States)

The mitochondrial genome’s non-recombinant mode of inheritance and relatively rapid rate of evolution has promoted its use as a marker for studying the biogeographic history and evolutionary interrelationships among many metazoan species. A modest portion of the mitochondrial genome has been define...

Zooplankton diversity across three Red Sea reefs using pyrosequencing

KAUST Repository

Pearman, John K.; El-Sherbiny, Mohsen M.; Lanzé n, Anders; Al-Aidaroos, Ali M.; Irigoien, Xabier

2014-01-01

% sequence similarity. A total of 754 and 854 metazoan OTUs were observed in the data set for the 1380F and 1389F primer sets respectively. The phylum Arthropoda dominated both primer sets accounting for ~60% of reads followed by Cnidaria (~20%). Only about

Three-dimensional reconstruction of the musculature of various life cycle stages of the cycliophoran Symbion americanus

DEFF Research Database (Denmark)

Cardoso Neves, Ricardo; Kristensen, Reinhardt Møbjerg; Wanninger, Andreas Wilhelm Georg

2009-01-01

Cycliophora is a very recently described phylum of acoelomate metazoans with a complex life cycle and a phylogenetic position that has been under debate ever since its discovery in 1995. Symbion americanus, which lives attached to the mouthparts of the American lobster, Homarus americanus...

MicroRNA pharmacogenomics

DEFF Research Database (Denmark)

Rukov, Jakob Lewin; Shomron, Noam

2011-01-01

polymorphisms, copy number variations or differences in gene expression levels of drug metabolizing or transporting genes and drug targets. In this review paper, we focus instead on microRNAs (miRNAs): small noncoding RNAs, prevalent in metazoans, that negatively regulate gene expression in many cellular...

Larval Myogenesis in the Articulate Brachiopod Argyrotheca cordata (Risso, 1826)

DEFF Research Database (Denmark)

Altenburger, Andreas; Wanninger, Andreas Wilhelm Georg

2008-01-01

Brachiopoda is a metazoan phylum with a fossil record dating back to the lower Cambrium and comprises over 12,000 extinct and 400 recent species. Despite some recent progress using mainly palaeontological and molecular datasets, the discussion concerning the phylogenetic position of Brachiopoda r...

Exploring microbial diversity of marine sponges by culture-dependent and molecular approaches

NARCIS (Netherlands)

Naim, M.A.

2015-01-01

Summary

Discovery of sponge-grade metazoans dated 650 million years ago proved that sponges have been around since the Precambrian era. Their resilience to ever-changing environmental conditions and their global distribution is one of the features attributed to the symbionts in

Control of endothelial cell tube formation by Notch ligand intracellular domain interactions with activator protein 1 (AP-1)

DEFF Research Database (Denmark)

Forghany, Zary; Robertson, Francesca; Lundby, Alicia

2018-01-01

Notch signaling is a ubiquitous signal transduction pathway found in most if not all metazoan cell types characterized to date. It is indispensable for cell differentiation as well as tissue growth, tissue remodelling and apoptosis. Although the canonical Notch signaling pathway is well character...

NIH Researchers Identify OCD Risk Gene

Science.gov (United States)

... News From NIH NIH Researchers Identify OCD Risk Gene Past Issues / Summer 2006 Table of Contents For ... and Alcoholism (NIAAA) have identified a previously unknown gene variant that doubles an individual's risk for obsessive- ...

RACE-OC Project: Rotation and variability in young stellar associations within 100 pc

OpenAIRE

Messina, S.; Desidera, S.; Turatto, M.; Lanzafame, A. C.; Guinan, E. F.

2010-01-01

Our goal is to determine the rotational and magnetic-related activity properties of stars at different stages of evolution. We have focussed our attention on 6 young loose stellar associations within 100 pc and ages in the range 8-70 Myr: TW Hydrae (~8 Myr), beta Pictoris (~10 Myr), Tucana/Horologium, Columba, Carina (~30 Myr), and AB Doradus (~70 Myr). Additional data on alpha Persei and the Pleiades from the literature is also considered. Rotational periods of stars showing rotational modul...

