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Sample records for echinoderm phosphorylated matrix

  1. A strategy to quantitate global phosphorylation of bone matrix proteins.

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    Sroga, Grażyna E; Vashishth, Deepak

    2016-04-15

    Current studies of protein phosphorylation focus primarily on the importance of specific phosphoproteins and their landscapes of phosphorylation in the regulation of different cellular functions. However, global changes in phosphorylation of extracellular matrix phosphoproteins measured "in bulk" are equally important. For example, correct global phosphorylation of different bone matrix proteins is critical to healthy tissue biomineralization. To study changes of bone matrix global phosphorylation, we developed a strategy that combines a procedure for in vitro phosphorylation/dephosphorylation of fully mineralized bone in addition to quantitation of the global phosphorylation levels of bone matrix proteins. For the first time, we show that it is possible to enzymatically phosphorylate/dephosphorylate fully mineralized bone originating from either cadaveric human donors or laboratory animals (mice). Using our strategy, we detected the difference in the global phosphorylation levels of matrix proteins isolated from wild-type and osteopontin knockout mice. We also observed that the global phosphorylation levels of matrix proteins isolated from human cortical bone were lower than those isolated from trabecular bone. The developed strategy has the potential to open new avenues for studies on the global phosphorylation of bone matrix proteins and their role in biomineralization as well for other tissues/cells and protein-based materials.

  2. Paleogenomics of echinoderms.

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    Bottjer, David J; Davidson, Eric H; Peterson, Kevin J; Cameron, R Andrew

    2006-11-10

    Paleogenomics propels the meaning of genomic studies back through hundreds of millions of years of deep time. Now that the genome of the echinoid Strongylocentrotus purpuratus is sequenced, the operation of its genes can be interpreted in light of the well-understood echinoderm fossil record. Characters that first appear in Early Cambrian forms are still characteristic of echinoderms today. Key genes for one of these characters, the biomineralized tissue stereom, can be identified in the S. purpuratus genome and are likely to be the same genes that were involved with stereom formation in the earliest echinoderms some 520 million years ago.

  3. Antimicrobial peptides in Echinoderms

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    C Li

    2010-05-01

    Full Text Available Antimicrobial peptides (AMPs are important immune effector molecules for invertebrates, including echinoderms, which lack a vertebrate-type adaptive immune system. Here we summarize the knowledge of such peptides in echinoderms. Strongylocins are a novel family of cysteine-rich AMPs, recently identified in the sea urchins, Strongylocentrotus droebachiensis and S. purpuratus. Although these molecules present diverse amino acid sequences, they share an identical cysteine arrangement pattern, dissimilar to other known AMPs. A family of heterodimeric AMPs, named centrocins, are also present in S. droebachiensis. Lysozymes and fragments of larger proteins, such as beta-thymocins, actin, histone 2A and filamin A have also been shown to display antimicrobial activities in echinoderms. Future studies on AMPs should be aimed in revealing how echinoderms use these AMPs in the immune response against microbial pathogens.

  4. Antimicrobial Peptides in Echinoderms

    OpenAIRE

    Li, C; Haug, T; K Stensvåg

    2010-01-01

    Antimicrobial peptides (AMPs) are important immune effector molecules for invertebrates, including echinoderms, which lack a vertebrate-type adaptive immune system. Here we summarize the knowledge of such peptides in echinoderms. Strongylocins are a novel family of cysteine-rich AMPs, recently identified in the sea urchins, Strongylocentrotus droebachiensis and S. purpuratus. Although these molecules present diverse amino acid sequences, they share an identical cysteine arrangement pattern, d...

  5. Echinoderms have bilateral tendencies.

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    Ji, Chengcheng; Wu, Liang; Zhao, Wenchan; Wang, Sishuo; Lv, Jianhao

    2012-01-01

    Echinoderms take many forms of symmetry. Pentameral symmetry is the major form and the other forms are derived from it. However, the ancestors of echinoderms, which originated from Cambrian period, were believed to be bilaterians. Echinoderm larvae are bilateral during their early development. During embryonic development of starfish and sea urchins, the position and the developmental sequence of each arm are fixed, implying an auxological anterior/posterior axis. Starfish also possess the Hox gene cluster, which controls symmetrical development. Overall, echinoderms are thought to have a bilateral developmental mechanism and process. In this article, we focused on adult starfish behaviors to corroborate its bilateral tendency. We weighed their central disk and each arm to measure the position of the center of gravity. We then studied their turning-over behavior, crawling behavior and fleeing behavior statistically to obtain the center of frequency of each behavior. By joining the center of gravity and each center of frequency, we obtained three behavioral symmetric planes. These behavioral bilateral tendencies might be related to the A/P axis during the embryonic development of the starfish. It is very likely that the adult starfish is, to some extent, bilaterian because it displays some bilateral propensity and has a definite behavioral symmetric plane. The remainder of bilateral symmetry may have benefited echinoderms during their evolution from the Cambrian period to the present.

  6. Phylogeny of Echinoderm Hemoglobins.

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    Ana B Christensen

    Full Text Available Recent genomic information has revealed that neuroglobin and cytoglobin are the two principal lineages of vertebrate hemoglobins, with the latter encompassing the familiar myoglobin and α-globin/β-globin tetramer hemoglobin, and several minor groups. In contrast, very little is known about hemoglobins in echinoderms, a phylum of exclusively marine organisms closely related to vertebrates, beyond the presence of coelomic hemoglobins in sea cucumbers and brittle stars. We identified about 50 hemoglobins in sea urchin, starfish and sea cucumber genomes and transcriptomes, and used Bayesian inference to carry out a molecular phylogenetic analysis of their relationship to vertebrate sequences, specifically, to assess the hypothesis that the neuroglobin and cytoglobin lineages are also present in echinoderms.The genome of the sea urchin Strongylocentrotus purpuratus encodes several hemoglobins, including a unique chimeric 14-domain globin, 2 androglobin isoforms and a unique single androglobin domain protein. Other strongylocentrotid genomes appear to have similar repertoires of globin genes. We carried out molecular phylogenetic analyses of 52 hemoglobins identified in sea urchin, brittle star and sea cucumber genomes and transcriptomes, using different multiple sequence alignment methods coupled with Bayesian and maximum likelihood approaches. The results demonstrate that there are two major globin lineages in echinoderms, which are related to the vertebrate neuroglobin and cytoglobin lineages. Furthermore, the brittle star and sea cucumber coelomic hemoglobins appear to have evolved independently from the cytoglobin lineage, similar to the evolution of erythroid oxygen binding globins in cyclostomes and vertebrates.The presence of echinoderm globins related to the vertebrate neuroglobin and cytoglobin lineages suggests that the split between neuroglobins and cytoglobins occurred in the deuterostome ancestor shared by echinoderms and vertebrates.

  7. The negative impact of α-ketoglutarate dehydrogenase complex deficiency on matrix substrate-level phosphorylation.

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    Kiss, Gergely; Konrad, Csaba; Doczi, Judit; Starkov, Anatoly A; Kawamata, Hibiki; Manfredi, Giovanni; Zhang, Steven F; Gibson, Gary E; Beal, M Flint; Adam-Vizi, Vera; Chinopoulos, Christos

    2013-06-01

    A decline in α-ketoglutarate dehydrogenase complex (KGDHC) activity has been associated with neurodegeneration. Provision of succinyl-CoA by KGDHC is essential for generation of matrix ATP (or GTP) by substrate-level phosphorylation catalyzed by succinyl-CoA ligase. Here, we demonstrate ATP consumption in respiration-impaired isolated and in situ neuronal somal mitochondria from transgenic mice with a deficiency of either dihydrolipoyl succinyltransferase (DLST) or dihydrolipoyl dehydrogenase (DLD) that exhibit a 20-48% decrease in KGDHC activity. Import of ATP into the mitochondrial matrix of transgenic mice was attributed to a shift in the reversal potential of the adenine nucleotide translocase toward more negative values due to diminished matrix substrate-level phosphorylation, which causes the translocase to reverse prematurely. Immunoreactivity of all three subunits of succinyl-CoA ligase and maximal enzymatic activity were unaffected in transgenic mice as compared to wild-type littermates. Therefore, decreased matrix substrate-level phosphorylation was due to diminished provision of succinyl-CoA. These results were corroborated further by the finding that mitochondria from wild-type mice respiring on substrates supporting substrate-level phosphorylation exhibited ~30% higher ADP-ATP exchange rates compared to those obtained from DLST(+/-) or DLD(+/-) littermates. We propose that KGDHC-associated pathologies are a consequence of the inability of respiration-impaired mitochondria to rely on "in-house" mitochondrial ATP reserves.

  8. Fertilization in echinoderms.

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    Santella, Luigia; Vasilev, Filip; Chun, Jong T

    2012-08-31

    For more than 150 years, echinoderm eggs have served as overly favored experimental model systems in which to study fertilization. Sea urchin and starfish belong to the same phylum and thus share many similarities in their fertilization patterns. However, several subtle but fundamental differences do exist in the fertilization of sea urchin and starfish, reflecting their phylogenetic bifurcation approximately 500 million years ago. In this article we review some of the seminal and recent findings that feature similarities and differences in sea urchin and starfish at fertilization.

  9. Molecular approach to echinoderm regeneration.

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    Thorndyke, M C; Chen, W C; Beesley, P W; Patruno, M

    2001-12-15

    Until very recently echinoderm regeneration research and indeed echinoderm research in general has suffered because of the lack of critical mass. In terms of molecular studies of regeneration, echinoderms in particular have lagged behind other groups in this respect. This is in sharp contrast to the major advances achieved with molecular and genetic techniques in the study of embryonic development in echinoderms. The aim of our studies has been to identify genes involved in the process of regeneration and in particular neural regeneration in different echinoderm species. Our survey included the asteroid Asterias rubens and provided evidence for the expression of Hox gene homologues in regenerating radial nerve cords. Present evidence suggests: 1) ArHox1 expression is maintained in intact radial nerve cord and may be upregulated during regeneration. 2) ArHox1 expression may contribute to the dedifferentiation and/or cell proliferation process during epimorphic regeneration. From the crinoid Antedon bifida, we have been successful in cloning a fragment of a BMP2/4 homologue (AnBMP2/4) and analysing its expression during arm regeneration. Here, we discuss the importance of this family of growth factors in several regulatory spheres, including maintaining the identity of pluripotent blastemal cells or as a classic skeletal morphogenic regulator. There is clearly substantial scope for future echinoderm research in the area of molecular biology and certain aspects are discussed in this review.

  10. Doxycycline inhibits leukemic cell migration via inhibition of matrix metalloproteinases and phosphorylation of focal adhesion kinase.

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    Wang, Chunhuai; Xiang, Ru; Zhang, Xiangzhong; Chen, Yunxian

    2015-09-01

    Doxycycline, a tetracycline-based antibiotic, has been reported to attenuate melanoma cell migration through inhibiting the focal adhesion kinase (FAK) signaling pathway. However, it remains to be elucidated whether doxycycline exerts this effect on leukemia cell migration. The present study aimed to examine the role of doxycycline in leukemia cell migration. The invasion capacities of the human leukemia cell lines KG1a (acute myelogenous leukemia) and K562 (chronic myelogenous leukemia) were evaluated using Matrigel® matrix‑coated Transwell® chamber assays; leukemic cell lines treated with doxycycline (1 µg/ml) or anti‑β1‑integrin antibodies were added to the upper chamber, while untreated cells were included as controls. Reverse transcription quantitative polymerase chain reaction was performed in order to further understand the influence of doxycycline treatment on the expression of FAK and gelatinases in the KG1a and K562 leukemic cell lines. In addition, FAK protein expression and phosphorylation were determined using western blot analysis in order to investigate the mechanism by which doxycycline inhibited leukemic cell migration. The results revealed that doxycycline treatment significantly attenuated the migration of KG1a and K562 cells, which was demonstrated to be associated with inhibition of the expression and phosphorylation of FAK. In addition, doxycycline treatment inhibited matrix metalloproteinase (MMP)‑2 and MMP‑9 expression. Furthermore, incubation with blocking anti‑β1‑integrin antibodies had an analogous inhibitory effect on leukemic cell migration to that of doxycycline. In conclusion, the results of the present study suggested that doxycycline attenuated leukemic cell migration through inhibiting the FAK signaling pathway. Therefore, doxycycline may have potential for use as a novel strategy for the treatment of leukemia.

  11. [The echinoderms (Echinodermata) from El Salvador].

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    Enrique Barraza, José; Roberto Hasbún, Carlos

    2005-12-01

    A list of echinoderms from El Salvador (tropical eastern Pacific) is presented. The results were obtained from field surveys (between the years 2000 and 2004), the scarce literature sources, and Internet information. A total of 37 species and six genera are reported. The most abundant echinoderms in rocky shores were: Phataria unifascialis, Echinometra vanbrunti, Holothuria kefersteini, as well as Astropecten armatus in soft bottoms.

  12. The inorganic constituents of echinoderms

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    Clarke, F.W.; Wheeler, W.C.

    1915-01-01

    In a recent paper on the composition of crinoid skeletons we showed that crinoids contain large quantities of magnesia, and that its proportion varies with the temperature of the water in which the creatures live. This result was so novel and surprising that it seemed desirable to examine other echinoderms and to ascertain whether they showed the same characteristics and regularity. A number of sea urchins and starfishes were therefore studied, their inorganic constituents being analyzed in the same manner as those of the crinoids

  13. Phylotranscriptomic analysis uncovers a wealth of tissue inhibitor of metalloproteinases variants in echinoderms.

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    Clouse, Ronald M; Linchangco, Gregorio V; Kerr, Alexander M; Reid, Robert W; Janies, Daniel A

    2015-12-01

    Tissue inhibitors of metalloproteinases (TIMPs) help regulate the extracellular matrix (ECM) in animals, mostly by inhibiting matrix metalloproteinases (MMPs). They are important activators of mutable collagenous tissue (MCT), which have been extensively studied in echinoderms, and the four TIMP copies in humans have been studied for their role in cancer. To understand the evolution of TIMPs, we combined 405 TIMPs from an echinoderm transcriptome dataset built from 41 specimens representing all five classes of echinoderms with variants from protostomes and chordates. We used multiple sequence alignment with various stringencies of alignment quality to cull highly divergent sequences and then conducted phylogenetic analyses using both nucleotide and amino acid sequences. Phylogenetic hypotheses consistently recovered TIMPs as diversifying in the ancestral deuterostome and these early lineages continuing to diversify in echinoderms. The four vertebrate TIMPs diversified from a single copy in the ancestral chordate, all other copies being lost. Consistent with greater MCT needs owing to body wall liquefaction, evisceration, autotomy and reproduction by fission, holothuroids had significantly more TIMPs and higher read depths per contig. Ten cysteine residues, an HPQ binding site and several other residues were conserved in at least 70% of all TIMPs. The conservation of binding sites and the placement of echinoderm TIMPs involved in MCT modification suggest that ECM regulation remains the primary function of TIMP genes, although within this role there are a large number of specialized copies.

  14. Are echinoderms of interest to biotechnology?

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    Petzelt, C

    2005-01-01

    The huge potential of echinoderms as a so far fairly untapped source of bioactive molecules is described. Examples are presented that show the usefulness of echinoderm-derived molecules for therapeutic application in selected fields of cancer research, in the control of bacterial growth as substances with new antibiotic properties, and finally in the context of technical applications such as antifouling substances. The molecules described here are but the mere beginning of a commercial exploitation of echinoderms and may incite a deeper involvement of biotechnology-oriented research in this material.

  15. [Echinoderms (Echinodermata) of the Mexican Caribbean].

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    Laguarda-Figueras, Alfredo; Solis-Marín, Francisco A; Durán-González, Alicia; Ahearn, Cynthia Gust; Buitrón Sánchez, Blanca Estela; Torres-Vega, Juan

    2005-12-01

    A systematic list of the echinoderms of the Mexican Caribbean based on museum specimens of the Colección Nacional de Equinodermos, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México and the National Museum of Natural History, Smithsonian Institution, Washington, D.C. is presented. This list reveals an important echinoderm biodiversity in the Mexican Caribbean, where five of the six echinoderm classes are represented. A total of 178 echinoderm species is recorded, distributed in 113 genera, 51 families and 22 orders. 30 new records for the Mexican Caribbean are presents: Crínoidea (three), Asteroidea (two), Ophiuroidea (eleven), Echinoidea (one), Holothuroidea (thirteen).

  16. Arrays in rays: terminal addition in echinoderms and its correlation with gene expression.

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    Mooi, Rich; David, Bruno; Wray, Gregory A

    2005-01-01

    The echinoderms are deuterostomes that superimpose radial symmetry upon bilateral larval morphology. Consequently, they are not the first animals that come to mind when the concepts of segmentation and terminal addition are being discussed. However, it has long been recognized that echinoderms have serial elements along their radii formed in accordance with the ocular plate rule (OPR). The OPR is a special case of terminal growth, forming elements of the ambulacra that define the rays in echinoderms. New elements are added at the terminus of the ray, which may or may not be marked by a calcified element called the terminal plate (the "ocular" of sea urchins). The OPR operates in every echinoderm, from the occasionally bizarre fossils of the Cambrian to the most familiar extant taxa. Using the OPR and other criteria of recognition, echinoderm body wall can be divided into two main regions: extraxial components are associated with the somatocoels, axial components (formed in accordance with the OPR) with the hydrocoel. We compare patterns of development in axial regions of echinoderms with those found in the anterior-posterior axes of the earliest echinoderms as well as other invertebrates. Although axial and extraxial skeletons appear to be composed of the same biomineral matrix, the genes involved in patterning these two skeletal components are likely distinct. During development of the axial skeleton, for instance, the genes engrailed and orthodenticle are expressed in spatial and temporal patterns consistent with the OPR. Other genes such as distal-less seem to demarcate early ontogenetic boundaries between the axial rudiment and the extraxial larval body. There is a complex and pervasive reorganization of gene expression domains to produce the highly divergent morphologies seen in the Echinodermata. We integrate morphological and genetic information, particularly with respect to the origins of radial symmetry in the rudiment, and the concomitant development of

  17. Neural control of muscle relaxation in echinoderms.

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    Elphick, M R; Melarange, R

    2001-03-01

    Smooth muscle relaxation in vertebrates is regulated by a variety of neuronal signalling molecules, including neuropeptides and nitric oxide (NO). The physiology of muscle relaxation in echinoderms is of particular interest because these animals are evolutionarily more closely related to the vertebrates than to the majority of invertebrate phyla. However, whilst in vertebrates there is a clear structural and functional distinction between visceral smooth muscle and skeletal striated muscle, this does not apply to echinoderms, in which the majority of muscles, whether associated with the body wall skeleton and its appendages or with visceral organs, are made up of non-striated fibres. The mechanisms by which the nervous system controls muscle relaxation in echinoderms were, until recently, unknown. Using the cardiac stomach of the starfish Asterias rubens as a model, it has been established that the NO-cGMP signalling pathway mediates relaxation. NO also causes relaxation of sea urchin tube feet, and NO may therefore function as a 'universal' muscle relaxant in echinoderms. The first neuropeptides to be identified in echinoderms were two related peptides isolated from Asterias rubens known as SALMFamide-1 (S1) and SALMFamide-2 (S2). Both S1 and S2 cause relaxation of the starfish cardiac stomach, but with S2 being approximately ten times more potent than S1. SALMFamide neuropeptides have also been isolated from sea cucumbers, in which they cause relaxation of both gut and body wall muscle. Therefore, like NO, SALMFamides may also function as 'universal' muscle relaxants in echinoderms. The mechanisms by which SALMFamides cause relaxation of echinoderm muscle are not known, but several candidate signal transduction pathways are discussed here. The SALMFamides do not, however, appear to act by promoting release of NO, and muscle relaxation in echinoderms is therefore probably regulated by at least two neuronal signalling systems acting in parallel. Recently, other

  18. Matrix density alters zyxin phosphorylation, which limits peripheral process formation and extension in endothelial cells invading 3D collagen matrices.

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    Abbey, Colette A; Bayless, Kayla J

    2014-09-01

    This study was designed to determine the optimal conditions required for known pro-angiogenic stimuli to elicit successful endothelial sprouting responses. We used an established, quantifiable model of endothelial cell (EC) sprout initiation where ECs were tested for invasion in low (1 mg/mL) and high density (5 mg/mL) 3D collagen matrices. Sphingosine 1-phosphate (S1P) alone, or S1P combined with stromal derived factor-1α (SDF) and phorbol ester (TPA), elicited robust sprouting responses. The ability of these factors to stimulate sprouting was more effective in higher density collagen matrices. S1P stimulation resulted in a significant increase in invasion distance, and with the exception of treatment groups containing phorbol ester, invasion distance was longer in 1mg/mL compared to 5mg/mL collagen matrices. Closer examination of cell morphology revealed that increasing matrix density and supplementing with SDF and TPA enhanced the formation of multicellular structures more closely resembling capillaries. TPA enhanced the frequency and size of lumen formation and correlated with a robust increase in phosphorylation of p42/p44 Erk kinase, while S1P and SDF did not. Also, a higher number of significantly longer extended processes formed in 5mg/mL compared to 1mg/mL collagen matrices. Because collagen matrices at higher density have been reported to be stiffer, we tested for changes in the mechanosensitive protein, zyxin. Interestingly, zyxin phosphorylation levels inversely correlated with matrix density, while levels of total zyxin did not change significantly. Immunofluorescence and localization studies revealed that total zyxin was distributed evenly throughout invading structures, while phosphorylated zyxin was slightly more intense in extended peripheral processes. Silencing zyxin expression increased extended process length and number of processes, while increasing zyxin levels decreased extended process length. Altogether these data indicate that ECs

  19. Lower Miocene echinoderms of Jamaica, West Indies

    NARCIS (Netherlands)

    Donovan, S.K.; Portell, R.W.; Veltkamp, C.J.

    2005-01-01

    Despite being diverse globally, Miocene echinoids are poorly known from Jamaica. Moderately diverse echinoids and other echinoderms have been identified mainly from fragmentary specimens collected from chalks and mass-flow deposits of the Lower Miocene Montpelier Formation, White Limestone Group, ne

  20. Antimicrobial peptides in echinoderm host defense.

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    Li, Chun; Blencke, Hans-Matti; Haug, Tor; Stensvåg, Klara

    2015-03-01

    Antimicrobial peptides (AMPs) are important effector molecules in innate immunity. Here we briefly summarize characteristic traits of AMPs and their mechanisms of antimicrobial activity. Echinoderms live in a microbe-rich marine environment and are known to express a wide range of AMPs. We address two novel AMP families from coelomocytes of sea urchins: cysteine-rich AMPs (strongylocins) and heterodimeric AMPs (centrocins). These peptide families have conserved preprosequences, are present in both adults and pluteus stage larvae, have potent antimicrobial properties, and therefore appear to be important innate immune effectors. Strongylocins have a unique cysteine pattern compared to other cysteine-rich peptides, which suggests a novel AMP folding pattern. Centrocins and SdStrongylocin 2 contain brominated tryptophan residues in their native form. This review also includes AMPs isolated from other echinoderms, such as holothuroidins, fragments of beta-thymosin, and fragments of lectin (CEL-III). Echinoderm AMPs are crucial molecules for the understanding of echinoderm immunity, and their potent antimicrobial activity makes them potential precursors of novel drug leads.

  1. MATRIX METALLOPROTEINS (MMP)-MEDIATED PHOSPHORYLATION OF THE EPIDERMAL GROWTH FACTOR RECEPTOR (EGFR) IN HUMAN AIRWAY EPITHELIAL CELLS (HAEC) EXPOSED TO ZINC (ZN)

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    Matrix Metalloproteinase (MMP)-Mediated Phosphorylation of The Epidermal Growth Factor Receptor (EGFR) in Human Airway Epithelial Cells (HAEC) Exposed to Zinc (Zn)Weidong Wu, James M. Samet, Robert Silbajoris, Lisa A. Dailey, Lee M. Graves, and Philip A. BrombergCenter fo...

  2. Evolution of mitochondrial gene orders in echinoderms.

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    Perseke, Marleen; Fritzsch, Guido; Ramsch, Kai; Bernt, Matthias; Merkle, Daniel; Middendorf, Martin; Bernhard, Detlef; Stadler, Peter F; Schlegel, Martin

    2008-05-01

    A comprehensive analysis of the mitochondrial gene orders of all previously published and two novel Antedon mediterranea (Crinoidea) and Ophiura albida (Ophiuroidea) complete echinoderm mitochondrial genomes shows that all major types of rearrangement operations are necessary to explain the evolution of mitochondrial genomes. In addition to protein coding genes we include all tRNA genes as well as the control region in our analysis. Surprisingly, 7 of the 16 genomes published in the GenBank database contain misannotations, mostly unannotated tRNAs and/or mistakes in the orientation of tRNAs, which we have corrected here. Although the gene orders of mt genomes appear very different, only 8 events are necessary to explain the evolutionary history of echinoderms with the exception of the ophiuroids. Only two of these rearrangements are inversions, while we identify three tandem-duplication-random-loss events and three transpositions.

  3. Plated Cambrian bilaterians reveal the earliest stages of echinoderm evolution.

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    Samuel Zamora

    Full Text Available Echinoderms are unique in being pentaradiate, having diverged from the ancestral bilaterian body plan more radically than any other animal phylum. This transformation arises during ontogeny, as echinoderm larvae are initially bilateral, then pass through an asymmetric phase, before giving rise to the pentaradiate adult. Many fossil echinoderms are radial and a few are asymmetric, but until now none have been described that show the original bilaterian stage in echinoderm evolution. Here we report new fossils from the early middle Cambrian of southern Europe that are the first echinoderms with a fully bilaterian body plan as adults. Morphologically they are intermediate between two of the most basal classes, the Ctenocystoidea and Cincta. This provides a root for all echinoderms and confirms that the earliest members were deposit feeders not suspension feeders.

  4. C-opsin expressing photoreceptors in echinoderms.

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    Ullrich-Lüter, Esther M; D'Aniello, Salvatore; Arnone, Maria I

    2013-07-01

    Today's progress in molecular analysis and, in particular, the increased availability of genome sequences have enabled us to investigate photoreceptor cells (PRCs) in organisms that were formerly inaccessible to experimental manipulation. Our studies of marine non-chordate deuterostomes thus aim to bridge a gap of knowledge regarding the evolution of deuterostome PRCs prior to the emergence of vertebrates' eyes. In this contribution, we will show evidence for expression of a c-opsin photopigment, which, according to our phylogenetic analysis, is closely related to an assemblage of chordate visual c-opsins. An antibody raised against sea urchins' c-opsin protein (Sp-Opsin1) recognizes epitopes in a variety of tissues of different echinoderms. While in sea urchins this c-opsin is expressed in locomotory and buccal tube feet, spines, pedicellaria, and epidermis, in brittlestars and starfish we found the immuno-reaction to be located exclusively in cells within the animals' spines. Structural characteristics of these c-opsin+ PRC types include the close vicinity/connection to nerve strands and a, so far unexplored, conspicuous association with the animals' calcite skeleton, which previously has been hypothesized to play a role in echinoderm photobiology. These features are discussed within the context of the evolution of photoreceptors in echinoderms and in deuterostomes generally.

  5. Primary structure and phosphorylation of dentin matrix protein 1 (DMP1) and dentin phosphophoryn (DPP) uniquely determine their role in biomineralization.

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    Deshpande, Atul Suresh; Fang, Ping-An; Zhang, Xiaoyuan; Jayaraman, Thottala; Sfeir, Charles; Beniash, Elia

    2011-08-08

    The SIBLING (small integrin-binding ligand N-linked glycoproteins) family is the major group of noncollagenous proteins in bone and dentin. These extremely acidic and highly phosphorylated extracellular proteins play critical roles in the formation of collagenous mineralized tissues. Whereas the lack of individual SIBLINGs causes significant mineralization defects in vivo, none of them led to a complete cessation of mineralization suggesting that these proteins have overlapping functions. To assess whether different SIBLINGs regulate biomineralization in a similar manner and how phosphorylation impacts their activity, we studied the effects of two SIBLINGs, dentin matrix protein 1 (DMP1) and dentin phosphophoryn (DPP), on mineral morphology and organization in vitro. Our results demonstrate distinct differences in the effects of these proteins on mineralization. We show that phosphorylation has a profound effect on the regulation of mineralization by both proteins. Specifically, both phosphorylated proteins facilitated organized mineralization of collagen fibrils and phosphorylated DMP1-induced formation of organized mineral bundles in the absence of collagen. In summary, these results indicate that the primary structure and phosphorylation uniquely determine functions of individual SIBLINGs in regulation of mineral morphology and organization.

  6. Life history evolution and comparative developmental biology of echinoderms.

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    Hart, Michael W

    2002-01-01

    Evolutionary biologists studying life history variation have used echinoderms in experimental, laboratory, and field studies of life history evolution. This focus on echinoderms grew originally from the tradition of comparative embryology, in which echinoderms were central. The tools for obtaining and manipulating echinoderm gametes and larvae were taken directly from comparative embryological research. In addition, the comparative embryologists employed a diverse array of echinoderms, not a few model species, and this diversity has led to a broad understanding of the development, function, and evolution of echinoderm larvae. As a result, this branch of life history evolution has deep roots in comparative developmental biology of echinoderms. Here two main aspects of this relationship are reviewed. The first is a broad range of studies of fertilization biology, dispersal, population genetics, functional morphology, and asexual reproduction in which developmental biologists might take a keen interest because of the historical origins of this research in echinoderm comparative embryology. The second is a similarly broad variety of topics in life history research in which evolutionary biologists require techniques or data from developmental biology in order to make progress on understanding patterns of life history variation among echinoderm species and higher taxa. Both sets of topics provide opportunities for interaction and collaboration.

  7. Exploring Canadian Echinoderm Diversity through DNA Barcodes

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    2016-01-01

    DNA barcoding has proven an effective tool for species identification in varied groups of marine invertebrates including crustaceans, molluscs, polychaetes and echinoderms. In this study, we further validate its utility by analyzing almost half of the 300 species of Echinodermata known from Canadian waters. COI sequences from 999 specimens were assigned to 145 BINs. In most cases, species discrimination was straightforward due to the large difference (25-fold) between mean intra- (0.48%) and inter- (12.0%) specific divergence. Six species were flagged for further taxonomic investigation because specimens assigned to them fell into two or three discrete sequence clusters. The potential influence of larval dispersal capacity and glacial events on patterns of genetic diversity is discussed for 19 trans-oceanic species. Although additional research is needed to clarify biogeographic patterns and resolve taxonomic questions, this study represents an important step in the assembly of a DNA barcode library for all Canadian echinoderms, a valuable resource for future biosurveillance programs. PMID:27870868

  8. Regeneration in Echinoderms: repair, regrowth, cloning

    Directory of Open Access Journals (Sweden)

    MD Candia Carnevali

    2006-06-01

    Full Text Available Regenerative potential is expressed to a maximum extent in echinoderms. It is a commonphenomenon in all the classes, extensively employed to reconstruct external appendages and internalorgans often subjected to amputation, self-induced or traumatic, rapidly followed by completesuccessful re-growth of the lost parts. Regeneration has been studied in adult individuals as well as inlarvae. In armed echinoderms, regeneration of arms is obviously frequent: in many cases, thedetached body fragments can undergo phenomena of partial or total regeneration independently of thedonor animal, and, in a few cases (asteroids, the individual autotomised arms can even regenerate toproduce new complete adults, offering superb examples of cloning strategies. In the species examinedso far most results throw light on aspects related to wound healing, growth, morphogenesis anddifferentiation, even though in most cases many crucial questions remain unanswered. The presentpaper provides an overview of the current understanding of the phenomenon and covers the mainbiological aspects of regeneration giving an idea of the “state of the art” across the phylum in terms ofexperimental approaches and representative models.

  9. [Echinoderms from Marino Ballena National Park, Pacific, Costa Rica].

    Science.gov (United States)

    Alvarado, Juan José; Fernández, Cindy

    2005-12-01

    A total of 25 species of echinoderms (four asteroids, six ophiuroids, five echinoids and ten holothurians) were recorded at Marino Ballena National Park, using 25 m2 quadrants, parallel to the coast, at seven sites. The ophiuroids were the most abundant group with 581 individuals and the asteroids the less abundant (48 individuals). Echinoderms densities were low, with the exception of the ophiuroids. Diversity, density and the number of groups were higher where sedimentation was lower. We suggest that sedimentation is having a negative effect on the diversity of echinoderms and on the development of the coral reefs in this park.

  10. Biodiversity of Echinoderms at Kuta Bay, West Nusa Tenggara

    Directory of Open Access Journals (Sweden)

    Eddy Yusron

    2009-04-01

    Full Text Available Observation on echinoderms diversity was carriedout at coastal waters of Kuta bay in the Nusa Tenggara Barat, Nopember 2005. A total of 21 species of echinoderms,consist of 4 species Holothuroidea, 7 species Echinoidea, 5 species Asteroidea and 5 species Ophiuroidea have beenfound in the Kuta of Nusa Tenggara Barat. The Echinoidea were relatively common in the sea gras zone. On the basisof population density, Echinoidea was the dominant group and relatively highest in the individual density. In generalthe number of species of echinoderm fauna is smaller than in the Sekotong Lombok Barat Bay.

  11. mTOR mediates human trophoblast invasion through regulation of matrix-remodeling enzymes and is associated with serine phosphorylation of STAT3

    Energy Technology Data Exchange (ETDEWEB)

    Busch, Susann [Placenta-Lab, Department of Obstetrics, Friedrich-Schiller-University Jena, Bachstrasse 18, 07740 Jena (Germany); Renaud, Stephen J. [Department of Anatomy and Cell Biology, Queen' s University, Kingston, Ontario, Canada K7L3N6 (Canada); Schleussner, Ekkehard [Placenta-Lab, Department of Obstetrics, Friedrich-Schiller-University Jena, Bachstrasse 18, 07740 Jena (Germany); Graham, Charles H. [Department of Anatomy and Cell Biology, Queen' s University, Kingston, Ontario, Canada K7L3N6 (Canada); Markert, Udo R., E-mail: markert@med.uni-jena.de [Placenta-Lab, Department of Obstetrics, Friedrich-Schiller-University Jena, Bachstrasse 18, 07740 Jena (Germany)

    2009-06-10

    The intracellular signaling molecule mammalian target of rapamycin (mTOR) is essential for cell growth and proliferation. It is involved in mouse embryogenesis, murine trophoblast outgrowth and linked to tumor cell invasiveness. In order to assess the role of mTOR in human trophoblast invasion we analyzed the in vitro invasiveness of HTR-8/SVneo immortalized first-trimester trophoblast cells in conjunction with enzyme secretion upon mTOR inhibition and knockdown of mTOR protein expression. Additionally, we also tested the capability of mTOR to trigger signal transducer and activator of transcription (STAT)-3 by its phosphorylation status. Rapamycin inhibited mTOR kinase activity as demonstrated with a lower phosphorylation level of the mTOR substrate p70 S6 kinase (S6K). With the use of rapamycin and siRNA-mediated mTOR knockdown we could show that cell proliferation, invasion and secretion of matrix-metalloproteinases (MMP)-2 and -9, urokinase-like plasminogen activator (uPA) and its major physiological uPA inhibitor (PAI)-1 were inhibited. While tyrosine phosphorylation of STAT3 was unaffected by mTOR inhibition and knockdown, serine phosphorylation was diminished. We conclude that mTOR signaling is one major mechanism in a tightly regulated network of intracellular signal pathways including the JAK/STAT system to regulate invasion in human trophoblast cells by secretion of enzymes that remodel the extra-cellular matrix (ECM) such as MMP-2, -9, uPA and PAI-1. Dysregulation of mTOR may contribute to pregnancy-related pathologies caused through impaired trophoblast invasion.

  12. Casein kinase II protein kinase is bound to lamina-matrix and phosphorylates lamin-like protein in isolated pea nuclei

    Science.gov (United States)

    Li, H.; Roux, S. J.

    1992-01-01

    A casein kinase II (CK II)-like protein kinase was identified and partially isolated from a purified envelope-matrix fraction of pea (Pisum sativum L.) nuclei. When [gamma-32P]ATP was directly added to the envelope-matrix preparation, the three most heavily labeled protein bands had molecular masses near 71, 48, and 46 kDa. Protein kinases were removed from the preparation by sequential extraction with Triton X-100, EGTA, 0.3 M NaCl, and a pH 10.5 buffer, but an active kinase still remained bound to the remaining lamina-matrix fraction after these treatments. This kinase had properties resembling CK II kinases previously characterized from animal and plant sources: it preferred casein as an artificial substrate, could use GTP as efficiently as ATP as the phosphoryl donor, was stimulated by spermine, was calcium independent, and had a catalytic subunit of 36 kDa. Some animal and plant CK II kinases have regulatory subunits near 29 kDa, and a lamina-matrix-bound protein of this molecular mass was recognized on immunoblot by anti-Drosophila CK II polyclonal antibodies. Also found associated with the envelope-matrix fraction of pea nuclei were p34cdc2-like and Ca(2+)-dependent protein kinases, but their properties could not account for the protein kinase activity bound to the lamina. The 71-kDa substrate of the CK II-like kinase was lamin A-like, both in its molecular mass and in its cross-reactivity with anti-intermediate filament antibodies. Lamin phosphorylation is considered a crucial early step in the entry of cells into mitosis, so lamina-bound CK II kinases may be important control points for cellular proliferation.

  13. Deformation and fracture of echinoderm collagen networks

    CERN Document Server

    Ovaska, Markus; Miksic, Amandine; Sugni, Michela; Di Benedetto, Cristiano; Ferrario, Cinzia; Leggio, Livio; Guidetti, Luca; Alava, Mikko J; La Porta, Caterina A M; Zapperi, Stefano

    2016-01-01

    Collagen networks provide the main structural component of most tissues and represent an important ingredient for bio-mimetic materials for bio-medical applications. Here we study the mechanical properties of stiff collagen networks derived from three different echinoderms and show that they exhibit non-linear stiffening followed by brittle fracture. The disordered nature of the network leads to strong sample-to-sample fluctuations in elasticity and fracture strength. We perform numerical simulations of a three dimensional model for the deformation of a cross-linked elastic fibril network which is able to reproduce the macroscopic features of the experimental results and provide insights into the internal mechanics of stiff collagen networks. Our numerical model provides an avenue for the design of collagen membranes with tunable mechanical properties.

  14. Calcium pathway machinery at fertilization in echinoderms.

    Science.gov (United States)

    Ramos, Isabela; Wessel, Gary M

    2013-01-01

    Calcium signaling in cells directs diverse physiological processes. The calcium waves triggered by fertilization is a highly conserved calcium signaling event essential for egg activation, and has been documented in every egg tested. This activity is one of the few highly conserved events of egg activation through the course of evolution. Echinoderm eggs, as well as many other cell types, have three main intracellular Ca(2+) mobilizing messengers - IP3, cADPR and NAADP. Both cADPR and NAADP were identified as Ca(2+) mobilizing messengers using the sea urchin egg homogenate, and this experimental system, along with the intact urchin and starfish oocyte/egg, continues to be a vital tool for investigating the mechanism of action of calcium signals. While many of the major regulatory steps of the IP3 pathway are well resolved, both cADPR and NAADP remain understudied in terms of our understanding of the fundamental process of egg activation at fertilization. Recently, NAADP has been shown to trigger Ca(2+) release from acidic vesicles, separately from the ER, and a new class of calcium channels, the two-pore channels (TPCs), was identified as the likely targets for this messenger. Moreover, it was found that both cADPR and NAADP can be synthesized by the same family of enzymes, the ADP-rybosyl cyclases (ARCs). In this context of increasing amount of information, the potential coupling and functional roles of different messengers, intracellular stores and channels in the formation of the fertilization calcium wave in echinoderms will be critically evaluated.

  15. A hexamer origin of the echinoderms' five rays.

    Science.gov (United States)

    de Lussanet, Marc H E

    2011-01-01

    Of the major deuterostome groups, the echinoderms with their multiple forms and complex development are arguably the most mysterious. Although larval echinoderms are bilaterally symmetric, the adult body seems to abandon the larval body plan and to develop independently a new structure with different symmetries. The prevalent pentamer structure, the asymmetry of Lovén's rule and the variable location of the periproct and madrepore present enormous difficulties in homologizing structures across the major clades, despite the excellent fossil record. This irregularity in body forms seems to place echinoderms outside the other deuterostomes. Here I propose that the predominant five-ray structure is derived from a hexamer structure that is grounded directly in the structure of the bilaterally symmetric larva. This hypothesis implies that the adult echinoderm body can be derived directly from the larval bilateral symmetry and thus firmly ranks even the adult echinoderms among the bilaterians. In order to test the hypothesis rigorously, a model is developed in which one ray is missing between rays IV-V (Lovén's schema) or rays C-D (Carpenter's schema). The model is used to make predictions, which are tested and verified for the process of metamorphosis and for the morphology of recent and fossil forms. The theory provides fundamental insight into the M-plane and the Ubisch', Lovén's, and Carpenter's planes and generalizes them for all echinoderms. The theory also makes robust predictions about the evolution of the pentamer structure and its developmental basis.

  16. Environmental Induction of Polyembryony in Echinoid Echinoderms.

    Science.gov (United States)

    Allen, Jonathan D; Armstrong, Anne Frances; Ziegler, Shelby L

    2015-12-01

    Polyembryony, or the production of multiple offspring from a single zygote, is a widespread phenomenon in the animal kingdom. Various types of polyembryony have been described in arthropods, bryozoans, chordates, cnidarians, echinoderms, and platyhelminthes. We describe the induction of polyembryony in embryos of the sand dollar Echinarachnius parma and the pencil urchin Eucidaris tribuloides in response to elevated temperature and reduced salinity. Data on the environmental variation in temperature and salinity that normally occurs during the spawning season, combined with the range of laboratory conditions over which polyembryony was induced, suggest that polyembryony may occur frequently in these species under natural conditions. We tested an additional two species of echinoids for similar responses, but found little evidence for polyembryony in the green urchin Strongylocentrotus droebachiensis or the variegated urchin Lytechinus variegatus, suggesting that polyembryony is not a universal response of echinoids to fluctuations in temperature and salinity. The unexpected developmental changes that we observed in response to present-day fluctuations in temperature and salinity suggest that ongoing and future environmental shifts may drive substantial changes in marine invertebrate developmental patterns, and that these changes will be different across taxa.