Distributed Coordinate Descent Method for Learning with Big Data

OpenAIRE

Richtárik, Peter; Takáč, Martin

2013-01-01

In this paper we develop and analyze Hydra: HYbriD cooRdinAte descent method for solving loss minimization problems with big data. We initially partition the coordinates (features) and assign each partition to a different node of a cluster. At every iteration, each node picks a random subset of the coordinates from those it owns, independently from the other computers, and in parallel computes and applies updates to the selected coordinates based on a simple closed-form formula. We give bound...

Distributed Persistent Identifiers System Design

Directory of Open Access Journals (Sweden)

Pavel Golodoniuc

2017-06-01

Full Text Available The need to identify both digital and physical objects is ubiquitous in our society. Past and present persistent identifier (PID systems, of which there is a great variety in terms of technical and social implementation, have evolved with the advent of the Internet, which has allowed for globally unique and globally resolvable identifiers. PID systems have, by in large, catered for identifier uniqueness, integrity, and persistence, regardless of the identifier’s application domain. Trustworthiness of these systems has been measured by the criteria first defined by Bütikofer (2009 and further elaborated by Golodoniuc 'et al'. (2016 and Car 'et al'. (2017. Since many PID systems have been largely conceived and developed by a single organisation they faced challenges for widespread adoption and, most importantly, the ability to survive change of technology. We believe that a cause of PID systems that were once successful fading away is the centralisation of support infrastructure – both organisational and computing and data storage systems. In this paper, we propose a PID system design that implements the pillars of a trustworthy system – ensuring identifiers’ independence of any particular technology or organisation, implementation of core PID system functions, separation from data delivery, and enabling the system to adapt for future change. We propose decentralisation at all levels — persistent identifiers and information objects registration, resolution, and data delivery — using Distributed Hash Tables and traditional peer-to-peer networks with information replication and caching mechanisms, thus eliminating the need for a central PID data store. This will increase overall system fault tolerance thus ensuring its trustworthiness. We also discuss important aspects of the distributed system’s governance, such as the notion of the authoritative source and data integrity

Frizzled7: A Promising Achilles’ Heel for Targeting the Wnt Receptor Complex to Treat Cancer

Science.gov (United States)

Phesse, Toby; Flanagan, Dustin; Vincan, Elizabeth

2016-01-01

Frizzled7 is arguably the most studied member of the Frizzled family, which are the cognate Wnt receptors. Frizzled7 is highly conserved through evolution, from Hydra through to humans, and is expressed in diverse organisms, tissues and human disease contexts. Frizzled receptors can homo- or hetero-polymerise and associate with several co-receptors to transmit Wnt signalling. Notably, Frizzled7 can transmit signalling via multiple Wnt transduction pathways and bind to several different Wnt ligands, Frizzled receptors and co-receptors. These promiscuous binding and functional properties are thought to underlie the pivotal role Frizzled7 plays in embryonic developmental and stem cell function. Recent studies have identified that Frizzled7 is upregulated in diverse human cancers, and promotes proliferation, progression and invasion, and orchestrates cellular transitions that underscore cancer metastasis. Importantly, Frizzled7 is able to regulate Wnt signalling activity even in cancer cells which have mutations to down-stream signal transducers. In this review we discuss the various aspects of Frizzled7 signalling and function, and the implications these have for therapeutic targeting of Frizzled7 in cancer. PMID:27196929

29 CFR 4010.7 - Identifying information.

Science.gov (United States)

2010-07-01

... 29 Labor 9 2010-07-01 2010-07-01 false Identifying information. 4010.7 Section 4010.7 Labor Regulations Relating to Labor (Continued) PENSION BENEFIT GUARANTY CORPORATION CERTAIN REPORTING AND DISCLOSURE REQUIREMENTS ANNUAL FINANCIAL AND ACTUARIAL INFORMATION REPORTING § 4010.7 Identifying information...

Identifying Critical Cross-Cultural School Psychology Competencies.

Science.gov (United States)

Rogers, Margaret R.; Lopez, Emilia C.

2002-01-01

Study sought to identify critical cross-cultural competencies for school psychologists. To identify the competencies, an extensive literature search about cross-cultural school psychology competencies was conducted, as well as a questionnaire to ask expert panelists. The 102 competencies identified cover 14 major domains of professional activities…

Somatic retrotransposition alters the genetic landscape of the human brain

NARCIS (Netherlands)

Baillie, J.K.; Barnett, M.W.; Upton, K.R.; Gerhardt, D.J.; Richmond, T.A.; De Sapio, F.; Brennan, P.; Rizzu, P.; Smith, S.; Fell, M.; Talbot, R.T.; Gustincich, S.; Freeman, T.C.; Mattick, J.S.; Hume, D.A.; Heutink, P.; Carninci, P.; Jeddeloh, J.A.; Faulkner, G.J.

2011-01-01

Retrotransposons are mobile genetic elements that use a germline 'copy-and-paste' mechanism to spread throughout metazoan genomes1. At least 50 per cent of the human genome is derived from retrotransposons, with three active families (L1, Alu and SVA) associated with insertional mutagenesis and

Patterning and shaping the endoderm in vivo and in culture

DEFF Research Database (Denmark)

Kraus, Marine R C; Grapin-Botton, Anne

2012-01-01

The definitive endoderm (DE) was first defined as the innermost germ layer found in all metazoan embryos. During development, it gives rise to a vast array of specialized epithelial cell types lining the respiratory and digestive systems, and contributes to associated organs such as thyroid, thymus...

The complete mitochondrial genome of a stonefly species, Togoperla sp. (Plecoptera: Perlidae).

Science.gov (United States)

Wang, Kai; Wang, Yuyu; Yang, Ding

2016-05-01

The complete mitochondrial (mt) genome of a stonefly species, Togoperla sp. (Plecoptera: Perlidae), was sequenced. The 15,723 bp long genome has the standard metazoan complement of 37 genes and an A+T-rich region, which is the same as the insect ancestral genome arrangement.

Use of Drosophila to study DNA repair

International Nuclear Information System (INIS)

Boyd, J.B.; Harris, P.V.; Sakaguchi, K.

1988-01-01

This paper discusses Drosophila, the premier metazoan organism for analyzing many fundamental features of eukaryotic gene regulation. The authors present adaptations of several approaches for studying DNA repair to an analysis of repair-defective mutants in Drosophila. A current understanding of Drosophila DNA repair is described

Journal of Biosciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

2009-01-05

Jan 5, 2009 ... Ancient metazoan organisms arose from unicellular eukaryotes that had billions of years of genetic evolution behind them. The transcription factor networks present in single-celled ancestors at the origin of the Metazoa (multicellular animals) were already capable of mediating the switching of the ...

UBL5 is essential for pre-mRNA splicing and sister chromatid cohesion in human cells

DEFF Research Database (Denmark)

Oka, Yasuyoshi; Varmark, Hanne; Vitting-Seerup, Kristoffer

2014-01-01

UBL5 is an atypical ubiquitin-like protein, whose function in metazoans remains largely unexplored. We show that UBL5 is required for sister chromatid cohesion maintenance in human cells. UBL5 primarily associates with spliceosomal proteins, and UBL5 depletion decreases pre-mRNA splicing efficien...

Sexual selection in marine plankton

DEFF Research Database (Denmark)

Sichlau, Mie Hylstofte

Copepods are among the most abundant metazoans on the planet and play an important role in the marine food web. Many aspects of their ecology have consequently been studied, including details of their reproductive biology and mating behaviour. Sexual selection, the part of evolution which selects...

Patterning and lifetime of plasma membrane-localized cellulose synthase is dependent on actin organization in Arabidopsis interphase cells

NARCIS (Netherlands)

Sampathkumar, A.; Gutierrez, R.; McFarlane, H.E.; Bringmann, M.; Lindeboom, J.J.; Emons, A.M.C.; Samuels, L.; Ketelaar, T.; Ehrhardt, D.W.; Persson, S.