  17. Basic fibroblast growth factor induces matrix metalloproteinase-13 via ERK MAP kinase-altered phosphorylation and sumoylation of Elk-1 in human adult articular chondrocytes

    Directory of Open Access Journals (Sweden)

    Hee-Jeong Im

    2009-10-01

    Full Text Available Hee-Jeong Im,1–4 Andrew D Sharrocks,5 Xia Lin,6 Dongyao Yan,1 Jaesung Kim,1 Andre J van Wijnen,7 Robert A Hipskind81Departments of Biochemistry, 2Internal Medicine, 3Section of Rheumatology, Orthopedic Surgery, 4Rush University Medical Center, and Department of Bioengineering; University of Illinois at Chicago, IL USA; 5Faculty of Life Sciences, University of Manchester, Oxford Rd, Manchester, UK; 6Michael D DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas, USA; 7Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA, USA; 8Institute De Genetique Moleculaire de Montpellier, FranceAbstract: Degradation of the extracellular matrix (ECM by matrix metalloproteinases (MMPs and release of basic fibroblast growth factor (bFGF are principal aspects of the pathology of osteoarthritis (OA. ECM disruption leads to bFGF release, which activates the extracellular signal-regulated kinase/mitogen-activated protein kinase (ERK/MAPK pathway and its downstream target the Ets-like transcription factor Elk-1. Previously we demonstrated that the bFGF-ERK-Elk-1 signaling axis is responsible for the potent induction of MMP-13 in human primary articular chondrocytes. Here we report that, in addition to phosphorylation of Elk-1, dynamic posttranslational modification of Elk-1 by small ubiquitin-related modifier (SUMO serves as an important mechanism through which MMP-13 gene expression is regulated. We show that bFGF activates Elk-1 mainly through the ERK pathway and that increased phosphorylation of Elk-1 is accompanied by decreased conjugation of SUMO to Elk-1. Reporter gene assays reveal that phosphorylation renders Elk-1 competent for induction of MMP-13 gene transcription, while sumoylation has the opposite effect. Furthermore, we demonstrate that the SUMO-conjugase Ubc9 acts as a key mediator for Elk-1 sumoylation. Taken together, our results suggest that sumoylation antagonizes the phosphorylation

  18. Historical aspects of meetings, publication series, and digital resources dedicated to echinoderms

    Directory of Open Access Journals (Sweden)

    Alexander Ziegler

    2014-03-01

    Full Text Available Half a century after the first scientific meeting dedicated to marine spiny-skinned animals (Deuterostomia: Echinodermata was held in Washington, DC, we take this opportunity to provide information on a number of historical aspects related to the echinoderm scientific community. Apart from shedding light on the historical origins of modern echinoderm conferences, the present contribution presents photographs taken during the first meeting of echinoderm researchers in 1963 as well as during the first installments of the International Echinoderm Conference and the European Conference on Echinoderms. Furthermore, we provide background information on publication series dedicated solely to the Echinodermata as well as descriptions of selected digital resources that focus on echinoderms. Finally, we present a number of echinoderm conference logos and flyers in addition to selected information about specific echinoderm meetings.

  19. Ultraviolet radiation and echinoderms: past, present and future perspectives.

    Science.gov (United States)

    Lamare, Miles; Burritt, David; Lister, Kathryn

    2011-01-01

    There is general consensus that solar ultraviolet radiation (UVR) negatively impacts many marine species. Echinoderms are ubiquitous within the marine environment, with members of the phyla often long-lived and numerically dominant within the benthic macrofauna, consequently the impact of UVR on the population dynamics of these organisms will influence marine communities and ecosystems. Research to date has shown that exposure of echinoderms to solar UVR can, affect reproduction and development, change behaviour, cause numerous biochemical and physiological changes and potentially cause increased mutation rates, by causing DNA damage. There is also considerable evidence that echinoderms utilise several different mechanisms to protect themselves against excessive UVR and subsequent UVR-induced damage. However, these protective mechanisms may pose conflicting selection pressures on echinoderms, as UVR is an additional stressor in oceans subjected to anthropogenic-induced climate change. This review summarises our knowledge of the effects of UVR on the Echinodermata. We outline the research conducted to date, highlight key studies on UVR that have utilised echinoderms and look to the future of UVR research in a rapidly changing ocean.

  20. Echinoderms: their culture and bioactive compounds.

    Science.gov (United States)

    Kelly, M S

    2005-01-01

    Of the five extant classes of echinoderms, it is the sea urchins (Echinoidea) and the sea cucumbers (Holothuroidea) that are both commercially fished and heavily overexploited. In sea urchins, it is the gonad of both males and females, normally referred to as'roe', that is a sought-after food. In the sea cucumber, the principal product is the boiled and dried body-wall or 'bêche-de-mer' for which there is an increasing demand. Many sea urchin and sea cucumber fisheries still have no management system or restrictions in place, and for those that do, the prognosis for catches to continue even at a reduced level is poor. Cultivation of these species increasingly becomes a necessity, both for stock enhancement programs and as a means to meet market demand. Sea urchin culture has been practised on a large scale in Japan for many decades, and effective methods for the culture and reseeding of species in these waters have been long established. Juvenile urchins are produced in their millions in state-sponsored hatcheries, for release to managed areas of seafloor. Outside of Japan, sea urchin cultivation is still a fairly recent practice, less than 10 years old, and largely still at a research level, although a range of species are now being produced in a variety of different culture systems. It is essential that the culture systems are adapted to be species-specific and meet with local environmental constraints. Sea cucumber cultivation originated in Japan in the 1930s and is now well established there and in China. Methods for mass cultivation of the tropical Holothuria scabra are now well established and practised in India, Australia, Indonesia, the Maldives and the Solomon Islands, with the focus of the research effort for both temperate and tropical species being centred on the production of juveniles in hatcheries for the restoration and enhancement of wild stocks. Like many other marine organisms, echinoderms have been, and continue to be, examined as a source of

  1. Cambrian stalked echinoderms show unexpected plasticity of arm construction.

    Science.gov (United States)

    Zamora, S; Smith, A B

    2012-01-22

    Feeding arms carrying coelomic extensions of the theca are thought to be unique to crinoids among stemmed echinoderms. However, a new two-armed echinoderm from the earliest Middle Cambrian of Spain displays a highly unexpected morphology. X-ray microtomographic analysis of its arms shows they are polyplated in their proximal part with a dorsal series of uniserial elements enclosing a large coelomic lumen. Distally, the arm transforms into the more standard biserial structure of a blastozoan brachiole. Phylogenetic analysis demonstrates that this taxon lies basal to rhombiferans as sister-group to pleurocystitid and glyptocystitid blastozoans, drawing those clades deep into the Cambrian. We demonstrate that Cambrian echinoderms show surprising variability in the way their appendages are constructed, and that the appendages of at least some blastozoans arose as direct outgrowths of the body in much the same way as the arms of crinoids.

  2. Microlens arrays in the complex visual system of Cretaceous echinoderms.

    Science.gov (United States)

    Gorzelak, Przemysław; Salamon, Mariusz A; Lach, Rafał; Loba, Michał; Ferré, Bruno

    2014-04-01

    It has long been assumed that photosensitivity in echinoderms is mainly related to diffuse photoreception mediated by photosensitive regions embedded within the dermis. Recent studies, however, have shown that some extant echinoderms may also display modified ossicles with microlenses acting as sophisticated photosensory organs. Thanks to their remarkable properties, these calcitic microlenses serve as an inspiration for scientists across various disciplines among which bio-inspired engineering. However, the evolutionary origins of these microlenses remain obscure. Here we provide microstructural evidence showing that analogous spherical calcitic lenses had been acquired in some brittle stars and starfish of Poland by the Late Cretaceous (Campanian, ~79 Ma). Specimens from Poland described here had a highly developed visual system similar to that of modern forms. We suggest that such an optimization of echinoderm skeletons for both mechanical and optical purposes reflects escalation-related adaptation to increased predation pressure during the so-called Mesozoic Marine Revolution.

  3. [Echinoderms (Echinodermata) from the Gulf of California, Mexico].

    Science.gov (United States)

    Solís-Marín, Francisco A; Laguarda-Figueras, Alfredo; Durán-González, Alicia; Ahearn, Cynthia Gust; Torres Vega, Juan

    2005-12-01

    A systematic list of the echinoderms of the Gulf of California, based on museum specimens of the Colección Nacional de Equinodermos, Instituto de Ciencias del Mar y Limnologia, Universidad Nacional Autónoma de México and the National Museum of Natural History, Smithsonian Institution, Washington, D.C. is presented. A total of 193 echinoderm species is recorded, distributed in 108 genera, 51 families and 19 orders. 12 new records for the Gulf of California are presented: Asteroidea (four), Ophiuroidea (three) and Holothuroidea (five).

  4. PROPOSAL OF SANITARY MANAGEMENT OF EDIBLE ECHINODERMS IN SARDINIA

    Directory of Open Access Journals (Sweden)

    G. Terrosu

    2011-01-01

    Full Text Available Sea urchin (Paracentrotus lividus is an edible echinoderm very common in the Mediterranean sea. In the Sardinian gastronomic tradition it represents a product very used in some periods of the year, but in practice the sanitary controls by the competent authorities are very difficult. The Reg. (EC n. 853/2004 provides that, as regards as the control on production, echinoderms are assimilable to live bivalve molluscs, with the exception of the provisions on purification. In this work a proposal for the sanitary management of the phases of gathering, transport and selling of the sea urchins has been studied.

  5. Functional evolution of Ets in echinoderms with focus on the evolution of echinoderm larval skeletons.

    Science.gov (United States)

    Koga, Hiroyuki; Matsubara, Mioko; Fujitani, Haruka; Miyamoto, Norio; Komatsu, Miéko; Kiyomoto, Masato; Akasaka, Koji; Wada, Hiroshi

    2010-09-01

    Convergent evolution of echinoderm pluteus larva was examined from the standpoint of functional evolution of a transcription factor Ets1/2. In sea urchins, Ets1/2 plays a central role in the differentiation of larval skeletogenic mesenchyme cells. In addition, Ets1/2 is suggested to be involved in adult skeletogenesis. Conversely, in starfish, although no skeletogenic cells differentiate during larval development, Ets1/2 is also expressed in the larval mesoderm. Here, we confirmed that the starfish Ets1/2 is indispensable for the differentiation of the larval mesoderm. This result led us to assume that, in the common ancestors of echinoderms, Ets1/2 activates the transcription of distinct gene sets, one for the differentiation of the larval mesoderm and the other for the development of the adult skeleton. Thus, the acquisition of the larval skeleton involved target switching of Ets1/2. Specifically, in the sea urchin lineage, Ets1/2 activated a downstream target gene set for skeletogenesis during larval development in addition to a mesoderm target set. We examined whether this heterochronic activation of the skeletogenic target set was achieved by the molecular evolution of the Ets1/2 transcription factor itself. We tested whether starfish Ets1/2 induced skeletogenesis when injected into sea urchin eggs. We found that, in addition to ectopic induction of mesenchyme cells, starfish Ets1/2 can activate some parts of the skeletogenic pathway in these mesenchyme cells. Thus, we suggest that the nature of the transcription factor Ets1/2 did not change, but rather that some unidentified co-factor(s) for Ets1/2 may distinguish between targets for the larval mesoderm and for skeletogenesis. Identification of the co-factor(s) will be key to understanding the molecular evolution underlying the evolution of the pluteus larvae.

  6. Marine-derived collagen biomaterials from echinoderm connective tissues

    KAUST Repository

    Ferrario, Cinzia

    2016-03-31

    The use of marine collagens is a hot topic in the field of tissue engineering. Echinoderms possess unique connective tissues (Mutable Collagenous Tissues, MCTs) which can represent an innovative source of collagen to develop collagen barrier-membranes for Guided Tissue Regeneration (GTR). In the present work we used MCTs from different echinoderm models (sea urchin, starfish and sea cucumber) to produce echinoderm-derived collagen membranes (EDCMs). Commercial membranes for GTR or soluble/reassembled (fibrillar) bovine collagen substrates were used as controls. The three EDCMs were similar among each other in terms of structure and mechanical performances and were much thinner and mechanically more resistant than the commercial membranes. Number of fibroblasts seeded on sea-urchin membranes were comparable to the bovine collagen substrates. Cell morphology on all EDCMs was similar to that of structurally comparable (reassembled) bovine collagen substrates. Overall, echinoderms, and sea urchins particularly, are alternative collagen sources to produce efficient GTR membranes. Sea urchins display a further advantage in terms of eco-sustainability by recycling tissues from food wastes.

  7. Echinoderms: potential model systems for studies on muscle regeneration.

    Science.gov (United States)

    García-Arrarás, José E; Dolmatov, Igor Yu

    2010-01-01

    Organisms of the phylum Echinodermata show some of the most impressive regenerative feats within the animal kingdom. Following injury or self-induced autotomy, species in this phylum can regenerate most tissues and organs, being the regeneration of the muscular systems one of the best studied. Even though echinoderms are closely related to chordates, they are little known in the biomedical field, and therefore their uses to study pharmacological effects on muscle formation and/or regeneration have been extremely limited. In order to rectify this lack of knowledge, we describe here the echinoderm muscular systems, particularly the somatic and visceral muscle components. In addition, we provide details of the processes that are known to take place during muscle regeneration, namely dedifferentiation, myogenesis and new muscle formation. Finally, we provide the available information on molecular and pharmacological studies that involve echinoderm muscle regeneration. We expect that by making this information accessible, researchers consider the use of echinoderms as model systems for pharmacological studies in muscle development and regeneration.

  8. Impact of near-future ocean acidification on echinoderms.

    Science.gov (United States)

    Dupont, S; Ortega-Martínez, O; Thorndyke, M

    2010-03-01

    As a consequence of increasing atmospheric CO(2), the world's oceans are warming and slowly becoming more acidic (ocean acidification, OA) and profound changes in marine ecosystems are certain. Calcification is one of the primary targets for studies of the impact of CO(2)-driven climate change in the oceans and one of the key marine groups most likely to be impacted by predicted climate change events are the echinoderms. Echinoderms are a vital component of the marine environment with representatives in virtually every ecosystem, where they are often keystone ecosystem engineers. This paper reviews and analyses what is known about the impact of near-future ocean acidification on echinoderms. A global analysis of the literature reveals that echinoderms are surprisingly robust to OA and that important differences in sensitivity to OA are observed between populations and species. However, this is modulated by parameters such as (1) exposure time with rare longer term experiments revealing negative impacts that are hidden in short or midterm ones; (2) bottlenecks in physiological processes and life-cycle such as stage-specific developmental phenomena that may drive the whole species responses; (3) ecological feedback transforming small scale sub lethal effects into important negative effects on fitness. We hypothesize that populations/species naturally exposed to variable environmental pH conditions may be pre-adapted to future OA highlighting the importance to understand and monitor environmental variations in order to be able to to predict sensitivity to future climate changes. More stress ecology research is needed at the frontier between ecotoxicology and ecology, going beyond standardized tests using model species in order to address multiple water quality factors (e.g. pH, temperature, toxicants) and organism health. However, available data allow us to conclude that near-future OA will have negative impact on echinoderm taxa with likely significant consequences

  9. Vimentin Levels and Serine 71 Phosphorylation in the Control of Cell-Matrix Adhesions, Migration Speed, and Shape of Transformed Human Fibroblasts.

    Science.gov (United States)

    Terriac, Emmanuel; Coceano, Giovanna; Mavajian, Zahra; Hageman, Tijmen A G; Christ, Andreas F; Testa, Ilaria; Lautenschläger, Franziska; Gad, Annica K B

    2017-01-22

    Metastasizing tumor cells show increased expression of the intermediate filament (IF) protein vimentin, which has been used to diagnose invasive tumors for decades. Recent observations indicate that vimentin is not only a passive marker for carcinoma, but may also induce tumor cell invasion. To clarify how vimentin IFs control cell adhesions and migration, we analyzed the nanoscale (30-50 nm) spatial organization of vimentin IFs and cell-matrix adhesions in metastatic fibroblast cells, using three-color stimulated emission depletion (STED) microscopy. We also studied whether wild-type and phospho-deficient or -mimicking mutants of vimentin changed the size and lifetime of focal adhesions (FAs), cell shape, and cell migration, using live-cell total internal reflection imaging and confocal microscopy. We observed that vimentin exists in fragments of different lengths. Short fragments were mostly the size of a unit-length filament and were mainly localized close to small cell-matrix adhesions. Long vimentin filaments were found in the proximity of large FAs. Vimentin expression in these cells caused a reduction in FAs size and an elongated cell shape, but did not affect FA lifetime, or the speed or directionality of cell migration. Expression of a phospho-mimicking mutant (S71D) of vimentin increased the speed of cell migration. Taken together, our results suggest that in highly migratory, transformed mesenchymal cells, vimentin levels control the cell shape and FA size, but not cell migration, which instead is linked to the phosphorylation status of S71 vimentin. These observations are consistent with the possibility that not only levels, but also the assembly status of vimentin control cell migration.

  10. Marine echinoderms as reservoirs of antimicrobial resistant bacteria

    Directory of Open Access Journals (Sweden)

    Catarina Marinho

    2014-06-01

    Full Text Available Echinoderms are benthic animals that play an important ecological role in marine communities occupying diverse trophic levels in the marine food chains. The majority of echinoderms feed on small particles of edible matter, although they can eat many kinds of food (Clark, 1968. Although, some echinoderms species has been facing an emerging demand for human consumption, particularly in Asian and Mediterranean cuisine, where these animals can be eaten raw (Kelly, 2005; Micael et al., 2009. Echinoderms own an innate immune mechanism that allows them to defend themselves from high concentrations of bacteria, viruses and fungus they are often exposed, on marine sediment (Janeway and Medzhitov, 1998, Cooper, 2003. The most frequent genera of gut bacteria in echinoderms are Vibrio, Pseudomonas, Flavobacterium, and Aeromonas; nevertheless Enterococcus spp. and Escherichia coli are also present (Harris, 1993; Marinho et al., 2013. Moreover, fecal resistant bacteria found in the aquatic environment might represent an index of marine pollution (Foti et al., 2009, Kummerer, 2009. Several studies had been lead in order to identify environmental reservoirs for antibiotic-resistant bacteria in populations of fish, echinoderms and marine mammals, and they all support the thesis that these animals may serve as reservoirs since they had acquired resistant microbial species (Johnson et al., 1998, Marinho et al., 2013, Miranda and Zemelman, 2001. However, to our knowledge, there are only available in bibliography one study of antimicrobial resistant bacteria isolated from marine echinoderms (Marinho et al., 2013, which stats that their provenience in this environment is still unclear. Antimicrobial resistance outcomes from the intensive use of antimicrobial drugs in human activities associated with various mechanisms for bacteria genetic transfer (Barbosa and Levy, 2000, Coque et al., 2008. Antibiotic-resistant bacteria enter into water environments where they are

  11. Ancestral echinoderms from the Chengjiang deposits of China.

    Science.gov (United States)

    Shu, D-G; Morris, S Conway; Han, J; Zhang, Z-F; Liu, J-N

    2004-07-22

    Deuterostomes are a remarkably diverse super-phylum, including not only the chordates (to which we belong) but groups as disparate as the echinoderms and the hemichordates. The phylogeny of deuterostomes is now achieving some degree of stability, especially on account of new molecular data, but this leaves as conjectural the appearance of extinct intermediate forms that would throw light on the sequence of evolutionary events leading to the extant groups. Such data can be supplied from the fossil record, notably those deposits with exceptional soft-part preservation. Excavations near Kunming in southwestern China have revealed a variety of remarkable early deuterostomes, including the vetulicolians and yunnanozoans. Here we describe a new group, the vetulocystids. They appear to have similarities not only to the vetulicolians but also to the homalozoans, a bizarre group of primitive echinoderms whose phylogenetic position has been highly controversial.

  12. Echinoderms from Middle and Upper Ordovician rocks of Kentucky

    Science.gov (United States)

    Parsley, R.L.

    1981-01-01

    The Middle and Upper Ordovician limestones of Kentucky, especially the Lexington Limestone, have yielded a diverse silicified echinoderm fauna, including: Stylophora-Enoploura cf. E. punctata; Paracrinoidea-A mygdalocystites; Crinoidea, Inadunata-Hybocrir/us tumidus, Hybocystites problem,aticus, Carabocrinus sp., Cupulocrinus sp., Heterocrinus sp.; Cyclocystoidea-Cyclocystoides sp. A rhombiferan cystoid, A mecystis laevis, from the Edinburg Formation, Virginia, is also discussed. No new taxa are introduced.

  13. Environmental factors influencing asexual reproductive processes in echinoderms

    OpenAIRE

    Mladenov, Pv

    1996-01-01

    This review provides a brief update of the occurrence and adaptive significance of asexual reproduction in echinoderms. It then focuses on the state of knowledge of biotic and abiotic factors that influence asexual processes in this group, particularly factors that may play a role in regulating the expression and relative proportion of asexual versus sexual phenotypes within populations of species, as well as factors modulating and triggering asexual processes. The information presented in th...

  14. Motoric impairment following manganese exposure in asteroid echinoderms.

    Science.gov (United States)

    Sköld, Helen Nilsson; Baden, Susanne P; Looström, Jakob; Eriksson, Susanne P; Hernroth, Bodil E

    2015-10-01

    In the oceans, naturally occurring manganese (Mn) is released from the sediments during events of hypoxia. While neuro- and immuno-toxic effects of bioavailable manganese are well documented for crustaceans, studies of similar effects of manganese on other marine invertebrates are comparatively few. Here, we developed a new functional test "the repeated turning assay" to investigate if manganese exposure at ∼12 mg L(-1) affected motoric behaviour of two asteroid echinoderms, the Common sea star, Asterias rubens, and the Black brittle star, Ophiocomina nigra. By measuring of the turning-over capacity, from dorsal to ventral position, after one and two weeks of manganese exposure, we showed that for both species Mn exposure significantly delayed the ability to turn. After a recovery period of two weeks, the capacity of turning-over was not restored to that of unexposed animals neither for A. rubens nor for O. nigra. Further investigation of sea stars showed that Mn accumulated ∼5 fold in the tube feet, organs involved in their turning-over activity, and the high concentration remained after the recovery period. In the tube feet we also recorded an increased activity of acetylcholinesterase (AChE), here used as a proxy for neuromuscular disturbances. The results indicated that Mn induces neuromuscular disturbance in echinoderms which is important news, given that previous studies have concluded that adult echinoderms are relatively tolerant to Mn.

  15. Endogenous and exogenous control of gametogenesis and spawning in echinoderms.

    Science.gov (United States)

    Mercier, Annie; Hamel, Jean-François

    2009-01-01

    Most echinoderms display seasonal or other temporal cycles of reproduction that presumably result from the complex interplay of endogenous and exogenous signals. Various environmental, chemical and hormonal factors, acting directly or indirectly, individually or in combination, have been proposed to cue, favour or modulate a suite of reproductive functions from the onset of gametogenesis to gamete release. From as early as the nineteenth century, an astonishing array of studies has been published on topics related to the control of reproduction in echinoderms, ranging from fortuitous behavioural observations to complex experimental demonstrations and molecular analyses. Although the exact pathways involved in the perception of external signals and their transduction into coordinated spawning events remain obscure for most species, significant advances have been made that shed new light on the information gathered over decades of research. By compiling the existing literature (over 1000 references), interpreting the main results, critically assessing the methodologies used and reviewing the emerging hypotheses, we endeavour to draw a clearer picture of the existing knowledge and to provide a framework for future investigation of the mechanisms that underlie reproductive strategies in echinoderms and, by extension, in other marine invertebrates.

  16. The biology of the germ line in echinoderms.

    Science.gov (United States)

    Wessel, Gary M; Brayboy, Lynae; Fresques, Tara; Gustafson, Eric A; Oulhen, Nathalie; Ramos, Isabela; Reich, Adrian; Swartz, S Zachary; Yajima, Mamiko; Zazueta, Vanessa

    2014-08-01

    The formation of the germ line in an embryo marks a fresh round of reproductive potential. The developmental stage and location within the embryo where the primordial germ cells (PGCs) form, however, differs markedly among species. In many animals, the germ line is formed by an inherited mechanism, in which molecules made and selectively partitioned within the oocyte drive the early development of cells that acquire this material to a germ-line fate. In contrast, the germ line of other animals is fated by an inductive mechanism that involves signaling between cells that directs this specialized fate. In this review, we explore the mechanisms of germ-line determination in echinoderms, an early-branching sister group to the chordates. One member of the phylum, sea urchins, appears to use an inherited mechanism of germ-line formation, whereas their relatives, the sea stars, appear to use an inductive mechanism. We first integrate the experimental results currently available for germ-line determination in the sea urchin, for which considerable new information is available, and then broaden the investigation to the lesser-known mechanisms in sea stars and other echinoderms. Even with this limited insight, it appears that sea stars, and perhaps the majority of the echinoderm taxon, rely on inductive mechanisms for germ-line fate determination. This enables a strongly contrasted picture for germ-line determination in this phylum, but one for which transitions between different modes of germ-line determination might now be experimentally addressed.

  17. [Echinoderms (Echinodermata) from the Mexican waters of the Gulf of Mexico].

    Science.gov (United States)

    Durán-González, Alicia; Laguarda-Figueras, Alfredo; Solís-Marin, Francisco A; Buitrón Sánchez, Blanca Estela; Ahearn, Cynthia Gust; Torres-Vega, Juan

    2005-12-01

    We present a systematic list of the echinoderms from Gulf of Mexico's Mexican waters based on specimens of the Colecci6n Nacional de Equinodermos, Instituto de Ciencias del Mar y Limnologia, Universidad Nacional Aut6noma de México and the National Museum of Natural History, Smithsonian Institution, Washington, D.C. This list reveals an important echinoderm biodiversity present in the Gulf of Mexico, where five of the six echinoderm classes are represented. A total of 209 echinoderm species is recorded, distributed in 129 genera, 63 families and 25 orders. 31 new records for the Gulf of Mexico are presented: Asteroidea (16), Ophiuroidea (nine), Echinoidea (one) and Holothuroidea (five).

  18. Coupling of metal-organic frameworks-containing monolithic capillary-based selective enrichment with matrix-assisted laser desorption ionization-time-of-flight mass spectrometry for efficient analysis of protein phosphorylation.

    Science.gov (United States)

    Li, Daojin; Yin, Danyang; Chen, Yang; Liu, Zhen

    2017-05-19

    Protein phosphorylation is a major post-translational modification, which plays a vital role in cellular signaling of numerous biological processes. Mass spectrometry (MS) has been an essential tool for the analysis of protein phosphorylation, for which it is a key step to selectively enrich phosphopeptides from complex biological samples. In this study, metal-organic frameworks (MOFs)-based monolithic capillary has been successfully prepared as an effective sorbent for the selective enrichment of phosphopeptides and has been off-line coupled with matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) for efficient analysis of phosphopeptides. Using š-casein as a representative phosphoprotein, efficient phosphorylation analysis by this off-line platform was verified. Phosphorylation analysis of a nonfat milk sample was also demonstrated. Through introducing large surface areas and highly ordered pores of MOFs into monolithic column, the MOFs-based monolithic capillary exhibited several significant advantages, such as excellent selectivity toward phosphopeptides, superb tolerance to interference and simple operation procedure. Because of these highly desirable properties, the MOFs-based monolithic capillary could be a useful tool for protein phosphorylation analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Affinity-tagged phosphorylation assay by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (ATPA-MALDI): application to calcium/calmodulin-dependent protein kinase.

    Science.gov (United States)

    Kinumi, Tomoya; Niki, Etsuo; Shigeri, Yasushi; Matsumoto, Hiroyuki

    2005-12-01

    A matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based kinase assay using a peptide substrate tagged with a biotinyl group has been developed. The peptide moiety was designed to serve as an efficient substrate for calcium/calmodulin-dependent protein kinase II, based on the in vivo phosphorylation site of phosrestin I, a Drosophila homolog of arrestin. In the assay, the quantitative relationship was determined from the ratio of the peak areas between the two peaks respectively representing the unphosphorylated and the phosphorylated substrate. Attempts to assay phosphorylated peptides directly from the reaction mixture, gave inaccurate results because of the high noise level caused by the presence of salts and detergents. In contrast, after purifying the substrate peptides with the biotin affinity tag using streptavidin-coated magnetic beads, peak areas accurately represented the ratio between the unphosphorylated and phosphorylated peptide. By changing the substrate peptide to a peptide sequence that serves as a kinase substrate, it is expected that an efficient non-radioactive protein kinase assay using MALDI-TOF MS can be developed for any type of protein kinase. We call this technique "Affinity-Tagged Phosphorylation Assay by MALDI-TOF MS (ATPA-MALDI)." ATPA-MALDI should serve as a quick and efficient non-radioactive protein kinase assay by MALDI-TOF MS.

  20. Evolution of echinoderms may not have required modification of the ancestral deuterostome HOX gene cluster: first report of PG4 and PG5 Hox orthologues in echinoderms.

    Science.gov (United States)

    Long, Suzanne; Martinez, Pedro; Chen, Wei-Chung; Thorndyke, Michael; Byrne, Maria

    2003-11-01

    Is the extreme derivation of the echinoderm body plan reflected in a derived echinoderm Hox genotype? Building on previous work, we exploited the sequence conservation of the homeobox to isolate putative orthologues of several Hox genes from two asteroid echinoderms. The 5-peptide motif (LPNTK) diagnostic of PG4 Hox genes was identified immediately downstream of one of the partial homeodomains from Patiriella exigua. This constitutes the first unequivocal report of a PG4 Hox gene orthologue from an echinoderm. Subsequent screenings identified genes of both PG4 and PG4/5 in Asterias rubens. Although in echinoids only a single gene (PG4/5) occupies these two contiguous cluster positions, we conclude that the ancestral echinoderm must have had the complete deuterostome suite of medial Hox genes, including orthologues of both PG4 and PG4/5 (=PG5). The reported absence of PG4 in the HOX cluster of echinoids is therefore a derived state, and the ancestral echinoderm probably had a HOX cluster not dissimilar to that of other deuterostomes. Modification of the ancestral deuterostome Hox genotype may not have been required for evolution of the highly derived echinoderm body plan.

  1. Diversity in the fertilization envelopes of echinoderms.

    Science.gov (United States)

    Oulhen, Nathalie; Reich, Adrian; Wong, Julian L; Ramos, Isabela; Wessel, Gary M

    2013-01-01

    Cell surface changes in an egg at fertilization are essential to begin development and for protecting the zygote. Most fertilized eggs construct a barrier around themselves by modifying their original extracellular matrix. This construction usually results from calcium-induced exocytosis of cortical granules, the contents of which in sea urchins function to form the fertilization envelope (FE), an extracellular matrix of cortical granule contents built upon a vitelline layer scaffold. Here, we examined the molecular mechanism of this process in sea stars, a close relative of the sea urchins, and analyze the evolutionary changes that likely occurred in the functionality of this structure between these two organisms. We find that the FE of sea stars is more permeable than in sea urchins, allowing diffusion of molecules in excess of 2 megadaltons. Through a proteomic and transcriptomic approach, we find that most, but not all, of the proteins present in the sea urchin envelope are present in sea stars, including SFE9, proteoliaisin, and rendezvin. The mRNAs encoding these FE proteins accumulated most densely in early oocytes, and then beginning with vitellogenesis, these mRNAs decreased in abundance to levels nearly undetectable in eggs. Antibodies to the SFE9 protein of sea stars showed that the cortical granules in sea star also accumulated most significantly in early oocytes, but different from sea urchins, they translocated to the cortex of the oocytes well before meiotic initiation. These results suggest that the preparation for cell surface changes in sea urchins has been shifted to later in oogenesis, and perhaps reflects the meiotic differences among the species-sea star oocytes are stored in prophase of meiosis and fertilized during the meiotic divisions, as in most animals, whereas sea urchins are one of the few taxons in which eggs have completed meiosis prior to fertilization.

  2. Diversity in the fertilization envelopes of echinoderms

    Science.gov (United States)

    Oulhen, Nathalie; Reich, Adrian; Wong, Julian L.; Wessel, Gary M.

    2013-01-01

    Cell surface changes in an egg at fertilization are essential to begin development and for protecting the zygote. Most fertilized eggs construct a barrier around themselves by modifying their original extracellular matrix. This construction usually results from calcium induced exocytosis of cortical granules, the contents of which in sea urchins function to form the fertilization envelope (FE), an extracellular matrix of cortical granule contents built upon a vitelline layer scaffold. Here we examined the molecular mechanism of this process in sea stars, a close relative of the sea urchins, and analyze the evolutionary changes that likely occurred in the functionality of this structure between these two organisms. We find that the FE of sea stars is more permeable than in sea urchins, allowing diffusion of molecules in excess of 2 megadaltons. Through a proteomic and transcriptomic approach, we find that most, but not all of the proteins present in the sea urchin envelope are present in sea stars, including SFE9, proteoliaisin, rendezvin, and ovoperoxidase. The mRNAs encoding these FE proteins accumulated most densely in early oocytes, and then beginning with vitellogenesis, these mRNAs deceased in abundance to levels nearly undetectable in eggs. Antibodies to the SFE9 protein of sea stars showed that the cortical granules in sea star also accumulated most significantly in early oocytes, and different from sea urchins, they translocated to the cortex of the oocytes well before meiotic initiation. These results suggest that the preparation of the cell surface changes in sea urchins has been shifted to later in oogenesis and perhaps reflects the meiotic differences among the species–sea star oocytes are stored in prophase of meiosis and fertilized during the meiotic divisions, as in most animals, whereas sea urchins are one of the few taxa in which eggs have completed meiosis prior to fertilization. PMID:23331915

  3. Every which way--nanos gene regulation in echinoderms.

    Science.gov (United States)

    Oulhen, Nathalie; Wessel, Gary M

    2014-03-01

    Nanos is an essential factor of germ line success in all animals tested. This gene encodes a Zn-finger RNA-binding protein that in complex with its partner pumilio binds to and changes the fate of several known transcripts. We summarize here the documented functions of Nanos in several key organisms, and then emphasize echinoderms as a working model for how nanos expression is regulated. Nanos presence outside of the target cells is often detrimental to the animal, and in sea urchins, nanos expression appears to be regulated at every step of transcription, and post-transcriptional activity, making this gene product exciting, every which way.

  4. SALMFamide salmagundi: the biology of a neuropeptide family in echinoderms.

    Science.gov (United States)

    Elphick, Maurice R

    2014-09-01

    The SALMFamides are a family of neuropeptides that occur in species belonging to the phylum Echinodermata. The prototypes for this neuropeptide family (S1 and S2) were discovered in starfish but subsequently SALMFamides were identified in other echinoderms. There are two types of SALMFamides: L-type, which have the C-terminal motif SxLxFamide, and F-type, which have the C-terminal motif SxFxFamide. They are derived from two types of precursor proteins: an L-type SALMFamide precursor, which comprises only L-type or L-type-like SALMFamides and an F-type SALMFamide precursor, which contains several F-type or F-type-like SALMFamides and, typically, one or more L-type SALMFamides. Thus, SALMFamides occur as heterogeneous mixtures of neuropeptides - a SALMFamide salmagundi. SALMFamides are produced by distinct populations of neurons in echinoderm larval and adult nervous systems and are present in the innervation of neuromuscular organs. Both L-type and F-type SALMFamides cause muscle relaxation in echinoderms and, for example, in starfish this effect of SALMFamides may mediate neural control of cardiac stomach eversion in species that feed extra-orally (e.g., Asterias rubens). The SALMFamide S1 also causes inhibition of neural release of a relaxin-like gonadotropin in the starfish Asterina pectinifera. An important issue that remains to be resolved are the relationships of SALMFamides with neuropeptides that have been identified in other phyla. However, it has been noted that the C-terminal SxLxFamide motif of L-type SALMFamides is a feature of some members of a bilaterian neuropeptide family that includes gonadotropin-inhibitory hormone (GnIH) in vertebrates and SIFamide-type neuropeptides in protostomes. Similarly, the C-terminal FxFamide motif of F-type SALMFamides is a feature of vertebrate QRFP (26RFa)-type neuropeptides. These sequence similarities may provide a basis for molecular identification of receptors that mediate effects of SALMFamides. Furthermore

  5. Regeneration of spines and pedicellariae in echinoderms: a review.

    Science.gov (United States)

    Dubois, P; Ameye, L

    2001-12-15

    Morphogenesis of tissues during regeneration of echinoderm spines and pedicellariae is reviewed. Regeneration of the skeleton is rather well documented while that of associated soft tissues is poorly investigated. In particular, little information is available on the early regeneration stages which follow wound healing. From the available information, it is suggested that regeneration of broken spines proceeds through a morphallactic process of which the organizational information, as well as the involved cells, lies in the stump. In contrast, regeneration of removed spines and pedicellariae may depend on an epimorphic process whose organizational information could be located in the mutable connective tissue that joins the appendage to the main body wall.

  6. Echinoderm Fauna of Chuuk, The Federated States of Micronesia

    Directory of Open Access Journals (Sweden)

    Lee, Taekjun

    2014-04-01

    Full Text Available Micronesia is an island nation located north of Papua New Guinea in the Pacific Ocean. A survey was conducted on Chuuk, which is one of the four main islands of Micronesia, from 11-25 Nov 2012. Echinoderms collected at one intertidal area as well as at 16 SCUBA diving points of 10-40 m depths in the subtidal zone were identified based on morphological characteristics. In total, 35 species from 165 individuals were identified: two crinoids, eight asteroids, four ophiuroids, seven echinoids, and 14 holothuroids. Among them, one asteroid, one ophiuroid, one echinoid, and two holothuroids were newly recorded from Micronesia.

  7. Diversity assessment of echinoderms from Mudasalodai and Pazhayar in the southeast coast of India

    Institute of Scientific and Technical Information of China (English)

    Maheswaran Murugan; Narendran Rajendran; Sundaravarman Kasirajan; Pravinkumar Moorthy; Gunalan Balakrishnan

    2016-01-01

    Objective: To study the echinoderms diversity in Mudasalodai and Pazhayar landing centers during November 2012 to December 2014. Methods: All the collected echinoderm samples were stored at 4 °C until further use. Results: As many as 19 species of echinoderms were recorded in both stations and it belongs to 10 families, three classes such as Asteroidea, Echinoidea and Ophiuroidea. The percentage composition varied from 0.15% to 73%. The species diversity ranged from 1.031 to 2.6; species richness was from 1.02 to 4.06 and species evenness ranged from 0.93 to 0.99. K-dominance curve drawn paralleled the trend of diversity indices. Cluster and multidimensional scaling showed the similarity in echinoderms composition within the stations. Conclusions: The present investigation is evident that the echinoderm occurrence was predominant during the summer season and proved statistically by using SPSS Primer 6.0.

  8. Cambrian spiral-plated echinoderms from Gondwana reveal the earliest pentaradial body plan.

    Science.gov (United States)

    Smith, Andrew B; Zamora, Samuel

    2013-08-22

    Echinoderms are unique among animal phyla in having a pentaradial body plan, and their fossil record provides critical data on how this novel organization came about by revealing intermediate stages. Here, we report a spiral-plated animal from the early Cambrian of Morocco that is the most primitive pentaradial echinoderm yet discovered. It is intermediate between helicoplacoids (a bizarre group of spiral-bodied echinoderms) and crown-group pentaradiate echinoderms. By filling an important gap, this fossil reveals the common pattern that underpins the body plans of the two major echinoderm clades (pelmatozoans and eleutherozoans), showing that differential growth played an important role in their divergence. It also adds to the striking disparity of novel body plans appearing in the Cambrian explosion.

  9. Diversity assessment of echinoderms from Mudasalodai and Pazhayar in the southeast coast of India

    Directory of Open Access Journals (Sweden)

    Maheswaran Murugan

    2016-02-01

    Full Text Available Objective: To study the echinoderms diversity in Mudasalodai and Pazhayar landing centers during November 2012 to December 2014. Methods: All the collected echinoderm samples were stored at 4 °C until further use. Results: As many as 19 species of echinoderms were recorded in both stations and it belongs to 10 families, three classes such as Asteroidea, Echinoidea and Ophiuroidea. The percentage composition varied from 0.15% to 73%. The species diversity ranged from 1.031 to 2.6; species richness was from 1.02 to 4.06 and species evenness ranged from 0.93 to 0.99. K-dominance curve drawn paralleled the trend of diversity indices. Cluster and multidimensional scaling showed the similarity in echinoderms composition within the stations. Conclusions: The present investigation is evident that the echinoderm occurrence was predominant during the summer season and proved statistically by using SPSS Primer 6.0.

  10. Large-scale spatial distribution patterns of echinoderms in nearshore rocky habitats.

    Science.gov (United States)

    Iken, Katrin; Konar, Brenda; Benedetti-Cecchi, Lisandro; Cruz-Motta, Juan José; Knowlton, Ann; Pohle, Gerhard; Mead, Angela; Miloslavich, Patricia; Wong, Melisa; Trott, Thomas; Mieszkowska, Nova; Riosmena-Rodriguez, Rafael; Airoldi, Laura; Kimani, Edward; Shirayama, Yoshihisa; Fraschetti, Simonetta; Ortiz-Touzet, Manuel; Silva, Angelica

    2010-11-05

    This study examined echinoderm assemblages from nearshore rocky habitats for large-scale distribution patterns with specific emphasis on identifying latitudinal trends and large regional hotspots. Echinoderms were sampled from 76 globally-distributed sites within 12 ecoregions, following the standardized sampling protocol of the Census of Marine Life NaGISA project (www.nagisa.coml.org). Sample-based species richness was overall low (2 cm in 1 m(2) quadrats) was highest in the Caribbean ecoregions and echinoids dominated these assemblages with an average of 5 ind m(-2). In contrast, intertidal echinoderm assemblages collected from clearings of 0.0625 m(2) quadrats had the highest abundance and richness in the Northeast Pacific ecoregions where asteroids and holothurians dominated with an average of 14 ind 0.0625 m(-2). Distinct latitudinal trends existed for abundance and richness in intertidal assemblages with declines from peaks at high northern latitudes. No latitudinal trends were found for subtidal echinoderm assemblages with either sampling technique. Latitudinal gradients appear to be superseded by regional diversity hotspots. In these hotspots echinoderm assemblages may be driven by local and regional processes, such as overall productivity and evolutionary history. We also tested a set of 14 environmental variables (six natural and eight anthropogenic) as potential drivers of echinoderm assemblages by ecoregions. The natural variables of salinity, sea-surface temperature, chlorophyll a, and primary productivity were strongly correlated with echinoderm assemblages; the anthropogenic variables of inorganic pollution and nutrient contamination also contributed to correlations. Our results indicate that nearshore echinoderm assemblages appear to be shaped by a network of environmental and ecological processes, and by the differing responses of various echinoderm taxa, making generalizations about the patterns of nearshore rocky habitat echinoderm assemblages

  11. Large-Scale Spatial Distribution Patterns of Echinoderms in Nearshore Rocky Habitats

    Science.gov (United States)

    Iken, Katrin; Konar, Brenda; Benedetti-Cecchi, Lisandro; Cruz-Motta, Juan José; Knowlton, Ann; Pohle, Gerhard; Mead, Angela; Miloslavich, Patricia; Wong, Melisa; Trott, Thomas; Mieszkowska, Nova; Riosmena-Rodriguez, Rafael; Airoldi, Laura; Kimani, Edward; Shirayama, Yoshihisa; Fraschetti, Simonetta; Ortiz-Touzet, Manuel; Silva, Angelica

    2010-01-01

    This study examined echinoderm assemblages from nearshore rocky habitats for large-scale distribution patterns with specific emphasis on identifying latitudinal trends and large regional hotspots. Echinoderms were sampled from 76 globally-distributed sites within 12 ecoregions, following the standardized sampling protocol of the Census of Marine Life NaGISA project (www.nagisa.coml.org). Sample-based species richness was overall low (2 cm in 1 m2 quadrats) was highest in the Caribbean ecoregions and echinoids dominated these assemblages with an average of 5 ind m−2. In contrast, intertidal echinoderm assemblages collected from clearings of 0.0625 m2 quadrats had the highest abundance and richness in the Northeast Pacific ecoregions where asteroids and holothurians dominated with an average of 14 ind 0.0625 m−2. Distinct latitudinal trends existed for abundance and richness in intertidal assemblages with declines from peaks at high northern latitudes. No latitudinal trends were found for subtidal echinoderm assemblages with either sampling technique. Latitudinal gradients appear to be superseded by regional diversity hotspots. In these hotspots echinoderm assemblages may be driven by local and regional processes, such as overall productivity and evolutionary history. We also tested a set of 14 environmental variables (six natural and eight anthropogenic) as potential drivers of echinoderm assemblages by ecoregions. The natural variables of salinity, sea-surface temperature, chlorophyll a, and primary productivity were strongly correlated with echinoderm assemblages; the anthropogenic variables of inorganic pollution and nutrient contamination also contributed to correlations. Our results indicate that nearshore echinoderm assemblages appear to be shaped by a network of environmental and ecological processes, and by the differing responses of various echinoderm taxa, making generalizations about the patterns of nearshore rocky habitat echinoderm assemblages

  12. Large-scale spatial distribution patterns of echinoderms in nearshore rocky habitats.

    Directory of Open Access Journals (Sweden)

    Katrin Iken

    Full Text Available This study examined echinoderm assemblages from nearshore rocky habitats for large-scale distribution patterns with specific emphasis on identifying latitudinal trends and large regional hotspots. Echinoderms were sampled from 76 globally-distributed sites within 12 ecoregions, following the standardized sampling protocol of the Census of Marine Life NaGISA project (www.nagisa.coml.org. Sample-based species richness was overall low (2 cm in 1 m(2 quadrats was highest in the Caribbean ecoregions and echinoids dominated these assemblages with an average of 5 ind m(-2. In contrast, intertidal echinoderm assemblages collected from clearings of 0.0625 m(2 quadrats had the highest abundance and richness in the Northeast Pacific ecoregions where asteroids and holothurians dominated with an average of 14 ind 0.0625 m(-2. Distinct latitudinal trends existed for abundance and richness in intertidal assemblages with declines from peaks at high northern latitudes. No latitudinal trends were found for subtidal echinoderm assemblages with either sampling technique. Latitudinal gradients appear to be superseded by regional diversity hotspots. In these hotspots echinoderm assemblages may be driven by local and regional processes, such as overall productivity and evolutionary history. We also tested a set of 14 environmental variables (six natural and eight anthropogenic as potential drivers of echinoderm assemblages by ecoregions. The natural variables of salinity, sea-surface temperature, chlorophyll a, and primary productivity were strongly correlated with echinoderm assemblages; the anthropogenic variables of inorganic pollution and nutrient contamination also contributed to correlations. Our results indicate that nearshore echinoderm assemblages appear to be shaped by a network of environmental and ecological processes, and by the differing responses of various echinoderm taxa, making generalizations about the patterns of nearshore rocky habitat echinoderm

  13. An evolutionary transition of Vasa regulation in echinoderms.

    Science.gov (United States)

    Juliano, Celina E; Wessel, Gary M

    2009-01-01

    Vasa, a DEAD box helicase, is a germline marker that may also function in multipotent cells. In the embryo of the sea urchin Strongylocentrotus purpuratus, Vasa protein is posttranscriptionally enriched in the small micromere lineage, which results from two asymmetric cleavage divisions early in development. The cells of this lineage are subsequently set aside during embryogenesis for use in constructing the adult rudiment. Although this mode of indirect development is prevalent among echinoderms, early asymmetric cleavage divisions are a derived feature in this phylum. The goal of this study is to explore how vasa is regulated in key members of the phylum with respect to the evolution of the micromere and small micromere lineages. We find that although striking similarities exist between the vasa mRNA expression patterns of several sea urchins and sea stars, the time frame of enriched protein expression differs significantly. These results suggest that a conserved mechanism of vasa regulation was shifted earlier in sea urchin embryogenesis with the derivation of micromeres. These data also shed light on the phenotype of a sea urchin embryo upon removal of the Vasa-positive micromeres, which appears to revert to a basal mechanism used by extant sea stars and pencil urchins to regulate Vasa protein accumulation. Furthermore, in all echinoderms tested here, Vasa protein and/or message is enriched in the larval coelomic pouches, the site of adult rudiment formation, thus suggesting a conserved role for vasa in undifferentiated multipotent cells set aside during embryogenesis for use in juvenile development.

  14. Echinoderms as blueprints for biocalcification: regulation of skeletogenic genes and matrices.

    Science.gov (United States)

    Matranga, Valeria; Bonaventura, Rosa; Costa, Caterina; Karakostis, Konstantinos; Pinsino, Annalisa; Russo, Roberta; Zito, Francesca

    2011-01-01

    Echinoderms have an extensive endoskeleton composed of magnesian calcite, a form of calcium carbonate that contains small amounts of magnesium carbonate and occluded matrix proteins. Adult sea urchins have several calcified structures, including test, teeth, and spines, composed of numerous ossicles which form a three-dimensional meshwork of mineral trabeculae, the stereom. The biomineral development begins in 24-hour-old embryos within the primary mesenchyme cells (PMCs), the only cells producing a set of necessary matrix proteins. The deposition of the biomineral occurs in a privileged extracellular space produced by the fused filopodial processes of the PMCs. We showed for the first time that signals from ectoderm cells overlying PMCs play an important role in the regulation of biomineralization-related genes. It is believed that growth factors are produced by ectoderm cells and released into the blastocoel where they interact with cognate receptor tyrosine kinases restricted to PMCs, which activate signaling cascades regulating the expression of biomineralization-related genes. We demonstrated the implication of a TGF-beta family factor by a perturbation model in which skeleton elongation was indirectly blocked by monoclonal antibodies to an extracellular matrix (ECM) protein located on the apical surface of ectoderm. Thus, it was inferred that interfering with the binding of the ECM ligand, a member of the discoidin family, to its cell surface receptor, a βC integrin, disrupts the ectodermal cell signaling cascade, resulting in reduced or aberrant skeletons. During the last few years, we analyzed the expression of biomineralization-related genes in other examples of experimentally induced skeleton malformations, produced by the exposure to toxic metals, such as Cd and Mn or ionizing radiations, such as UV-B and X-rays. Besides the obvious toxicological implication, since the mis-expression of spicule matrix genes paralleled skeleton defects, we believe that

  15. Echinoderm Fauna of Kosrae, The Federation States of Micronesia

    Directory of Open Access Journals (Sweden)

    Taekjun Lee

    2013-01-01

    Full Text Available Micronesia is an island nation located north of Papua New Guinea in the Pacific Ocean. A survey was executed on Kosrae, which is one of the four main islands of Micronesia, during January 23-30, 2011 and January 8-15, 2012. The echinoderms were collected at eight intertidal areas and at 12 SCUBA diving points at depths of 10-50 m in the subtidal zone. They were identified based on morphological characteristics. In total, 50 species from 276 individuals were identified: three crinoids, 11 asteroids, seven ophiuroids, 10 echinoids, and 19 holothuroids. Among them, two crinoids, five asteroids, three ophiuroids, four echinoids and two holothuroids were newly recorded from Kosrae.

  16. The skeleton of postmetamorphic echinoderms in a changing world.

    Science.gov (United States)

    Dubois, Philippe

    2014-06-01

    Available evidence on the impact of acidification and its interaction with warming on the skeleton of postmetamorphic (juvenile and adult) echinoderms is reviewed. Data are available on sea urchins, starfish, and brittle stars in 33 studies. Skeleton growth of juveniles of all sea urchin species studied so far is affected from pH 7.8 to 7.6 in seawater, values that are expected to be reached during the 21st century. Growth in adult sea urchins (six species studied) is apparently only marginally affected at seawater pH relevant to this century. The interacting effect of temperature differed according to studies. Juvenile starfish as well as adults seem to be either not impacted or even boosted by acidification. Brittle stars show moderate effects at pH below or equal to 7.4. Dissolution of the body wall skeleton is unlikely to be a major threat to sea urchins. Spines, however, due to their exposed position, are more prone to this threat, but their regeneration abilities can probably ensure their maintenance, although this could have an energetic cost and induce changes in resource allocation. No information is available on skeleton dissolution in starfish, and the situation in brittle stars needs further assessment. Very preliminary evidence indicates that mechanical properties in sea urchins could be affected. So, although the impact of ocean acidification on the skeleton of echinoderms has been considered as a major threat from the first studies, we need a better understanding of the induced changes, in particular the functional consequences of growth modifications and dissolution related to mechanical properties. It is suggested to focus studies on these aspects.

  17. Inhibition of Nonsmall Cell Lung Cancer Cell Migration by Protein Arginine Methyltransferase 1-small Hairpin RNA Through Inhibiting Epithelial-mesenchymal Transition,Extracellular Matrix Degradation, and Src Phosphorylation In Vitro

    Institute of Scientific and Technical Information of China (English)

    Ting Zhang; Ge Cui; Yun-Liang Yao; Yue Guo; Qi-Chun Wang; Xi-Ning Li; Wen-Ming Feng

    2015-01-01

    Background:Protein arginine methyltransferases 1 (PRMT1) is over-expressed in a variety of cancers,including lung cancer,and is correlated with a poor prognosis of tumor development.This study aimed to investigate the role of PRMT1 in nonsmall cell lung cancer (NSCLC) migration in vitro.Methods:In this study,PRMT1 expression in the NSCLC cell line A549 was silenced using lentiviral vector-mediated short hairpin RNAs.Cell migration was measured using both scratch wound healing and transwell cell migration assays.The mRNA expression levels of matrix metalloproteinase 2 (MMP-2) and tissue inhibitor ofmetalloproteinase 1,2 (TIMP l,2) were measured using quantitative real-time reverse transcription-polymerase chain reaction.The expression levels of protein markers for epithelial-mesenchymal transition (EMT) (E-cadherin,N-cadherin),focal adhesion kinase (FAK),Src,AKT,and their corresponding phosphorylated states were detected by Western blot.Results:Cell migration was significantly inhibited in the PRMT1 silenced group compared to the control group.The mRNA expression of MMP-2 decreased while TIMP 1 and TIMP2 increased significantly.E-cadherin mRNA expression also increased while N-cadherin decreased.Only phosphorylated Src levels decreased in the silenced group while FAK or AKT remained unchanged.Conclusions:PRMT1-small hairpin RNA inhibits the migration abilities of NSCLC A549 cells by inhibiting EMT,extracellular matrix degradation,and Src phosphorylation in vitro.

  18. Conservation of sequence and function in fertilization of the cortical granule serine protease in echinoderms.

    Science.gov (United States)

    Oulhen, Nathalie; Xu, Dongdong; Wessel, Gary M

    2014-08-01

    Conservation of the cortical granule serine protease during fertilization in echinoderms was tested both functionally in sea stars, and computationally throughout the echinoderm phylum. We find that the inhibitor of serine protease (soybean trypsin inhibitor) effectively blocks proper transition of the sea star fertilization envelope into a protective sperm repellent, whereas inhibitors of the other main types of proteases had no effect. Scanning the transcriptomes of 15 different echinoderm ovaries revealed sequences of high conservation to the originally identified sea urchin cortical serine protease, CGSP1. These conserved sequences contained the catalytic triad necessary for enzymatic activity, and the tandemly repeated LDLr-like repeats. We conclude that the protease involved in the slow block to polyspermy is an essential and conserved element of fertilization in echinoderms, and may provide an important reagent for identification and testing of the cell surface proteins in eggs necessary for sperm binding.

  19. Understanding form and function of the stem in early flattened echinoderms (pleurocystitids) using a microstructural approach.

    Science.gov (United States)

    Gorzelak, Przemysław; Zamora, Samuel

    2016-01-01

    Pleurocystitid rhombiferans are among the most unusual echinoderms whose mode of life has been long debated. These echinoderms are usually interpreted as vagile epibenthic echinoderms, moving over the sea bottom by means of a flexible stem. Although their life habits and posture are reasonably well understood, the mechanisms that control the movement of stem are highly controversial. Specifically, it is unknown whether the stem flexibility was under the control of muscles or ligamentary mutable collagenous tissues (MCTs). Here, we reconstruct palaeoanatomy of the two Ordovician pleurocystitid rhombiferans (Pleurocystites and Amecystis) based on stereom microstructure. We show that the articular facets of columnals in pleurocystitid rhombiferans are composed of fine labyrinthic stereom. Comparison with modern echinoderms suggests that this type of stereom was associated with muscles implying that their stem was a muscular locomotory organ supporting an active mode of life.

  20. Diagenesis of echinoderm skeletons: Constraints on paleoseawater Mg/Ca reconstructions

    Science.gov (United States)

    Gorzelak, Przemysław; Krzykawski, Tomasz; Stolarski, Jarosław

    2016-09-01

    One of the most profound environmental changes thought to be reflected in chemical composition of numerous geological archives is Mg/Ca ratio of the seawater, which has varied dramatically throughout the Phanerozoic. Echinoderms that today typically form high magnesium calcite skeletons are increasingly being utilized as a proxy for interpreting secular changes in seawater chemistry. However, accurate characterization of the diagenetic changes of their metastable high magnesium calcite skeletons is a prerequisite for assessing their original, major-element geochemical composition. Here we expand the existing models of diagenesis of echinoderm skeleton by integration of various analytical methods that up to now rarely have been used to assess the diagenetic changes of fossil echinoderms. We validated the preservation of a suite of differently preserved echinoderm ossicles, mostly crinoids, ranging in age from the Cambrian through Recent. In 13 of 99 fossil echinoderm ossicles we found well-preserved porous microstructure (stereom), non-luminescent behaviour or blotchy dark color in cathodoluminescence, and distinct nanostructural features (layered and nanocomposite structure). Moreover, in representatives of such preserved samples, distribution of sulphates associated with organic matter is identical to those in Recent echinoderms. Only such ossicles, despite of local micrometer-scale diagenetic changes, were herein considered well-preserved, retaining their original major-element skeletal composition. By contrast, majority of samples show transformation to the stable low magnesium calcite that leads to obliteration of the primary geochemical and micro/nanostructural features and is accompanied with increase in cathodoluminescence emission intensity. Using only well-preserved fossil echinoderm samples, we found purely random variation in Mg/Ca in echinoderm skeletons through the observed time series; any periodicities in echinoderm skeletal Mg/Ca ratio which might

  1. Hydromechanical considerations on the origin of the pentaradial body structure of echinoderms

    OpenAIRE

    2005-01-01

    When echinoderms are conceptualized as hydraulic entities, the early evolution of this group can be presented in a scenario which describes how a bilateral ancestor (an enteropneust-like organism) gradually evolved into a pentaradial echinoderm. According to this scenario, the arms are outgrowths from the anterior/posterior body axis of the bilateral pterobranchia-like intermediate. These outgrowths developed when the originally U-shaped mesentery of the intestinal tract formed loops, and cor...

  2. Notes on the Echinoderm Fauna of the Tanjung Merah Bay Waters Sulawesi Utara

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    Susetiono

    2005-12-01

    Full Text Available A total of 21 species of echinoderms, belonging to of 5 species holothuroidea, 5 species of asteroidea, 4 species echinoidea and 7 species ophiuroidea have been found in the Tanjung Merah of Sulawesi Utara. The Ophiuroidea were relatively common in the sea grass zone. On the basis of population density, Ophiuroidea was the dominant group and relatively highest in the individual density. The species composition, community structure, zonation, and spatial distribution of echinoderm fauna are discussed in this paper.

  3. Buffer capacity of the coelomic fluid in echinoderms.

    Science.gov (United States)

    Collard, Marie; Laitat, Kim; Moulin, Laure; Catarino, Ana I; Grosjean, Philippe; Dubois, Philippe

    2013-09-01

    The increase in atmospheric CO2 due to anthropogenic activity results in an acidification of the surface waters of the oceans. The impact of these chemical changes depends on the considered organisms. In particular, it depends on the ability of the organism to control the pH of its inner fluids. Among echinoderms, this ability seems to differ significantly according to species or taxa. In the present paper, we investigated the buffer capacity of the coelomic fluid in different echinoderm taxa as well as factors modifying this capacity. Euechinoidea (sea urchins except Cidaroidea) present a very high buffer capacity of the coelomic fluid (from 0.8 to 1.8mmolkg(-1) SW above that of seawater), while Cidaroidea (other sea urchins), starfish and holothurians have a significantly lower one (from -0.1 to 0.4mmolkg(-1) SW compared to seawater). We hypothesize that this is linked to the more efficient gas exchange structures present in the three last taxa, whereas Euechinoidea evolved specific buffer systems to compensate lower gas exchange abilities. The constituents of the buffer capacity and the factors influencing it were investigated in the sea urchin Paracentrotus lividus and the starfish Asterias rubens. Buffer capacity is primarily due to the bicarbonate buffer system of seawater (representing about 63% for sea urchins and 92% for starfish). It is also partly due to coelomocytes present in the coelomic fluid (around 8% for both) and, in P. lividus only, a compound of an apparent size larger than 3kDa is involved (about 15%). Feeding increased the buffer capacity in P. lividus (to a difference with seawater of about 2.3mmolkg(-1) SW compared to unfed ones who showed a difference of about 0.5mmolkg(-1) SW) but not in A. rubens (difference with seawater of about 0.2 for both conditions). In P. lividus, decreased seawater pH induced an increase of the buffer capacity of individuals maintained at pH7.7 to about twice that of the control individuals and, for those at pH7

  4. Rise of echinoderms in the Paleozoic evolutionary fauna: Significance of paleoenvironmental controls

    Energy Technology Data Exchange (ETDEWEB)

    Guensburg, T.E. (Rock Valley College, Rockford, IL (United States)); Sprinkle, J. (Univ. of Texas, Austin (United States))

    1992-05-01

    Echinoderms were a major enduring component of Paleozoic marine faunas beginning with the rapid diversification of crinoids and other classes in the Early Ordovician. This diversification was triggered by increased availability of habitable areas accompanying sea-level rise and changed sedimentation styles. Newly collected Early Ordovician echinoderms facilitate determination in detail of life modes and important adaptations during this transition interval. Substrate consistency and stability were crucial spatial limiting factors that resulted in heterogeneous distribution patterns for echinoderm classes. Crinoids were overwhelmingly large-food-groove suspension feeders with relatively open filtration fans attached by small discs to hardground surfaces in shallow water. They were preadapted for this life mode. Rhombiferans were mobile small-food-groove suspension feeders; they lived on soft substrates at various depths. Several important crinoid clades underwent a second phase of diversification during the Middle Ordovician by developing holdfasts adapted to soft substrates and densely pinnulate arms with small food grooves, leading to dominance of this class among Paleozoic echinoderms. The authors findings are in basic agreement with the overall onshore diversification pattern of most Paleozoic benthic invertebrates, but they argue for an extrinsic environmental control (substrate availability) for the observed echinoderm distribution.

  5. Comparing dynamic connective tissue in echinoderms and sponges: morphological and mechanical aspects and environmental sensitivity.

    Science.gov (United States)

    Sugni, Michela; Fassini, Dario; Barbaglio, Alice; Biressi, Anna; Di Benedetto, Cristiano; Tricarico, Serena; Bonasoro, Francesco; Wilkie, Iain C; Candia Carnevali, Maria Daniela

    2014-02-01

    Echinoderms and sponges share a unique feature that helps them face predators and other environmental pressures. They both possess collagenous tissues with adaptable viscoelastic properties. In terms of morphology these structures are typical connective tissues containing collagen fibrils, fibroblast- and fibroclast-like cells, as well as unusual components such as, in echinoderms, neurosecretory-like cells that receive motor innervation. The mechanisms underpinning the adaptability of these tissues are not completely understood. Biomechanical changes can lead to an abrupt increase in stiffness (increasing protection against predation) or to the detachment of body parts (in response to a predator or to adverse environmental conditions) that are regenerated. Apart from these advantages, the responsiveness of echinoderm and sponge collagenous tissues to ionic composition and temperature makes them potentially vulnerable to global environmental changes.

  6. Temporal and Spatial Distribution Patterns of Echinoderm Larvae in La Parguera, Puerto Rico

    Directory of Open Access Journals (Sweden)

    Stacey M Williams

    2010-10-01

    Full Text Available This study describes temporal and spatial abundance patterns of echinoderm larvae in La Parguera, Puerto Rico. For the temporal study, larvae were sampled by a series of monthly tows taken with a 64μm mesh net between the new and full moon from April 2005 to July 2006, September 2006 and August 2007. In order to measure spatial variation of echinoderm larval bundances, oblique tows were taken with 64 and 202μm mesh nets at seven different sites within the shelf, at the shelf-edge, and at a nearby oceanic stations during August 2007. Overall, Echinoidea (sea urchin exhibited the highest abundance with a total of 11 921 larvae, representing 52.5% of the total collection. Ophiuroidea (brittle star ranked second in abundance with 45.6% of the total larvae. Holothuroidea (sea cucumber and Asteroidea larvae (sea star accounted for less than 2% of the total echinoderm larval collection. Early larval stages (2-8 day old of Diadema antillarum represented 20% of the total Echinoidea larvae. There was no marked seasonal trend of echinoderm larval abundance; Echinoidea and Ophiuroidea larvae were present in all monthly samples indicating that reproduction occurs year-round. Peak abundances of later-stage Echinoidea larvae were observed during January, July and October and of later-stage Ophiuroidea larvae during June, August and October. The observed peaks of later-stage larval abundances may be indicative of higher recruitment activity during these months. There was a significant difference of echinoderm larval abundance between spatial stations, with higher abundances collected at the shelf-edge. Later-stage (~24 day old D. antillarum larvae were mostly collected at shelf-edge and oceanic locations. In addition, the 64mm mesh net was more efficient for collection of echinoderm larvae than the 202mm mesh net. Rev. Biol. Trop. 58 (Suppl. 3: 81-88. Epub 2010 October 01.

  7. Echinoderm Biodiversity in the Takofi Coastal Waters, Moti Island, North Maluku

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    Eddy Yusron

    2006-04-01

    Full Text Available A total of 22 echinoderm species were found in Takofi waters, North Maluku. They were represented by 6 species of holothuroidea, 4 species of asteroidea, 5 species of echinoidea and 7 species of ophiuroidea. The Ophiuroidea were relatively common in seagrass area. The quantitative analysis on the abundance data revealed the highest diversity index of faunal assemblage at station II (H'=1.19. The highest evenness index was exhibited by the echinoderms from station III (J = 0.99, while the highest species richness was represented by them from station I (D = 1.22.

  8. Inventory of echinoderms in the Iles Eparses (Europa, Glorieuses, Juan de Nova), Mozambique Channel, France

    Science.gov (United States)

    Conand, C.; Mulochau, T.; Stöhr, S.; Eléaume, M.; Chabanet, P.

    2016-04-01

    The multidisciplinary programme BioReCIE (Biodiversity, Resources and Conservation of coral reefs at Eparses Is.) inventoried multiple marine animal groups in order to provide information on the coral reef health of the Iles Eparses. All five classes of echinoderms were observed by visual census, photographed and later identified. About 100 species are reported, including a few unidentified ones which require further studies. The Holothuroidea and Ophiuroidea are the most diverse. One new species, the asterinid Aquilonastra chantalae O'Loughlin and McKenzie (2013), was discovered in addition to several new records of echinoderms. The illegal fishery targeting holothurians, which are presently highly valuable resources in this zone, is discussed.

  9. Stars in the Silurian sky: Echinoderm holdfasts from the Carnic Alps, Austria

    Energy Technology Data Exchange (ETDEWEB)

    Ferretti, A.; Ausich, W.I.; Corradini, C.; Corriga, M.G.; Schoenlaub, H.P.

    2016-07-01

    A small collection of echinoderm holdfasts from the Ludlow Cardiola Formation of the Carnic Alps (Austria) contains a wide range of morphologies as a response of environmental adaptation. In general, the holdfasts have a globous and massive dome-like profile with several processes arranged in a sub-radial disposition, so to create a sort of ‘star-like’ outline. A small central depression is common but not present on all specimens. The distinctive holdfasts are preserved in an iron-rich phase, documenting a substitution that has also affected other non-echinoderm calcareous material. (Author)

  10. Nouvelle interpretation des echinodermes de Collado de Tosas (Gerona, Espagne

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    Meléndez, B.

    1988-12-01

    Full Text Available The revision of the echinoderms from Collado de Tosas, based on the original specimens and additional material, is undertaken. The study shows that the initial attribution to the genus Trochocystites belonging to the Homalozoa Cincta has been induced by the tectonic deformation and the presence of recristallization lamellae in the natural molds. New observations allow to conclude without ambiguity that these skeletal elements are isolated columnals with a broad lumen, of crinoids. The presence of Cambrian in the section, established exclusively on the initial determinations, cannot longer be maintained.Los fósiles de Equinodermos del Collado de Tosas fueron dados a conocer en 1911 por F. Azpeitia que los atribuyó a Trochocystites bohemicus Bar. Posteriormente, M. Faura (1912 hizo notar la presencia de fósiles ordovícicos en esta misma localidad, y propuso una interpretación estratigráfica que incluía un contacto anómalo con el supuesto Cámbrico determinado por los Trochocystites. Todo ello fue revisado por B. Meléndez en 1954, que creyó poder confirmar que los fósiles en cuestión (fig. 1, eran realmente Carpoideos. El estudio de nuevo material recogido in situ, así como de los ejemplares conservados en el Museo del Seminario Conciliar de Barcelona, nos ha llevado a la conclusión de que la atribución inicial de estos discutidos fósiles al género Trochocystites, fue debida a la deformación tectónica que les ha dado forma ovalada, y a la presencia de láminas de recristalización, en disposición radial, en los moldes (fig. 6, lám. 1, que dan la falsa apariencia de placas marginales. Las nuevas observaciones nos permiten afirmar que estos fósiles son placas columnales, aisladas, probablemente del pedúnculo de Crinoides, con cavidad central muy amplia (Iám. 1, figs. 15, aunque eventualmente, también podrían haber pertenecido a Cystideos. En consecuencia, la presencia del Cámbrico en esta localidad, basada únicamente en la

  11. Endocrine disrupting compounds and echinoderms: new ecotoxicological sentinels for the marine ecosystem.

    Science.gov (United States)

    Sugni, Michela; Mozzi, Daniela; Barbaglio, Alice; Bonasoro, Francesco; Candia Carnevali, Maria Daniela

    2007-02-01

    Echinoderms are valuable test species in marine ecotoxicology and offer a wide range of biological processes appropriate for this approach. In spite of this potential, available data in literature are still rather limited, particularly with regard to the possible effects of endocrine disrupter compounds (EDCs). This review presents echinoderms as useful models for ecotoxicological tests and gives a brief overview of the most significant results obtained in recent years, particularly in the context of the COMPRENDO EU project. In this research project two different aspects of echinoderm physiology, plausibly regulated by humoral mechanisms, were investigated: reproductive biology and regenerative development. Selected EDCs suspected for their androgenic or antiandrogenic action were tested at low concentrations. The results obtained so far showed that different parameters such as regenerative growth, histological pattern, egg diameter and gonad maturation were affected by the exposure to the selected compounds. These results substantiate that reproductive and regenerative phenomena of echinoderms can be considered valuable alternative models for studies on EDCs and confirm that these compounds interfere with fundamental physiological processes, including growth, development and reproductive competence.

  12. [Taxonomic composition and distribution of the echinoderms associations in the littoral ecosystems from the Colombian Pacific].

    Science.gov (United States)

    Neira, Raúl; Cantera, Jaime R

    2005-12-01

    This paper examines published information and gray literature about taxonomy and ecology of echinoderm species of the Colombian Pacific Coast. Unpublished collection data of specimens kept in the Marine Sciences Museum of the University of Valle are also considered. Sixty-six species are found in coastal ecosystems and shallow bottoms of ten geographical, coastal and insular localities of the Pacific coast of Colombia. Main habitats having echinoderms are: rocky cliffs and shores, coral reefs, sand beaches, mud substrates, mangroves, and shallow bottoms of mud, sand, gravel and rocks. Regular Echinoidea and Asteroidea are the most diverse and abundant groups, mainly in subtidal rocky shallow bottoms and coral reefs. Ophiuroidea are abundant below rocky boulders. Irregular Echinoidea are abundant on sand beaches. The relatively high number of species shows that this geographical area presents a high diversity of echinoderms compared with other tropical shallow and littoral zones of the world. Rocky substrates and coral reefs are the ecosystems with the highest numbers of echinoderm species and individuals. A conservation status assessment is difficult because the lack of periodical sampling and few data about deep zones. In general, the species reported in the last 25 years, have not experimented important changes in their populations, although in some specific places, populations may decrease because human activities in coastal areas increase sedimentation rates change some rocky substrates to mud or sand.

  13. Neuritogenic activity of gangliosides from echinoderms and their structure-activity relationship.

    Science.gov (United States)

    Kaneko, Masafumi; Yamada, Koji; Miyamoto, Tomofumi; Inagaki, Masanori; Higuchi, Ryuichi

    2007-03-01

    The effects of the gangliosides isolated from echinoderms on the neuritogenesis of a rat pheochromocytoma cell line (PC-12 cells) in the presence of nerve growth factor were investigated. The results show that they displayed neuritogenic activity. Based on the observed results, a structure-activity relationship has been established.

  14. [Diversity and distribution of crustaceans and echinoderms and their relation with sedimentation levels in coral reefs].

    Science.gov (United States)

    Vázquez-Domínguez, Ella

    2003-03-01

    Seven reef formations were studied in South Caicos, Turks & Caicos, to determine the species richness, patterns of diversity and patterns of distribution of crustaceans and echinoderms, and to evaluate the relationship between these parameters and the degree of sedimentation of the different sites. The reefs showed a gradient from a high sedimentation level, almost totally covered by algae, to places with no sediment particles deposited over the corals. Sites were classified as with high, low or null sedimentation, and species richness, abundance, diversity, spatial distribution of species and similarity among sites were estimated. No unique pattern was found: for crustaceans as well as for echinoderms, the site with the highest diversity value and high equitability, presumably associated to the environmental heterogeneity of this reef formation, showed null sedimentation and an uniform and random pattern of distribution, crustaceans and echinoderms respectively. The two sites with the lowest diversity for both animal groups, although with different sedimentation levels, showed the lowest equitability value and were the only sites with an aggregated pattern of distribution. The next sites in diversity for crustaceans were those with high sedimentation, probably because most species present inhabit empty conchs, in the sediment, or among seagrass. For the echinoderms, on the contrary, the intermediate sites in diversity had low sedimentation; the habitat requirements for these species (inside sponges, over the corals or among rocks) may have determined this result. The sites with lowest diversity had high sedimentation levels. In these, crustaceans showed the lowest equitability values and an aggregated spatial distribution, while the community of echinoderms was dominated by one single species. Although only general descriptions can be elucidated with the present results, knowledge about the basic population characteristics and natural history of these reef

  15. Developmental gene regulatory network evolution: insights from comparative studies in echinoderms.

    Science.gov (United States)

    Hinman, Veronica F; Cheatle Jarvela, Alys M

    2014-03-01

    One of the central concerns of Evolutionary Developmental biology is to understand how the specification of cell types can change during evolution. In the last decade, developmental biology has progressed toward a systems level understanding of cell specification processes. In particular, the focus has been on determining the regulatory interactions of the repertoire of genes that make up gene regulatory networks (GRNs). Echinoderms provide an extraordinary model system for determining how GRNs evolve. This review highlights the comparative GRN analyses arising from the echinoderm system. This work shows that certain types of GRN subcircuits or motifs, i.e., those involving positive feedback, tend to be conserved and may provide a constraint on development. This conservation may be due to a required arrangement of transcription factor binding sites in cis regulatory modules. The review will also discuss ways in which novelty may arise, in particular through the co-option of regulatory genes and subcircuits. The development of the sea urchin larval skeleton, a novel feature that arose in echinoderms, has provided a model for study of co-option mechanisms. Finally, the types of GRNs that can permit the great diversity in the patterns of ciliary bands and their associated neurons found among these taxa are discussed. The availability of genomic resources is rapidly expanding for echinoderms, including genome sequences not only for multiple species of sea urchins but also a species of sea star, sea cucumber, and brittle star. This will enable echinoderms to become a particularly powerful system for understanding how developmental GRNs evolve.

  16. Notes on the Echinoderm Fauna of the Tapak Tuan Bay Waters, Aceh Selatan the Nangroe Aceh Darussalam

    Directory of Open Access Journals (Sweden)

    Eddy Yusron

    2003-12-01

    Full Text Available A total of 21 species of echinoderms, belonging to of 5 species Holothuroidea, 5 species of Asteroidea, 4 species Echinoidea and 7 species Ophiuroidea have been found in the Tapak Tuan of Aceh Selatan. The Ophiuroidea were relatively dominant in the sea grass zone. On the basis of population density, Ophiuroidea was the dominant group and relatively highest in the individual density. In general, the number of species of echinoderm fauna is smaller than that in the Sekotong Lombok Barat bay waters. The species composition, community structure, zonation, and spatial distribution of echinoderm fauna are discussed in this paper.

  17. Annotated catalogue of recent Echinoderm type specimens in the collection of the Rijksmuseum van Natuurlijke Historie at Leiden

    NARCIS (Netherlands)

    Jangoux, M.; Ridder, de C.

    1987-01-01

    The Leiden Museum houses 82 type specimens of recent echinoderms representing 59 nominal species, one nominal subspecies and one variety. Each species, subspecies or variety is presented (original name, current status, Museum characteristics, brief bibliography, and eventual remarks).

  18. No changes in contributions of echinoderms to the carbon budgets in shelf seas of China over the past five decades

    Science.gov (United States)

    Jin, Shaofei; Yan, Xiaodong; Zhang, Heng; Xiao, Ning; Zhang, Junlong; Liu, Wenliang; Xiong, Zhe

    2015-09-01

    The contribution over the past five decades of echinoderms to the regional carbon cycle of shelf sea areas in China, as well as the changes in calcium carbonate (CaCO3)/calcium carbonate carbon (CaCO3-C) standing stocks and production rates, was investigated using meta-analysis. We report results for water depths of echinoderm biomasses, and total macrobenthos biomasses showed no significant linear decline, but there was a significant decline for the biomass ratio of echinoderms to total macrobenthic biomass since the 1950s. However, there remain no convincing evidences to explain this due to a lack of environmental data. We suggest that studies on the responses of echinoderms to intense anthropogenic activities and climate change should concentrate on their roles in carbon budgets and macrobenthos community stability.

  19. Potential Anti-cancer and Anti-bacterial Activities of Philippine Echinoderm Extracts

    Directory of Open Access Journals (Sweden)

    Rodyl J. Layson

    2014-11-01

    Full Text Available In high-throughput search for bioactive compounds under resource-limited settings from Philippine echinoderms, the aqueous, methanol, chloroform and hexane extracts of seven Philippine echinoderms namely Holothuria nobilis (sea cucumber, Bohadscia marmorata (sea cucumber, Stichopus chloronatus (sea cucumber, Holothuria axiologa (sea cucumber, Linckia laevigata (starfish, Oreaster nodusus (starfish and Ophiocoma ochoenleinii (brittle star were screened for antitumor and antibacterial activity. Antitumor activity was determined using brine shrimp lethality assay while antibacterial assay was performed using turbidimetric method. Both assays utilized 96-well microtiter plates to facilitate speed and ease in screening. The chloroform extract of H. nobilis gave a positive result on antitumor activity while almost all sample extracts showed antibacterial activity against E. coli.

  20. [The role of heterochrony in the establishment of archetype in higher Echinoderm taxa].

    Science.gov (United States)

    Rozhnov, S V

    2009-01-01

    The analysis based on paleontological data shows that the body plans of higher echinoderm taxa were established through the combination of previously developed characters. These combinations appeared due to various heterochronies and resulted in more or less complete filling of the morphological space of logical capabilities. The maximum rank of new taxa decreased with time. New body plans of higher taxa did not replace the old plans but rather overlay them, extending the hierarchy of body plans and the respective hierarchy of taxa. The macroevolution of echinoderms and other metazoans progressed from the formation of an archetype (a general body plan) to individual details, the development of structural plans of lower levels. Heterochrony resulted in mosaic evolution and obscurity of intermediate forms.

  1. Earliest crinoids: New evidence for the origin of the dominant Paleozoic echinoderms

    Science.gov (United States)

    Guensburg, Thomas E.; Sprinkle, James

    2001-02-01

    The oldest crinoids have been discovered in Early Ordovician strata of the western United States. A set of emergent crinoid traits based on these and other early crinoids enables reinterpretation of crinoid origins and early history. The new fossils retain primitive echinoderm characteristics, including ambulacral floor plates and largely unorganized cup plating, a first for crinoids. They lack shared derived characteristics linking them to other stalked echinoderms, including blastozoans. Contrary to current widespread opinion, crinoids originated as an independent group during the Cambrian, apparently from an edrioasteroid ancestor. All four major Paleozoic crinoid clades had evolved by the early Ibexian (Tremadocian), and this initial diversification slightly preceded those of most other Paleozoic evolutionary fauna components. These earliest crinoids attached to carbonate hardgrounds developed on sponge-algal mounds, intraformational conglomerates, and grainstones.

  2. Comparative DNA Damage and Repair in Echinoderm Coelomocytes Exposed to Genotoxicants

    OpenAIRE

    El-Bibany, Ameena H.; Bodnar, Andrea G.; Reinardy, Helena C.

    2014-01-01

    The capacity to withstand and repair DNA damage differs among species and plays a role in determining an organism's resistance to genotoxicity, life history, and susceptibility to disease. Environmental stressors that affect organisms at the genetic level are of particular concern in ecotoxicology due to the potential for chronic effects and trans-generational impacts on populations. Echinoderms are valuable organisms to study the relationship between DNA repair and resistance to genotoxic st...

  3. Hydromechanical considerations on the evolution and diversification of the echinoderm bauplans

    OpenAIRE

    Gudo, Michael

    2005-01-01

    The pentaradial organisation of echinoderms is postulated to have evolved as the result of the reorganisation of the internal U-shaped mesentery of the intestinal tract during inflation of the trunk of a pterobranch-like ancestor. Under this scenario, loops of the mesentery developed between five hydraulic bulges by three different mechanisms: (1) by the early formation of two additional loops resulting directly in five hydraulic bulges, (2) by the subsequent formation of two additional loops...

  4. The A/P axis in echinoderm ontogeny and evolution: evidence from fossils and molecules

    Science.gov (United States)

    Peterson, K. J.; Arenas-Mena, C.; Davidson, E. H.

    2000-01-01

    Even though echinoderms are members of the Bilateria, the location of their anterior/posterior axis has remained enigmatic. Here we propose a novel solution to the problem employing three lines of evidence: the expression of a posterior class Hox gene in the coeloms of the nascent adult body plan within the larva; the anatomy of certain early fossil echinoderms; and finally the relation between endoskeletal plate morphology and the associated coelomic tissues. All three lines of evidence converge on the same answer, namely that the location of the adult mouth is anterior, and the anterior/posterior axis runs from the mouth through the adult coelomic compartments. This axis then orients the animal such that there is but a single plane of symmetry dividing the animal into left and right halves. We tentatively hypothesize that this plane of symmetry is positioned along the dorsal/ventral axis. These axis identifications lead to the conclusion that the five ambulacra are not primary body axes, but instead are outgrowths from the central anterior/posterior axis. These identifications also shed insight into several other evolutionary mysteries of various echinoderm clades such as the independent evolution of bilateral symmetry in irregular echinoids, but do not elucidate the underlying mechanisms of the adult coelomic architecture.

  5. The A/P axis in echinoderm ontogeny and evolution: evidence from fossils and molecules

    Science.gov (United States)

    Peterson, K. J.; Arenas-Mena, C.; Davidson, E. H.

    2000-01-01

    Even though echinoderms are members of the Bilateria, the location of their anterior/posterior axis has remained enigmatic. Here we propose a novel solution to the problem employing three lines of evidence: the expression of a posterior class Hox gene in the coeloms of the nascent adult body plan within the larva; the anatomy of certain early fossil echinoderms; and finally the relation between endoskeletal plate morphology and the associated coelomic tissues. All three lines of evidence converge on the same answer, namely that the location of the adult mouth is anterior, and the anterior/posterior axis runs from the mouth through the adult coelomic compartments. This axis then orients the animal such that there is but a single plane of symmetry dividing the animal into left and right halves. We tentatively hypothesize that this plane of symmetry is positioned along the dorsal/ventral axis. These axis identifications lead to the conclusion that the five ambulacra are not primary body axes, but instead are outgrowths from the central anterior/posterior axis. These identifications also shed insight into several other evolutionary mysteries of various echinoderm clades such as the independent evolution of bilateral symmetry in irregular echinoids, but do not elucidate the underlying mechanisms of the adult coelomic architecture.