2013-01-01

The actin and microtubule cytoskeletons regulate cell shape across phyla, from bacteria to metazoans. In organisms with cell walls, the wall acts as a primary constraint of shape, and generation of specific cell shape depends on cytoskeletal organization for wall deposition and/or cell expansion. In

Parameter identifiability of linear dynamical systems

Science.gov (United States)

Glover, K.; Willems, J. C.

1974-01-01

It is assumed that the system matrices of a stationary linear dynamical system were parametrized by a set of unknown parameters. The question considered here is, when can such a set of unknown parameters be identified from the observed data? Conditions for the local identifiability of a parametrization are derived in three situations: (1) when input/output observations are made, (2) when there exists an unknown feedback matrix in the system and (3) when the system is assumed to be driven by white noise and only output observations are made. Also a sufficient condition for global identifiability is derived.

MXLKID: a maximum likelihood parameter identifier

International Nuclear Information System (INIS)

Gavel, D.T.

1980-07-01

MXLKID (MaXimum LiKelihood IDentifier) is a computer program designed to identify unknown parameters in a nonlinear dynamic system. Using noisy measurement data from the system, the maximum likelihood identifier computes a likelihood function (LF). Identification of system parameters is accomplished by maximizing the LF with respect to the parameters. The main body of this report briefly summarizes the maximum likelihood technique and gives instructions and examples for running the MXLKID program. MXLKID is implemented LRLTRAN on the CDC7600 computer at LLNL. A detailed mathematical description of the algorithm is given in the appendices. 24 figures, 6 tables

Rooted triple consensus and anomalous gene trees

Directory of Open Access Journals (Sweden)

Schmidt Heiko A

2008-04-01

Full Text Available Abstract Background Anomalous gene trees (AGTs are gene trees with a topology different from a species tree that are more probable to observe than congruent gene trees. In this paper we propose a rooted triple approach to finding the correct species tree in the presence of AGTs. Results Based on simulated data we show that our method outperforms the extended majority rule consensus strategy, while still resolving the species tree. Applying both methods to a metazoan data set of 216 genes, we tested whether AGTs substantially interfere with the reconstruction of the metazoan phylogeny. Conclusion Evidence of AGTs was not found in this data set, suggesting that erroneously reconstructed gene trees are the most significant challenge in the reconstruction of phylogenetic relationships among species with current data. The new method does however rule out the erroneous reconstruction of deep or poorly resolved splits in the presence of lineage sorting.

β-Catenin-Dependent Wnt Signaling in C. elegans: Teaching an Old Dog a New Trick

Science.gov (United States)

Jackson, Belinda M.; Eisenmann, David M.

2012-01-01

Wnt signaling is an evolutionarily ancient pathway used to regulate many events during metazoan development. Genetic results from Caenorhabditis elegans more than a dozen years ago suggested that Wnt signaling in this nematode worm might be different than in vertebrates and Drosophila: the worm had a small number of Wnts, too many β-catenins, and some Wnt pathway components functioned in an opposite manner than in other species. Work over the ensuing years has clarified that C. elegans does possess a canonical Wnt/β-catenin signaling pathway similar to that in other metazoans, but that the majority of Wnt signaling in this species may proceed via a variant Wnt/β-catenin signaling pathway that uses some new components (mitogen-activated protein kinase signaling enzymes), and in which some conserved pathway components (β-catenin, T-cell factor [TCF]) are used in new and interesting ways. This review summarizes our current understanding of the canonical and novel TCF/β-catenin-dependent signaling pathways in C. elegans. PMID:22745286

From Fossil Parasitoids to Vectors: Insects as Parasites and Hosts.