  6. Proteome characterization of sea star coelomocytes--the innate immune effector cells of echinoderms.

    Science.gov (United States)

    Franco, Catarina F; Santos, Romana; Coelho, Ana V

    2011-09-01

    Sea star coelomic fluid is in contact with all internal organs, carrying signaling molecules and a large population of circulating cells, the coelomocytes. These cells, also known as echinoderm blood cells, are responsible for the innate immune responses and are also known to have an important role in the first stage of regeneration, i.e. wound closure, necessary to prevent disruption of the body fluid balance and to limit the invasion of pathogens. This study focuses on the proteome characterization of these multifunctional cells. The identification of 358 proteins was achieved using a combination of two techniques for protein separation (1-D SDS-PAGE followed by nanoLC and 2-D SDS-PAGE) and MALDI-TOF/TOF MS for protein identification. To our knowledge, the present report represents the first comprehensive list of sea star coelomocyte proteins, constituting an important database to validate many echinoderm-predicted proteins. Evidence for new pathways in these particular echinoderm cells are also described, and thus representing a valuable resource to stimulate future studies aiming to unravel the homology with vertebrate immune cells and particularly the origins of the immune system itself.

  7. Identification of echinoderms (Echinodermata) from an anchialine cave in Cozumel Island, Mexico, using DNA barcodes.

    Science.gov (United States)

    Bribiesca-Contreras, Guadalupe; Solís-Marín, Francisco A; Laguarda-Figueras, Alfredo; Zaldívar-Riverón, Alejandro

    2013-11-01

    The echinoderm species richness of the Aerolito de Paraiso anchialine cave, on Cozumel Island, in the Mexican Caribbean, is assessed on the basis of morphological and DNA barcoding data. We included specimens from this cave system and from different open sea areas, and employed two different approaches for species delineation based on DNA barcoding data: a 2% cox1 divergence and the general mixed Yule-coalescent (GMYC) approaches. We subsequently compared the results derived from these approaches with our morphospecies discrimination. A total of 188 cox1 sequences belonging to specimens of four echinoderm classes were examined. The 2% cox1 divergence and GMYC approaches recovered 78 and 70 putative species, respectively, 24 and 22 of which corresponded to specimens from the anchialine system. Of 26 echinoderm species identified in the cave system, seven appear to be endemic to it. Among these are Copidaster carvenicola Solís-Marín & Laguarda-Figueras, 2010, two morphologically distinctive, undescribed species belonging to Asterinides and Ophionereis and four probably cryptic undescribed species originally assigned to Amphipholis squamata (Delle Chiaje, 1839), Astropecten duplicatus Gray, 1840, Copidaster lymani (AH Clark, 1948) and Ophiothrix angulata (Say, 1825). Further research and protection of this particularly fragile ecosystem becomes urgent because construction of tourism developments is planned nearby.

  8. [The anteroposterior axis in echinoderms and displacement of the mouth in their phylogeny and ontogeny].

    Science.gov (United States)

    Rozhnov, S V

    2012-01-01

    The difference in the position of the anteroposterior axis in larval and adult echinoderms is related to the displacement of the mouth from the anterior end of the body to the posterior end in the phylogeny of echinoderms, which occurred in the course of the reorganization of their body plan from bilateral asymmetrical to radiosymmetrical. Traces of this phylogenetic process have been especially fully preserved in the ontogeny of crinoids. Other recent echinoderms have largely lost such traces. Dislocation of Hox-genes in sea urchins, resulting from the translocation of these genes to the 5' end of the chromosome and inversion of the anterior Hox-genes, is explained by the necessity to preserve the spatial and temporal colinearity in the course of the convergence of the starting and final stages of the mouth displacement process, similar to the elevation process in crinoids, and inclusion in the basic body plan of the structure of a rudiment now regulated directly by the anterior Hox-genes.

  9. Late Cretaceous-Early Palaeogene echinoderms and the K/T boundary in the southeast Netherlands and northeast Belgium — Part 6: Conclusions

    NARCIS (Netherlands)

    Jagt, J.W.M.

    2000-01-01

    The palaeobiology of echinoderms occurring in the Meerssen and Geulhem members is discussed and changes in diversity across the K/T boundary are documented. Using literature data on the ecology of extant faunas, the various echinoderm groups are considered. Naturally, such data can only be applied w

  10. Late Cretaceous-Early Palaeogene echinoderms and the K/T boundary in the southeast Netherlands and northeast Belgium — Part 6: Conclusions

    NARCIS (Netherlands)

    Jagt, J.W.M.

    2000-01-01

    The palaeobiology of echinoderms occurring in the Meerssen and Geulhem members is discussed and changes in diversity across the K/T boundary are documented. Using literature data on the ecology of extant faunas, the various echinoderm groups are considered. Naturally, such data can only be applied

  11. Early post-metamorphic, Carboniferous blastoid reveals the evolution and development of the digestive system in echinoderms.

    Science.gov (United States)

    Rahman, Imran A; Waters, Johnny A; Sumrall, Colin D; Astolfo, Alberto

    2015-10-01

    Inferring the development of the earliest echinoderms is critical to uncovering the evolutionary assembly of the phylum-level body plan but has long proven problematic because early ontogenetic stages are rarely preserved as fossils. Here, we use synchrotron tomography to describe a new early post-metamorphic blastoid echinoderm from the Carboniferous (approx. 323 Ma) of China. The resulting three-dimensional reconstruction reveals a U-shaped tubular structure in the fossil interior, which is interpreted as the digestive tract. Comparisons with the developing gut of modern crinoids demonstrate that crinoids are an imperfect analogue for many extinct groups. Furthermore, consideration of our findings in a phylogenetic context allows us to reconstruct the evolution and development of the digestive system in echinoderms more broadly; there was a transition from a straight to a simple curved gut early in the phylum's evolution, but additional loops and coils of the digestive tract (as seen in crinoids) were not acquired until much later.

  12. [Diversity and abundance of echinoderms from the reef lagoon at Cahuita National Park, Caribbean from Costa Rica].

    Science.gov (United States)

    Bolaños, Natalie; Bourg, Amandine; Gómez, Javier; Alvarado, Juan José

    2005-12-01

    A total of 15 species of echinoderms (one asteroid, seven ophiuroids, five echinoids and two holothurians) were recorded at the Cahuita National Park reef lagoon, between September and October 2003, using a 1 m2 quadrant. The sites with coral substrate and algae were the most diverse, while those with seagrass and sand were the least. Ophiuroids were the most abundant group with 170 individuals, asteroids were the least abundant. Adding other studies and reports of echinoderms to this study, a total of 23 species have been found at Cahuita National Park, which is the most diverse area on the Caribbean of Costa Rica. We report nine new echinoderm records for Costa Rica's Caribbean.

  13. Uncoupling of complex regulatory patterning during evolution of larval development in echinoderms

    Directory of Open Access Journals (Sweden)

    Jennings Charlotte K

    2010-11-01

    Full Text Available Abstract Background Conservation of orthologous regulatory gene expression domains, especially along the neuroectodermal anterior-posterior axis, in animals as disparate as flies and vertebrates suggests that common patterning mechanisms have been conserved since the base of Bilateria. The homology of axial patterning is far less clear for the many marine animals that undergo a radical transformation in body plan during metamorphosis. The embryos of these animals are microscopic, feeding within the plankton until they metamorphose into their adult forms. Results We describe here the localization of 14 transcription factors within the ectoderm during early embryogenesis in Patiria miniata, a sea star with an indirectly developing planktonic bipinnaria larva. We find that the animal-vegetal axis of this very simple embryo is surprisingly well patterned. Furthermore, the patterning that we observe throughout the ectoderm generally corresponds to that of "head/anterior brain" patterning known for hemichordates and vertebrates, which share a common ancestor with the sea star. While we suggest here that aspects of head/anterior brain patterning are generally conserved, we show that another suite of genes involved in retinal determination is absent from the ectoderm of these echinoderms and instead operates within the mesoderm. Conclusions Our findings therefore extend, for the first time, evidence of a conserved axial pattering to echinoderm embryos exhibiting maximal indirect development. The dissociation of head/anterior brain patterning from "retinal specification" in echinoderm blastulae might reflect modular changes to a developmental gene regulatory network within the ectoderm that facilitates the evolution of these microscopic larvae.

  14. Oral region homologies in paleozoic crinoids and other plesiomorphic pentaradial echinoderms.

    Science.gov (United States)

    Kammer, Thomas W; Sumrall, Colin D; Zamora, Samuel; Ausich, William I; Deline, Bradley

    2013-01-01

    The phylogenetic relationships between major groups of plesiomorphic pentaradial echinoderms, the Paleozoic crinoids, blastozoans, and edrioasteroids, are poorly understood because of a lack of widely recognized homologies. Here, we present newly recognized oral region homologies, based on the Universal Elemental Homology model for skeletal plates, in a wide range of fossil taxa. The oral region of echinoderms is mainly composed of the axial, or ambulacral, skeleton, which apparently evolved more slowly than the extraxial skeleton that forms the majority of the body. Recent phylogenetic hypotheses have focused on characters of the extraxial skeleton, which may have evolved too rapidly to preserve obvious homologies across all these groups. The axial skeleton conserved homologous suites of characters shared between various edrioasteroids and specific blastozoans, and between other blastozoans and crinoids. Although individual plates can be inferred as homologous, no directly overlapping suites of characters are shared between edrioasteroids and crinoids. Six different systems of mouth (peristome) plate organization (Peristomial Border Systems) are defined. These include four different systems based on the arrangement of the interradially-positioned oral plates and their peristomial cover plates, where PBS A1 occurs only in plesiomorphic edrioasteroids, PBS A2 occurs in plesiomorphic edrioasteroids and blastozoans, and PBS A3 and PBS A4 occur in blastozoans and crinoids. The other two systems have radially-positioned uniserial oral frame plates in construction of the mouth frame. PBS B1 has both orals and uniserial oral frame plates and occurs in edrioasterid and possibly edrioblastoid edrioasteroids, whereas PBS B2 has exclusively uniserial oral frame plates and is found in isorophid edrioasteroids and imbricate and gogiid blastozoans. These different types of mouth frame construction offer potential synapomorphies to aid in parsimony-based phylogenetics for

  15. Oral region homologies in paleozoic crinoids and other plesiomorphic pentaradial echinoderms.

    Directory of Open Access Journals (Sweden)

    Thomas W Kammer

    Full Text Available The phylogenetic relationships between major groups of plesiomorphic pentaradial echinoderms, the Paleozoic crinoids, blastozoans, and edrioasteroids, are poorly understood because of a lack of widely recognized homologies. Here, we present newly recognized oral region homologies, based on the Universal Elemental Homology model for skeletal plates, in a wide range of fossil taxa. The oral region of echinoderms is mainly composed of the axial, or ambulacral, skeleton, which apparently evolved more slowly than the extraxial skeleton that forms the majority of the body. Recent phylogenetic hypotheses have focused on characters of the extraxial skeleton, which may have evolved too rapidly to preserve obvious homologies across all these groups. The axial skeleton conserved homologous suites of characters shared between various edrioasteroids and specific blastozoans, and between other blastozoans and crinoids. Although individual plates can be inferred as homologous, no directly overlapping suites of characters are shared between edrioasteroids and crinoids. Six different systems of mouth (peristome plate organization (Peristomial Border Systems are defined. These include four different systems based on the arrangement of the interradially-positioned oral plates and their peristomial cover plates, where PBS A1 occurs only in plesiomorphic edrioasteroids, PBS A2 occurs in plesiomorphic edrioasteroids and blastozoans, and PBS A3 and PBS A4 occur in blastozoans and crinoids. The other two systems have radially-positioned uniserial oral frame plates in construction of the mouth frame. PBS B1 has both orals and uniserial oral frame plates and occurs in edrioasterid and possibly edrioblastoid edrioasteroids, whereas PBS B2 has exclusively uniserial oral frame plates and is found in isorophid edrioasteroids and imbricate and gogiid blastozoans. These different types of mouth frame construction offer potential synapomorphies to aid in parsimony

  16. Comparative DNA damage and repair in echinoderm coelomocytes exposed to genotoxicants.

    Science.gov (United States)

    El-Bibany, Ameena H; Bodnar, Andrea G; Reinardy, Helena C

    2014-01-01

    The capacity to withstand and repair DNA damage differs among species and plays a role in determining an organism's resistance to genotoxicity, life history, and susceptibility to disease. Environmental stressors that affect organisms at the genetic level are of particular concern in ecotoxicology due to the potential for chronic effects and trans-generational impacts on populations. Echinoderms are valuable organisms to study the relationship between DNA repair and resistance to genotoxic stress due to their history and use as ecotoxicological models, little evidence of senescence, and few reported cases of neoplasia. Coelomocytes (immune cells) have been proposed to serve as sensitive bioindicators of environmental stress and are often used to assess genotoxicity; however, little is known about how coelomocytes from different echinoderm species respond to genotoxic stress. In this study, DNA damage was assessed (by Fast Micromethod) in coelomocytes of four echinoderm species (sea urchins Lytechinus variegatus, Echinometra lucunter lucunter, and Tripneustes ventricosus, and a sea cucumber Isostichopus badionotus) after acute exposure to H2O2 (0-100 mM) and UV-C (0-9999 J/m2), and DNA repair was analyzed over a 24-hour period of recovery. Results show that coelomocytes from all four echinoderm species have the capacity to repair both UV-C and H2O2-induced DNA damage; however, there were differences in repair capacity between species. At 24 hours following exposure to the highest concentration of H2O2 (100 mM) and highest dose of UV-C (9999 J/m2) cell viability remained high (>94.6 ± 1.2%) but DNA repair ranged from 18.2 ± 9.2% to 70.8 ± 16.0% for H2O2 and 8.4 ± 3.2% to 79.8 ± 9.0% for UV-C exposure. Species-specific differences in genotoxic susceptibility and capacity for DNA repair are important to consider when evaluating ecogenotoxicological model organisms and assessing overall impacts of genotoxicants in the environment.

  17. Comparative DNA damage and repair in echinoderm coelomocytes exposed to genotoxicants.

    Directory of Open Access Journals (Sweden)

    Ameena H El-Bibany

    Full Text Available The capacity to withstand and repair DNA damage differs among species and plays a role in determining an organism's resistance to genotoxicity, life history, and susceptibility to disease. Environmental stressors that affect organisms at the genetic level are of particular concern in ecotoxicology due to the potential for chronic effects and trans-generational impacts on populations. Echinoderms are valuable organisms to study the relationship between DNA repair and resistance to genotoxic stress due to their history and use as ecotoxicological models, little evidence of senescence, and few reported cases of neoplasia. Coelomocytes (immune cells have been proposed to serve as sensitive bioindicators of environmental stress and are often used to assess genotoxicity; however, little is known about how coelomocytes from different echinoderm species respond to genotoxic stress. In this study, DNA damage was assessed (by Fast Micromethod in coelomocytes of four echinoderm species (sea urchins Lytechinus variegatus, Echinometra lucunter lucunter, and Tripneustes ventricosus, and a sea cucumber Isostichopus badionotus after acute exposure to H2O2 (0-100 mM and UV-C (0-9999 J/m2, and DNA repair was analyzed over a 24-hour period of recovery. Results show that coelomocytes from all four echinoderm species have the capacity to repair both UV-C and H2O2-induced DNA damage; however, there were differences in repair capacity between species. At 24 hours following exposure to the highest concentration of H2O2 (100 mM and highest dose of UV-C (9999 J/m2 cell viability remained high (>94.6 ± 1.2% but DNA repair ranged from 18.2 ± 9.2% to 70.8 ± 16.0% for H2O2 and 8.4 ± 3.2% to 79.8 ± 9.0% for UV-C exposure. Species-specific differences in genotoxic susceptibility and capacity for DNA repair are important to consider when evaluating ecogenotoxicological model organisms and assessing overall impacts of genotoxicants in the environment.

  18. Signal transduction at fertilization: the Ca2+ release pathway in echinoderms and other invertebrate deuterostomes.

    Science.gov (United States)

    Townley, Ian K; Roux, Michelle M; Foltz, Kathy R

    2006-04-01

    Gamete interaction and fusion triggers a number of events that lead to egg activation and development of a new organism. A key event at fertilization is the rise in intracellular calcium. In deuterostomes, this calcium is released from the egg's endoplasmic reticulum and is necessary for proper activation. This article reviews recent data regarding how gamete interaction triggers the initial calcium release, focusing on the echinoderms (invertebrate deuterostomes) as model systems. In eggs of these animals, Src-type kinases and phospholipase C-gamma are required components of the initial calcium trigger pathway in eggs.

  19. Ammonium and phosphate excretion in three common echinoderms from Philippine coral reefs.

    Science.gov (United States)

    Dy; Yap

    2000-08-30

    The ammonium and phosphate excretion and oxygen consumption of three species of echinoderms (Tripneustes gratilla, Protoreaster nodosus and Ophiorachna incrassata) commonly encountered in Philippine coral reefs were investigated in relation to time of day (i.e. daytime between 10:00 and 12:00 h vs. nighttime between 22:00 and 24:00 h) and their recent feeding history (i.e. recently-collected vs. short-term starvation for 3+/-1 days). The experiment used whole organism incubations and followed a nested hierarchical design. Ammonium excretion rates were 1447+/-310 nmolg(-1) DWh(-1) (mean+/-S.E., n=24) for T. gratilla, 361+/-33 for O. incrassata and 492+/-38 for P. nodosus. Ammonium excretion differed significantly among species, time of incubation and recent feeding history. Interaction between species and recent feeding history was also significant. The organisms excreted more ammonium during daytime except for starved specimens of O. incrassata. In addition, animals that were starved in the laboratory for a few days had a tendency to excrete more ammonium than recently-collected specimens. Phosphate excretion rates were 25+/-13 nmolg(-1) DWh(-1) for T. gratilla, 10+/-2 for O. incrassata and 4+/-1 for P. nodosus. There were no significant differences in phosphate excretion among the three species of echinoderms, their recent feeding history and time of day. Oxygen consumption rates were 286+/-24 µg O(2)g(-1) DWh(-1) for T. gratilla, 64+/-3 for O. incrassata and 54+/-3 for P. nodosus. Oxygen consumption differed significantly among species and recent feeding history but differed only slightly with time of incubation. There was a significant correlation between oxygen consumption and ammonium excretion (r=0.48, P=0.018), and between oxygen consumption and phosphate excretion (r=0.41, P=0.047) for T. gratilla. The nutrient excretion by tropical echinoderms is another pathway by which inorganic nutrients are regenerated in coral reef communities. However, the quantity

  20. Studying the Relative Strengths of Environmental Factors that Influence Echinoderm Body Size Trends

    Science.gov (United States)

    Low, A.; Randhawa, S.; Heim, N. A.; Payne, J.

    2013-12-01

    Body size is often a useful metric in observing how a clade responds to environmental changes. Previous research has uncovered how environmental factors such as carbon dioxide and oxygen levels influence body size evolution. However, we wanted to look into how these natural factors interact and which factors seem to have a stronger relative influence on echinoderm body size. We analyzed carbon dioxide levels, a proxy for paleotemperature, oxygen levels, and sea level. Our research process involved measuring and calculating the volume of Phanerozoic echinoderm fossils recorded in the Treatise on Invertebrate Paleontology, plotting their mean volumes over various natural factors, and using statistical tools such as correlation tests and the PaleoTS statistical analysis software to compare the relative strengths of these factors. Furthermore, we divided our data into the following three subsets to uncover more specific relationships: 1) A set that included all data of the phylum Echinodermata 2) A set that focused on the two classes with the most recorded data, Echinoidea and Crinoidea 3) A set that focused on the crinoid specimens that originated in the Paleozoic and in the post-Paleozoic. In the first subset, echinoderms had the strongest correlation with carbon dioxide, a proxy for temperature, and possessed a weaker correlation with oxygen. In the second subset, we discovered that the echinoid data also possessed a strong correlation with carbon dioxide and a weaker correlation with oxygen. For crinoids, we found that the class as a whole showed no strong correlation with any measured environmental factors. However, when we divided the crinoids based on age, we found that both Paleozoic and post-Paleozoic crinoids individually correlated strongly with sea level. However, some uncertainty with this correlation arose as the comparison of the environmental correlate models suggested that an unbiased random walk was the best fit for the data. This stands as a sharp

  1. Phosphorylation Modulates Ameloblastin Self-assembly and Ca2+ Binding

    Directory of Open Access Journals (Sweden)

    Øystein Stakkestad

    2017-07-01

    Full Text Available Ameloblastin (AMBN, an important component of the self-assembled enamel extra cellular matrix, contains several in silico predicted phosphorylation sites. However, to what extent these sites actually are phosphorylated and the possible effects of such post-translational modifications are still largely unknown. Here we report on in vitro experiments aimed at investigating what sites in AMBN are phosphorylated by casein kinase 2 (CK2 and protein kinase A (PKA and the impact such phosphorylation has on self-assembly and calcium binding. All predicted sites in AMBN can be phosphorylated by CK2 and/or PKA. The experiments show that phosphorylation, especially in the exon 5 derived part of the molecule, is inversely correlated with AMBN self-assembly. These results support earlier findings suggesting that AMBN self-assembly is mostly dependent on the exon 5 encoded region of the AMBN gene. Phosphorylation was significantly more efficient when the AMBN molecules were in solution and not present as supramolecular assemblies, suggesting that post-translational modification of AMBN must take place before the enamel matrix molecules self-assemble inside the ameloblast cell. Moreover, phosphorylation of exon 5, and the consequent reduction in self-assembly, seem to reduce the calcium binding capacity of AMBN suggesting that post-translational modification of AMBN also can be involved in control of free Ca2+ during enamel extra cellular matrix biomineralization. Finally, it is speculated that phosphorylation can provide a functional crossroad for AMBN either to be phosphorylated and act as monomeric signal molecule during early odontogenesis and bone formation, or escape phosphorylation to be subsequently secreted as supramolecular assemblies that partake in enamel matrix structure and mineralization.

  2. Developmental gene regulatory network architecture across 500 million years of echinoderm evolution

    Science.gov (United States)

    Hinman, Veronica F.; Nguyen, Albert T.; Cameron, R. Andrew; Davidson, Eric H.

    2003-01-01

    Evolutionary change in morphological features must depend on architectural reorganization of developmental gene regulatory networks (GRNs), just as true conservation of morphological features must imply retention of ancestral developmental GRN features. Key elements of the provisional GRN for embryonic endomesoderm development in the sea urchin are here compared with those operating in embryos of a distantly related echinoderm, a starfish. These animals diverged from their common ancestor 520-480 million years ago. Their endomesodermal fate maps are similar, except that sea urchins generate a skeletogenic cell lineage that produces a prominent skeleton lacking entirely in starfish larvae. A relevant set of regulatory genes was isolated from the starfish Asterina miniata, their expression patterns determined, and effects on the other genes of perturbing the expression of each were demonstrated. A three-gene feedback loop that is a fundamental feature of the sea urchin GRN for endoderm specification is found in almost identical form in the starfish: a detailed element of GRN architecture has been retained since the Cambrian Period in both echinoderm lineages. The significance of this retention is highlighted by the observation of numerous specific differences in the GRN connections as well. A regulatory gene used to drive skeletogenesis in the sea urchin is used entirely differently in the starfish, where it responds to endomesodermal inputs that do not affect it in the sea urchin embryo. Evolutionary changes in the GRNs since divergence are limited sharply to certain cis-regulatory elements, whereas others have persisted unaltered.

  3. How do changes in parental investment influence development in echinoid echinoderms?

    Science.gov (United States)

    Alcorn, Nicholas J; Allen, Jonathan D

    2009-01-01

    Understanding the relationship between egg size, development time, and juvenile size is critical to explaining patterns of life-history evolution in marine invertebrates. Currently there is conflicting information about the effects of changes in egg size on the life histories of echinoid echinoderms. We sought to resolve this conflict by manipulating egg size and food level during the development of two planktotrophic echinoid echinoderms: the green sea urchin, Strongylocentrotus droebachiensis and the sand dollar, Echinarachnius parma. Based on comparative datasets, we predicted that decreasing food availability and egg size would increase development time and reduce juvenile size. To test our prediction, blastomere separations were performed in both species at the two-cell stage to reduce egg volume by 50%, producing whole- and half-size larvae that were reared to metamorphosis under high or low food levels. Upon settlement, age at metamorphosis, juvenile size, spine number, and spine length were measured. As predicted, reducing egg size and food availability significantly increased age at metamorphosis and reduced juvenile quality. Along with previous egg size manipulations in other echinoids, this study suggests that the relationship between egg size, development time, and juvenile size is strongly dependent upon the initial size of the egg.

  4. Heterogeneous generation of new cells in the adult echinoderm nervous system

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    Vladimir S. Mashanov

    2015-09-01

    Full Text Available Adult neurogenesis, generation of new functional cells in the mature central nervous system (CNS, has been documented in a number of diverse organisms, ranging from humans to invertebrates. However, the origin and evolution of this phenomenon is still poorly understood for many of the key phylogenetic groups. Echinoderms are one such phylum, positioned as a sister group to chordates within the monophyletic clade Deuterostomia. They are well known for the ability of their adult organs, including the CNS, to completely regenerate after injury. Nothing is known, however, about production of new cells in the nervous tissue under normal physiological conditions in these animals. In this study, we show that new cells are continuously generated in the mature radial nerve cord (RNC of the sea cucumber Holothuria glaberrima. Importantly, this neurogenic activity is not evenly distributed, but is significantly more extensive in the lateral regions of the RNC than along the midline. Some of the new cells generated in the apical region of the ectoneural neuroepithelium leave their place of origin and migrate basally to populate the neural parenchyma. Gene expression analysis showed that generation of new cells in the adult sea cucumber CNS is associated with transcriptional activity of genes known to be involved in regulation of various aspects of neurogenesis in other animals. Further analysis of one of those genes, the transcription factor Myc showed that it is expressed, in some, but not all radial glial cells, suggesting heterogeneity of this CNS progenitor cell population in echinoderms.

  5. Fibronectin phosphorylation by ecto-protein kinase

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    Imada, Sumi; Sugiyama, Yayoi; Imada, Masaru (Meiji Institute of Health Science, Odawara (Japan))

    1988-12-01

    The presence of membrane-associated, extracellular protein kinase (ecto-protein kinase) and its substrate proteins was examined with serum-free cultures of Swiss 3T3 fibroblast. When cells were incubated with ({gamma}-{sup 32})ATP for 10 min at 37{degree}C, four proteins with apparent molecular weights between 150 and 220 kDa were prominently phosphorylated. These proteins were also radiolabeled by lactoperoxidase catalyzed iodination and were sensitive to mild tryptic digestion, suggesting that they localized on the cell surface or in the extracellular matrix. Phosphorylation of extracellular proteins with ({gamma}-{sup 32}P)ATP in intact cell culture is consistent with the existence of ecto-protein kinase. Anti-fibronectin antibody immunoprecipitated one of the phosphoproteins which comigrated with a monomer and a dimer form of fibronectin under reducing and nonreducing conditions of electrophoresis, respectively. The protein had affinity for gelatin as demonstrated by retention with gelatin-conjugated agarose. This protein substrate of ecto-protein kinase was thus concluded to be fibronectin. The sites of phosphorylation by ecto-protein kinase were compared with those of intracellularly phosphorylated fibronectin by the analysis of radiolabeled amino acids and peptides. Ecto-protein kinase phosphorylated fibronectin at serine and threonine residues which were distinct from the sites of intracellular fibronectin phosphorylation.

  6. Phylogenetic position of Licnophora, Lechriopyla, and Schizocaryum, three unusual ciliates (phylum Ciliophora) endosymbiotic in echinoderms (phylum Echinodermata).

    Science.gov (United States)

    Lynn, Denis H; Strüder-Kypke, Michaela

    2002-01-01

    Various echinoderms are colonized by species from several classes of the Phylum Ciliophora, indicating that the echinoderm "habitat" has been invaded independently on numerous occasions throughout evolutionary history. Two "echinoderm" ciliates whose phylogenetic positions have been problematic are Licnophora macfarlandi Stevens, 1901 and Schizocaryum dogieli Poljansky and Golikova, 1957. Licnophora macfarlandi is an endosymbiont of the respiratory trees of holothuroids, and S. dogieli is found in the esophagus of echinoids. A third species, Lechriopyla mystax Lynch, 1930, is a plagiopylid ciliate found in the intestine of echinoids. Host echinoderms were collected near the Friday Harbor Laboratories, San Juan Island, WA. Specimens of S. dogieli and L. mystax were obtained from the esophagus and intestine, respectively, of the sea urchin Strongylocentrotus pallidus. Specimens of L. macfarlandi were collected from the fluid obtained from the respiratory trees of Parastichopus californicus. Using small subunit ribosomal RNA (SSrRNA) sequences of these three ciliates and a global alignment of SSrRNA sequences of other ciliates, we established the following. 1) Licnophora is a spirotrich ciliate, clearly related to the hypotrichs and stichotrichs; this is corroborated by its possession of macronuclear replication bands. 2) Lechriopyla is the sister genus to Plagiopyla and is a member of the Class Plagiopylea, which was predicted based on its cytology. 3) Schizocaryum clusters in the Class Oligohymenophorea and is most closely related to the scuticociliates; there are currently no morphological features known to relate Schizocaryum to the scuticociliates.

  7. Late Cretaceous-Early Palaeogene echinoderms and the K/T boundary in the southeast Netherlands and northeast Belgium —

    NARCIS (Netherlands)

    Jagt, J.W.M.; Kutscher, M.

    2000-01-01

    The present paper is divided into two parts. In the first, all Campanian, Maastrichtian and Danian ophiuroids known to date from the extended type area of the Maastrichtian Stage, are described and illustrated. The geographic and stratigraphic distribution of this diverse echinoderm group are docume

  8. Annotated Catalogue of recent echinoderm type specimen in the collection of the Zoölogisch Museum Amsterdam

    NARCIS (Netherlands)

    Jangoux, Michel

    1991-01-01

    The Amsterdam Museum houses 2,047 type specimens of recent echinoderms representing 441 nominal species, 5 nominal subspecies, and 11 nominal varieties. Each species, subspecies or variety is presented (original name, current status, museum characteristics, brief bibliography, and eventual remarks).

  9. Volume regulation of intestinal cells of echinoderms: Putative role of ion transporters (Na(+)/K(+)-ATPase and NKCC).

    Science.gov (United States)

    Castellano, Giovanna C; Souza, Marta M; Freire, Carolina A

    2016-11-01

    Echinoderms are exclusively marine osmoconformer invertebrates. Some species occupy the challenging intertidal region. Upon salinity changes, the extracellular osmotic concentration of these animals also varies, exposing tissues and cells to osmotic challenges. Cells and tissues may then respond with volume regulation mechanisms, which involve transport of ions and water into and/or out of the cells, through ion transporters, such as the Na(+)/K(+)-ATPase and NKCC. The goal of this study was to relate the cell volume regulation capacity of echinoderm intestinal cells Na(+)/K(+)-ATPase and NKCC activities, in three echinoderm species: Holothuria grisea, Arbacia lixula, and Echinometra lucunter. Isolated cells of these species displayed some control of their cell volume upon exposure to anisosmotic media (isolated intestinal cells, calcein fluorescence as indicator of volume change), with a distinct higher capacity shown by H. grisea, which did not swell even upon 50% hyposmotic shock. The holothuroid cells showed indirect evidence (effect of furosemide) of the participation of NKCC in this process, with a secretory function, and of a secondary role by the NKA (effect of ouabain). Other mechanisms are probably responsible for this function in the urchins. Variable expression of these transporters, and others not examined here, may to some extent account for the variability in cell volume regulation capacity in echinoderm cells.

  10. Echinoderms associated with reef formations in Zihuatanejo and Acapulco, Guerrero, Mexico

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    Pablo Zamorano

    2009-12-01

    Full Text Available Knowledge of echinoderms from Zihuatanejo and Acapulco, Guerrero is currently limited to taxonomic listings. This work attempts to characterize better the community of these organisms associatedto coral reefs in this region using band transects of 50 m length by 1 m width. Two samplings were carried out in 2004, one in the rainy season and other in the dry season. Ten species, three Asteroidea,six Echinoidea and one Holothuroidea, were found. The mean values obtained for diversity in the 13 study sites (1.036 bits ind-1 are considered low when compared with the maximum possible diversity(3.322 bits ind-1, and this is likely due to the dominance of the black sea urchin Diadema mexicanum and the starsh Phataria unifascialis, with densities reported of 1.45±0.60 ind m-2 and 0.12±0.02 ind m-2, respectively. The highest diversity was associated with low tide, which is not different between localities.The spatial arrangement of the echinoderm species composition obtained by the multidimensional scaling analysis denotes the formation of ve conglomerates according to similarity, where the substratum and reef cover are the possible determinant variables. The four predominant species (D. mexicanum, P. unifascialis, Toxopneustes roseus and Hesperocidaris asteriscus, whose densities were compared with those of other sites of the Oriental Tropical Pacic, show, in general, inferior values for Echinoidea and intermediate values for the Asteroidea. For the specic case of D. mexicanum, there are differences in the densities between localities, depths, and time of year, and the mean value obtained of 1.45±0.60 ind m-2 was low compared to densities recorded in other zones. Also, it was observed that in some localities, such as Playa Coral, Caleta de Chon, Punta del Cerro Colorado, and Zacatoso, the sea urchin densities increased considerably during the rainy season, and these high densities maintain a positive correlation with coral cover, which is indicative

  11. Mg isotopes in biocarbonates: new insight into vital effects associated to echinoderms and bivalves calcification

    Science.gov (United States)

    Planchon, F.; Hermans, J.; Borremans, C.; Dubois, P.; Poulain, C.; Paulet, Y.; Andre, L.

    2007-12-01

    Mg isotopes can be helpful tracers to reveal the fundamental pathways of Mg incorporation during biomineralisation. We report in this study a detailed characterisation of the Mg isotopic signatures of different biominerals: high magnesium calcitic skeletons of selected echinoderms (sea urchins and starfish) and low magnesium aragonitic shells of a bivalve species (clam). State of the art analytical procedures were applied including sample purification step followed by high precision measurements using MC-ICP-MS (Nu instrument) in dry plasma conditions. 26Mg/24Mg and 25Mg/24Mg are expressed as per mil deviations from the DSM3 (Dead Sea Metal 3) reference standard in delta notation (d26Mg and d25Mg). For echinoderms, we considered: (a) adult specimens of six starfish species (Asteria r., Marthasterias g., Anseropoda p., Asterina g., Echinaster s. and Henricia o.), sampled in Brittany (France); (b) a sea urchin species (Paracentrotus lividus) with field samples (Mediterranean Sea, Marseille, France) and culture specimen under T and S controlled conditions. In vivo endoskeletons display negative, but different d26Mg values of -3.06 for starfish (with uniform interspecies signatures) and -2.65 for sea urchin. Relative to seawater signature (-0.82), all echinoderms favour the incorporation of light isotopes during biocalcification. The d26Mg depletion is lower than theoretically expected from a inorganic calcite precipitation from seawater (at -3.5). These differences suggest that on its route from seawater to the shell, Mg isotopes are partly biologically fractionationated through "vital effects" leaving heavier Mg isotopic signatures. Taken into account that calcification in echinoderms is an intra- cellular process involving transient amorphous calcium carbonate (ACC) phase, the observed bio-fractionation factors can be related to: (1) changes in the isotopic composition of the precipitating intracellular fluids due to active pumping in and out of the cell; (2) a

  12. Interfibrillar stiffening of echinoderm mutable collagenous tissue demonstrated at the nanoscale

    Science.gov (United States)

    Mo, Jingyi; Blowes, Liisa M.; Egertová, Michaela; Terrill, Nicholas J.; Wang, Wen; Elphick, Maurice R.; Gupta, Himadri S.

    2016-01-01

    The mutable collagenous tissue (MCT) of echinoderms (e.g., sea cucumbers and starfish) is a remarkable example of a biological material that has the unique attribute, among collagenous tissues, of being able to rapidly change its stiffness and extensibility under neural control. However, the mechanisms of MCT have not been characterized at the nanoscale. Using synchrotron small-angle X-ray diffraction to probe time-dependent changes in fibrillar structure during in situ tensile testing of sea cucumber dermis, we investigate the ultrastructural mechanics of MCT by measuring fibril strain at different chemically induced mechanical states. By measuring a variable interfibrillar stiffness (EIF), the mechanism of mutability at the nanoscale can be demonstrated directly. A model of stiffness modulation via enhanced fibrillar recruitment is developed to explain the biophysical mechanisms of MCT. Understanding the mechanisms of MCT quantitatively may have applications in development of new types of mechanically tunable biomaterials. PMID:27708167

  13. Troponin-I is present as an essential component of muscles in echinoderm larvae

    Science.gov (United States)

    Yaguchi, Shunsuke; Yaguchi, Junko; Tanaka, Hiroyuki

    2017-01-01

    The troponin complex, composed of Troponin-I, Troponin-T and Troponin-C, is an essential mediator of the contraction of striated muscle downstream of calcium signaling in almost all bilaterians. However, in echinoderms and hemichordates, collectively termed Ambulacraria, the components of the troponin complex have never been isolated, thus suggesting that these organisms lost the troponin system during evolution. Here, by analyzing genomic information from sea urchins, we identify the troponin-I gene and isolate its complete mRNA sequence. Using this information, we reveal that the larval muscles express this gene and its translated product and that the protein is definitely a functional molecule expressed in sea urchin larvae by showing that Troponin-I morphants are unable to swallow algae. We conclude that muscular contraction in all bilaterians universally depends on a regulatory system mediated by Troponin-I, which emerged in the common ancestor of bilaterians. PMID:28272398

  14. Echinodermata das praias de Salvador (Bahia, Brasil The Echinoderms of Salvador beaches (Bahia, Brazil

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    Orane Falcão de Souza Alves

    2000-06-01

    Full Text Available This paper presents 28 species of Echinoderms collected on 5 beaches of Salvador (12º54' to 13º01' S and 38º26' to 38º33' W, Brazil, which are distributed in 19 families. Ophiuroidea represented 53,6% of the collected species, followed by Echinoidea (28,6%, Asteroidea (7,1%, Holothuroidea (7,1%, and Crinoidea (3,6%. Ophiuroidea and Echinoidea were the most frequent groups, occurring at all the studied beaches while Crinoidea occurred only on 20% of them. Most of the species are characterized as belonging to the tropical warm waters, some to the shallow coastal areas and some having a broad bathymetric distribution. The richness of species values on beaches ranged from 7 to 24, at Itapua Beach, and from 2 to 14 among different kinds of habitats, where protected ones showed higher values.

  15. Ancestral state reconstruction by comparative analysis of a GRN kernel operating in echinoderms.

    Science.gov (United States)

    Erkenbrack, Eric M; Ako-Asare, Kayla; Miller, Emily; Tekelenburg, Saira; Thompson, Jeffrey R; Romano, Laura

    2016-01-01

    Diverse sampling of organisms across the five major classes in the phylum Echinodermata is beginning to reveal much about the structure and function of gene regulatory networks (GRNs) in development and evolution. Sea urchins are the most studied clade within this phylum, and recent work suggests there has been dramatic rewiring at the top of the skeletogenic GRN along the lineage leading to extant members of the euechinoid sea urchins. Such rewiring likely accounts for some of the observed developmental differences between the two major subclasses of sea urchins-cidaroids and euechinoids. To address effects of topmost rewiring on downstream GRN events, we cloned four downstream regulatory genes within the skeletogenic GRN and surveyed their spatiotemporal expression patterns in the cidaroid Eucidaris tribuloides. We performed phylogenetic analyses with homologs from other non-vertebrate deuterostomes and characterized their spatiotemporal expression by quantitative polymerase chain reaction (qPCR) and whole-mount in situ hybridization (WMISH). Our data suggest the erg-hex-tgif subcircuit, a putative GRN kernel, exhibits a mesoderm-specific expression pattern early in Eucidaris development that is directly downstream of the initial mesodermal GRN circuitry. Comparative analysis of the expression of this subcircuit in four echinoderm taxa allowed robust ancestral state reconstruction, supporting hypotheses that its ancestral function was to stabilize the mesodermal regulatory state and that it has been co-opted and deployed as a unit in mesodermal subdomains in distantly diverged echinoderms. Importantly, our study supports the notion that GRN kernels exhibit structural and functional modularity, locking down and stabilizing clade-specific, embryonic regulatory states.

  16. Dynamic evolution of toll-like receptor multigene families in echinoderms.

    Science.gov (United States)

    Buckley, Katherine M; Rast, Jonathan P

    2012-01-01

    The genome sequence of the purple sea urchin, Strongylocentrotus purpuratus, a large and long-lived invertebrate, provides a new perspective on animal immunity. Analysis of this genome uncovered a highly complex immune system in which the gene families that encode homologs of the pattern recognition receptors that form the core of vertebrate innate immunity are encoded in large multigene families. The sea urchin genome contains 253 Toll-like receptor (TLR) sequences, more than 200 Nod-like receptors and 1095 scavenger receptor cysteine-rich domains, a 10-fold expansion relative to vertebrates. Given their stereotypic protein structure and simple intron-exon architecture, the TLRs are the most tractable of these families for more detailed analysis. A role for these receptors in immune defense is suggested by their similarity to TLRs in other organisms, sequence diversity, and expression in immunologically active tissues, including phagocytes. The complexity of the sea urchin TLR multigene families is largely derived from expansions independent of those in vertebrates and protostomes, although a small family of TLRs with structure similar to that of Drosophila Toll can be traced to an ancient eumetazoan ancestor. Several other echinoderm sequences are now available, including Lytechinus variegatus, as well as partial sequences from two other sea urchin species. Here, we present an analysis of the invertebrate deuterostome TLRs with emphasis on the echinoderms. Representatives of most of the S. purpuratus TLR subfamilies and homologs of the mccTLR sequences are found in L. variegatus, although the L. variegatus TLR gene family is notably smaller (68 TLR sequences). The phylogeny of these genes within sea urchins highlights lineage-specific expansions at higher resolution than is evident at the phylum level. These analyses identify quickly evolving TLR subfamilies that are likely to have novel immune recognition functions and other, more stable, subfamilies that may

  17. Determination of Gonyautoxin-4 in Echinoderms and Gastropod Matrices by Conversion to Neosaxitoxin Using 2-Mercaptoethanol and Post-Column Oxidation Liquid Chromatography with Fluorescence Detection.

    Science.gov (United States)

    Silva, Marisa; Rey, Verónica; Botana, Ana; Vasconcelos, Vitor; Botana, Luis

    2015-12-30

    Paralytic Shellfish Toxin blooms are common worldwide, which makes their monitoring crucial in the prevention of poisoning incidents. These toxins can be monitored by a variety of techniques, including mouse bioassay, receptor binding assay, and liquid chromatography with either mass spectrometric or pre- or post-column fluorescence detection. The post-column oxidation liquid chromatography with fluorescence detection method, used routinely in our laboratory, has been shown to be a reliable method for monitoring paralytic shellfish toxins in mussel, scallop, oyster and clam species. However, due to its high sensitivity to naturally fluorescent matrix interferences, when working with unconventional matrices, there may be problems in identifying toxins because of naturally fluorescent interferences that co-elute with the toxin peaks. This can lead to erroneous identification. In this study, in order to overcome this challenge in echinoderm and gastropod matrices, we optimized the conversion of Gonyautoxins 1 and 4 to Neosaxitoxin with 2-mercaptoethanol. We present a new and less time-consuming method with a good recovery (82.2%, RSD 1.1%, n = 3), requiring only a single reaction step.

  18. Temporal and Spatial Distribution Patterns of Echinoderm Larvae in La Parguera, Puerto Rico

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    Stacey M Williams

    2010-10-01

    Full Text Available This study describes temporal and spatial abundance patterns of echinoderm larvae in La Parguera, Puerto Rico. For the temporal study, larvae were sampled by a series of monthly tows taken with a 64μm mesh net between the new and full moon from April 2005 to July 2006, September 2006 and August 2007. In order to measure spatial variation of echinoderm larval bundances, oblique tows were taken with 64 and 202μm mesh nets at seven different sites within the shelf, at the shelf-edge, and at a nearby oceanic stations during August 2007. Overall, Echinoidea (sea urchin exhibited the highest abundance with a total of 11 921 larvae, representing 52.5% of the total collection. Ophiuroidea (brittle star ranked second in abundance with 45.6% of the total larvae. Holothuroidea (sea cucumber and Asteroidea larvae (sea star accounted for less than 2% of the total echinoderm larval collection. Early larval stages (2-8 day old of Diadema antillarum represented 20% of the total Echinoidea larvae. There was no marked seasonal trend of echinoderm larval abundance; Echinoidea and Ophiuroidea larvae were present in all monthly samples indicating that reproduction occurs year-round. Peak abundances of later-stage Echinoidea larvae were observed during January, July and October and of later-stage Ophiuroidea larvae during June, August and October. The observed peaks of later-stage larval abundances may be indicative of higher recruitment activity during these months. There was a significant difference of echinoderm larval abundance between spatial stations, with higher abundances collected at the shelf-edge. Later-stage (~24 day old D. antillarum larvae were mostly collected at shelf-edge and oceanic locations. In addition, the 64mm mesh net was more efficient for collection of echinoderm larvae than the 202mm mesh net. Rev. Biol. Trop. 58 (Suppl. 3: 81-88. Epub 2010 October 01.Este estudio describe patrones de abundancia temporal y espacial de larvas de

  19. Late Cretaceous-Early Palaeogene echinoderms and the K/Tboundary in the southeast Netherlands and northeast Belgium - Part 2: Crinoids

    NARCIS (Netherlands)

    Jagt, J.W.M.

    1999-01-01

    All Campanian, Maastrichtian and Danian articulate (cladid) crinoids known to date from the extendedtype area of the Maastrichtian Stage, are described and illustrated. The geographic and stratigraphicdistribution of this unexpectedly diverse echinoderm group are documented. A total of twentygenera

  20. An evolutionary scenario for the origin of pentaradial echinoderms-implications from the hydraulic principles of form determination.

    Science.gov (United States)

    Gudo, Michael

    2005-01-01

    The early evolutionary history of echinoderms was reconstructed on the basis of structural-functional considerations and application of the quasi-engineering approach of 'Konstruktions-Morphologie'. According to the presented evolutionary scenario, a bilaterally symmetrical ancestor, such as an enteropneust-like organism, became gradually modified into a pentaradial echinoderm by passing through an intermediate pterobranch-like stage. The arms of a pentaradial echinoderm are identified as hydraulic outgrowths from the central coelomic cavity of the bilateral ancestor which developed due to a shortening of the body in length but widening in the diameter. The resulting pentaradial symmetry is a consequence of mechanical laws that dictate minimal contact surface areas among hydraulic pneumatic entities. These developed in the coelomic cavity (metacoel) in the bilaterally symmetrical ancestor, when from the already U-shaped mesentery with the intestinal tract two additional U-shaped bows developed directly or subsequently. During the subsequent development tensile chords of the mesentery 'sewed' the gut with the body wall first in three and secondly in five 'seams'. During the direct development five 'seams' between tensile chords and body wall developed straightly. These internal tensile chords subdivide the body coelom into five hydraulic subsystems ('pneus'), which eventually arrange in a pentaradial pattern. The body could then enlarge only between the tensile chords, which means that five hydraulic bulges developed. These bulges initially supported the tentacles and finally each of them enclosed the tentacle until only the feather-like appendages of the tentacles projected over the surface. The tentacles with their feathers were transformed into the ambulacral system, and the bulges become the arms. These morphological transformations were accompanied and partly determined by specific histological modifications, such as the development of mutable connective

  1. Structure and anticoagulant activity of sulfated fucans. Comparison between the regular, repetitive, and linear fucans from echinoderms with the more heterogeneous and branched polymers from brown algae.

    Science.gov (United States)

    Pereira, M S; Mulloy, B; Mourão, P A

    1999-03-19

    Sulfated fucans are among the most widely studied of all the sulfated polysaccharides of non-mammalian origin that exhibit biological activities in mammalian systems. Examples of these polysaccharides extracted from echinoderms have simple structures, composed of oligosaccharide repeating units within which the residues differ by specific patterns of sulfation among different species. In contrast the algal fucans may have some regular repeating structure but are clearly more heterogeneous when compared with the echinoderm fucans. The structures of the sulfated fucans from brown algae also vary from species to species. We compared the anticoagulant activity of the regular and repetitive fucans from echinoderms with that of the more heterogeneous fucans from three species of brown algae. Our results indicate that different structural features determine not only the anticoagulant potency of the sulfated fucans but also the mechanism by which they exert this activity. Thus, the branched fucans from brown algae are direct inhibitors of thrombin, whereas the linear fucans from echinoderms require the presence of antithrombin or heparin cofactor II for inhibition of thrombin, as reported for mammalian glycosaminoglycans. The linear sulfated fucans from echinoderms have an anticoagulant action resembling that of mammalian dermatan sulfate and a modest action through antithrombin. A single difference of one sulfate ester per tetrasaccharide repeating unit modifies the anticoagulant activity of the polysaccharide markedly. Possibly the spatial arrangements of sulfate esters in the repeating tetrasaccharide unit of the echinoderm fucan mimics the site in dermatan sulfate with high affinity for heparin cofactor II.

  2. The mechanically adaptive connective tissue of echinoderms: its potential for bio-innovation in applied technology and ecology.

    Science.gov (United States)

    Barbaglio, A; Tricarico, S; Ribeiro, A; Ribeiro, C; Sugni, M; Di Benedetto, C; Wilkie, I; Barbosa, M; Bonasoro, F; Candia Carnevali, M D

    2012-05-01

    Echinoderms possess unique connective tissues, called mutable collagenous tissues (MCTs), which undergo nervously mediated, drastic and reversible or irreversible changes in their mechanical properties. Connective tissue mutability influences all aspects of echinoderm biology and is a key-factor in the ecological success of the phylum. Due to their sensitivity to endogenous or exogenous agents, MCTs may be targets for a number of common pollutants, with potentially drastic effects on vital functions. Besides its ecological relevance, MCT represents a topic with relevance to several applied fields. A promising research route looks at MCTs as a source of inspiration for the development of novel biomaterials. This contribution presents a review of MCT biology, which incorporates recent ultrastructural, biomolecular and biochemical analyses carried out in a biotechnological context.

  3. Hydroxylation of a conserved tRNA modification establishes non-universal genetic code in echinoderm mitochondria.

    Science.gov (United States)

    Nagao, Asuteka; Ohara, Mitsuhiro; Miyauchi, Kenjyo; Yokobori, Shin-Ichi; Yamagishi, Akihiko; Watanabe, Kimitsuna; Suzuki, Tsutomu

    2017-09-01

    The genetic code is not frozen but still evolving, which can result in the acquisition of 'dialectal' codons that deviate from the universal genetic code. RNA modifications in the anticodon region of tRNAs play a critical role in establishing such non-universal genetic codes. In echinoderm mitochondria, the AAA codon specifies asparagine instead of lysine. By analyzing mitochondrial (mt-) tRNA(Lys) isolated from the sea urchin (Mesocentrotus nudus), we discovered a novel modified nucleoside, hydroxy-N(6)-threonylcarbamoyladenosine (ht(6)A), 3' adjacent to the anticodon (position 37). Biochemical analysis revealed that ht(6)A37 has the ability to prevent mt-tRNA(Lys) from misreading AAA as lysine, thereby indicating that hydroxylation of N(6)-threonylcarbamoyladenosine (t(6)A) contributes to the establishment of the non-universal genetic code in echinoderm mitochondria.

  4. The skeletal proteome of the brittle star Ophiothrix spiculata identifies C-type lectins and other proteins conserved in echinoderm skeleton formation

    Directory of Open Access Journals (Sweden)

    Brian T. Livingston

    2016-07-01

    Full Text Available Determining the identity and functional role of proteins involved in biomineralization and the formation of skeletons is critical to our understanding of the process. Proteomics has allowed rapid characterization of the proteins occluded within mineralized tissue, but the large numbers of proteins detected makes it difficult to assign the relative importance of each protein. We have taken a comparative approach, examining the skeletal proteome of different species of echinoderms in order to identify the proteins that are conserved and likely to be important. Our previous study comparing the skeletal proteome of the brittle star Ophiocoma wendtii to the published proteomes of the sea urchin Strongylocentrotus purpuratus revealed some conservation of proteins, but indicated that the C-type lectin domain-containing spicule matrix proteins abundant in the sea urchin skeletal proteome were not conserved in the brittle star. Here we examine the skeletal proteome of a different species of brittle star, Ophiothrix spiculata. We have isolated the proteins from the skeleton of O. spiculata and performed LC/MS/MS to identify peptides present. Comparison to transcriptome and genome databases revealed the proteins present in the O. spiculata proteome. Despite being diverged for several million years, the two brittle stars have very similar proteins in their skeletons. Included is a fibrinogen C-like lectin and several C-type lectins proteins, which we describe in detail. The unusual number of C-type lectins found in the S. purpuatus skeleton and the repetitive regions seen in those spicule matrix proteins are not present in O. spiculata.

  5. Developmental origin of the adult nervous system in a holothurian: an attempt to unravel the enigma of neurogenesis in echinoderms.

    Science.gov (United States)

    Mashanov, Vladimir S; Zueva, Olga R; Heinzeller, Thomas; Aschauer, Beate; Dolmatov, Igor Yu

    2007-01-01

    In adult echinoderms, the nervous system includes the ectoneural and hyponeural subsystems. The former has been believed to develop from the ectoderm, whereas the latter is considered to be mesodermal in origin. However, this view has not been substantially supported by embryological examinations. Our study deals with the developmental origin of the nervous system in the direct-developing sea cucumber Eupentacta fraudatrix. The rudiment of the adult nervous system develops from ectodermally derived cells, which ingress into the primary body cavity from the floor of the vestibule. At the earliest stages, only the rudiment of the ectoneural nerve ring is laid down. The radial nerve cords and tentacular nerves grow out from this subcutaneous rudiment. The ectoneural cords do not develop simultaneously but make their appearance in the following order: unpaired mid-ventral cord, paired dorsal lateral cords, and ventral lateral cords. These transitional developmental stages probably recapitulate the evolution of the echinoderm body plan. The holothurian hyponeural subsystem, as other regions of the metazoan nervous system, has an ectodermal origin. It originally appears as a narrow band of tissue, which bulges out of the basal region of the ectoneural neuroepithelium. Our data combined with those of other workers strongly suggest that the adult nervous tissue in echinoderms develops separately from the superficial larval system of ciliary nerves. Therefore, our data are neither in strict accordance with Garstang's hypothesis nor do they allow to refuse it. Nevertheless, in addition to ciliary bands, other areas of neurogenetic epidermis must be taken into account.

  6. Abundance and size patterns of echinoderms in coastal soft-bottoms at Deception Island (South Shetland Islands, Antarctica)

    Science.gov (United States)

    Angulo-Preckler, Carlos; Tuya, Fernando; Avila, Conxita

    2017-04-01

    Deception Island is an active volcano in Antarctic waters under high sedimentation regimes, which may affect the abundance and structure of soft-bottom assemblages. During the summer of 2012-2013, a survey of the shallow water soft-bottom assemblages of Deception Island was carried out to examine patterns of abundance and size structure of the three dominant echinoderms (Ophionotus victoriae, Sterechinus neumayeri and Odontaster validus) at 8 locations encompassing a gradient in proximity from the open ocean, including two depths (5 vs. 15 m) per location. Abundance patterns of the three species varied with depth; organisms were typically more abundant at 15 relative to 5 m depth. Our results partially supported the hypothesis that echinoderms from locations adjacent to the open ocean present larger abundances. Body sizes varied significantly among locations and depths for the three species and some places presented a density-size pattern. High sedimentation rates, combined with low ice-related disturbance, may be the reason behind the large abundances of echinoderms found in this waters.

  7. Echinoderms in Shallow-Bottom from Ahumadera Sector, Cispatá Bay, Cordoba, Colombian Caribbean

    Directory of Open Access Journals (Sweden)

    Jorge Alexander QUIRÓS RODRÍGUEZ

    2014-10-01

    Full Text Available This study represents a report of the echinoderm fauna found in shallow waters of the sector La Ahumadera, Cispatá Bay, Colombian Caribbean. The area is formed by a plain substrate type soft sand-mud colonized by sponges in punta Terraplén and sandy with seagrass (Thalassia testudinum, macroalgae and sponges in punta Robalo. Were identified ten species of echinoderms belonging to four classes (Asteroidea, Ophiuroidea, Echinoidea and Holothuroidea, distributed in eight families and nine genera. The number of taxa identified corresponds to 4.1% of the species recorded for the Colombian Caribbean, and shows the representation of species of echinoderms in this sector. The most abundant species in punta Robalo were Encope michelini (24,3% and Ophiothrix angulata, while in punta Terraplén were O. angulata (36,7% and Ophiactis savignyi (16,5%. Higher richness (S= 9, diversity (H’= 2.64 and evenness (U= 0.92 were found in punta Robalo compared to values from Terraplén (S= 6, H’= 2.39 and U= 0.83. Both stations showed a similarity index (Is of 0.66.Among the species identified, the following are new records for the department of Córdoba: Holothuria floridana, Encope michelini and Mellita quinquiesperforata.EQUINODERMOS EN FONDOS SOMEROS DEL SECTOR LA AHUMADERA, BAHÍA DE CISPATÁ, CÓRDOBA, CARIBE COLOMBIANO Este estudio representa un reporte de la fauna de equinodermos que se encuentran en fondos someros del sector La Ahumadera, bahía de Cispatá, Caribe colombiano. El área está formada por un sustrato de tipo fango-arenoso colonizado por esponjas en punta Terraplén, y arenoso con pasto marino (Thalassia testudinum, macroalgas y esponjas en punta Robalo. Se identificaron diez especies de equinodermos que pertenecen a cuatro clases (Asteroidea, Ophiuroidea, Echinoidea y Holothuroidea, distribuidas en ocho familias y nueve géneros. El número de taxones identificados corresponde al 4,1% de las especies registradas para el Caribe colombiano

  8. Protein phosphorylation and photorespiration.

    Science.gov (United States)

    Hodges, M; Jossier, M; Boex-Fontvieille, E; Tcherkez, G

    2013-07-01

    Photorespiration allows the recycling of carbon atoms of 2-phosphoglycolate produced by ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) oxygenase activity, as well as the removal of potentially toxic metabolites. The photorespiratory pathway takes place in the light, encompasses four cellular compartments and interacts with several other metabolic pathways and functions. Therefore, the regulation of this cycle is probably of paramount importance to plant metabolism, however, our current knowledge is poor. To rapidly respond to changing conditions, proteins undergo a number of different post-translational modifications that include acetylation, methylation and ubiquitylation, but protein phosphorylation is probably the most common. The reversible covalent addition of a phosphate group to a specific amino acid residue allows the modulation of protein function, such as activity, subcellular localisation, capacity to interact with other proteins and stability. Recent data indicate that many photorespiratory enzymes can be phosphorylated, and thus it seems that the photorespiratory cycle is, in part, regulated by protein phosphorylation. In this review, the known phosphorylation sites of each Arabidopsis thaliana photorespiratory enzyme and several photorespiratory-associated proteins are described and discussed. A brief account of phosphoproteomic protocols is also given since the published data compiled in this review are the fruit of this approach.

  9. Echinoderms from Azores islands: an unexpected source of antibiotic resistant Enterococcus spp. and Escherichia coli isolates.

    Science.gov (United States)

    Marinho, Catarina; Silva, Nuno; Pombo, Sofia; Santos, Tiago; Monteiro, Ricardo; Gonçalves, Alexandre; Micael, Joana; Rodrigues, Pedro; Costa, Ana Cristina; Igrejas, Gilberto; Poeta, Patrícia

    2013-04-15

    The prevalence of antibiotic resistance and the implicated mechanisms of resistance were evaluated in Enterococcus spp. and Escherichia coli, isolated from a total of 250 faecal samples of echinoderms collected from Azorean waters (Portugal). A total of 144 enterococci (120 Enterococcus faecium, 14 E. hirae, 8 E. faecalis, 2 E. gallinarum) and 10 E. coli were recovered. High percentages of resistance in enterococci were found for erythromycin, ampicillin, tetracyclin and ciprofloxacin. The erm(A) or erm(B), tet(M) and/or tet(L), vat(D), aac(6')-aph(2″) and aph(3')-IIIa genes were found in isolates resistant to erythromycin, tetracycline, quinupristin/dalfopristin, high-level gentamicin and high-level kanamycin, respectively. Resistance in E. coli isolates was detected for streptomycin, amikacin, tetracycline and tobramycin. The aadA gene was found in streptomycin-resistant isolates and tet(A)+tet(B) genes in tetracycline-resistant isolates. The data recovered are essential to improve knowledge about the dissemination of resistant strains through marine ecosystems and the possible implications involved in transferring these resistances either to other animals or to humans.

  10. Cambrian cinctan echinoderms shed light on feeding in the ancestral deuterostome.

    Science.gov (United States)

    Rahman, Imran A; Zamora, Samuel; Falkingham, Peter L; Phillips, Jeremy C

    2015-11-07

    Reconstructing the feeding mode of the latest common ancestor of deuterostomes is key to elucidating the early evolution of feeding in chordates and allied phyla; however, it is debated whether the ancestral deuterostome was a tentaculate feeder or a pharyngeal filter feeder. To address this, we evaluated the hydrodynamics of feeding in a group of fossil stem-group echinoderms (cinctans) using computational fluid dynamics. We simulated water flow past three-dimensional digital models of a Cambrian fossil cinctan in a range of possible life positions, adopting both passive tentacular feeding and active pharyngeal filter feeding. The results demonstrate that an orientation with the mouth facing downstream of the current was optimal for drag and lift reduction. Moreover, they show that there was almost no flow to the mouth and associated marginal groove under simulations of passive feeding, whereas considerable flow towards the animal was observed for active feeding, which would have enhanced the transport of suspended particles to the mouth. This strongly suggests that cinctans were active pharyngeal filter feeders, like modern enteropneust hemichordates and urochordates, indicating that the ancestral deuterostome employed a similar feeding strategy.

  11. Eggs as energy: revisiting the scaling of egg size and energetic content among echinoderms.

    Science.gov (United States)

    Moran, A L; McAlister, J S; Whitehill, E A G

    2013-08-01

    Marine organisms exhibit substantial life-history diversity, of which egg size is one fundamental parameter. The size of an egg is generally assumed to reflect the amount of energy it contains and the amount of per-offspring maternal investment. Egg size and energy are thought to scale isometrically. We investigated this relationship by updating published datasets for echinoderms, increasing the number of species over those in previous studies by 62%. When we plotted egg energy versus egg size in the updated dataset we found that planktotrophs have a scaling factor significantly lower than 1, demonstrating an overall trend toward lower energy density in larger planktotrophic eggs. By looking within three genera, Echinometra, Strongylocentrotus, and Arbacia, we also found that the scaling exponent differed among taxa, and that in Echinometra, energy density was significantly lower in species with larger eggs. Theoretical models generally assume a strong tradeoff between egg size and fecundity that limits energetic investment and constrains life-history evolution. These data suggest that the evolution of egg size and egg energy content can be decoupled, possibly facilitating response to selective factors such as sperm limitation which could act on volume alone.

  12. Comparative study of reproductive synchrony at various scales in deep-sea echinoderms

    Science.gov (United States)

    Baillon, Sandrine; Hamel, Jean-François; Mercier, Annie

    2011-03-01

    This study examined the influence of temporal and spatial factors on the determination of reproductive cycles in selected deep-water echinoderms. The prevalence of inter-individual synchrony in the gametogenesis of three ubiquitous species, Phormosoma placenta (Echinoidea), Hippasteria phrygiana (Asteroidea) and Mesothuria lactea (Holothuroidea) collected off the coast of Newfoundland and Labrador (eastern Canada), was determined. Analyses revealed diverse degrees of gametogenic asynchrony at the scales examined (within trawls, between trawls over similar or different periods, as well as among depths and locations over the same period). Taken as a whole, samples did not show any annual or seasonal patterns, whereas some sets of samples, taken over a particular time period in the same area and at the same depth, revealed well synchronized maturing and/or spawning periods in P. placenta and H. phrygiana. This study presents evidence that determination of reproductive cycles in many deep-sea species may be affected by low sampling resolution inherent to most deep-sea studies. More accurate assessments of reproductive patterns and periodicities may require much tighter collection designs as several species are likely to rely on long-term or transient pairing and aggregation to synchronize their breeding activities.

  13. Steroid levels in crinoid echinoderms are altered by exposure to model endocrine disruptors.

    Science.gov (United States)

    Lavado, Ramón; Barbaglio, Alice; Carnevali, M Daniela Candia; Porte, Cinta

    2006-06-01

    Sexual steroids (testosterone and estradiol) were measured in the whole body of wild specimens of the crinoid Antedon mediterranea collected from the Tyrrhenian Sea (Italy). Testosterone levels (274-1,488 pg/g wet weight (w.w.)) were higher than those of estradiol (60-442 pg/g w.w.) and no significant differences between males and females were observed. No clear seasonal trend was either detected - individuals from February, June and October 2004 analyzed - apart from a peak of estradiol in males in autumn. Nonetheless, dramatic changes on tissue steroid levels were observed when individuals were exposed to model androgenic and anti-androgenic compounds for 2 and 4 weeks. The selected compounds were 17 alpha-methyltestosterone (17 alpha-MT), triphenyltin (TPT), fenarimol (FEN), cyproterone acetate (CPA), and p,p'-DDE. Endogenous testosterone levels were significantly increased after exposure to 17 alpha-MT, TPT and FEN, while different responses were observed for estradiol; 17 alpha-MT and FEN increased endogenous estradiol (up to seven-fold), and TPT lead to a significant decrease. Concerning the anti-androgenic compounds, CPA significantly reduced testosterone in a dose-dependent manner without altering estradiol levels, whereas specimens exposed to p,p'-DDE at a low dose (24 ng/L) for 4 weeks showed a four-fold increase in T levels. Overall, the data show the ability of the selected compounds to alter endogenous steroid concentrations in A. mediterranea, and suggest the existence in this echinoderm species of vertebrate-like mechanisms that can be affected by exposure to androgenic and anti-androgenic chemicals.

  14. Regenerative response and endocrine disrupters in crinoid echinoderms: an old experimental model, a new ecotoxicological test.

    Science.gov (United States)

    Candia Carnevali, M D

    2005-01-01

    The regenerative phenomena that reproduce developmental processes in adult organisms and are regulated by endocrine and neurohumoral mechanisms can provide new sensitive tests for monitoring the effects of exposure to anthropogenic chemicals such as endocrine disrupter (ED) contaminants. These pollutants in fact can be bioaccumulated by the organisms, causing dysfunctions in steroid hormone production/metabolism and activities and inducing dramatic effects on reproductive competence, development and growth in many animals, man included. Current research is exploring the effects of exposure to different classes of compounds well known for their ED activity, such as polychlorinated biphenyls (PCBs), nonylphenols and organotins, on regenerative potential of echinoderms, a relatively unexplored and promising applied approach which offers the unique chance to study physiological developmental processes in adult animals. The selected test species is the crinoid Antedon mediterranea, which represents a valuable experimental model for investigation into the regenerative process from the macroscopic to the molecular level. The present study employs an integrated approach which combines exposure experiments, chemical analysis and biological analysis utilizing classical methods of light (LM) and electron (TEM and SEM) microscopy and immunocytochemistry. The experiments were carried out on experimentally induced arm regenerations in controlled conditions with exposure concentrations comparable to those of moderately polluted coastal zones in order to reproduce common conditions of exposure to environmental contaminants. The results of the exposure tests were analysed in terms of effects at the whole organism, at the tissue and cellular level, and possible sites of action of EDs. Our results show that prolonged exposure to these compounds significantly affects the regenerative mechanisms by inducing appreciable anomalies in terms of regeneration times, overall growth, general

  15. Dynamic evolution of toll-like receptor multigene families in echinoderms

    Directory of Open Access Journals (Sweden)

    Katherine M Buckley

    2012-06-01

    Full Text Available The genome of the purple sea urchin, Strongylocentrotus purpuratus, was the first to be sequenced from a long-lived large invertebrate. Analysis of this genome uncovered a surprisingly complex immune system in which the moderately sized sets of pattern recognition receptors that form the core of vertebrate innate immunity are encoded in large multigene families. The sea urchin genome contains 253 Toll-like receptor (TLR genes, more than 200 Nod-like receptors and 1095 scavenger receptor cysteine-rich domains, a ten-fold expansion relative to vertebrates. Given their stereotypic structure and simple intron-exon architecture, the TLRs are the most tractable of these families for more detailed analysis. An immune defense role for these receptors is suggested by their sequence diversity and expression in immunologically active tissues, including phagocytes. This complexity of the sea urchin TLR multigene families largely derives from expansions that are independent of those in vertebrates and protostomes, although a small family of TLRs with structure similar to that of Drosophila Toll likely originated in an ancient eumetazoan ancestor. Several other invertebrate deuterostome genomes have been sequenced, including the cephalochordate, Branchiostoma floridae and the sea urchin Lytechinus variegatus, as well as partial sequences from two other sea urchin species. Here, we present an analysis of the invertebrate deuterostome TLRs with emphasis on the echinoderms. Representatives of most of the S. purpuratus TLR subfamilies and homologs of the protostome-like sequences are found in L. variegatus. The phylogeny of these genes within sea urchins highlights lineage-specific expansions at higher resolution than is evident at the phylum level. These analyses identify quickly evolving TLR subfamilies that are likely to have novel functions and other, more stable, subfamilies that may function similarly to those of vertebrates.

  16. Effects of manganese and hypoxia on coelomocyte renewal in the echinoderm, Asterias rubens (L.)

    Energy Technology Data Exchange (ETDEWEB)

    Oweson, Carolina [Department of Marine Ecology, University of Gothenburg, Kristineberg 566, SE-450 34 Fiskebaeckskil (Sweden); Li Chenghua; Soederhaell, Irene [Department of Comparative Physiology, Evolutionary Biology Centre, Uppsala University, Norbyvaegen 18a, SE-752 36 Uppsala (Sweden); Hernroth, Bodil, E-mail: bodil.hernroth@marecol.gu.se [Royal Swedish Academy of Sciences, Kristineberg 566, SE-450 34 Fiskebaeckskil (Sweden); Biomedical Group, Kristianstad University, SE-291 88 Kristianstad (Sweden)

    2010-10-01

    Manganese (Mn) is a naturally abundant metal and particularly so in soft-bottom oceanic sediments where it generally occurs bound in a four-valent colloidal state as MnO{sub 2}. When hypoxic conditions occur in bottom waters, the metal reduces to the bioavailable ion Mn{sup 2+} and can reach concentrations known to have immunotoxic effects in the crustacean Nephrops norvegicus, reducing numbers of circulating haemocytes as a consequence. However, we have previously shown that Mn seems to have a contrasting effect on the echinoderm Asterias rubens in which it triggers the proliferation of haematopoietic cells and increases coelomocyte numbers. Since elevated Mn levels mostly co-occur with hypoxia in nature, here we investigated whether hypoxia has a negative effect on haematopoiesis. Proliferation and differentiation of coelomocytes and cells in the coelomic epithelium of A. rubens were compared after 3 days of exposure to realistic levels of Mn, hypoxia or a combination of these two parameters. We can confirm that Mn elevated numbers of coelomocytes and increased proliferation of epithelial cells, but hypoxia did not affect these levels. However, hypoxia did affect differentiation of these cells as judged by investigating the expression of a Runt domain transcription factor, which was also cloned and sequenced. Through comparative quantification using a real time PCR technique, we found that exposure to hypoxia had a clearly stimulating effect on mRNA expression of Runt gene in both coelomocytes and epithelial cells. These results indicate that during hypoxic conditions the composition of coelomocyte sub-populations changed.

  17. Bathymetric and interspecific variability in maternal reproductive investment and diet of eurybathic echinoderms

    Science.gov (United States)

    Ross, David A. N.; Hamel, Jean-François; Mercier, Annie

    2013-10-01

    While conditions in shallow-water and deep-sea environments differ markedly, it remains unclear how eurybathic species adapt their life histories to cope with these changes. The present study compared indicators of maternal reproductive investment of three common echinoderms collected shallower than 20 m and deeper than 850 m: Cucumaria frondosa (Holothuroidea), Solaster endeca and Henricia sanguinolenta (Asteroidea). Depth-specific and species-specific differences were found in gonad indices (GI), potential fecundity, oocyte size frequency, as well as lipid classes and fatty acids measured in gonad tissue and oocytes. The asteroids, S. endeca and H. sanguinolenta, exemplified the interspecific trade-off between size and number of oocytes: the former had fewer larger oocytes than the latter, with higher total lipid proportions in them. However, intraspecifically, larger oocytes found in deep specimens of S. endeca did not translate into lower fecundity but rather into a seemingly higher GI, indicating greater investment per oocyte without reducing fecundity. Oocytes were absent in specimens of C. frondosa sampled in deep water, suggesting delayed or impaired maturation at the limit of their depth tolerance. Analysis of S. endeca sterol proportions in gonads and oocytes across depths showed higher sterol input into oocytes in females from the deep. Gonads of S. endeca and H. sanguinolenta contained similar essential fatty acids, but showed significant differences in major fatty acids and some of the less dominant ones, indicating diet specificities. Analyses within S. endeca showed evidence of similar feeding mode (carnivory) at both depths, but suggested shifts in the diet or synthesis of fatty acids, presumably reflecting differences in available food sources and/or adaptations to their respective environments.

  18. Effect of the East Siberian barrier on the echinoderm dispersal in the Arctic Ocean

    Science.gov (United States)

    Mironov, A. N.; Dilman, A. B.

    2010-06-01

    The distributional patterns were analyzed for 43 species and 33 genera of echinoderms in the Laptev and East Siberian seas and for 59 species and 35 genera of the asteroid species in the Arctic Ocean. The probable colonization route through the Arctic was suggested for each species based on (1) the distributional patterns of the Arctic species, (2) the distributional patterns of the closely related species, and (3) the location of the center of the diversity of the species belonging to a certain genus. The species of the Pacific origin prevailed in the asteroid fauna of the Arctic seas. The asteroid species diversity and the ratio of the species of Pacific origin decreased from the Barents towards the Laptev Sea and increased, respectively, in the East Siberian and the Chukchee seas. The species range limits were found for 19 species in the East Siberian Sea compared to only 3 species in the Laptev Sea. The East Siberian Sea was a limiting area for the dispersal of four species groups: (1) invaders from the North Pacific dispersing along the Asian coast of the Arctic (shallow-water stenobathic species), (2) invaders from the North Pacific dispersing along the American coast of the Arctic and further on back into the Arctic along the Eurasian coast (secondarily Atlantic species); (3) originally invaders from the Northern Atlantic; (4) representatives of the Arctic autochthonous fauna. A great width of the biotic boundaries (i.e., the zones of the species range boundaries crowding) was typical for the Arctic Basin, which was a sign of their young geological age.

  19. Novel insights into the echinoderm nervous system from histaminergic and FMRFaminergic-like cells in the sea cucumber Leptosynapta clarki.

    Science.gov (United States)

    Hoekstra, Luke A; Moroz, Leonid L; Heyland, Andreas

    2012-01-01

    Understanding of the echinoderm nervous system is limited due to its distinct organization in comparison to other animal phyla and by the difficulty in accessing it. The transparent and accessible, apodid sea cucumber Leptosynapta clarki provides novel opportunities for detailed characterization of echinoderm neural systems. The present study used immunohistochemistry against FMRFamide and histamine to describe the neural organization in juvenile and adult sea cucumbers. Histaminergic- and FMRFaminergic-like immunoreactivity is reported in several distinct cell types throughout the body of L. clarki. FMRFamide-like immunoreactive cell bodies were found in the buccal tentacles, esophageal region and in proximity to the radial nerve cords. Sensory-like cells in the tentacles send processes toward the circumoral nerve ring, while unipolar and bipolar cells close to the radial nerve cords display extensive processes in close association with muscle and other cells of the body wall. Histamine-like immunoreactivity was identified in neuronal somatas located in the buccal tentacles, circumoral nerve ring and in papillae distributed across the body. The tentacular cells send processes into the nerve ring, while the processes of cells in the body wall papillae extend to the surface epithelium and radial nerve cords. Pharmacological application of histamine produced a strong coordinated, peristaltic response of the body wall suggesting the role of histamine in the feeding behavior. Our immunohistochemical data provide evidence for extensive connections between the hyponeural and ectoneural nervous system in the sea cucumber, challenging previously held views on a clear functional separation of the sub-components of the nervous system. Furthermore, our data indicate a potential function of histamine in coordinated, peristaltic movements; consistent with feeding patterns in this species. This study on L. clarki illustrates how using a broader range of neurotransmitter systems

  20. Phosphorylation of formate dehydrogenase in potato tuber mitochondria

    DEFF Research Database (Denmark)

    Bykova, N.V.; Stensballe, A.; Egsgaard, H.

    2003-01-01

    Two highly phosphorylated proteins were detected after two-dimensional (blue native/SDS-PAGE) gel electrophoretic separation of the matrix fraction isolated from potato tuber mitochondria. These two phosphoproteins were identified by mass spectrometry as formate dehydrogenase (FDH) and the E1alpha...

  1. Serine phosphorylation of syndecan-2 proteoglycan cytoplasmic domain

    DEFF Research Database (Denmark)

    Oh, E S; Couchman, J R; Woods, A

    1997-01-01

    Protein kinase C (PKC) is involved in cell-matrix and cell-cell adhesion, and the cytoplasmic domain of syndecan-2 contains two serines (residues 197 and 198) which lie in a consensus sequence for phosphorylation by PKC. Other serine and threonine residues are present but not in a consensus seque...

  2. Determination of GPCR Phosphorylation Status: Establishing a Phosphorylation Barcode.

    Science.gov (United States)

    Prihandoko, Rudi; Bradley, Sophie J; Tobin, Andrew B; Butcher, Adrian J

    2015-06-01

    G protein-coupled receptors (GPCRs) are rapidly phosphorylated following agonist occupation in a process that mediates receptor uncoupling from its cognate G protein, a process referred to as desensitization. In addition, this process provides a mechanism by which receptors can engage with arrestin adaptor molecules and couple to downstream signaling pathways. The importance of this regulatory process has been highlighted recently by the understanding that ligands can direct receptor signaling along one pathway in preference to another, the phenomenon of signaling bias that is partly mediated by the phosphorylation status or phosphorylation barcode of the receptor. Methods to determine the phosphorylation status of a GPCR in vitro and in vivo are necessary to understand not only the physiological mechanisms involved in GPCR signaling, but also to fully examine the signaling properties of GPCR ligands. This unit describes detailed methods for determining the overall phosphorylation pattern on a receptor (the phosphorylation barcode), as well as mass spectrometry approaches that can define the precise sites that become phosphorylated. These techniques, coupled with the generation and characterization of receptor phosphorylation-specific antibodies, provide a full palate of techniques necessary to determine the phosphorylation status of any given GPCR subtype.

  3. Protein tyrosine phosphorylation in streptomycetes.

    Science.gov (United States)

    Waters, B; Vujaklija, D; Gold, M R; Davies, J

    1994-07-01

    Using phosphotyrosine-specific antibodies, we demonstrate that in several Streptomyces spp. a variety of proteins are phosphorylated on tyrosine residues. Tyrosine phosphorylation was found in a number of Streptomyces species including Streptomyces lividans, Streptomyces hygroscopicus and Streptomyces lavendulae. Each species exhibited a unique pattern of protein tyrosine phosphorylation. Moreover, the patterns of tyrosine phosphorylation varied during the growth phase and were also influenced by culture conditions. We suggest that metabolic shifts during the complex growth cycle of these filamentous bacteria, and possibly secondary metabolic pathways, may be controlled by the action of protein tyrosine kinases and phosphatases, as has been demonstrated in signal transduction pathways in eukaryotic organisms.

  4. Does hybridization increase evolutionary rate? Data from the 28S-rDNA D8 domain in echinoderms.

    Science.gov (United States)

    Chenuil, Anne; Egea, Emilie; Rocher, Caroline; Touzet, Hélène; Féral, Jean-Pierre

    2008-11-01

    The divergent domain D8 of the large ribosomal RNA is very variable and extended in vertebrates compared to other eukaryotes. We provide data from 31 species of echinoderms and present the first comparative analysis of the D8 in nonvertebrate deuterostomes. In addition, we obtained 16S mitochondrial DNA sequences for the sea urchin taxa and analyzed single-strand conformation polymorphism (SSCP) of D8 in several populations within the species complex Echinocardium cordatum. A common secondary structure supported by compensatory substitutions and indels is inferred for echinoderms. Variation mostly arises at the tip of the longest stem (D8a), and the most variable taxa also display the longest and most stable D8. The most stable variants are the only ones displaying bulges in the terminal part of the stem, suggesting that selection, rather than maximizing stability of the D8 secondary structure, maintains it in a given range. Striking variation in D8 evolutionary rates was evidenced among sea urchins, by comparison with both 16S mitochondrial DNA and paleontological data. In Echinocardium cordatum and Strongylocentrotus pallidus and S. droebachiensis, belonging to very distant genera, the increase in D8 evolutionary rate is extreme. Their highly stable D8 secondary structures rule out the possibility of pseudogenes. These taxa are the only ones in which interspecific hybridization was reported. We discuss how evolutionary rates may be affected in nuclear relative to mitochondrial genes after hybridization, by selective or mutational processes such as gene silencing and concerted evolution.

  5. On the sites of secondary podia formation in a juvenile echinoid: growth of the body types in echinoderms.

    Science.gov (United States)

    Morris, Valerie B

    2009-12-01

    The growth of the adult echinoderm body is addressed here in the echinoid Holopneustes purpurescens in a study of the early development of the secondary podia along the five radial canals of the adult rudiment. At a stage when the first four secondary podia have formed along each radius oral to the primary podium, two podia are on one side of the radius and two are on the other side, all at a different distance from the primary podium. The pattern of the connexions of these secondary podia to the radial canals changes in successive radii in a manner similar to Lovén's law for skeletal plates and matches the reported sequence in the times at which the first ambulacral skeletal plates form in the adult echinoid rudiment. A similar pattern is described for the reported origins of the secondary podia in apodid holothurians. A common plan for the growth of the body types is described for echinoids, asteroids, holothurians and concentricycloids. The five metameric series of secondary podia formed in echinoderms have a coelomic developmental origin like the single metameric series of somites formed in the axial structures of chordates.

  6. Localization of Neuropeptide Gene Expression in Larvae of an Echinoderm, the Starfish Asterias rubens

    Science.gov (United States)

    Mayorova, Tatiana D.; Tian, Shi; Cai, Weigang; Semmens, Dean C.; Odekunle, Esther A.; Zandawala, Meet; Badi, Yusef; Rowe, Matthew L.; Egertová, Michaela; Elphick, Maurice R.

    2016-01-01

    patterns of expression suggesting potential roles for neuropeptides in the attachment process. Lastly, expression of several neuropeptide precursors is associated with ciliary bands, suggesting potential roles for the neuropeptides derived from these precursors in control of larval locomotion and/or feeding. In conclusion, our findings provide novel perspectives on the evolution and development of neuropeptide signaling systems and neuroanatomical insights into neuropeptide function in echinoderm larvae. PMID:27990106

  7. Ocean acidification has little effect on developmental thermal windows of echinoderms from Antarctica to the tropics.

    Science.gov (United States)

    Karelitz, Sam E; Uthicke, Sven; Foo, Shawna A; Barker, Mike F; Byrne, Maria; Pecorino, Danilo; Lamare, Miles D

    2017-02-01

    As the ocean warms, thermal tolerance of developmental stages may be a key driver of changes in the geographical distributions and abundance of marine invertebrates. Additional stressors such as ocean acidification may influence developmental thermal windows and are therefore important considerations for predicting distributions of species under climate change scenarios. The effects of reduced seawater pH on the thermal windows of fertilization, embryology and larval morphology were examined using five echinoderm species: two polar (Sterechinus neumayeri and Odontaster validus), two temperate (Fellaster zelandiae and Patiriella regularis) and one tropical (Arachnoides placenta). Responses were examined across 12-13 temperatures ranging from -1.1 °C to 5.7 °C (S. neumayeri), -0.5 °C to 10.7 °C (O. validus), 5.8 °C to 27 °C (F. zelandiae), 6.0 °C to 27.1 °C (P. regularis) and 13.9 °C to 34.8 °C (A. placenta) under present-day and near-future (2100+) ocean acidification conditions (-0.3 pH units) and for three important early developmental stages 1) fertilization, 2) embryo (prehatching) and 3) larval development. Thermal windows for fertilization were broad and were not influenced by a pH decrease. Embryological development was less thermotolerant. For O. validus, P. regularis and A. placenta, low pH reduced normal development, albeit with no effect on thermal windows. Larval development in all five species was affected by both temperature and pH; however, thermal tolerance was not reduced by pH. Results of this study suggest that in terms of fertilization and development, temperature will remain as the most important factor influencing species' latitudinal distributions as the ocean continues to warm and decrease in pH, and that there is little evidence of a synergistic effect of temperature and ocean acidification on the thermal control of species ranges.