Science.gov (United States)

Nagler, Christina; Haug, Joachim T

2015-01-01

Within Metazoa, it has been proposed that as many as two-thirds of all species are parasitic. This propensity towards parasitism is also reflected within insects, where several lineages independently evolved a parasitic lifestyle. Parasitic behaviour ranges from parasitic habits in the strict sense, but also includes parasitoid, phoretic or kleptoparasitic behaviour. Numerous insects are also the host for other parasitic insects or metazoans. Insects can also serve as vectors for numerous metazoan, protistan, bacterial and viral diseases. The fossil record can report this behaviour with direct (parasite associated with its host) or indirect evidence (insect with parasitic larva, isolated parasitic insect, pathological changes of host). The high abundance of parasitism in the fossil record of insects can reveal important aspects of parasitic lifestyles in various evolutionary lineages. For a comprehensive view on fossil parasitic insects, we discuss here different aspects, including phylogenetic systematics, functional morphology and a direct comparison of fossil and extant species. Copyright © 2015 Elsevier Ltd. All rights reserved.

Structural Molecular Components of Septate Junctions in Cnidarians Point to the Origin of Epithelial Junctions in Eukaryotes

KAUST Repository

Ganot, P.

2014-09-21

Septate junctions (SJs) insure barrier properties and control paracellular diffusion of solutes across epithelia in invertebrates. However, the origin and evolution of their molecular constituents in Metazoa have not been firmly established. Here, we investigated the genomes of early branching metazoan representatives to reconstruct the phylogeny of the molecular components of SJs. Although Claudins and SJ cytoplasmic adaptor components appeared successively throughout metazoan evolution, the structural components of SJs arose at the time of Placozoa/Cnidaria/Bilateria radiation. We also show that in the scleractinian coral Stylophora pistillata, the structural SJ component Neurexin IV colocalizes with the cortical actin network at the apical border of the cells, at the place of SJs. We propose a model for SJ components in Cnidaria. Moreover, our study reveals an unanticipated diversity of SJ structural component variants in cnidarians. This diversity correlates with gene-specific expression in calcifying and noncalcifying tissues, suggesting specific paracellular pathways across the cell layers of these diploblastic animals.

Intergenerational epigenetic inheritance in reef-building corals

KAUST Repository

Liew, Yi Jin

2018-02-22

The notion that intergenerational or transgenerational inheritance operates solely through genetic means is slowly being eroded: epigenetic mechanisms have been shown to induce heritable changes in gene activity in plants and metazoans. Inheritance of DNA methylation provides a potential pathway for environmentally induced phenotypes to contribute to evolution of species and populations. However, in basal metazoans, it is unknown whether inheritance of CpG methylation patterns occurs across the genome (as in plants) or as rare exceptions (as in mammals). Here, we demonstrate genome-wide intergenerational transmission of CpG methylation patterns from parents to sperm and larvae in a reef-building coral. We also show variation in hypermethylated genes in corals from distinct environments, indicative of responses to variations in temperature and salinity. These findings support a role of DNA methylation in the transgenerational inheritance of traits in corals, which may extend to enhancing their capacity to adapt to climate change.

Intergenerational epigenetic inheritance in reef-building corals

KAUST Repository

Liew, Yi Jin; Howells, Emily J.; Wang, Xin; Michell, Craig; Burt, John A.; Idaghdour, Youssef; Aranda, Manuel

2018-01-01

The notion that intergenerational or transgenerational inheritance operates solely through genetic means is slowly being eroded: epigenetic mechanisms have been shown to induce heritable changes in gene activity in plants and metazoans. Inheritance of DNA methylation provides a potential pathway for environmentally induced phenotypes to contribute to evolution of species and populations. However, in basal metazoans, it is unknown whether inheritance of CpG methylation patterns occurs across the genome (as in plants) or as rare exceptions (as in mammals). Here, we demonstrate genome-wide intergenerational transmission of CpG methylation patterns from parents to sperm and larvae in a reef-building coral. We also show variation in hypermethylated genes in corals from distinct environments, indicative of responses to variations in temperature and salinity. These findings support a role of DNA methylation in the transgenerational inheritance of traits in corals, which may extend to enhancing their capacity to adapt to climate change.