  8. Energetic costs of loss and regeneration of arms in stellate echinoderms.

    Science.gov (United States)

    Lawrence, John M

    2010-10-01

    Loss of arms has energetic consequences for stellate echinoderms (crinoids, ophiuroids, and asteroids). The energetic cost of losing an arm includes loss of investment, decrease in ability to obtain nutrients and allocation of nutrients to regeneration of the lost arms at a cost to other body compartments. The cost to other body compartments is low when food availability is very low or very high. The cost becomes apparent when food availability is sufficient to support production but not high enough that the cost of regeneration has no effect on production of other body compartments. Loss of investment is greater in asteroids than in crinoids and ophiuroids because of greater development of the body wall and presence of gonads and pyloric caeca in the arms. The cost of regeneration of organic matter in an arm can be estimated from the amount of organic matter present in intact arms and the cost of anabolism. Protein production is the primary cost of regeneration of an arm because of the high concentration of protein in the regenerated arm and the high anabolic cost of protein production. A major energetic cost of loss of arms that affects regeneration is decrease in food consumption. It is necessary to separate cost of decrease in consumption from cost of regeneration. Comparison of intact and regenerating individuals requires they consume the same amount of food. The cost of regeneration will also be affected by the quality of food because of the nutrient requirements for growth. Because the quantity and quality of the food ingested is not known, it is not possible to quantify the cost of regeneration in the field. Asteroids appear to be a good model for the study of regeneration in the laboratory because it is possible to control the quantity and quality of food they ingest. They are also a good model for the study of the evolutionary significance of regeneration by comparing individuals that have lost arms and are regenerating them to those that have lost arms

  9. Localization of neuropeptide gene expression in larvae of an echinoderm, the starfish Asterias rubens

    Directory of Open Access Journals (Sweden)

    Tatiana D Mayorova

    2016-12-01

    distinctive patterns of expression suggesting potential roles for neuropeptides in the attachment process. Lastly, expression of several neuropeptide precursors is associated with ciliary bands, suggesting potential roles for the neuropeptides derived from these precursors in control of larval locomotion and/or feeding. In conclusion, our findings provide novel perspectives on the evolution and development of neuropeptide signaling systems and neuroanatomical insights into neuropeptide function in echinoderm larvae.

  10. Phosphorylation of chicken growth hormone

    Energy Technology Data Exchange (ETDEWEB)

    Aramburo, C.; Montiel, J.L. (Universidad Nacional Autonoma de Mexico (Mexico)); Donoghue, D.; Scanes, C.G. (Rutgers Univ., New Brunswick, NJ (USA)); Berghman, L.R. (Laboratory for Neuroendocrinology and Immunological Biotechnology, Louvain (Belgium))

    1990-01-01

    The possibility that chicken growth hormone (cGH) can be phosphorylated has been examined. Both native and biosynthetic cGH were phosphorylated by cAMP-dependent protein kinase (and {gamma}-{sup 32}P-ATP). The extent of phosphorylation was however less than that observed with ovine prolactin. Under the conditions employed, glycosylated cGH was not phosphorylated. Chicken anterior pituitary cells in primary culture were incubated in the presence of {sup 32}P-phosphate. Radioactive phosphate was incorporated in vitro into the fraction immunoprecipitable with antisera against cGH. Incorporation was increased with cell number and time of incubation. The presence of GH releasing factor (GRF) increased the release of {sup 32}P-phosphate labeled immunoprecipitable GH into the incubation media but not content of immunoprecipitable GH in the cells. The molecular weight of the phosphorylated immunoreactive cGH in the cells corresponded to cGH dimer.

  11. Late Cretaceous-Early Palaeogene echinoderms and the K/T boundary in the southeast Netherlands and northeast Belgium - Part 1: Introduction and stratigraphy

    NARCIS (Netherlands)

    Jagt, J.W.M.

    1999-01-01

    In a series of papers describing Late Cretaceous and Early Palaeogene echinoderm faunas (exclusiveof holothurians) of the Maastrichtian type area, the present contribution comprises a detailed accountof the litho- and chronostratigraphy and biozonations of these deposits, and of localities from whic

  12. Late Cretaceous-Early Palaeogene echinoderms and the K/T boundary in the southeast Netherlands and northeast Belgium — Part 4: Echinoids

    NARCIS (Netherlands)

    Jagt, J.W.M.

    2000-01-01

    All Campanian, Maastrichtian and Danian echinoids known to date from the extended type area of the Maastrichtian Stage are listed and, with a few exceptions, also illustrated. The geographic and stratigraphic distribution of these echinoderms are documented. A total of 55 (sub)genera and 119 (sub)sp

  13. Ventralization of an indirect developing hemichordate by NiCl₂ suggests a conserved mechanism of dorso-ventral (D/V) patterning in Ambulacraria (hemichordates and echinoderms).

    Science.gov (United States)

    Röttinger, E; Martindale, M Q

    2011-06-01

    One of the earliest steps in embryonic development is the establishment of the future body axes. Morphological and molecular data place the Ambulacraria (echinoderms and hemichordates) within the Deuterostomia and as the sister taxon to chordates. Extensive work over the last decades in echinoid (sea urchins) echinoderms has led to the characterization of gene regulatory networks underlying germ layer specification and axis formation during embryogenesis. However, with the exception of recent studies from a direct developing hemichordate (Saccoglossus kowalevskii), very little is known about the molecular mechanism underlying early hemichordate development. Unlike echinoids, indirect developing hemichordates retain the larval body axes and major larval tissues after metamorphosis into the adult worm. In order to gain insight into dorso-ventral (D/V) patterning, we used nickel chloride (NiCl₂), a potent ventralizing agent on echinoderm embryos, on the indirect developing enteropneust hemichordate, Ptychodera flava. Our present study shows that NiCl₂ disrupts the D/V axis and induces formation of a circumferential mouth when treated before the onset of gastrulation. Molecular analysis, using newly isolated tissue-specific markers, shows that the ventral ectoderm is expanded at expense of dorsal ectoderm in treated embryos, but has little effect on germ layer or anterior-posterior markers. The resulting ventralized phenotype, the effective dose, and the NiCl₂ sensitive response period of Ptychodera flava, is very similar to the effects of nickel on embryonic development described in larval echinoderms. These strong similarities allow one to speculate that a NiCl₂ sensitive pathway involved in dorso-ventral patterning may be shared between echinoderms, hemichordates and a putative ambulacrarian ancestor. Furthermore, nickel treatments ventralize the direct developing hemichordate, S. kowalevskii indicating that a common pathway patterns both larval and adult

  14. Matrix theory

    CERN Document Server

    Franklin, Joel N

    2003-01-01

    Mathematically rigorous introduction covers vector and matrix norms, the condition-number of a matrix, positive and irreducible matrices, much more. Only elementary algebra and calculus required. Includes problem-solving exercises. 1968 edition.

  15. Directional and quantitative phosphorylation networks

    DEFF Research Database (Denmark)

    Jørgensen, Claus; Linding, Rune

    2008-01-01

    for unravelling phosphorylation-mediated cellular interaction networks. In particular, we will discuss how the combination of new quantitative mass-spectrometric technologies and computational algorithms together are enhancing mapping of these largely uncharted dynamic networks. By combining quantitative...

  16. Echinoderm Distribution and Habitat, Aquatic Invasive Species (AIS) animal distribution in Wisconsin - Chinese/Japanese/Banded mystery snails, Published in 2009, 1:24000 (1in=2000ft) scale, Wisconsin DNR Bureau of Watershed Management.

    Data.gov (United States)

    NSGIC GIS Inventory (aka Ramona) — This Echinoderm Distribution and Habitat dataset, published at 1:24000 (1in=2000ft) scale, was produced all or in part from Field Observation information as of 2009....

  17. Integrin Ligation Results in Nephrin Tyrosine Phosphorylation In Vitro.

    Directory of Open Access Journals (Sweden)

    Rakesh Verma

    Full Text Available Nephrin is expressed at the basolateral aspect of podocytes and is an important signaling protein at the glomerular slit diaphragm. In vitro studies have demonstrated that Nephrin phosphorylation-dependent signaling is able to assemble a protein complex that is able to polymerize actin. However, proximal signaling events that result in nephrin tyrosine phosphorylation are not well understood. Nephrin deletion in mice and human nephrin mutations result in developmental failure of the podocyte intercellular junction resutling in proteinuria. This has been presumed to be due to a failure to respond to an external polarized cue in the absence of nephrin or a failure to transduce an outside-in signal in patients with nephrin mutations. The nephrin extracellular domain binds to itself or neph1 across the foot process intercellular junction. Nephrin is tyrosine phosphorylation-silent in healthy glomeruli when presumably the nephrin extracellular domain is in an engaged state. These observations raise the possibility of an alternate proximal signaling mechanism that might be responsible for nephrin tyrosine phosphorylation. Here we present data showing that integrin engagement at the basal aspect of cultured podocytes results in nephrin tyrosine phosphorylation. This is abrogated by incubating podocytes with an antibody that prevents integrin β1 ligation and activation in response to binding to extracellular matrix. Furthermore, nephrin tyrosine phosphorylation was observed in podocytes expressing a membrane-targeted nephrin construct that lacks the extracellular domain. We propose, integrin-activation based signaling might be responsible for nephrin phosphorylation rather than engagment of the nephrin extracellular domain by a ligand.

  18. Chemistry of Phosphorylated Formaldehyde Derivatives. Part I

    Directory of Open Access Journals (Sweden)

    Vasily P. Morgalyuk

    2014-08-01

    Full Text Available The underinvestigated derivatives of unstable phosphorylated formaldehyde acetals and some of the structurally related compounds, such as thioacetals, aminonitriles, aminomethylphosphinoyl compounds, are considered. Separately considered are halogen aminals of phosphorylated formaldehyde, acetals of phosphorylated formaldehyde of H-phosphinate-type and a phosphorylated gem-diol of formaldehyde. Synthetic methods, chemical properties and examples of practical applications are given.

  19. Development of the five primary podia from the coeloms of a sea star larva: homology with the echinoid echinoderms and other deuterostomes.

    Science.gov (United States)

    Morris, Valerie B; Selvakumaraswamy, Paulina; Whan, Renée; Byrne, Maria

    2009-04-07

    Confocal laser scanning microscopy of larvae of the asteroid Parvulastra exigua was used to investigate the development of the five primary podia from the coeloms in the echinoderm phylum in an approach to the problem of morphological homology in the deuterostome phyla. The development is shown from an early brachiolaria larval stage to a pre-settlement late brachiolaria larval stage. In the early brachiolaria larva, a single enterocoele connected to the archenteron has formed into two lateral coeloms and an anterior coelom. The primary podia form from the coelomic regions on the left side of the brachiolaria larva, while on the right the coelomic regions connect with the exterior through the pore canal and hydropore. The anterior coelom forms the coelom of the brachia. Homology between the primary podia of the asteroid and the echinoid classes of echinoderms is described and extended to coeloms of other deuterostome phyla.

  20. Adjusting ammonium uptake via phosphorylation.

    Science.gov (United States)

    Lanquar, Viviane; Frommer, Wolf B

    2010-06-01

    In plants, AMT/MEP/Rh superfamily mediates high affinity ammonium uptake. AMT/MEP transporters form a trimeric complex, which requires a productive interaction between subunits in order to be functional. The AMT/MEP C-terminal domain is highly conserved in more than 700 AMT homologs from cyanobacteria to higher plants with no cases found to be lacking this domain. AMT1;1 exists in active and inactive states, probably controlled by the spatial positioning of the C-terminus. Ammonium triggers the phosphorylation of a conserved threonine residue (T460) in the C-terminus of AMT1;1 in a time- and concentration-dependent manner. The T460 phosphorylation level correlates with a decrease of root ammonium uptake. We propose that ammonium-induced phosphorylation modulates ammonium uptake as a general mechanism to protect against ammonium toxicity.

  1. Matrix Factorization and Matrix Concentration

    OpenAIRE

    Mackey, Lester

    2012-01-01

    Motivated by the constrained factorization problems of sparse principal components analysis (PCA) for gene expression modeling, low-rank matrix completion for recommender systems, and robust matrix factorization for video surveillance, this dissertation explores the modeling, methodology, and theory of matrix factorization.We begin by exposing the theoretical and empirical shortcomings of standard deflation techniques for sparse PCA and developing alternative methodology more suitable for def...

  2. Propofol directly increases tau phosphorylation.

    Directory of Open Access Journals (Sweden)

    Robert A Whittington

    Full Text Available In Alzheimer's disease (AD and other tauopathies, the microtubule-associated protein tau can undergo aberrant hyperphosphorylation potentially leading to the development of neurofibrillary pathology. Anesthetics have been previously shown to induce tau hyperphosphorylation through a mechanism involving hypothermia-induced inhibition of protein phosphatase 2A (PP2A activity. However, the effects of propofol, a common clinically used intravenous anesthetic, on tau phosphorylation under normothermic conditions are unknown. We investigated the effects of a general anesthetic dose of propofol on levels of phosphorylated tau in the mouse hippocampus and cortex under normothermic conditions. Thirty min following the administration of propofol 250 mg/kg i.p., significant increases in tau phosphorylation were observed at the AT8, CP13, and PHF-1 phosphoepitopes in the hippocampus, as well as at AT8, PHF-1, MC6, pS262, and pS422 epitopes in the cortex. However, we did not detect somatodendritic relocalization of tau. In both brain regions, tau hyperphosphorylation persisted at the AT8 epitope 2 h following propofol, although the sedative effects of the drug were no longer evident at this time point. By 6 h following propofol, levels of phosphorylated tau at AT8 returned to control levels. An initial decrease in the activity and expression of PP2A were observed, suggesting that PP2A inhibition is at least partly responsible for the hyperphosphorylation of tau at multiple sites following 30 min of propofol exposure. We also examined tau phosphorylation in SH-SY5Y cells transfected to overexpress human tau. A 1 h exposure to a clinically relevant concentration of propofol in vitro was also associated with tau hyperphosphorylation. These findings suggest that propofol increases tau phosphorylation both in vivo and in vitro under normothermic conditions, and further studies are warranted to determine the impact of this anesthetic on the acceleration of

  3. Nucleoside phosphorylation in amide solutions

    Science.gov (United States)

    Schoffstall, A. M.; Kokko, B.

    1978-01-01

    The paper deals with phosphorylation in possible prebiotic nonaqueous solvents. To this end, phosphorylation of nucleosides using inorganic phosphates in amide solutions is studied at room and elevated temperatures. Reaction proceeds most readily in formamide and N-methylformamide. Products obtained at elevated temperature are nucleotides, nucleoside 2',3'-cyclic phosphates, and when the phosphate concentration is high, nucleoside diphosphates. At room temperature, adenosine afforded a mixture of nucleotides, but none of the cyclic nucleotide. Conditions leading to the highest relative percentage of cyclic nucleotide involve the use of low concentrations of phosphate and an excess of nucleoside.

  4. Properties of phosphorylated thymidylate synthase

    DEFF Research Database (Denmark)

    Frączyk, Tomasz; Ruman, Tomasz; Wilk, Piotr;

    2015-01-01

    Thymidylate synthase (TS) may undergo phosphorylation endogenously in mammalian cells, and as a recombinant protein expressed in bacterial cells, as indicated by the reaction of purified enzyme protein with Pro-Q® Diamond Phosphoprotein Gel Stain (PGS). With recombinant human, mouse, rat, Trichin......Thymidylate synthase (TS) may undergo phosphorylation endogenously in mammalian cells, and as a recombinant protein expressed in bacterial cells, as indicated by the reaction of purified enzyme protein with Pro-Q® Diamond Phosphoprotein Gel Stain (PGS). With recombinant human, mouse, rat...

  5. Subcuticular bacteria associated with two common New Zealand echinoderms: Characterization using 16S rRNA sequence analysis and fluorescence in situ hybridization.

    Science.gov (United States)

    Lawrence, Scott A; O'Toole, Ronan; Taylor, Michael W; Davy, Simon K

    2010-02-01

    Many echinoderms contain subcuticular bacteria (SCB), symbionts which reside in the lumen between the host's epidermal cells and outer cuticle. This relationship is common, existing in about 60% of echinoderms studied so far, yet the function of SCB remains largely unknown. In this study, phylogenetic analysis was carried out on 16S rRNA sequences obtained from echinoderm-associated bacteria, resulting in the identification of four species of putative SCB. All four bacteria were identified from the holothurian Stichopus mollis, and two of the four were also found in the asteroid Patiriella sp. Two of these bacteria belong to the Alphaproteobacteria, and two to the Gammaproteobacteria. In addition to phylogenetic analysis, fluorescence in situ hybridization (FISH) assays were carried out on Patiriella sp., S. mollis, and the asteroid Astrostole scabra. Results showed that Patiriella sp. and S. mollis contain SCB, in agreement with the phylogenetic analysis, while SCB were not detected in A. scabra. Of the bacteria detected using FISH, more than 80% were recognized as belonging to the Alphaproteobacteria in both host species. However, in S. mollis about 20% of the detected SCB successfully hybridized with the Gammaproteobacteria-specific probe, whereas bacteria belonging to this class were never observed in Patiriella sp. This is only the second study to characterize SCB by molecular means, and is the first to identify SCB in situ using FISH.

  6. Equinodermos del Parque Nacional Isla Isabel, Nayarit, México Echinoderms of the National Park Isla Isabel, Nayarit, Mexico

    Directory of Open Access Journals (Sweden)

    Eduardo Ríos-Jara

    2008-06-01

    Full Text Available Se describe la composición específica de equinodermos del Parque Nacional Isla Isabel, ubicado en el Pacífico central mexicano. Los muestreos y recolectas se realizaron durante octubre de 2004, marzo y julio de 2005 mediante búsqueda directa en diferentes playas rocosas y mediante transectos en banda en los sustratos rocoso y arenoso del submareal hasta los 19 m de profundidad. Se incluyen también ejemplares recolectados con redes de arrastre en el barco camaronero "América" en aguas adyacentes. Se registraron 299 individuos correspondientes a 31 especies y 19 familias de equinodermos. La mayor abundancia se registró en las regiones norte (43% y este (39% de la isla donde existe mayor heterogeneidad de sustratos y la menor en la oeste (3%. La mayor riqueza de especies correspondió a las zonas este (36%, norte (31% y sur (29% de la isla. Los holoturoideos fueron los más diversos con 10 especies. Las especies más importantes de acuerdo al índice de valor biológico son: Diadema mexicanum, Toxopneustes roseus, Phataria unifascialis, Pharia pyramidatus, Ophiocoma alexandri, Holothuria lubrica, Isostichopus fuscus y Eucidaris thouarsii representando el 60% de los individuos. La afinidad de especies es mayor con el golfo de California que con la región centro-sur del Pacífico.This study describes the species composition of echinoderms from Isla Isabel National Park, in the central Mexican Pacific. The samplings and collection transects band were made in October 2004, March and July 2005 by direct search on several rocky beaches, and on rocky and sandy substrates in subtidal areas to 19 m depth. The specimens collected with a trawling net from the shrimp vessel "America" in adjacent waters were also included. A total of 299 organisms belonging to 31 species and 19 families of echinoderms were registered. The greatest abundance was recorded in the nothern (43% and eastern (39% regions of the island where there is greater substrate

  7. Tyrosine phosphorylation in human lymphomas

    NARCIS (Netherlands)

    Haralambieva, E; Jones, M.; Roncador, GM; Cerroni, L; Lamant, L; Ott, G; Rosenwald, A; Sherman, C; Thorner, P; Kusec, R; Wood, KM; Campo, E; Falini, B; Ramsay, A; Marafioti, T; Stein, H; Kluin, PM; Pulford, K; Mason, DY

    2002-01-01

    In a previous study, we showed that the high level of protein tyrosine phosphorylation present in lymphomas containing an anaplastic lymphoma kinase (ALK) can be demonstrated in routinely processed paraffin tissue sections using immunolabelling techniques. In the present study we investigated

  8. SYMPOSIUM ON PLANT PROTEIN PHOSPHORYLATION

    Energy Technology Data Exchange (ETDEWEB)

    JOHN C WALKER

    2011-11-01

    Protein phosphorylation and dephosphorylation play key roles in many aspects of plant biology, including control of cell division, pathways of carbon and nitrogen metabolism, pattern formation, hormonal responses, and abiotic and biotic responses to environmental signals. A Symposium on Plant Protein Phosphorylation was hosted on the Columbia campus of the University of Missouri from May 26-28, 2010. The symposium provided an interdisciplinary venue at which scholars studying protein modification, as it relates to a broad range of biological questions and using a variety of plant species, presented their research. It also provided a forum where current international challenges in studies related to protein phosphorylation could be examined. The symposium also stimulated research collaborations through interactions and networking among those in the research community and engaged students and early career investigators in studying issues in plant biology from an interdisciplinary perspective. The proposed symposium, which drew 165 researchers from 13 countries and 21 States, facilitated a rapid dissemination of acquired knowledge and technical expertise regarding protein phosphorylation in plants to a broad range of plant biologists worldwide.

  9. Thiamine phosphorylated derivatives and bioelectrogenesis.

    Science.gov (United States)

    Schoffeniels, E

    1983-09-01

    Kinetic as well as thermodynamic considerations favour the idea that the change in sodium conductance explaining the action potential, must result from a bimolecular reaction system. The fact that thiamine phosphorylated derivatives are associated with the specific protein forming the sodium channel could well mean that these thiamine derivatives and more specifically thiamine triphosphate are directly involved in the conductance change.

  10. Biocatalytic asymmetric phosphorylation of mevalonate

    NARCIS (Netherlands)

    Matsumi, R.; Hellriegel, C.; Schoenenberger, B.; Milesi, T.; Oost, van der J.; Wohlgemuth, R.

    2014-01-01

    The excellent selectivity of the mevalonate kinase-catalyzed phosphorylation of mevalonate simplifies lengthy multi-step routes to (R)-mevalonate-5-phosphate to a one-step biocatalytic reaction, because the phosphate group can be transferred directly and without any additional reaction steps

  11. Matrix calculus

    CERN Document Server

    Bodewig, E

    1959-01-01

    Matrix Calculus, Second Revised and Enlarged Edition focuses on systematic calculation with the building blocks of a matrix and rows and columns, shunning the use of individual elements. The publication first offers information on vectors, matrices, further applications, measures of the magnitude of a matrix, and forms. The text then examines eigenvalues and exact solutions, including the characteristic equation, eigenrows, extremum properties of the eigenvalues, bounds for the eigenvalues, elementary divisors, and bounds for the determinant. The text ponders on approximate solutions, as well

  12. Evolution of a pentameral body plan was not linked to translocation of anterior Hox genes: the echinoderm HOX cluster revisited.

    Science.gov (United States)

    Byrne, Maria; Martinez, Pedro; Morris, Valerie

    2016-01-01

    Echinodermata is a large phylum of marine invertebrates characterized by an adult, pentameral body plan. This morphology is clearly derived as all members of Deuterostomia (the superphylum to which they belong) have a bilateral body plan. The origin of the pentameral plan has been the subject of intense debate. It is clear that the ancestor of Echinodermata had a bilateral plan but how this ancestor transformed its body "architecture" in such a drastic manner is not clear. Data from the fossil record and ontogeny are sparse and, so far, not very informative. The sequencing of the sea urchin genome a decade ago opened the possibility that the pentameral body plan was a consequence of a broken Hox cluster and a series of papers dwelt on the putative relationship between Hox gene arrangements in the chromosomes and the origin of pentamery. This relationship, sound as it was, is challenged by the revelation that the sea star HOX cluster is, in fact, intact, thus falsifying the hypothesis of a direct relationship between HOX cluster arrangement and the origin of the pentameral body plan. Here, we explore the relationship between Hox gene arrangements and echinoderm body "architecture," the expression of Hox genes in development and alternative scenarios for the origin of pentamery, with putative roles for signaling centers in generating multiple axes.

  13. Coelomogenesis during the abbreviated development of the echinoid Heliocidaris erythrogramma and the developmental origin of the echinoderm pentameral body plan.

    Science.gov (United States)

    Morris, Valerie B

    2011-01-01

    The development of the coeloms is described in an echinoid with an abbreviated larval development and shows the early morphogenesis of the coeloms of the adult stage. The development is described from images obtained by laser scanning confocal microscopy. The development in Heliocidaris erythrogramma is asymmetric with a larger left coelom forming on the larval-left side and a smaller right coelom forming on the larval-right side. The right coelom forms after the development of the left coelom is well advanced. The hydrocoele forms from the anterior part of the left coelom. The five lobes of the hydrocoele from which the pentamery of the adult derives take shape on the outer, distal wall of the anterior part of the left coelom. The hydrocoele separates from the more posterior part of the left coelom, which becomes the left posterior coelom. The lobes of the hydrocoele are named, based on the site of the connexion of the stone canal to the hydrocoele. The mouth is assumed to form by penetration through only the outer, distal wall of the hydrocoele and the ectoderm. Both larval and adult polarities are evident in this larva. A comparison with coelomogenesis in the asteroid Parvulastra exigua, which also has an abbreviated development, leads to predictions of homology between the echinoderm and chordate phyla that do not require the hypothesis of a dorsoventral inversion event in chordates.

  14. Neuropeptides and polypeptide hormones in echinoderms: new insights from analysis of the transcriptome of the sea cucumber Apostichopus japonicus.

    Science.gov (United States)

    Rowe, Matthew L; Achhala, Sufyan; Elphick, Maurice R

    2014-02-01

    Echinoderms are of special interest for studies in comparative endocrinology because of their phylogenetic position in the animal kingdom as deuterostomian invertebrates. Furthermore, their pentaradial symmetry as adult animals provides a unique context for analysis of the physiological and behavioral roles of peptide signaling systems. Here we report the first extensive survey of neuropeptide and peptide hormone precursors in a species belonging to the class Holothuroidea. Transcriptome sequence data obtained from the sea cucumber Apostichopus japonicus were analyzed to identify homologs of precursor proteins that have recently been identified in the sea urchin Strongylocentrotus purpuratus (class Echinoidea). A total of 17 precursor proteins have been identified in A. japonicus, including precursors of peptides related to thyrotropin-releasing hormone, pedal peptide/orcokinin-type peptides, AN peptides/tachykinins, luqins, corticotropin-releasing hormone (CRH), GPA2-type glycoprotein hormone subunits and bursicon. In addition, an unusual finding was an A. japonicus calcitonin-type precursor protein (AjCTLPP), the first to be discovered that comprises two calcitonin-like peptides; this contrasts with the products of the alternatively-spliced calcitonin/CGRP gene in vertebrates, which comprise either calcitonin or CGRP. Collectively, the data obtained provide new insights on the evolution and diversity of neuropeptides and polypeptide hormones. Furthermore, because A. japonicus is one of several sea cucumber species that are used for human consumption, our findings may have practical and economic impact by providing a basis for neuroendocrine-based strategies to improve methods of aquaculture.

  15. A Prejudiced Review of Ancient Parasites and Their Host Echinoderms: CSI Fossil Record or Just an Excuse for Speculation?

    Science.gov (United States)

    Donovan, Stephen K

    2015-01-01

    Recognizing the presence of a parasite and identifying it is a relatively straightforward task for the twenty-first century parasitologist. Not so the pursuit of ancient parasites in fossil organisms, a much more difficult proposition. Herein, Boucot's seven-tiered scheme of reliability classes is applied as a measure of confidence of the recognition of putative parasitism in two echinoderm classes, Upper Palaeozoic crinoids and a Cretaceous echinoid (high confidence is 1, low confidence 7). Of the five examples, the parasitic(?) organism is preserved in only two of them. A zaphrentoid coral on the camerate crinoid Amphoracrinus may have robbed food from the arms (Category 1 or 2B). A pit in what appears to be a carefully selected site on the disparid crinoid Synbathocrinus is associated with a growth deformity of the cup (Category 4). Multiple pits in an Amphoracrinus theca are also associated with a deformed cup, but it is more difficult to interpret (Category 4 or 7). Some specimens of the camerate crinoid Neoplatycrinites have circular grooves or depressions posteriorly, presumably produced by coprophagic/parasitic platyceratid gastropods (Category 1). Site selectivity of pits in the echinoid Hemipneustes places them preferentially adjacent to respiratory tube feet (Category 4). From these examples it is deduced that sparse infestations of borings or epizoozoic organisms permit a more confident interpretation of organism/organism interactions; dense accumulations, possibly following multiple spatfalls, mask such patterns.

  16. Apparent selection intensity for the cytochrome oxidase subunit I gene varies with mode of reproduction in echinoderms.

    Science.gov (United States)

    Foltz, David W; Hrincevich, Adam W; Rocha-Olivares, Axayácatl

    2004-10-01

    When most amino acid substitutions in protein-coding genes are slightly deleterious rather than selectively neutral, life history differences can potentially modify the effective population size or the selective regime, resulting in altered ratios of non-synonymous to synonymous substitutions among taxa. We studied substitution patterns for the mitochondrial cytochrome oxidase subunit I (COI) gene in a sea star genus (Leptasterias spp.) with an obligate brood-protecting mode of reproduction and small-scale population genetic subdivision, and compared the results to available COI sequences in nine other genera of echinoderms with pelagic larvae: three sea stars, five sea urchins and one brittle star. We predicted that this life history difference would be associated with differences in the ratio of non-synonymous (dN) to synonymous (dS) substitution rates. Leptasterias had a significantly greater dN/dS ratio (both between species and within species), a significantly smaller transition/transversion rate ratio, and a significantly lower average nucleotide diversity within species, than did the non-brooding genera. Other explanations for the results, such as altered mutation rates or selective sweeps, were not supported by the data analysis. These findings highlight the potential influence of reproductive traits and other life history factors on patterns of nucleotide substitution within and between species.

  17. Inter-annual variability and potential for selectivity in the diets of deep-water Antarctic echinoderms

    Science.gov (United States)

    Wigham, B. D.; Galley, E. A.; Smith, C. R.; Tyler, P. A.

    2008-11-01

    The continental shelf of the West Antarctic Peninsula (WAP) is a highly productive region but also unusually deep as a result of isostatic depression by the polar ice cap. The close coupling of surface processes with those of the benthos would be expected in such a seasonally variable environment; however, the cold, deep conditions of the WAP shelf may allow for the persistence of organic material in the sediments as a "food bank". Chlorophyll and carotenoid pigments were determined from the gut contents of seven species of echinoderm and from the surficial sediment on the bathyal continental shelf. Samples were collected as part of the FOODBANCS programme during successive cruises in austral spring (October 2000) and austral autumn (March 2001). Pigments were identified and quantified using reverse-phase high-performance liquid chromatography (HPLC). A lack of qualitative selectivity was observed among species, compared to that observed for deep-water assemblages at temperate latitudes, supporting the theory of a persistent "food bank". However, significant quantitative differences were observed among species and between years and sampling location on the shelf. Species differences were marked between those we classified as "true" deposit feeders and those species whose diet also may be supplemented by scavenging and/or grazing.

  18. Affinity chromatography of phosphorylated proteins.

    Science.gov (United States)

    Tchaga, Grigoriy S

    2008-01-01

    This chapter covers the use of immobilized metal ion affinity chromatography (IMAC) for enrichment of phosphorylated proteins. Some requirements for successful enrichment of these types of proteins are discussed. An experimental protocol and a set of application data are included to enable the scientist to obtain high-yield results in a very short time with pre-packed phospho-specific metal ion affinity resin (PMAC).

  19. Cell entry of Lassa virus induces tyrosine phosphorylation of dystroglycan.

    Science.gov (United States)

    Moraz, Marie-Laurence; Pythoud, Christelle; Turk, Rolf; Rothenberger, Sylvia; Pasquato, Antonella; Campbell, Kevin P; Kunz, Stefan

    2013-05-01

    The extracellular matrix (ECM) receptor dystroglycan (DG) serves as a cellular receptor for the highly pathogenic arenavirus Lassa virus (LASV) that causes a haemorrhagic fever with high mortality in human. In the host cell, DG provides a molecular link between the ECM and the actin cytoskeleton via the adapter proteins utrophin or dystrophin. Here we investigated post-translational modifications of DG in the context of LASV cell entry. Using the tyrosine kinase inhibitor genistein, we found that tyrosine kinases are required for efficient internalization of virus particles, but not virus-receptor binding. Engagement of cellular DG by LASV envelope glycoprotein (LASV GP) in human epithelial cells induced tyrosine phosphorylation of the cytoplasmic domain of DG. LASV GP binding to DG further resulted in dissociation of the adapter protein utrophin from virus-bound DG. This virus-induced dissociation of utrophin was affected by genistein treatment, suggesting a role of receptor tyrosine phosphorylation in the process.

  20. Matrix Thermalization

    CERN Document Server

    Craps, Ben; Nguyen, Kévin

    2016-01-01

    Matrix quantum mechanics offers an attractive environment for discussing gravitational holography, in which both sides of the holographic duality are well-defined. Similarly to higher-dimensional implementations of holography, collapsing shell solutions in the gravitational bulk correspond in this setting to thermalization processes in the dual quantum mechanical theory. We construct an explicit, fully nonlinear supergravity solution describing a generic collapsing dilaton shell, specify the holographic renormalization prescriptions necessary for computing the relevant boundary observables, and apply them to evaluating thermalizing two-point correlation functions in the dual matrix theory.

  1. Multi-residue analysis of 36 priority and emerging pollutants in marine echinoderms (Holothuria tubulosa) and marine sediments by solid-liquid extraction followed by dispersive solid phase extraction and liquid chromatography-tandem mass spectrometry analysis.

    Science.gov (United States)

    Martín, J; Zafra-Gómez, A; Hidalgo, F; Ibáñez-Yuste, A J; Alonso, E; Vilchez, J L

    2017-05-01

    Marine echinoderms are filter-feeding invertebrates widely distributed along the coasts, and which are therefore extensively exposed to anthropogenic xenobiotics. They can serve as good sentinels for monitoring a large variety of contaminants in marine ecosystems. In this context, a multi-residue analytical method has been validated and applied to Holothuria tubulosa specimens and marine sediments for the determination of 36 organic compounds, which belong to some of the most problematic groups of emerging and priority pollutants (perfluoroalkyl compounds, estrogens, parabens, benzophenones, plasticizers, surfactants, brominated flame retardants and alkylphenols). Lyophilization of samples prior to solvent extraction and clean-up of extracts with C18, followed by liquid chromatography-tandem mass spectrometry analysis, is proposed. A Box-Behnken design was used for optimization of the most influential variables affecting the extraction and clean-up steps. For validation, matrix-matched calibration and recovery assay were applied. Linearity (% r(2)) higher than 99%, recoveries between 80% and 114% (except in LAS and NP1EO), RSD (precision) lower than 15% and limits of quantification between 0.03 and 12.5ngg(-1) dry weight (d.w.) were achieved. The method was applied to nine samples of Holothuria collected along the coast of Granada (Spain), and to marine sediments around the animals. The results demonstrated high bioaccumulation of certain pollutants. A total of 25 out of the 36 studied compounds were quantified, being surfactants, alkylphenols, perfluoroalkyl compounds, triclocarban and parabens the most frequently detected. Nonylphenol was found in the highest concentration (340 and 323ngg(-1) d.w. in sediment and Holothuria samples, respectively).

  2. Optimizing preservation protocols to extract high-quality RNA from different tissues of echinoderms for next-generation sequencing.

    Science.gov (United States)

    Pérez-Portela, Rocío; Riesgo, Ana

    2013-09-01

    Transcriptomic information provides fundamental insights into biological processes. Extraction of quality RNA is a challenging step, and preservation and extraction protocols need to be adjusted in many cases. Our objectives were to optimize preservation protocols for isolation of high-quality RNA from diverse echinoderm tissues and to compare the utility of parameters as absorbance ratios and RIN values to assess RNA quality. Three different tissues (gonad, oesophagus and coelomocytes) were selected from the sea urchin Arbacia lixula. Solid tissues were flash-frozen and stored at -80 °C until processed. Four preservation treatments were applied to coelomocytes: flash freezing and storage at -80 °C, RNAlater and storage at -20 °C, preservation in TRIzol reagent and storage at -80 °C and direct extraction with TRIzol from fresh cells. Extractions of total RNA were performed with a modified TRIzol protocol for all tissues. Our results showed high values of RNA quantity and quality for all tissues, showing nonsignificant differences among them. However, while flash freezing was effective for solid tissues, it was inadequate for coelomocytes because of the low quality of the RNA extractions. Coelomocytes preserved in RNAlater displayed large variability in RNA integrity and insufficient RNA amount for further isolation of mRNA. TRIzol was the most efficient system for stabilizing RNA which resulted on high RNA quality and quantity. We did not detect correlation between absorbance ratios and RNA integrity. The best strategies for assessing RNA integrity was the visualization of 18S rRNA and 28S rRNA bands in agarose gels and estimation of RIN values with Agilent Bioanalyzer chips. © 2013 John Wiley & Sons Ltd.

  3. Development of an embryonic skeletogenic mesenchyme lineage in a sea cucumber reveals the trajectory of change for the evolution of novel structures in echinoderms

    Directory of Open Access Journals (Sweden)

    McCauley Brenna S

    2012-08-01

    Full Text Available Abstract Background The mechanisms by which the conserved genetic “toolkit” for development generates phenotypic disparity across metazoans is poorly understood. Echinoderm larvae provide a great resource for understanding how developmental novelty arises. The sea urchin pluteus larva is dramatically different from basal echinoderm larval types, which include the auricularia-type larva of its sister taxon, the sea cucumbers, and the sea star bipinnaria larva. In particular, the pluteus has a mesodermally-derived larval skeleton that is not present in sea star larvae or any outgroup taxa. To understand the evolutionary origin of this structure, we examined the molecular development of mesoderm in the sea cucumber, Parastichopus parvimensis. Results By comparing gene expression in sea urchins, sea cucumbers and sea stars, we partially reconstructed the mesodermal regulatory state of the echinoderm ancestor. Surprisingly, we also identified expression of the transcription factor alx1 in a cryptic skeletogenic mesenchyme lineage in P. parvimensis. Orthologs of alx1 are expressed exclusively within the sea urchin skeletogenic mesenchyme, but are not expressed in the mesenchyme of the sea star, which suggests that alx1+ mesenchyme is a synapomorphy of at least sea urchins and sea cucumbers. Perturbation of Alx1 demonstrates that this protein is necessary for the formation of the sea cucumber spicule. Overexpression of the sea star alx1 ortholog in sea urchins is sufficient to induce additional skeleton, indicating that the Alx1 protein has not evolved a new function during the evolution of the larval skeleton. Conclusions The proposed echinoderm ancestral mesoderm state is highly conserved between the morphologically similar, but evolutionarily distant, auricularia and bipinnaria larvae. However, the auricularia, but not bipinnaria, also develops a simple skelotogenic cell lineage. Our data indicate that the first step in acquiring these novel

  4. Sulfated fucans from echinoderms have a regular tetrasaccharide repeating unit defined by specific patterns of sulfation at the 0-2 and 0-4 positions.

    Science.gov (United States)

    Mulloy, B; Ribeiro, A C; Alves, A P; Vieira, R P; Mourão, P A

    1994-09-02

    Sulfated fucans from echinoderms (sea cucumber and sea urchin) have a linear backbone of 1-->3-linked alpha-L-fucopyranose with some sulfate substitution at the 2- and 4-positions. NMR spectroscopy indicates that both polysaccharides have a tetrasaccharide repeat unit in which the separate residues differ only in the extent and position of their sulfate substitution. The sea urchin fucan has the structure, [formula: see text] This type of regular structure has not previously been described, and is in contrast with the random arrangement of substituents on the similar 1-->3-linked alpha-L-fucopyranose backbone of the fucoidans from brown algae.

  5. Los equinodermos (Echinodermata de bahía Chamela, Jalisco, México The echinoderms (Echinodermata from bahía Chamela, Jalisco, Mexico

    Directory of Open Access Journals (Sweden)

    Eduardo Ríos-Jara

    2013-03-01

    Full Text Available Cuarenta especies de equinodermos fueron recolectadas en las zonas intermareal y submareal somero de 14 sitios de bahía Chamela. Destacan 7 nuevos registros para la costa de Jalisco. Los análisis de escalonamiento multidimensional no métrico y el índice de similitud de Jaccard permitieron identificar grupos y entidades aisladas de acuerdo a la contribución y frecuencia de las especies de 4 clases de equinodermos en los sitios de la bahía y en otras localidades del Pacífico tropical mexicano (PTM. La mayor similitud se presentó con las localidades del golfo de California. Los índices de distinción taxonómica promedio (Δ+ y su variación (Λ+ fueron utilizados para analizar la diversidad de equinodermos en los niveles de especie, género, familia, orden y clase para cada sitio de la bahía y para distintas localidades del PTM de acuerdo al número de jerarquías taxonómicas de alto orden y la variabilidad en su diversidad taxonómica. La riqueza de especies de Chamela representa el 20% de la diversidad total de equinodermos de las zonas intermareal y submareal somero del PTM, lo que indica su importancia en la contribución a la diversidad taxonómica de la región.Forty species of echinoderms were collected in the intertidal and shallow subtidal zones of 14 sites of bahía Chamela. Of particular importance are 7 new records of species for the coast of Jalisco. A nonmetric multidimensional scaling analysis and the Jaccard's similarity index identified different groups and isolated entities according to the contribution and the frequency of species of 4 classes of echinoderms in the bay and in other localities of the Mexican Tropical Pacific (MTP. The highest similarity of species was with the localities of the Gulf of California. The indices of average taxonomic distinctness (Δ+ and the variation in the taxonomic distinctness (Λ+ were estimated to analyze the diversity of echinoderms at the taxonomic levels of species, genus, family

  6. Phosphorylation of brain proteins in generalized convulsions

    Energy Technology Data Exchange (ETDEWEB)

    Horan, M.P.