Apoptotic markers in protozoan parasites

Directory of Open Access Journals (Sweden)

Fasel Nicolas

2010-11-01

Full Text Available Abstract The execution of the apoptotic death program in metazoans is characterized by a sequence of morphological and biochemical changes that include cell shrinkage, presentation of phosphatidylserine at the cell surface, mitochondrial alterations, chromatin condensation, nuclear fragmentation, membrane blebbing and the formation of apoptotic bodies. Methodologies for measuring apoptosis are based on these markers. Except for membrane blebbing and formation of apoptotic bodies, all other events have been observed in most protozoan parasites undergoing cell death. However, while techniques exist to detect these markers, they are often optimised for metazoan cells and therefore may not pick up subtle differences between the events occurring in unicellular organisms and multi-cellular organisms. In this review we discuss the markers most frequently used to analyze cell death in protozoan parasites, paying special attention to changes in cell morphology, mitochondrial activity, chromatin structure and plasma membrane structure/permeability. Regarding classical regulators/executors of apoptosis, we have reviewed the present knowledge of caspase-like and nuclease activities.

Anaerobic animals from an ancient, anoxic ecological niche

Directory of Open Access Journals (Sweden)

Martin William

2010-04-01

Full Text Available Abstract Tiny marine animals that complete their life cycle in the total absence of light and oxygen are reported by Roberto Danovaro and colleagues in this issue of BMC Biology. These fascinating animals are new members of the phylum Loricifera and possess mitochondria that in electron micrographs look very much like hydrogenosomes, the H2-producing mitochondria found among several unicellular eukaryotic lineages. The discovery of metazoan life in a permanently anoxic and sulphidic environment provides a glimpse of what a good part of Earth's past ecology might have been like in 'Canfield oceans', before the rise of deep marine oxygen levels and the appearance of the first large animals in the fossil record roughly 550-600 million years ago. The findings underscore the evolutionary significance of anaerobic deep sea environments and the anaerobic lifestyle among mitochondrion-bearing cells. They also testify that a fuller understanding of eukaryotic and metazoan evolution will come from the study of modern anoxic and hypoxic habitats.

Hydrogel-Tissue Chemistry: Principles and Applications.

Science.gov (United States)

Gradinaru, Viviana; Treweek, Jennifer; Overton, Kristin; Deisseroth, Karl

2018-05-20

Over the past five years, a rapidly developing experimental approach has enabled high-resolution and high-content information retrieval from intact multicellular animal (metazoan) systems. New chemical and physical forms are created in the hydrogel-tissue chemistry process, and the retention and retrieval of crucial phenotypic information regarding constituent cells and molecules (and their joint interrelationships) are thereby enabled. For example, rich data sets defining both single-cell-resolution gene expression and single-cell-resolution activity during behavior can now be collected while still preserving information on three-dimensional positioning and/or brain-wide wiring of those very same neurons-even within vertebrate brains. This new approach and its variants, as applied to neuroscience, are beginning to illuminate the fundamental cellular and chemical representations of sensation, cognition, and action. More generally, reimagining metazoans as metareactants-or positionally defined three-dimensional graphs of constituent chemicals made available for ongoing functionalization, transformation, and readout-is stimulating innovation across biology and medicine.

Identifying Information Focuses in Listening Comprehension

Science.gov (United States)

Zhang, Hong-yan

2011-01-01

The study explains the process of learners' listening comprehension within Halliday's information theory in functional grammar, including the skills of identifying focuses while listening in college English teaching. Identifying information focuses in listening is proved to improve the students' communicative listening ability by the means of a…

EZID: Long term identifiers made easy (Invited)

Science.gov (United States)

Starr, J.