    1986-01-01

    Phosphorylation of neuronal proteins is being proposed as a modulating influence on several aspects of neuronal function. By labeling proteins with radioactive phosphorus (/sup 32/P) and then separating these proteins by polyacrylamide gel electrophoresis, the author can determine what factors change the phosphorylation of these proteins. They have used such a system to analyze the effects of generalized convulsions on protein phosphorylation. Electroshock (ES) and pentylenetetrazol (PTZ) were utilized to produce generalized convulsions. Brain membranes, taken from rats immediately after a convulsion, exhibited an increase in protein phosphorylation in vitro. The most noticeable change took place in proteins in the 18,000-20,000 MW range. They have designated these proteins as the low molecular weight (LMW) proteins. The change in phosphorylation was basically the same after one convulsions as after six daily convulsions. Twenty-four hours after a single convulsion no change in phosphorylation was observed. When rat membranes are exposed to PTZ in vitro, phosphorylation is increased at 20 sec but has returned to control level at 90 sec of incubation. This effect is produced without a convulsion. In general, as the concentration of magnesium is increased from 5 mM to 10 mM phosphorylation is increased. Increasing the incubation time from 20 sec to 90 sec and increasing the calcium concentration to 10 mM both decrease phosphorylation of the LMW proteins. Human temporal cortex samples present with phosphorylated proteins having patterns very similar to those in rat membranes.

  7. Matrix inequalities

    CERN Document Server

    Zhan, Xingzhi

    2002-01-01

    The main purpose of this monograph is to report on recent developments in the field of matrix inequalities, with emphasis on useful techniques and ingenious ideas. Among other results this book contains the affirmative solutions of eight conjectures. Many theorems unify or sharpen previous inequalities. The author's aim is to streamline the ideas in the literature. The book can be read by research workers, graduate students and advanced undergraduates.

  8. Species composition and faunal characteristics of echinoderms in China seas%中国海棘皮动物的种类组成及区系特点

    Institute of Scientific and Technical Information of China (English)

    廖玉麟; 肖宁

    2011-01-01

    The echinoderms are important components of macrobenthos. In order to understand the diversity of echinoderm fauna of China seas, the characteristics of their fauna are analysed according to the species composition and distribution patterns. The effects of marine environmental factors such as temperature, currents and water mass to the distribution of echinoderms are also discussed. The results showed that the echinoderm fauna of China seas now comprise 591 species in 5 classes: 44 crinoids, 86 starfish, 93 sea urchins, 147 sea cucumbers, and 221 ophiuroids. There is significant difference in species composition of echinoderms between the Yellow Sea, the East China Sea and the South China Sea. Only 59 species are distributed in the Yellow Sea; more than 200 species are distributed in the East China Sea; the number of species known from the South China Sea is about 450. The distributional characteristic of species shows that the species number and the warm water species are on the increase from the north toward the south. It is worth mentioning that the cold water species dominated by the ophiuroids Ophiura sarsii vadicola and Ophiopholis mirabilis are found in large quantities in the deeper part of the Yellow Sea due to the existence of the Yellow Sea Cold water mass (where the summer bottom water temperature is not higher than 4-8℃ in the north, and 8-12 ℃ in the south) in the summer. Consequently, the present authors are of the opinion that the echinoderm fauna of the Yellow Sea should be considered as a constituent portion of the temperate fauna, being a subregion belonging to North Pacific Temperate Biotic Region. Of the 591 species of echinoderms, 34 species are elements of North temperate fauna (sharing 5.8%); 557 species are warm water species (sharing 94.2%), most species of which are widely distributed in Indo-west Pacific region. Generally speaking, the echinoderm fauna of China Seas is predominantly warm water elements.%棘皮动物是大型底栖

  9. Analysis of mitotic phosphorylation of Borealin

    Directory of Open Access Journals (Sweden)

    Date Dipali A

    2007-01-01

    Full Text Available Abstract Background The main role of the chromosomal passenger complex is to ensure that Aurora B kinase is properly localized and activated before and during mitosis. Borealin, a member of the chromosomal passenger complex, shows increased expression during G2/M phases and is involved in targeting the complex to the centromere and the spindle midzone, where it ensures proper chromosome segregation and cytokinesis. Borealin has a consensus CDK1 phosphorylation site, threonine 106 and can be phosphorylated by Aurora B Kinase at serine 165 in vitro. Results Here, we show that Borealin is phosphorylated during mitosis in human cells. Dephosphorylation of Borealin occurs as cells exit mitosis. The phosphorylated form of Borealin is found in an INCENP-containing complex in mitosis. INCENP-containing complexes from cells in S phase are enriched in the phosphorylated form suggesting that phosphorylation may encourage entry of Borealin into the chromosomal passenger complex. Although Aurora B Kinase is found in complexes that contain Borealin, it is not required for the mitotic phosphorylation of Borealin. Mutation of T106 or S165 of Borealin to alanine does not alter the electrophoretic mobility shift of Borealin. Experiments with cyclohexamide and the phosphatase inhibitor sodium fluoride suggest that Borealin is phosphorylated by a protein kinase that can be active in interphase and mitosis and that the phosphorylation may be regulated by a short-lived phosphatase that is active in interphase but not mitosis. Conclusion Borealin is phosphorylated during mitosis. Neither residue S165, T106 nor phosphorylation of Borealin by Aurora B Kinase is required to generate the mitotic, shifted form of Borealin. Suppression of phosphorylation during interphase is ensured by a labile protein, possibly a cell cycle regulated phosphatase.

  10. Matrix analysis

    CERN Document Server

    Bhatia, Rajendra

    1997-01-01

    A good part of matrix theory is functional analytic in spirit. This statement can be turned around. There are many problems in operator theory, where most of the complexities and subtleties are present in the finite-dimensional case. My purpose in writing this book is to present a systematic treatment of methods that are useful in the study of such problems. This book is intended for use as a text for upper division and gradu­ ate courses. Courses based on parts of the material have been given by me at the Indian Statistical Institute and at the University of Toronto (in collaboration with Chandler Davis). The book should also be useful as a reference for research workers in linear algebra, operator theory, mathe­ matical physics and numerical analysis. A possible subtitle of this book could be Matrix Inequalities. A reader who works through the book should expect to become proficient in the art of deriving such inequalities. Other authors have compared this art to that of cutting diamonds. One first has to...

  11. SIMAC - A phosphoproteomic strategy for the rapid separation of mono-phosphorylated from multiply phosphorylated peptides

    DEFF Research Database (Denmark)

    Thingholm, Tine E; Jensen, Ole N; Robinson, Phillip J

    2008-01-01

    spectrometric analysis, such as immobilized metal affinity chromatography or titanium dioxide the coverage of the phosphoproteome of a given sample is limited. Here we report a simple and rapid strategy - SIMAC - for sequential separation of mono-phosphorylated peptides and multiply phosphorylated peptides from...... and an optimized titanium dioxide chromatographic method. More than double the total number of identified phosphorylation sites was obtained with SIMAC, primarily from a three-fold increase in recovery of multiply phosphorylated peptides....

  12. Phosphorylation by Cdk1 induces Plk1-mediated vimentin phosphorylation during mitosis

    NARCIS (Netherlands)

    Yamaguchi, Tomoya; Goto, Hidemasa; Yokoyama, Tomoya; Silljé, Herman; Hanisch, Anja; Uldschmid, Andreas; Takai, Yasushi; Oguri, Takashi; Nigg, Erich A; Inagaki, Masaki

    2005-01-01

    Several kinases phosphorylate vimentin, the most common intermediate filament protein, in mitosis. Aurora-B and Rho-kinase regulate vimentin filament separation through the cleavage furrow-specific vimentin phosphorylation. Cdk1 also phosphorylates vimentin from prometaphase to metaphase, but its si

  13. Matrix pentagons

    CERN Document Server

    Belitsky, A V

    2016-01-01

    The Operator Product Expansion for null polygonal Wilson loop in planar maximally supersymmetric Yang-Mills theory runs systematically in terms of multiparticle pentagon transitions which encode the physics of excitations propagating on the color flux tube ending on the sides of the four-dimensional contour. Their dynamics was unravelled in the past several years and culminated in a complete description of pentagons as an exact function of the 't Hooft coupling. In this paper we provide a solution for the last building block in this program, the SU(4) matrix structure arising from internal symmetry indices of scalars and fermions. This is achieved by a recursive solution of the Mirror and Watson equations obeyed by the so-called singlet pentagons and fixing the form of the twisted component in their tensor decomposition. The non-singlet, or charged, pentagons are deduced from these by a limiting procedure.

  14. Characterizing the Microenvironment Surrounding Phosphorylated Protein Sites

    Institute of Scientific and Technical Information of China (English)

    Shi-Cai Fan; Xue-Gong Zhang

    2005-01-01

    Protein phosphorylation plays an important role in various cellular processes. Due to its high complexity, the mechanism needs to be further studied. In the last few years, many methods have been contributed to this field, but almost all of them investigated the mechanism based on protein sequences around protein sites. In this study, we implement an exploration by characterizing the microenvironment surrounding phosphorylated protein sites with a modified shell model, and obtain some significant properties by the rank-sum test, such as the lack of some classes of residues, atoms, and secondary structures. Furthermore, we find that the depletion of some properties affects protein phosphorylation remarkably. Our results suggest that it is a meaningful direction to explore the mechanism of protein phosphorylation from microenvironment and we expect further findings along with the increasing size of phosphorylation and protein structure data.

  15. Oxidative phosphorylation in cancer cells.

    Science.gov (United States)

    Solaini, Giancarlo; Sgarbi, Gianluca; Baracca, Alessandra

    2011-06-01

    Evidence suggests that mitochondrial metabolism may play a key role in controlling cancer cells life and proliferation. Recent evidence also indicates how the altered contribution of these organelles to metabolism and the resistance of cancer mitochondria against apoptosis-associated permeabilization are closely related. The hallmarks of cancer growth, increased glycolysis and lactate production in tumours, have raised attention due to recent observations suggesting a wide spectrum of oxidative phosphorylation deficit and decreased availability of ATP associated with malignancies and tumour cell expansion. More specifically, alteration in signal transduction pathways directly affects mitochondrial proteins playing critical roles in controlling the membrane potential as UCP2 and components of both MPTP and oxphos complexes, or in controlling cells life and death as the Bcl-2 proteins family. Moreover, since mitochondrial bioenergetics and dynamics, are also involved in processes of cells life and death, proper regulation of these mitochondrial functions is crucial for tumours to grow. Therefore a better understanding of the key pathophysiological differences between mitochondria in cancer cells and in their non-cancer surrounding tissue is crucial to the finding of tools interfering with these peculiar tumour mitochondrial functions and will disclose novel approaches for the prevention and treatment of malignant diseases. Here, we review the peculiarity of tumour mitochondrial bioenergetics and the mode it is linked to the cell metabolism, providing a short overview of the evidence accumulated so far, but highlighting the more recent advances.

  16. In vivo analysis of Yorkie phosphorylation sites.

    Science.gov (United States)

    Oh, H; Irvine, K D

    2009-04-30

    The co-activator Yorkie (Yki) mediates transcriptional regulation effected by the Drosophila Fat-Warts (Wts)-Hippo (Hpo) pathways. Yki is inhibited by Wts-mediated phosphorylation, and a Wts phosphorylation site at Ser168 has been identified. Here we identify two additional Wts phosphorylation sites on Yki, and examine the respective contribution of all three sites to Yki nuclear localization and activity. Our results show that although Ser168 is the most critical site, all three phosphorylation sites influence Yki localization and activity in vivo, and can be sites of regulation by Wts. Thus, investigations of the role of Yki and its mammalian homolog Yes-associated protein (YAP) in development and oncogenesis should include evaluations of additional sites. The WW domains of Yki are not required for its phosphorylation, but instead are positively required for its activity. We also identify two potential sites of phosphorylation by an unknown kinase, which could influence phosphorylation of Ser168 by Wts, suggesting that there are additional mechanisms for regulating Yki/YAP activity.

  17. Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome

    DEFF Research Database (Denmark)

    Mann, Matthias; Ong, Shao En; Grønborg, Mads

    2002-01-01

    In signal transduction in eukaryotes, protein phosphorylation is a key event. To understand signaling processes, we must first acquire an inventory of phosphoproteins and their phosphorylation sites under different conditions. Because phosphorylation is a dynamic process, elucidation of signaling...

  18. 棘皮动物呼吸代谢研究进展%PROGRESS OF STUDIES ON RESPIRATORY METABOLISM OF ECHINODERMS

    Institute of Scientific and Technical Information of China (English)

    包杰; 姜宏波; 董双林; 田相利

    2013-01-01

    Respiratory metabolism is one of the most important aspects of bioenergetics for aquatic animals, which as the major proportion of the energy expenditure was used to maintain their process of life activities. Therefore, the researches on the respiratory metabolism of aquatic animals could enrich the knowledge of their broad ecological and physiological patterns. The effect of biotic and abiotic factors on the respiratory metabolisms of aquatic animals, especially for fish, shrimp and shellfish, have been extensively reported at home and abroad. Echinoderms as benthic marine animals played the important role in maintenance of marine function and structure; thus, their respiratory metabolisms were paid much attention these years. This paper was a review about the progress of factors on the respiratory metabolisms of Echinoderms.%呼吸代谢是动物进行能量代谢的基本生理活动,动物所摄取的能量大部分都消耗在维持其生命活动的新陈代谢中,研究动物呼吸代谢可了解动物的生理状况及对外界环境条件的适应能力.目前有关鱼类、甲壳类和贝类等呼吸代谢的影响因素的研究国内外已有很多报道.棘皮动物作为海洋底层生物,对海洋生态系统结构和功能的维护具有非常重要的作用,因而对其呼吸生理生态的研究也越来越受到关注.本文就影响棘皮动物呼吸代谢的生物因素和非生物因素进行综合评述.

  19. The protein precursors of peptides that affect the mechanics of connective tissue and/or muscle in the echinoderm Apostichopus japonicus.

    Directory of Open Access Journals (Sweden)

    Maurice R Elphick

    Full Text Available Peptides that cause muscle relaxation or contraction or that modulate electrically-induced muscle contraction have been discovered in the sea cucumber Apostichopus japonicus (Phylum Echinodermata; Class Holothuroidea. By analysing transcriptome sequence data, here the protein precursors of six of these myoactive peptides (the SALMFamides Sticho-MFamide-1 and -2, NGIWYamide, stichopin, GN-19 and GLRFA have been identified, providing novel insights on neuropeptide and endocrine-type signalling systems in echinoderms. The A. japonicus SALMFamide precursor comprises eight putative neuropeptides including both L-type and F-type SALMFamides, which contrasts with previous findings from the sea urchin Strongylocentrotus purpuratus where L-type and F-type SALMFamides are encoded by different genes. The NGIWYamide precursor contains five copies of NGIWYamide but, unlike other NG peptide-type neuropeptide precursors in deuterostomian invertebrates, the NGIWYamide precursor does not have a C-terminal neurophysin domain, indicating loss of this character in holothurians. NGIWYamide was originally discovered as a muscle contractant, but it also causes stiffening of mutable connective tissue in the body wall of A. japonicus, whilst holokinins (PLGYMFR and derivative peptides cause softening of the body wall. However, the mechanisms by which these peptides affect the stiffness of body wall connective tissue are unknown. Interestingly, analysis of the A. japonicus transcriptome reveals that the only protein containing the holokinin sequence PLGYMFR is an alpha-5 type collagen. This suggests that proteolysis of collagen may generate peptides (holokinins that affect body wall stiffness in sea cucumbers, providing a novel perspective on mechanisms of mutable connective tissue in echinoderms.

  20. Acute effects of non-weathered and weathered crude oil and dispersant associated with the Deepwater Horizon incident on the development of marine bivalve and echinoderm larvae.

    Science.gov (United States)

    Stefansson, Emily S; Langdon, Chris J; Pargee, Suzanne M; Blunt, Susanna M; Gage, Susan J; Stubblefield, William A

    2016-08-01

    Acute toxicity tests (48-96-h duration) were conducted with larvae of 2 echinoderm species (Strongylocentrotus purpuratus and Dendraster excentricus) and 4 bivalve mollusk species (Crassostrea virginica, Crassostrea gigas, Mytilus galloprovincialis, and Mercenaria mercenaria). Developing larvae were exposed to water-accommodated fractions (WAFs) and chemically enhanced water-accommodated fractions (CEWAFs) of fresh and weathered oils collected from the Gulf of Mexico during the Deepwater Horizon incident. The WAFs (oils alone), CEWAFs (oils plus Corexit 9500A dispersant), and WAFs of Corexit alone were prepared using low-energy mixing. The WAFs of weathered oils had no effect on survival and development of echinoderm and bivalve larvae, whereas WAFs of fresh oils showed adverse effects on larval development. Similar toxicities were observed for weathered oil CEWAFs and WAFs prepared with Corexit alone for oyster (C. gigas and C. virginica) larvae, which were the most sensitive of the tested invertebrate species to Corexit. Mean 10% effective concentration values for total polycyclic aromatic hydrocarbons and dipropylene glycol n-butyl ether (a marker for Corexit) in the present study were higher than all concentrations reported in nearshore field samples collected during and after the Deepwater Horizon incident. The results suggest that water-soluble fractions of weathered oils and Corexit dispersant associated with the Deepwater Horizon incident had limited, if any, acute impacts on nearshore larvae of eastern oysters and clams, as well as other organisms with similar sensitivities to those of test species in the present study; however, exposure to sediments and long-term effects were not evaluated. Environ Toxicol Chem 2016;35:2016-2028. © 2016 SETAC.

  1. Structural basis of syndecan-4 phosphorylation as a molecular switch to regulate signaling

    DEFF Research Database (Denmark)

    Koo, Bon-Kyung; Jung, Young Sang; Shin, Joon

    2005-01-01

    The syndecan transmembrane proteoglycans are involved in the organization of the actin cytoskeleton and have important roles as cell surface receptors during cell-matrix interactions. We have shown that the syndecan-4 cytoplasmic domain (4L) forms oligomeric complexes that bind to and stimulate...... PKCalpha activity in the presence of PtdIns(4,5)P2, emphasizing the importance of multimerization in the regulation of PKCalpha activation. Oligomerization of the cytoplasmic domain of syndecan-4 is regulated either positively by PtdIns(4,5)P2 or negatively by phosphorylation of serine 183. Phosphorylation...... analysis showed that the overall conformation of p-4L is a compact intertwined dimer with an unusually symmetric clamp shape, and its molecular surface is mostly positively charged. The two parallel strands form a cavity in the center of the dimeric twist. An especially marked effect of phosphorylation...

  2. Phosphorylation of dynamin I on Ser-795 by protein kinase C blocks its association with phospholipids

    DEFF Research Database (Denmark)

    Powell, K A; Valova, V A; Malladi, C S

    2000-01-01

    Dynamin I is phosphorylated in nerve terminals exclusively in the cytosolic compartment and in vitro by protein kinase C (PKC). Dephosphorylation is required for synaptic vesicle retrieval, suggesting that its phosphorylation affects its subcellular localization. An in vitro phospholipid binding...... assay was established that prevents lipid vesiculation and dynamin lipid insertion into the lipid. Dynamin I bound the phospholipid in a concentration-dependent and saturable manner, with an apparent affinity of 230 +/- 51 nM. Optimal binding occurred with mixtures of phosphatidylserine...... and phosphatidylcholine of 1:3 with little binding to phosphatidylcholine or phosphatidylserine alone. Phospholipid binding was abolished after dynamin I phosphorylation by PKC and was restored after dephosphorylation by calcineurin. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry revealed...

  3. Riemann Zeta Matrix Function

    OpenAIRE

    Kargın, Levent; Kurt, Veli

    2015-01-01

    In this study, obtaining the matrix analog of the Euler's reflection formula for the classical gamma function we expand the domain of the gamma matrix function and give a infinite product expansion of sinπxP.  Furthermore we define Riemann zeta matrix function and evaluate some other matrix integrals. We prove a functional equation for Riemann zeta matrix function.

  4. Tyrosyl phosphorylation toggles a Runx1 switch

    OpenAIRE

    Benjamin G. Neel; Speck, Nancy A.

    2012-01-01

    The Runx1 transcription factor is post-translationally modified by seryl/threonyl phosphorylation, acetylation, and methylation that control its interactions with transcription factor partners and epigenetic coregulators. In this Perspective, the study by Huang et al. (in this issue), which describes how the regulation of Runx1 tyrosyl phosphorylation by Src family kinases and the Shp2 phosphatase toggle Runx1's interactions between different coregulatory molecules, is discussed.

  5. Compartment-Specific Phosphorylation of Squid Neurofilaments.

    Science.gov (United States)

    Grant, Philip; Pant, Harish C

    2016-01-01

    Studies of the giant axon and synapse of third-order neurons in the squid stellate ganglion have provided a vast literature on neuronal physiology and axon transport. Large neuronal size also lends itself to comparative biochemical studies of cell body versus axon. These have focused on the regulation of synthesis, assembly, posttranslational modification and function of neuronal cytoskeletal proteins (microtubules (MTs) and neurofilaments (NFs)), the predominant proteins in axoplasm. These contribute to axonal organization, stability, transport, and impulse transmission responsible for rapid contractions of mantle muscles underlying jet propulsion. Studies of vertebrate NFs have established an extensive literature on NF structure, organization, and function; studies of squid NFs, however, have made it possible to compare compartment-specific regulation of NF synthesis, assembly, and function in soma versus axoplasm. Since NFs contain over 100 eligible sites for phosphorylation by protein kinases, the compartment-specific patterns of phosphorylation have been a primary focus of biochemical studies. We have learned that NF phosphorylation is tightly compartmentalized; extensive phosphorylation occurs only in the axonal compartment in squid and in vertebrate neurons. This extensive phosphorylation plays a key role in organizing NFs, in association with microtubules (MTs), into a stable, dynamic functional lattice that supports axon growth, diameter, impulse transmission, and synaptic activity. To understand how cytoskeletal phosphorylation is topographically regulated, the kinases and phosphatases, bound to NFs isolated from cell bodies and axoplasm, have also been studied.

  6. Protein phosphorylation: Localization in regenerating optic axons

    Energy Technology Data Exchange (ETDEWEB)

    Larrivee, D. (Cornell Univ. Medical College, New York, NY (USA))

    1990-09-01

    A number of axonal proteins display changes in phosphorylation during goldfish optic nerve regeneration. (1) To determine whether the phosphorylation of these proteins was closely linked to their synthesis in the retinal ganglion cell body, cycloheximide was injected intraocularly into goldfish whose optic nerves had been regenerating for 3 weeks. Cycloheximide reduced the incorporation of (3H)proline and 32P orthophosphate into total nerve protein by 84% and 46%, respectively. Of the 20 individual proteins examined, 17 contained less than 15% of the (3H)proline label measured in corresponding controls, whereas 18 proteins contained 50% or more of the 32P label, suggesting that phosphorylation was largely independent of synthesis. (2) To determine whether the proteins were phosphorylated in the ganglion cell axons, axonal transport of proteins was blocked by intraocular injection of vincristine. Vincristine reduced (3H)proline labeling of total protein by 88% and 32P labeling by 49%. Among the individual proteins (3H)proline labeling was reduced by 90% or more in 18 cases but 32P labeling was reduced only by 50% or less. (3) When 32P was injected into the cranial cavity near the ends of the optic axons, all of the phosphoproteins were labeled more intensely in the optic tract than in the optic nerve. These results suggest that most of the major phosphoproteins that undergo changes in phosphorylation in the course of regeneration are phosphorylated in the optic axons.

  7. PKA regulates calcineurin function through the phosphorylation of RCAN1: Identification of a novel phosphorylation site

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Seon Sook; Lee, Eun Hye [Department of Molecular Bioscience, College of Biomedical Science, Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon 200-701 (Korea, Republic of); Lee, Kooyeon [Department of Bio-Health Technology, College of Biomedical Science, Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon 200-701 (Korea, Republic of); Jo, Su-Hyun, E-mail: suhyunjo@kangwon.ac.kr [Department of Physiology, BK21 Plus Graduate Program, Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon 200-701 (Korea, Republic of); Seo, Su Ryeon, E-mail: suryeonseo@kangwon.ac.kr [Department of Molecular Bioscience, College of Biomedical Science, Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon 200-701 (Korea, Republic of)

    2015-04-17

    Calcineurin is a calcium/calmodulin-dependent phosphatase that has been implicated in T cell activation through the induction of nuclear factors of activated T cells (NFAT). We have previously suggested that endogenous regulator of calcineurin (RCAN1, also known as DSCR1) is targeted by protein kinase A (PKA) for the control of calcineurin activity. In the present study, we characterized the PKA-mediated phosphorylation site in RCAN1 by mass spectrometric analysis and revealed that PKA directly phosphorylated RCAN1 at the Ser 93. PKA-induced phosphorylation and the increase in the half-life of the RCAN1 protein were prevented by the substitution of Ser 93 with Ala (S93A). Furthermore, the PKA-mediated phosphorylation of RCAN1 at Ser 93 potentiated the inhibition of calcineurin-dependent pro-inflammatory cytokine gene expression by RCAN1. Our results suggest the presence of a novel phosphorylation site in RCAN1 and that its phosphorylation influences calcineurin-dependent inflammatory target gene expression. - Highlights: • We identify novel phosphorylation sites in RCAN1 by LC-MS/MS analysis. • PKA-dependent phosphorylation of RCAN1 at Ser 93 inhibits calcineurin-mediated intracellular signaling. • We show the immunosuppressive function of RCAN1 phosphorylation at Ser 93 in suppressing cytokine expression.

  8. Ammonium Ion Exchanged Zeolite for Laser Desorption/Ionization Mass Spectrometry of Phosphorylated Peptides

    Directory of Open Access Journals (Sweden)

    Mengrui Yang

    2015-01-01

    Full Text Available α-Cyano-4-hydroxycinnamic acid (CHCA, an organic matrix molecule for matrix-assisted laser desorption/ionization mass spectrometry, was adsorbed to NH4+-type zeolite surface, and this new matrix was used for the detection of low-molecular-weight compounds. It was found that this matrix could simplify the mass spectrum in the low-molecular-weight region and prevent interference from fragments and alkali metal ion adducted species. CHCA adsorbed to NH4+-type ZSM5 zeolite (CHCA/NH4ZSM5 was used to measure atropine and aconitine, two toxic alkaloids in plants. In addition, CHCA/NH4ZSM5 enabled us to detect phosphorylated peptides; peaks of the protonated peptides had higher intensities than the peaks observed using CHCA only.

  9. Echinoderms as biological indicators of the quality of littoral waters in the Mar de Alboran (Western Mediterranean, Andalusia, Spain); Equinodermos como indicadores biologicos de la calidad de las aguas litorales en el Mar de Alboran (Mediterraneo Occidental, Andalucia, Espana)

    Energy Technology Data Exchange (ETDEWEB)

    Conesa Garcia, M. A.; Lozano Duran, R.; Pozo Camacho, E.; Ruiz Arias, R. [Colegio Maravillas, Benalmadena. Malaga (Spain)

    1999-07-01

    Since 1985, the European Foundation for Environmental Education (EFEE) has used the widely-known European Blue Flag and its logo as a distinction for beaches that comply with a series of environmental, aesthetic, microbiological and physico-chemical quality criteria. Although the Blue Flag has had a positive effect on the overall quality of bathing waters, its presence has not ensured that the flora and fauna of coastal waters were equally preserved. The results of this study indicate the many of the coastal areas studied, some of them holding the European Blue Flag, have a high level of bacterial pollution, with the associated negative impact on their biological diversity. Two scientific method used in sea ecology have been applied: the Jacard rate and the UPGMA algorithm (grouping according to the mean association). Samples of 20 echinoderms species (sea-urchins, starfish, and holothurian) were collected in 17 clearly defined beach strips along the coast of the Alboran Sea, in the Western Mediterranean Sea. The beach strips were evaluated according to their water pollution level. The results confirm the validity of some echinoderm species as good bio indicators of the quality of coastal fauna and flora. By simply evaluating the presence or absence of those easily identified species it is possible to assess the status of the coastal waters ecosystem. It is proposed to include a new logo that substitutes the laws European Blue Flags, with the shape of an echinoderm, using three different species to indicate the health status of the ecosystem. Seminars should be organized in Schools to present the usefulness of echinoderms as bio indicators in coastal areas, and to teach students the importance of preservation of the sea environment. (Author) 17 refs.

  10. Phosphorylation of Cdc5 regulates its accumulation

    Directory of Open Access Journals (Sweden)

    Simpson-Lavy Kobi J

    2011-12-01

    Full Text Available Abstract Background Cdc5 (polo kinase/Plk1 is a highly conserved key regulator of the S. cerevisiae cell cycle from S-phase until cytokinesis. However, much of the regulatory mechanisms that govern Cdc5 remain to be determined. Cdc5 is phosphorylated on up to 10 sites during mitosis. In this study, we investigated the function of phosphorylation site T23, the only full consensus Cdk1 (Cdc28 phosphorylation site present. Findings Cdc5T23A introduces a degron that reduces its cellular amount to undetectable levels, which are nevertheless sufficient for normal cell proliferation. The degron acts in cis and is reversed by N-terminal GFP-tagging. Cdk1 kinase activity is required to maintain Cdc5 levels during G2. This, Cdk1 inhibited, Cdc5 degradation is APC/CCdh1 independent and requires new protein synthesis. Cdc5T23E is hyperactive, and reduces the levels of Cdc5 (in trans and drastically reduces Clb2 levels. Conclusions Phosphorylation of Cdc5 by Cdk1 is required to maintain Cdc5 levels during G2. However, phosphorylation of T23 (probably by Cdk1 caps Cdc5 and other CLB2 cluster protein accumulation, preventing potential protein toxicity, which may arise from their overexpression or from APC/CCdh1 inactivation.

  11. Phosphorylation state-dependent interaction between AKAP7δ/γ and phospholamban increases phospholamban phosphorylation

    Science.gov (United States)

    Rigatti, Marc; Le, Andrew V.; Gerber, Claire; Moraru, Ion I.; Dodge-Kafka, Kimberly L.

    2016-01-01

    Changes in heart rate and contractility in response to sympathetic stimulation occur via activation of cAMP dependent protein kinase A (PKA), leading to phosphorylation of numerous substrates that alter Ca2+ cycling. Phosphorylation of these substrates is coordinated by A-kinase anchoring proteins (AKAPs), which recruit PKA to specific substrates [1]. Phosphorylation of the PKA substrate phospholamban (PLB) is a critical determinant of Ca2+ re-entry into the sarcoplasmic reticulum and is coordinated by AKAP7δ/γ [2,3]. Here, we further these findings by showing that phosphorylation of PLB requires interaction with AKAP7δ/γ and that this interaction occurs only when PLB is unphosphorylated. Additionally, we find that two mutants of PLB (R9C and Δ14), which are associated with dilated cardiomyopathy in humans, prevent association with AKAP7δ/γ and display reduced phosphorylation in vitro. This finding implicates the AKAP7δ/γ-PLB interaction in the pathology of the disease phenotype. Further exploration of the AKAP7δ/γ-PLB association demonstrated a phosphorylation state-dependence of the interaction. Computational modeling revealed that this mode of interaction allows for small amounts of AKAP and PKA (100–200nM) to regulate the phosphorylation of large quantities of PLB (50µM). Our results confirm that AKAP7γ/δ binding to PLB is important for phosphorylation of PLB, and describe a novel phosphorylation state-dependent binding mechanism that explains how phosphorylation of highly abundant PKA substrates can be regulated by AKAPs present at ~100–200 fold lower concentrations. PMID:26027516

  12. Stable isotope trophic patterns in echinoderm megafauna in close proximity to and remote from Gulf of Mexico lower slope hydrocarbon seeps

    Science.gov (United States)

    Carney, Robert Spencer

    2010-11-01

    Hydrocarbon-seep communities in the Gulf of Mexico have a high biomass that is exploited as a food source to varying degrees by the photosynthesis-dependent fauna inhabiting the surrounding mud bottom. A decline concurrent with ocean depth in detritus influx to that background habitat results in a much lower background biomass. The biomass contrast between population-rich seeps and depauperate mud bottom leads to the prediction that seep utilization by the background fauna should be extensive at all depths and should increase with depth. Species depth zonation makes like-species comparisons over the full depth of the Gulf of Mexico impossible. Seeps and normal bottom above 1000 m have different fauna from those below 1000 m. Lower slope seeps are surrounded by a fauna rich in echinoderm species, especially asteroids, ophiuroids, and holothuroids. All three taxa have species that are abundant within seeps and are probably endemic to them. They also contain species found only in mud background or within mud and seeps backgrounds. Tissue analyses of δ13C and δ15N of echinoderms collected by ROV within seeps and trawling away from seeps indicate a pattern of utilization similar to that found in upper slope seeps exploited by different taxa. Seastar and ophiuroid species abundant in or endemic to seeps have tissue isotope values reflecting seep chemosynthetic input via a free-living microbial detritus or predation. A single seep-endemic deposit-feeding holothuroid showed distinct seep tissue values. Background deposit-feeding holothuroids collected within seeps showed either no or only minor incorporation of seep carbon, indicating either a lack of access to seep detritus or short feeding times within the seep. A predicted extensive utilization of seep productivity at the deeper seeps was not found. Seeps may be relatively closed systems that require special adaptations of species in order for them to enter, exploit, and survive. Alternately, the surrounding deep

  13. Protein-Tyrosine Phosphorylation in Bacillus subtilis

    DEFF Research Database (Denmark)

    Mijakovic, Ivan; Petranovic, Dina; Bottini, N.

    2005-01-01

    phosphorylation, indicating that this post-translational modifi cation could regulate physiological processes ranging from stress response and exopolysaccharide synthesis to DNA metabolism. Some interesting work in this fi eld was done in Bacillus subtilis , and we here present the current state of knowledge...

  14. Mapping of p140Cap phosphorylation sites

    DEFF Research Database (Denmark)

    Repetto, Daniele; Aramu, Simona; Boeri Erba, Elisabetta

    2013-01-01

    Protein phosphorylation tightly regulates specific binding of effector proteins that control many diverse biological functions of cells (e. g. signaling, migration and proliferation). p140Cap is an adaptor protein, specifically expressed in brain, testis and epithelial cells, that undergoes phosp...

  15. Phosphorylation sites within Ebola virus nucleoprotein

    Institute of Scientific and Technical Information of China (English)

    Sora; Yasri; Viroj; Wiwanitkit

    2015-01-01

    To understand the infection process, the viral multiplication and entry to the cell is widely studied. The Ebola virus nucleoprotein is the important problem for the pathological process. Focusing on the specific biological process, the post translational modification is needed. Here, the authors used the bioinformatics study to find the phosphorylation sites within the Ebola virus nucleoprotein and could identify many new sites.

  16. Ion channels, phosphorylation and mammalian sperm capacitation.

    Science.gov (United States)

    Visconti, Pablo E; Krapf, Dario; de la Vega-Beltrán, José Luis; Acevedo, Juan José; Darszon, Alberto

    2011-05-01

    Sexually reproducing animals require an orchestrated communication between spermatozoa and the egg to generate a new individual. Capacitation, a maturational complex phenomenon that occurs in the female reproductive tract, renders spermatozoa capable of binding and fusing with the oocyte, and it is a requirement for mammalian fertilization. Capacitation encompasses plasma membrane reorganization, ion permeability regulation, cholesterol loss and changes in the phosphorylation state of many proteins. Novel tools to study sperm ion channels, image intracellular ionic changes and proteins with better spatial and temporal resolution, are unraveling how modifications in sperm ion transport and phosphorylation states lead to capacitation. Recent evidence indicates that two parallel pathways regulate phosphorylation events leading to capacitation, one of them requiring activation of protein kinase A and the second one involving inactivation of ser/thr phosphatases. This review examines the involvement of ion transporters and phosphorylation signaling processes needed for spermatozoa to achieve capacitation. Understanding the molecular mechanisms leading to fertilization is central for societies to deal with rising male infertility rates, to develop safe male gamete-based contraceptives and to preserve biodiversity through better assisted fertilization strategies.

  17. Ion channels, phosphorylation and mammalian sperm capacitation

    Institute of Scientific and Technical Information of China (English)

    Pablo E Visconti; Dario Krapf; José Luis de la Vega-Beltrán; Juan José Acevedo; Alberto Darszon

    2011-01-01

    Sexually reproducing animals require an orchestrated communication between spermatozoa and the egg to generate a new individual. Capacitation, a maturational complex phenomenon that occurs in the female reproductive tract, renders spermatozoa capable of binding and fusing with the oocyte, and it is a requirement for mammalian fertilization. Capacitation encompasses plasma membrane reorganization, ion permeability regulation, cholesterol loss and changes in the phosphorylation state of many proteins. Novel tools to study sperm ion channels, image intracellular ionic changes and proteins with better spatial and temporal resolution, are unraveling how modifications in sperm ion transport and phosphorylation states lead to capacitation. Recent evidence indicates that two parallel pathways regulate phosphorylation events leading to capacitation, one of them requiring activation of protein kinase A and the second one involving inactivation of ser/thr phosphatases. This review examines the involvement of ion transporters and phosphorylation signaling processes needed for spermatozoa to achieve capacitation. Understanding the molecular mechanisms leading to fertilization is central for societies to deal with rising male infertility rates, to develop safe male gamete-based contraceptives and to preserve biodiversity through better assisted fertilization strategies.

  18. Phosphorylated α-synuclein in Parkinson's disease

    DEFF Research Database (Denmark)

    Stewart, Tessandra; Sossi, Vesna; Aasly, Jan O;

    2015-01-01

    INTRODUCTION: α-Synuclein (α-syn) is a key protein in Parkinson's disease (PD), and one of its phosphorylated forms, pS129, is higher in PD patients than healthy controls. However, few studies have examined its levels in longitudinally collected cerebrospinal fluid (CSF) or in preclinical cases. ...

  19. Transferases for alkylation, glycosylation and phosphorylation

    NARCIS (Netherlands)

    Auriol, D.; ter Halle, R.; Lefèvre, F.; Visser, D.F.; Gordon, G.E.R.; Bode, M.L.; Mathiba, K.; Brady, D.; De Winter, K.; Desmet, T.; Cerdobbel, A.; Soetaert, W.; van Herk, T.; Hartog, A.F.; Wever, R.; Brzezińska-rodak, M.; Klimek-Ochab, M.; Żymańczyk-Duda, E.; Mukherjee, J.; Gupta, M.N.; Yin, W.B.; Li, S.M.; Gruber-Khadjawi, M.; Whittall, J.; Sutton, P.W.

    2012-01-01

    This chapter contains sections titled: Industrial Production of Caffeic Acid-α-D-O-Glucoside Enzymatic Synthesis of 5-Methyluridine by Transglycosylation of Guanosine and Thymine Preparation and Use of Sucrose Phosphorylase as Cross-Linked Enzyme Aggregate (CLEA) Enzymatic Synthesis of Phosphorylate

  20. First records, rediscovery and compilation of deep-sea echinoderms in the middle and lower continental slope of the Mediterranean Sea

    Directory of Open Access Journals (Sweden)

    Ariadna Mecho

    2014-06-01

    Full Text Available This study provides a compilation of all available information on deep-sea echinoderms from the middle and lower slopes of the Mediterranean Sea, with the aim of providing a unified source of information on the taxonomy of this group. Previous records of species are updated with new data obtained from 223 trawl hauls conducted in 11 cruises within the northwestern Mediterranean Sea between 800 m and 2845 m depth. Valid names, bathymetric ranges and geographic distributions are given for all species. The new data report, for the first time, the presence of the Atlantic echinoid Gracilechinus elegans (Düben and Koren, 1844 in the Mediterranean Sea. We also report the presence of the endemic holothurians Hedingia mediterranea (Bartolini Baldelli, 1914, dredged only once previously in 1914 in the Tyrrhenian Sea, and Penilpidia ludwigi (von Marenzeller, 1893, known previously only from three samples, two in the Aegean Sea and one in the Balearic Sea. Additionally, the deeper limits of the bathymetric distribution of four species have been expanded: the asteroid Ceramaster grenadensis (Perrier, 1881 to 2845 m; the echinoid Brissopsis lyrifera (Forbes, 1841 to 2250 m; and the holothurians Hedingia mediterranea and Holothuria (Panningothuria forskali Delle Chiaje, 1823, to 1500 m and 850 m, respectively.

  1. From gonadotropin-inhibitory hormone to SIFamides: are echinoderm SALMFamides the "missing link" in a bilaterian family of neuropeptides that regulate reproductive processes?

    Science.gov (United States)

    Elphick, Maurice R

    2013-11-01

    Gonadotropin-inhibitory hormone (GnIH) belongs to a family of vertebrate neuropeptides with a C-terminal PxRFamide motif, which exert effects by activating the G-protein coupled receptors NPFF1 and/or NPFF2. Comparative analysis of genome sequence data has revealed that orthologs of NPFF1/NPFF2-type receptors occur throughout the Bilateria and the neuropeptide ligand that activates the Drosophila NPFF1/NPFF2-type receptor has been identified as AYRKPPFNGSIFamide ("SIFamide"). Therefore, SIFamide-type neuropeptides, which occur throughout protostomian invertebrates, probably share a common evolutionary origin with vertebrate PxRFamide-type neuropeptides. Based on structural similarities, here SALMFamide neuropeptides are identified as candidate ligand components of this ancient bilaterian peptide-receptor signaling system in a deuterostomian invertebrate phylum, the echinoderms (e.g., starfish, sea urchins). Furthermore, functional studies provide evidence that PxRFamide/SALMFamide/SIFamide-type neuropeptides have evolutionarily conserved roles in regulation (typically inhibitory) of reproductive processes.

  2. AChE and EROD activities in two echinoderms, Holothuria leucospilota and Holoturia atra (Holothuroidea), in a coral reef (Reunion Island, South-western Indian Ocean).