2013-12-01

Scholarly research is producing ever increasing amounts of digital research data, and this data should be managed throughout the research life cycle both as part of good scientific practice, but also to comply with funder mandates, such as the 2013 OSTP Public Access Memo (http://www.whitehouse.gov/sites/default/files/microsites/ostp/ostp_public_access_memo_2013.pdf). By assigning unique and persistent identifiers to data objects, data managers can gain control and flexibility over what can be a daunting task. This is due to the fact that the objects can be moved to new locations without disruption to links, as long as the identifier target is maintained. EZID is a tool that makes assigning and maintaining unique, persistent identifiers easy. It was designed and built by California Digital Library (CDL) and has both a user interface and a RESTful API. EZID currently offers services for two globally unique, persistent identifier schemes: Digital Object Identifiers (DOIs) and Archival Resource Keys (ARKs). DOIs are identifiers originating from the publishing world and are in widespread use for journal articles. CDL is able to offer DOIs because of being a founding member of DataCite (http://www.datacite.org/), an international consortium established to provide easier access to scientific research data on the Internet. ARKs are identifiers originating from the library, archive and museum community. Like DOIs, they become persistent when the objects and identifier forwarding information is maintained. DOIs and ARKs have a key role in data management and, therefore, in data management plans. DOIs are the recommended identifier for use in data citation, and ARKs provide the maximum flexibility needed for data documentation and management throughout the early phases of a project. The two identifier schemes are able to be used together, and EZID is made to work with both. EZID clients, coming from education, research, government, and the private sector, are utilizing the

Football refereeing: Identifying innovative methods

Directory of Open Access Journals (Sweden)

Reza MohammadKazemi

2014-08-01

Full Text Available The aim of the present study is to identify the potentials innovation in football industry. Data were collected from 10 national and international referees, assistant referees and referees’ supervisors in Iran. In this study, technological innovations are identified that assist better refereeing performances. The analysis revealed a significant relationship between using new technologies and referees ‘performance. The results indicate that elite referees, assistant referees and supervisors agreed to use new technological innovations during the game. According to their comments, this kind of technology causes the referees’ performance development.

Ability of Slovakian Pupils to Identify Birds

Science.gov (United States)

Prokop, Pavol; Rodak, Rastislav

2009-01-01

A pupil's ability to identify common organisms is necessary for acquiring further knowledge of biology. We investigated how pupils were able to identify 25 bird species following their song, growth habits, or both features presented simultaneously. Just about 19% of birds were successfully identified by song, about 39% by growth habit, and 45% of…

The giant cold-water coral mound as a nested microbial/metazoan system: physical, chemical, biological and geological picture (ESF EuroDiversity MiCROSYSTEMS)

Science.gov (United States)

Henriet, J. P.; Microsystems Team

2009-04-01

The MiCROSYSTEMS project under the ESF EUROCORES EuroDiversity scheme is a holistic and multi-scale approach in studying microbial diversity and functionality in a nested microbial/metazoan system, which thrives in deep waters: the giant cold-water coral mound. Studies on prolific cold-water coral sites have been carried out from the canyons of the Bay of Biscay to the fjords of the Norwegian margin, while the Pen Duick carbonate mound province off Morocco developed into a joint natural lab for studying in particular the impact of biogeochemical and microbial processes on modern sedimentary diagenesis within the reef sediments, in complement to the studies on I0DP Exp. 307 cores (Challenger Mound, off Ireland). Major outcomes of this research can be summarized as follows. • IODP Exp. 307 on Challenger Mound had revealed a significant prokaryotic community both within and beneath the carbonate mound. MiCROSYSTEMS unveils a remarkable degree of compartmentalization in such community from the seawater, the coral skeleton surface and mucus to the reef sediments. The occurrence of such multiple and distinct microbial compartments associated with cold-water coral ecosystems promotes opportunities for microbial diversity in the deep ocean. • New cases of co-habitation of cold-water corals and giant deep-water oysters were discovered in the Bay of Biscay, which add a new facet of macrofaunal diversity to cold-water coral reef systems. • The discovery of giant, ancient coral graveyards on the Moroccan mounds not only fuels the debate about natural versus anthropogenic mass extinction, but these open frameworks simultaneously invite for the study of bio-erosion and early diagenesis, in particular organo-mineralization, and of the possible role and significance of these thick, solid rubble patches in 3D mound-building and consolidation. • The assessment of the carbonate budget of a modern cold-water coral mound (Challenger Mound) reveals that only 33 to 40 wt % of

IDENTIFIABILITY VERSUS HETEROGENEITY IN GROUNDWATER MODELING SYSTEMS

Directory of Open Access Journals (Sweden)

A M BENALI

2003-06-01

Full Text Available Review of history matching of reservoirs parameters in groundwater flow raises the problem of identifiability of aquifer systems. Lack of identifiability means that there exists parameters to which the heads are insensitive. From the guidelines of the study of the homogeneous case, we inspect the identifiability of the distributed transmissivity field of heterogeneous groundwater aquifers. These are derived from multiple realizations of a random function Y = log T  whose probability distribution function is normal. We follow the identifiability of the autocorrelated block transmissivities through the measure of the sensitivity of the local derivatives DTh = (∂hi  ∕ ∂Tj computed for each sample of a population N (0; σY, αY. Results obtained from an analysis of Monte Carlo type suggest that the more a system is heterogeneous, the less it is identifiable.

Phylogenetic relationships within major nematode clades based on multiple molecular markers

NARCIS (Netherlands)

Rybarczyk-Mydlowska, K.

2013-01-01

Nematodes are probably the most abundant Metazoans on our planet. They are present in densities of millions of individuals per square meter in soil and sediments. However, these inconspicuous animals are hardly known to the general public as most individuals are colorless and smaller than 1 mm.

Identifiability of PBPK Models with Applications to ...

Science.gov (United States)

Any statistical model should be identifiable in order for estimates and tests using it to be meaningful. We consider statistical analysis of physiologically-based pharmacokinetic (PBPK) models in which parameters cannot be estimated precisely from available data, and discuss different types of identifiability that occur in PBPK models and give reasons why they occur. We particularly focus on how the mathematical structure of a PBPK model and lack of appropriate data can lead to statistical models in which it is impossible to estimate at least some parameters precisely. Methods are reviewed which can determine whether a purely linear PBPK model is globally identifiable. We propose a theorem which determines when identifiability at a set of finite and specific values of the mathematical PBPK model (global discrete identifiability) implies identifiability of the statistical model. However, we are unable to establish conditions that imply global discrete identifiability, and conclude that the only safe approach to analysis of PBPK models involves Bayesian analysis with truncated priors. Finally, computational issues regarding posterior simulations of PBPK models are discussed. The methodology is very general and can be applied to numerous PBPK models which can be expressed as linear time-invariant systems. A real data set of a PBPK model for exposure to dimethyl arsinic acid (DMA(V)) is presented to illustrate the proposed methodology. We consider statistical analy

Contribuciones al conocimiento del género Phragmotheca cuatr. 1 (Bombacaceae-Quararibeae).

OpenAIRE

Fernández Alonso, José Luis

1996-01-01

Se comenta la posicidn sistemática de Phragmotheca en relacidn con la tribu Quararibeae y se incluye una clave para la separación de los géneros de bombacáceas de hoja entera o unifoliolada del norte de Suramdrica. Se revisa la utilidad'de algunos caracteres en la separación de las especies y se presenta una clave diagnbstica. Se describen e ilustran 4 nuevas especies y dos taxones infraespeclficos P. rubriflora, P. lemniscata, P. hydra, P. siderosa subsp. megacarpa, F! amazonl...

Towards Self-managed Pervasive Middleware using OWL/SWRL ontologies

DEFF Research Database (Denmark)

Zhang, Weishan; Hansen, Klaus Marius

2008-01-01

Self-management for pervasive middleware is important to realize the Ambient Intelligence vision. In this paper, we present an OWL/SWRL context ontologies based self-management approach for pervasive middleware where OWL ontology is used as means for context modeling. The context ontologies....../SWRL context ontologies based self-management approach with the self-diagnosis in Hydra middleware, using device state machine and other dynamic context information, for example web service calls. The evaluations in terms of extensibility, performance and scalability show that this approach is effective...

Identifying high-risk medication

DEFF Research Database (Denmark)

Sædder, Eva; Brock, Birgitte; Nielsen, Lars Peter

2014-01-01

salicylic acid, and beta-blockers; 30 drugs or drug classes caused 82 % of all serious MEs. The top ten drugs involved in fatal events accounted for 73 % of all drugs identified. CONCLUSION: Increasing focus on seven drugs/drug classes can potentially reduce hospitalizations, extended hospitalizations...