    Science.gov (United States)

    Kolasinski, Joanna; Taddei, Dorothée; Cuet, Pascale; Frouin, Patrick

    2010-01-01

    AChE and EROD activities were investigated in two holothurian species, Holothuria leucospilota and Holoturia atra, from a tropical coral reef. These organisms were collected from 3 back-reef stations, where temperature and salinity were homogeneous. The activity levels of both AChE and EROD varied significantly between the two species, but were in the range of values determined in other echinoderm species. AChE activity levels were higher in the longitudinal muscle than in the tentacle tegument. Among the several tissues tested, the digestive tract wall exhibited higher EROD activity levels. Sex did not influence AChE and EROD activity levels in both species. Animal biomass and EROD activity levels were only correlated in the tegument tissue of H. atra, and we hypothesize a possible influence of age. EROD activity did not show intraspecific variability. A significant relationship was found between AChE activity and Cuvierian tubules time of expulsion in Holothuria leucospilota. Individuals collected at the southern site presented both lower AChE activity levels and Cuvierian tubules time of expulsion, indicating possible neural disturbance. More information on holothurians biology and physiology is needed to further assess biomarkers in these key species. This study is the first of its kind performed in the coastal waters of Reunion Island and data obtained represent reference values.

  3. Matrix metalloproteinases in a sea urchin ligament with adaptable mechanical properties.

    Directory of Open Access Journals (Sweden)

    Ana R Ribeiro

    Full Text Available Mutable collagenous tissues (MCTs of echinoderms show reversible changes in tensile properties (mutability that are initiated and modulated by the nervous system via the activities of cells known as juxtaligamental cells. The molecular mechanism underpinning this mechanical adaptability has still to be elucidated. Adaptable connective tissues are also present in mammals, most notably in the uterine cervix, in which changes in stiffness result partly from changes in the balance between matrix metalloproteinases (MMPs and tissue inhibitors of metalloproteinases (TIMPs. There have been no attempts to assess the potential involvement of MMPs in the echinoderm mutability phenomenon, apart from studies dealing with a process whose relationship to the latter is uncertain. In this investigation we used the compass depressor ligaments (CDLs of the sea-urchin Paracentrotus lividus. The effect of a synthetic MMP inhibitor - galardin - on the biomechanical properties of CDLs in different mechanical states ("standard", "compliant" and "stiff" was evaluated by dynamic mechanical analysis, and the presence of MMPs in normal and galardin-treated CDLs was determined semi-quantitatively by gelatin zymography. Galardin reversibly increased the stiffness and storage modulus of CDLs in all three states, although its effect was significantly lower in stiff than in standard or compliant CDLs. Gelatin zymography revealed a progressive increase in total gelatinolytic activity between the compliant, standard and stiff states, which was possibly due primarily to higher molecular weight components resulting from the inhibition and degradation of MMPs. Galardin caused no change in the gelatinolytic activity of stiff CDLs, a pronounced and statistically significant reduction in that of standard CDLs, and a pronounced, but not statistically significant, reduction in that of compliant CDLs. Our results provide evidence that MMPs may contribute to the variable tensility of the

  4. Protein Synthesis Initiation Factors: Phosphorylation and Regulation

    Energy Technology Data Exchange (ETDEWEB)

    Karen S. Browning

    2009-06-15

    The initiation of the synthesis of proteins is a fundamental process shared by all living organisms. Each organism has both shared and unique mechanisms for regulation of this vital process. Higher plants provide for a major amount of fixation of carbon from the environment and turn this carbon into food and fuel sources for our use. However, we have very little understanding of how plants regulate the synthesis of the proteins necessary for these metabolic processes. The research carried out during the grant period sought to address some of these unknowns in the regulation of protein synthesis initiation. Our first goal was to determine if phosphorylation plays a significant role in plant initiation of protein synthesis. The role of phosphorylation, although well documented in mammalian protein synthesis regulation, is not well studied in plants. We showed that several of the factors necessary for the initiation of protein synthesis were targets of plant casein kinase and showed differential phosphorylation by the plant specific isoforms of this kinase. In addition, we identified and confirmed the phosphorylation sites in five of the plant initiation factors. Further, we showed that phosphorylation of one of these factors, eIF5, affected the ability of the factor to participate in the initiation process. Our second goal was to develop a method to make initiation factor 3 (eIF3) using recombinant methods. To date, we successfully cloned and expressed 13/13 subunits of wheat eIF3 in E. coli using de novo gene construction methods. The final step in this process is to place the subunits into three different plasmid operons for co-expression. Successful completion of expression of eIF3 will be an invaluable tool to the plant translation community.

  5. A Simple Hydraulic Analog Model of Oxidative Phosphorylation.

    Science.gov (United States)

    Willis, Wayne T; Jackman, Matthew R; Messer, Jeffrey I; Kuzmiak-Glancy, Sarah; Glancy, Brian

    2016-06-01

    Mitochondrial oxidative phosphorylation is the primary source of cellular energy transduction in mammals. This energy conversion involves dozens of enzymatic reactions, energetic intermediates, and the dynamic interactions among them. With the goal of providing greater insight into the complex thermodynamics and kinetics ("thermokinetics") of mitochondrial energy transduction, a simple hydraulic analog model of oxidative phosphorylation is presented. In the hydraulic model, water tanks represent the forward and back "pressures" exerted by thermodynamic driving forces: the matrix redox potential (ΔGredox), the electrochemical potential for protons across the mitochondrial inner membrane (ΔGH), and the free energy of adenosine 5'-triphosphate (ATP) (ΔGATP). Net water flow proceeds from tanks with higher water pressure to tanks with lower pressure through "enzyme pipes" whose diameters represent the conductances (effective activities) of the proteins that catalyze the energy transfer. These enzyme pipes include the reactions of dehydrogenase enzymes, the electron transport chain (ETC), and the combined action of ATP synthase plus the ATP-adenosine 5'-diphosphate exchanger that spans the inner membrane. In addition, reactive oxygen species production is included in the model as a leak that is driven out of the ETC pipe by high pressure (high ΔGredox) and a proton leak dependent on the ΔGH for both its driving force and the conductance of the leak pathway. Model water pressures and flows are shown to simulate thermodynamic forces and metabolic fluxes that have been experimentally observed in mammalian skeletal muscle in response to acute exercise, chronic endurance training, and reduced substrate availability, as well as account for the thermokinetic behavior of mitochondria from fast- and slow-twitch skeletal muscle and the metabolic capacitance of the creatine kinase reaction.

  6. The Matrix Cookbook

    DEFF Research Database (Denmark)

    Petersen, Kaare Brandt; Pedersen, Michael Syskind

    Matrix identities, relations and approximations. A desktop reference for quick overview of mathematics of matrices.......Matrix identities, relations and approximations. A desktop reference for quick overview of mathematics of matrices....

  7. Neurofilament Phosphorylation during Development and Disease: Which Came First, the Phosphorylation or the Accumulation?

    Directory of Open Access Journals (Sweden)

    Jeffrey M. Dale

    2012-01-01

    Full Text Available Posttranslational modification of proteins is a ubiquitous cellular mechanism for regulating protein function. Some of the most heavily modified neuronal proteins are cytoskeletal proteins of long myelinated axons referred to as neurofilaments (NFs. NFs are type IV intermediate filaments (IFs that can be composed of four subunits, neurofilament heavy (NF-H, neurofilament medium (NF-M, neurofilament light (NF-L, and α-internexin. Within wild type axons, NFs are responsible for mediating radial growth, a process that determines axonal diameter. NFs are phosphorylated on highly conserved lysine-serine-proline (KSP repeats located along the C-termini of both NF-M and NF-H within myelinated axonal regions. Phosphorylation is thought to regulate aspects of NF transport and function. However, a key pathological hallmark of several neurodegenerative diseases is ectopic accumulation and phosphorylation of NFs. The goal of this review is to provide an overview of the posttranslational modifications that occur in both normal and diseased axons. We review evidence that challenges the role of KSP phosphorylation as essential for radial growth and suggests an alternative role for NF phosphorylation in myelinated axons. Furthermore, we demonstrate that regulation of NF phosphorylation dynamics may be essential to avoiding NF accumulations.

  8. Matrix with Prescribed Eigenvectors

    Science.gov (United States)

    Ahmad, Faiz

    2011-01-01

    It is a routine matter for undergraduates to find eigenvalues and eigenvectors of a given matrix. But the converse problem of finding a matrix with prescribed eigenvalues and eigenvectors is rarely discussed in elementary texts on linear algebra. This problem is related to the "spectral" decomposition of a matrix and has important technical…

  9. BAD Phosphorylation: A Novel Link between Apoptosis and Cancer

    OpenAIRE

    Polzien, Lisa

    2011-01-01

    BAD (Bcl-2 antagonist of cell death, Bcl-2 associated death promoter) is a pro-apoptotic member of the Bcl-2 protein family that is regulated by phosphorylation in response to survival factors. Although much attention has been devoted to the identification of phosphorylation sites in murine BAD (mBAD), little data are available with respect to phosphorylation of human BAD (hBAD) protein. In this work, we investigated the quantitative contribution of BAD targeting kinases in phosphorylating se...

  10. Flux control through protein phosphorylation in yeast

    DEFF Research Database (Denmark)

    Chen, Yu; Nielsen, Jens

    2016-01-01

    describe the development of phosphoproteomics in yeast as well as approaches to analysing the phosphoproteomics data. Finally, we focus on integrated analyses with other omics data sets and genome-scale metabolic models. Despite the advances, future studies improving both experimental technologies......Protein phosphorylation is one of the most important mechanisms regulating metabolism as it can directly modify metabolic enzymes by the addition of phosphate groups. Attributed to such a rapid and reversible mechanism, cells can adjust metabolism rapidly in response to temporal changes. The yeast...... as well as identify mechanisms underlying human metabolic diseases. Here we collect functional phosphorylation events of 41 enzymes involved in yeast metabolism and demonstrate functional mechanisms and the application of this information in metabolic engineering. From a systems biology perspective, we...

  11. Phosphorylation sites within Ebola virus nucleoprotein

    Directory of Open Access Journals (Sweden)

    Sora Yasri

    2015-07-01

    Full Text Available To understand the infection process, the viral multiplication and entry to the cell is widely studied. The Ebola virus nucleoprotein is the important problem for the pathological process. Focusing on the specific biological process, the post translational modification is needed. Here, the authors used the bioinformatics study to find the phosphorylation sites within the Ebola virus nucleoprotein and could identify many new sites.

  12. Protein phosphorylation in bcterial signaling and regulation

    KAUST Repository

    Mijakovic, Ivan

    2016-01-26

    In 2003, it was demonstrated for the first time that bacteria possess protein-tyrosine kinases (BY-kinases), capable of phosphorylating other cellular proteins and regulating their activity. It soon became apparent that these kinases phosphorylate a number of protein substrates, involved in different cellular processes. More recently, we found out that BY-kinases can be activated by several distinct protein interactants, and are capable of engaging in cross-phosphorylation with other kinases. Evolutionary studies based on genome comparison indicate that BY-kinases exist only in bacteria. They are non-essential (present in about 40% bacterial genomes), and their knockouts lead to pleiotropic phenotypes, since they phosphorylate many substrates. Surprisingly, BY-kinase genes accumulate mutations at an increased rate (non-synonymous substitution rate significantly higher than other bacterial genes). One direct consequence of this phenomenon is no detectable co-evolution between kinases and their substrates. Their promiscuity towards substrates thus seems to be “hard-wired”, but why would bacteria maintain such promiscuous regulatory devices? One explanation is the maintenance of BY-kinases as rapidly evolving regulators, which can readily adopt new substrates when environmental changes impose selective pressure for quick evolution of new regulatory modules. Their role is clearly not to act as master regulators, dedicated to triggering a single response, but they might rather be employed to contribute to fine-tuning and improving robustness of various cellular responses. This unique feature makes BY-kinases a potentially useful tool in synthetic biology. While other bacterial kinases are very specific and their signaling pathways insulated, BY-kinase can relatively easily be engineered to adopt new substrates and control new biosynthetic processes. Since they are absent in humans, and regulate some key functions in pathogenic bacteria, they are also very promising

  13. Solid polymer electrolyte from phosphorylated chitosan

    Energy Technology Data Exchange (ETDEWEB)

    Fauzi, Iqbal, E-mail: arcana@chem.itb.ac.id; Arcana, I Made, E-mail: arcana@chem.itb.ac.id [Inorganic and Physical Chemistry Research Groups, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung 40132 (Indonesia)

    2014-03-24

    Recently, the need of secondary battery application continues to increase. The secondary battery which using a liquid electrolyte was indicated had some weakness. A solid polymer electrolyte is an alternative electrolytes membrane which developed in order to replace the liquid electrolyte type. In the present study, the effect of phosphorylation on to polymer electrolyte membrane which synthesized from chitosan and lithium perchlorate salts was investigated. The effect of the component’s composition respectively on the properties of polymer electrolyte, was carried out by analyzed of it’s characterization such as functional groups, ion conductivity, and thermal properties. The mechanical properties i.e tensile resistance and the morphology structure of membrane surface were determined. The phosphorylation processing of polymer electrolyte membrane of chitosan and lithium perchlorate was conducted by immersing with phosphoric acid for 2 hours, and then irradiated on a microwave for 60 seconds. The degree of deacetylation of chitosan derived from shrimp shells was obtained around 75.4%. Relative molecular mass of chitosan was obtained by viscometry method is 796,792 g/mol. The ionic conductivity of chitosan membrane was increase from 6.33 × 10{sup −6} S/cm up to 6.01 × 10{sup −4} S/cm after adding by 15 % solution of lithium perchlorate. After phosphorylation, the ionic conductivity of phosphorylated lithium chitosan membrane was observed 1.37 × 10{sup −3} S/cm, while the tensile resistance of 40.2 MPa with a better thermal resistance. On the strength of electrolyte membrane properties, this polymer electrolyte membrane was suggested had one potential used for polymer electrolyte in field of lithium battery applications.

  14. Linear motif atlas for phosphorylation-dependent signaling

    DEFF Research Database (Denmark)

    Miller, Martin Lee; Jensen, LJ; Diella, F;

    2008-01-01

    Systematic and quantitative analysis of protein phosphorylation is revealing dynamic regulatory networks underlying cellular responses to environmental cues. However, matching these sites to the kinases that phosphorylate them and the phosphorylation-dependent binding domains that may subsequently...... sequence models of linear motifs. The atlas is available as a community resource (http://netphorest.info)....

  15. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis

    DEFF Research Database (Denmark)

    Miller, Martin Lee; Brunak, Søren; Olsen, JV

    2010-01-01

    ) or CDK2 were almost fully phosphorylated in mitotic cells. In particular, nuclear proteins and proteins involved in regulating metabolic processes have high phosphorylation site occupancy in mitosis. This suggests that these proteins may be inactivated by phosphorylation in mitotic cells....

  16. Phosphorylation of erythrocyte membrane liberates calcium

    Energy Technology Data Exchange (ETDEWEB)

    Chauhan, V.P.S.; Brockerhoff, H.

    1986-05-01

    Phosphorylation of permeabilized erythrocyte ghost membranes with ATP results in an increase free calcium level as measured with the help of Ca/sup 2 +/ electrode and /sup 45/Ca. This effect could not be observed in the presence of p/sup -/ chloromercuric benzoate, an inhibitor of kinases. The rise in the free calcium due to phosphorylation of the membrane was accompanied by a decrease in the level of phosphatidylinositol (PI) and an increase in phosphatidylinositolmonophosphate (PIP) and phosphatidylinositolbisphosphate (PIP/sub 2/). These results support the proposal that an inositol shuttle, PI in equilibrium PIP in equilibrium PIP/sub 2/, operates to maintain the intracellular calcium concentration. The cation is believed to be sequestered in a cage formed by the head groups of two acidic phospholipid molecules, e.g., phosphatidylserine and phosphatidylinositol, with the participation of both PO and fatty acid ester CO groups. When the inositol group of such a cage is phosphorylated, inter-headgroup hydrogen bonding between the lipids is broken. As a result the cage opens and calcium is released.

  17. Phosphorylation of Astrin Regulates Its Kinetochore Function.

    Science.gov (United States)

    Chung, Hee Jin; Park, Ji Eun; Lee, Nam Soo; Kim, Hongtae; Jang, Chang-Young

    2016-08-19

    The error-free segregation of chromosomes, which requires the precisely timed search and capture of chromosomes by spindles during early mitotic and meiotic cell division, is responsible for genomic stability and is achieved by the spindle assembly checkpoint in the metaphase-anaphase transition. Mitotic kinases orchestrate M phase events, such as the reorganization of cell architecture and kinetochore (KT) composition with the exquisite phosphorylation of mitotic regulators, to ensure timely and temporal progression. However, the molecular mechanisms underlying the changes of KT composition for stable spindle attachment during mitosis are poorly understood. Here, we show that the sequential action of the kinase Cdk1 and the phosphatase Cdc14A control spindle attachment to KTs. During prophase, the mitotic spindle protein Spag5/Astrin is transported into centrosomes by Kinastrin and phosphorylated at Ser-135 and Ser-249 by Cdk1, which, in prometaphase, is loaded onto the spindle and targeted to KTs. We also demonstrate that Cdc14A dephosphorylates Astrin, and therefore the overexpression of Cdc14A sequesters Astrin in the centrosome and results in aberrant chromosome alignment. Mechanistically, Plk1 acts as an upstream kinase for Astrin phosphorylation by Cdk1 and targeting phospho-Astrin to KTs, leading to the recruitment of outer KT components, such as Cenp-E, and the stable attachment of spindles to KTs. These comprehensive findings reveal a regulatory circuit for protein targeting to KTs that controls the KT composition change of stable spindle attachment and chromosome integrity.

  18. Control mechanisms in mitochondrial oxidative phosphorylation

    Institute of Scientific and Technical Information of China (English)

    Jana Hroudová; Zdeněk Fi(s)ar

    2013-01-01

    Distribution and activity of mitochondria are key factors in neuronal development, synaptic plasticity and axogenesis. The majority of energy sources, necessary for cellular functions, originate from oxidative phosphorylation located in the inner mitochondrial membrane. The adenosine-5'- triphosphate production is regulated by many control mechanism–firstly by oxygen, substrate level, adenosine-5'-diphosphate level, mitochondrial membrane potential, and rate of coupling and proton leak. Recently, these mechanisms have been implemented by "second control mechanisms," such as reversible phosphorylation of the tricarboxylic acid cycle enzymes and electron transport chain complexes, allosteric inhibition of cytochrome c oxidase, thyroid hormones, effects of fatty acids and uncoupling proteins. Impaired function of mitochondria is implicated in many diseases ranging from mitochondrial myopathies to bipolar disorder and schizophrenia. Mitochondrial dysfunctions are usually related to the ability of mitochondria to generate adenosine-5'-triphosphate in response to energy demands. Large amounts of reactive oxygen species are released by defective mitochondria, similarly, decline of antioxidative enzyme activities (e.g. in the elderly) enhances reactive oxygen species production. We reviewed data concerning neuroplasticity, physiology, and control of mitochondrial oxidative phosphorylation and reactive oxygen species production.

  19. Mechanical, thermal and swelling properties of phosphorylated nanocellulose fibrils/PVA nanocomposite membranes.

    Science.gov (United States)

    Niazi, Muhammad Bilal Khan; Jahan, Zaib; Berg, Sigrun Sofie; Gregersen, Øyvind Weiby

    2017-12-01

    Cellulose nanofibrils (CNF) have strong reinforcing properties when incorporated in a compatible polymer matrix. This work reports the effect of the addition of phosphorylated nanocellulose (PCNF) on the mechanical, thermal and swelling properties of poly(vinyl alcohol) (PVA) nanocomposite membranes. The incorporation of nanocellulose in PVA reduced the crystallinity at 0%RH. However, when the films were exposed to higher humidities the crystallinity increased. No apparent trend is observed for mechanical properties for dry membranes (0% RH). However, at 93% RH the elastic modulus increased strongly from 0.12MPa to 0.82MPa when adding 6% PCNF. At higher humidities, the moisture uptake has large influence on storage modulus, tan δ and tensile properties. Membranes containing 1% PCNF absorbed most moisture. Swelling, thermal and mechanical properties indicate a good potential for applying of PVA/phosphorylated nanocellulose composite membranes for CO2 separation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Mode of interaction of ganglioside Langmuir monolayer originated from echinoderms: three binary systems of ganglioside/DPPC, ganglioside/DMPE, and ganglioside/cholesterol.

    Science.gov (United States)

    Hoda, Kazuki; Ikeda, Yuriko; Kawasaki, Hideya; Yamada, Koji; Higuchi, Ryuichi; Shibata, Osamu

    2006-09-01

    The surface pressure (pi)-area (A), the surface potential (DeltaV)-A, and the dipole moment (mu( perpendicular))-A isotherms were obtained for monolayers made from a ganglioside originated from echinoderms [Diadema setosum ganglioside (DSG-1)], dipalmitoylphosphatidylcholine (DPPC), dimyristoylphosphatidylethanolamine (DMPE), cholesterol (Ch), and their combinations. Monolayers spread on several different substrates were investigated at the air/water interface by the Wilhelmy method, ionizing electrode method, fluorescence microscopy (FM) and atomic force microscopy (AFM). Surface potentials (DeltaV) of pure components were analyzed using the three-layer model proposed by Demchak and Fort [R.J. Demchak, T. Fort, J. Colloid Interface Sci. 46 (1974) 191-202]. The new finding was that DSG-1 was stable and showed a liquid-expanded film and that its monolayer behavior of DeltaV was sensitive for the change of the NaCl concentration in the subphase. Moreover, the miscibility of DSG-1 and three major lipids in the two-component monolayers was examined by plotting the variation of the molecular area and the surface potential as a function of the DSG-1 molar fraction (X(DSG-1)), using the additivity rule. From the A-X(DSG-1) and DeltaV(m)-X(DSG-1) plots, partial molecular surface area (PMA) and apparent partial molecular surface potential (APSP) were determined at the discrete surface pressure. The PMA and APSP with the mole fraction were extensively discussed for the miscible system. The miscibility was also investigated from the two-dimensional phase diagrams. Furthermore, a regular surface mixture, for which the Joos equation was used for the analysis of the collapse pressure of two-component monolayers, allowed calculation of the interaction parameter (xi) and the interaction energy (-Deltavarepsilon) between them. The observations using fluorescence microscopy and AFM image also provide us the miscibility in the monolayer state.

  1. Linking genotoxic responses with cytotoxic and behavioural or physiological consequences: differential sensitivity of echinoderms (Asterias rubens) and marine molluscs (Mytilus edulis).

    Science.gov (United States)

    Canty, Martin N; Hutchinson, Thomas H; Brown, Rebecca J; Jones, Malcolm B; Jha, Awadhesh N

    2009-08-13

    the relevance of including adult echinoderms in environmental studies.

  2. Ancestral regulatory circuits governing ectoderm patterning downstream of Nodal and BMP2/4 revealed by gene regulatory network analysis in an echinoderm.

    Directory of Open Access Journals (Sweden)

    Alexandra Saudemont

    Full Text Available Echinoderms, which are phylogenetically related to vertebrates and produce large numbers of transparent embryos that can be experimentally manipulated, offer many advantages for the analysis of the gene regulatory networks (GRN regulating germ layer formation. During development of the sea urchin embryo, the ectoderm is the source of signals that pattern all three germ layers along the dorsal-ventral axis. How this signaling center controls patterning and morphogenesis of the embryo is not understood. Here, we report a large-scale analysis of the GRN deployed in response to the activity of this signaling center in the embryos of the Mediterranean sea urchin Paracentrotus lividus, in which studies with high spatial resolution are possible. By using a combination of in situ hybridization screening, overexpression of mRNA, recombinant ligand treatments, and morpholino-based loss-of-function studies, we identified a cohort of transcription factors and signaling molecules expressed in the ventral ectoderm, dorsal ectoderm, and interposed neurogenic ("ciliary band" region in response to the known key signaling molecules Nodal and BMP2/4 and defined the epistatic relationships between the most important genes. The resultant GRN showed a number of striking features. First, Nodal was found to be essential for the expression of all ventral and dorsal marker genes, and BMP2/4 for all dorsal genes. Second, goosecoid was identified as a central player in a regulatory sub-circuit controlling mouth formation, while tbx2/3 emerged as a critical factor for differentiation of the dorsal ectoderm. Finally, and unexpectedly, a neurogenic ectoderm regulatory circuit characterized by expression of "ciliary band" genes was triggered in the absence of TGF beta signaling. We propose a novel model for ectoderm regionalization, in which neural ectoderm is the default fate in the absence of TGF beta signaling, and suggest that the stomodeal and neural subcircuits that we

  3. Tyrosine phosphorylation of the human guanylyl cyclase C receptor

    Indian Academy of Sciences (India)

    Rashna Bhandari; Roy Mathew; K Vijayachandra; Sandhya S Visweswariah

    2000-12-01

    Tyrosine phosphorylation events are key components of several cellular signal transduction pathways. This study describes a novel method for identification of substrates for tyrosine kinases. Co-expression of the tyrosine kinase EphB1 with the intracellular domain of guanylyl cyclase C (GCC) in Escherichia coli cells resulted in tyrosine phosphorylation of GCC, indicating that GCC is a potential substrate for tyrosine kinases. Indeed, GCC expressed in mammalian cells is tyrosine phosphorylated, suggesting that tyrosine phosphorylation may play a role in regulation of GCC signalling. This is the first demonstration of tyrosine phosphorylation of any member of the family of membrane-associated guanylyl cyclases.

  4. A phosphorylation cascade controls the degradation of active SREBP1.

    Science.gov (United States)

    Bengoechea-Alonso, Maria T; Ericsson, Johan

    2009-02-27

    Sterol regulatory element-binding proteins (SREBPs) are a family of transcription factors that regulates cholesterol and lipid metabolism. The active forms of these transcription factors are targeted by a number of post-translational modifications, including phosphorylation. Phosphorylation of Thr-426 and Ser-430 in SREBP1a creates a docking site for the ubiquitin ligase Fbw7, resulting in the degradation of the transcription factor. Here, we identify a novel phosphorylation site in SREBP1a, Ser-434, which regulates the Fbw7-dependent degradation of SREBP1. We demonstrate that both SREBP1a and SREBP1c are phosphorylated on this residue (Ser-410 in SREBP1c). Importantly, we demonstrate that the mature form of endogenous SREBP1 is phosphorylated on Ser-434. Glycogen synthase kinase-3 phosphorylates Ser-434, and the phosphorylation of this residue is attenuated in response to insulin signaling. Interestingly, phosphorylation of Ser-434 promotes the glycogen synthase kinase-3-dependent phosphorylation of Thr-426 and Ser-430 and destabilizes SREBP1. Consequently, mutation of Ser-434 blocks the interaction between SREBP1 and Fbw7 and attenuates Fbw7-dependent degradation of SREBP1. Importantly, insulin fails to enhance the levels of mature SREBP1 in cells lacking Fbw7. Thus, the degradation of mature SREBP1 is controlled by cross-talk between multiple phosphorylated residues in its C-terminal domain and the phosphorylation of Ser-434 could function as a molecular switch to control these processes.

  5. Multistep phosphorylation systems: tunable components of biological signaling circuits.

    Science.gov (United States)

    Valk, Evin; Venta, Rainis; Ord, Mihkel; Faustova, Ilona; Kõivomägi, Mardo; Loog, Mart

    2014-11-05

    Multisite phosphorylation of proteins is a powerful signal processing mechanism that plays crucial roles in cell division and differentiation as well as in disease. We recently demonstrated a novel phenomenon in cell cycle regulation by showing that cyclin-dependent kinase-dependent multisite phosphorylation of a crucial substrate is performed sequentially in the N-to-C terminal direction along the disordered protein. The process is controlled by key parameters, including the distance between phosphorylation sites, the distribution of serines and threonines in sites, and the position of docking motifs. According to our model, linear patterns of phosphorylation along disordered protein segments determine the signal-response function of a multisite phosphorylation switch. Here we discuss the general advantages and engineering principles of multisite phosphorylation networks as processors of kinase signals. We also address the idea of using the mechanistic logic of linear multisite phosphorylation networks to design circuits for synthetic biology applications.

  6. Calcium regulation of oxidative phosphorylation in rat skeletal muscle mitochondria.

    Science.gov (United States)

    Kavanagh, N I; Ainscow, E K; Brand, M D

    2000-02-24

    Activation of oxidative phosphorylation by physiological levels of calcium in mitochondria from rat skeletal muscle was analysed using top-down elasticity and regulation analysis. Oxidative phosphorylation was conceptually divided into three subsystems (substrate oxidation, proton leak and phosphorylation) connected by the membrane potential or the protonmotive force. Calcium directly activated the phosphorylation subsystem and (with sub-saturating 2-oxoglutarate) the substrate oxidation subsystem but had no effect on the proton leak kinetics. The response of mitochondria respiring on 2-oxoglutarate at two physiological concentrations of free calcium was quantified using control and regulation analysis. The partial integrated response coefficients showed that direct stimulation of substrate oxidation contributed 86% of the effect of calcium on state 3 oxygen consumption, and direct activation of the phosphorylation reactions caused 37% of the increase in phosphorylation flux. Calcium directly activated phosphorylation more strongly than substrate oxidation (78% compared to 45%) to achieve homeostasis of mitochondrial membrane potential during large increases in flux.

  7. Phosphorylated testis-specific serine/threonine kinase 4 may phosphorylate Crem at Ser-117.

    Science.gov (United States)

    Fu, Guolong; Wei, Youheng; Wang, Xiaoli; Yu, Long

    2016-06-01

    We aimed to investigate the internal existence status of testis-specific serine/threonine kinase 4 (Tssk4) and the interaction of Tssk4 and Cre-responsive element modulator (Crem). The internal existence status of Tssk4 in testis of mice was detected using western blotting and dephosphorylation method. The interaction of Tssk4 and Crem was analyzed by western blotting, immunohistochemistry, immunofluorescence, in vitro co-immunoprecipitation assays, and in vitro kinase assay. The results revealed that Tssk4 existed in testis both in phosphorylation and unphosphorylation status by a temporal manner with the development of testis. Immunofluorescence results showed that Tssk4 had identical distribution pattern with Crem in testis, which was utterly different to the localization of Cre-responsive element binding (Creb). In conclusion, our study demonstrated that phosphorylated Tssk4 might participate in testis genes expressions by phosphorylating Crem at Ser-117.

  8. Parallelism in matrix computations

    CERN Document Server

    Gallopoulos, Efstratios; Sameh, Ahmed H

    2016-01-01

    This book is primarily intended as a research monograph that could also be used in graduate courses for the design of parallel algorithms in matrix computations. It assumes general but not extensive knowledge of numerical linear algebra, parallel architectures, and parallel programming paradigms. The book consists of four parts: (I) Basics; (II) Dense and Special Matrix Computations; (III) Sparse Matrix Computations; and (IV) Matrix functions and characteristics. Part I deals with parallel programming paradigms and fundamental kernels, including reordering schemes for sparse matrices. Part II is devoted to dense matrix computations such as parallel algorithms for solving linear systems, linear least squares, the symmetric algebraic eigenvalue problem, and the singular-value decomposition. It also deals with the development of parallel algorithms for special linear systems such as banded ,Vandermonde ,Toeplitz ,and block Toeplitz systems. Part III addresses sparse matrix computations: (a) the development of pa...

  9. Phosphine in various matrixes

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    Matrix-bound phosphine was determined in the Jiaozhou Bay coastal sediment, in prawn-pond bottom soil, in the eutrophic lake Wulongtan, in the sewage sludge and in paddy soil as well. Results showed that matrix-bound phosphine levels in freshwater and coastal sediment, as well as in sewage sludge, are significantly higher than that in paddy soil. The correlation between matrix bound phosphine concentrations and organic phosphorus contents in sediment samples is discussed.

  10. Genetic Manipulation of Neurofilament Protein Phosphorylation.

    Science.gov (United States)

    Jones, Maria R; Villalón, Eric; Garcia, Michael L

    2016-01-01

    Neurofilament biology is important to understanding structural properties of axons, such as establishment of axonal diameter by radial growth. In order to study the function of neurofilaments, a series of genetically modified mice have been generated. Here, we describe a brief history of genetic modifications used to study neurofilaments, as well as an overview of the steps required to generate a gene-targeted mouse. In addition, we describe steps utilized to analyze neurofilament phosphorylation status using immunoblotting. Taken together, these provide comprehensive analysis of neurofilament function in vivo, which can be applied to many systems.

  11. The Phosphorylation and Distribution of Cortactin Downstream of Integrin α9β1 Affects Cancer Cell Behaviour

    DEFF Research Database (Denmark)

    Høye, Anette M; Couchman, John R; Wewer, Ulla M;

    2016-01-01

    Integrins, a family of heterodimeric adhesion receptors are implicated in cell migration, development and cancer progression. They can adopt conformations that reflect their activation states and thereby impact adhesion strength and migration. Integrins in an intermediate activation state may...... localises, upon integrin activation. This was commensurate with reduced migration. The localisation and phosphorylation of cortactin Y470 was regulated by Yes kinase and PTEN phosphatase. Cortactin levels influenced fibronectin matrix assembly and active β1 integrin on the cell surface, being inversely...... correlated with migratory behaviour. This study underlines the complex interplay between cortactin and α9β1 integrin that regulates cell-extracellular matrix interactions....

  12. Phenobarbital Meets Phosphorylation of Nuclear Receptors.

    Science.gov (United States)

    Negishi, Masahiko

    2017-05-01

    Phenobarbital was the first therapeutic drug to be characterized for its induction of hepatic drug metabolism. Essentially at the same time, cytochrome P450, an enzyme that metabolizes drugs, was discovered. After nearly 50 years of investigation, the molecular target of phenobarbital induction has now been delineated to phosphorylation at threonine 38 of the constitutive androstane receptor (NR1I3), a member of the nuclear receptor superfamily. Determining this mechanism has provided us with the molecular basis to understand drug induction of drug metabolism and disposition. Threonine 38 is conserved as a phosphorylation motif in the majority of both mouse and human nuclear receptors, providing us with an opportunity to integrate diverse functions of nuclear receptors. Here, I review the works and accomplishments of my laboratory at the National Institutes of Health National Institute of Environmental Health Sciences and the future research directions of where our study of the constitutive androstane receptor might take us. U.S. Government work not protected by U.S. copyright.

  13. Modelling the Krebs cycle and oxidative phosphorylation.

    Science.gov (United States)

    Korla, Kalyani; Mitra, Chanchal K

    2014-01-01

    The Krebs cycle and oxidative phosphorylation are the two most important sets of reactions in a eukaryotic cell that meet the major part of the total energy demands of a cell. In this paper, we present a computer simulation of the coupled reactions using open source tools for simulation. We also show that it is possible to model the Krebs cycle with a simple black box with a few inputs and outputs. However, the kinetics of the internal processes has been modelled using numerical tools. We also show that the Krebs cycle and oxidative phosphorylation together can be combined in a similar fashion - a black box with a few inputs and outputs. The Octave script is flexible and customisable for any chosen set-up for this model. In several cases, we had no explicit idea of the underlying reaction mechanism and the rate determining steps involved, and we have used the stoichiometric equations that can be easily changed as and when more detailed information is obtained. The script includes the feedback regulation of the various enzymes of the Krebs cycle. For the electron transport chain, the pH gradient across the membrane is an essential regulator of the kinetics and this has been modelled empirically but fully consistent with experimental results. The initial conditions can be very easily changed and the simulation is potentially very useful in a number of cases of clinical importance.

  14. Prebiotic Phosphorylation Reactions on the Early Earth

    Directory of Open Access Journals (Sweden)

    Maheen Gull

    2014-07-01

    Full Text Available Phosphorus (P is an essential element for life. It occurs in living beings in the form of phosphate, which is ubiquitous in biochemistry, chiefly in the form of C-O-P (carbon, oxygen and phosphorus, C-P, or P-O-P linkages to form life. Within prebiotic chemistry, several key questions concerning phosphorus chemistry have developed: what were the most likely sources of P on the early Earth? How did it become incorporated into the biological world to form the P compounds that life employs today? Can meteorites be responsible for the delivery of P? What were the most likely solvents on the early Earth and out of those which are favorable for phosphorylation? Or, alternatively, were P compounds most likely produced in relatively dry environments? What were the most suitable temperature conditions for phosphorylation? A route to efficient formation of biological P compounds is still a question that challenges astrobiologists. This article discusses these important issues related to the origin of biological P compounds.

  15. Phosphorylation regulates coilin activity and RNA association

    Directory of Open Access Journals (Sweden)

    Hanna J. Broome

    2013-02-01

    The Cajal body (CB is a domain of concentrated components found within the nucleus of cells in an array of species that is functionally important for the biogenesis of telomerase and small nuclear ribonucleoproteins. The CB is a dynamic structure whose number and size change during the cell cycle and is associated with other nuclear structures and gene loci. Coilin, also known as the marker protein for the CB, is a phosphoprotein widely accepted for its role in maintaining CB integrity. Recent studies have been done to further elucidate functional activities of coilin apart from its structural role in the CB in an attempt to explore the rationale for coilin expression in cells that have few CBs or lack them altogether. Here we show that the RNA association profile of coilin changes in mitosis with respect to that during interphase. We provide evidence of transcriptional and/or processing dysregulation of several CB-related RNA transcripts as a result of ectopic expression of both wild-type and phosphomutant coilin proteins. We also show apparent changes in transcription and/or processing of these transcripts upon coilin knockdown in both transformed and primary cell lines. Additionally, we provide evidence of specific coilin RNase activity regulation, on both U2 and hTR transcripts, by phosphorylation of a single residue, serine 489. Collectively, these results point to additional functions for coilin that are regulated by phosphorylation.

  16. Patience of matrix games

    DEFF Research Database (Denmark)

    Hansen, Kristoffer Arnsfelt; Ibsen-Jensen, Rasmus; Podolskii, Vladimir V.;

    2013-01-01

    For matrix games we study how small nonzero probability must be used in optimal strategies. We show that for image win–lose–draw games (i.e. image matrix games) nonzero probabilities smaller than image are never needed. We also construct an explicit image win–lose game such that the unique optimal...

  17. Patience of matrix games

    DEFF Research Database (Denmark)

    Hansen, Kristoffer Arnsfelt; Ibsen-Jensen, Rasmus; Podolskii, Vladimir V.

    2013-01-01

    For matrix games we study how small nonzero probability must be used in optimal strategies. We show that for image win–lose–draw games (i.e. image matrix games) nonzero probabilities smaller than image are never needed. We also construct an explicit image win–lose game such that the unique optimal...

  18. Transfer function matrix

    Science.gov (United States)

    Seraji, H.

    1987-01-01

    Given a multivariable system, it is proved that the numerator matrix N(s) of the transfer function evaluated at any system pole either has unity rank or is a null matrix. It is also shown that N(s) evaluated at any transmission zero of the system has rank deficiency. Examples are given for illustration.

  19. Kinetic analyses of phosphorylated and non-phosphorylated eIFiso4E binding to mRNA cap analogues.

    Science.gov (United States)

    Khan, Mateen A; Goss, Dixie J

    2017-08-08

    Phosphorylation of eukaryotic initiation factors was previously shown to interact with m(7)G cap and play an important role in the regulation of translation initiation of protein synthesis. To gain further insight into the phosphorylation process of plant protein synthesis, the kinetics of phosphorylated wheat eIFiso4E binding to m(7)G cap analogues were examined. Phosphorylation of wheat eIFiso4E showed similar kinetic effects to human eIF4E binding to m(7)-G cap. Phosphorylation of eIFiso4E decreased the kinetic rate (2-fold) and increased the dissociation rate (2-fold) as compared to non-phosphorylated eIFiso4E binding to both mono- and di-nucleotide analogues at 22°C. Phosphorylated and non-phosphorylated eIFiso4E-m(7)G cap binding rates were found to be independent of concentration, suggesting conformational changes were rate limiting. Rate constant for phosphorylated and non-phosphorylated eIFiso4E binding to m(7)-G cap increased with temperature. Phosphorylation of eIFiso4E decreased (2-fold) the activation energy for both m(7)-G cap analogues binding as compared to non-phosphorylated eIFiso4E. The reduced energy barrier for the formation of eIFiso4E-m(7)-G cap complex suggests a more stable platform for further initiation complex formation and possible means of adapting variety of environmental conditions. Furthermore, the formation of phosphorylated eIFiso4E-cap complex may contribute to modulation of the initiation of protein synthesis in plants. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Chemoselective synthesis and analysis of naturally occurring phosphorylated cysteine peptides

    Science.gov (United States)

    Bertran-Vicente, Jordi; Penkert, Martin; Nieto-Garcia, Olaia; Jeckelmann, Jean-Marc; Schmieder, Peter; Krause, Eberhard; Hackenberger, Christian P. R.

    2016-09-01

    In contrast to protein O-phosphorylation, studying the function of the less frequent N- and S-phosphorylation events have lagged behind because they have chemical features that prevent their manipulation through standard synthetic and analytical methods. Here we report on the development of a chemoselective synthetic method to phosphorylate Cys side-chains in unprotected peptides. This approach makes use of a reaction between nucleophilic phosphites and electrophilic disulfides accessible by standard methods. We achieve the stereochemically defined phosphorylation of a Cys residue and verify the modification using electron-transfer higher-energy dissociation (EThcD) mass spectrometry. To demonstrate the use of the approach in resolving biological questions, we identify an endogenous Cys phosphorylation site in IICBGlc, which is known to be involved in the carbohydrate uptake from the bacterial phosphotransferase system (PTS). This new chemical and analytical approach finally allows further investigating the functions and significance of Cys phosphorylation in a wide range of crucial cellular processes.

  1. Phosphorylation modifies the molecular stability of β-amyloid deposits

    Science.gov (United States)

    Rezaei-Ghaleh, Nasrollah; Amininasab, Mehriar; Kumar, Sathish; Walter, Jochen; Zweckstetter, Markus

    2016-04-01

    Protein aggregation plays a crucial role in neurodegenerative diseases. A key feature of protein aggregates is their ubiquitous modification by phosphorylation. Little is known, however, about the molecular consequences of phosphorylation of protein aggregates. Here we show that phosphorylation of β-amyloid at serine 8 increases the stability of its pathogenic aggregates against high-pressure and SDS-induced dissociation. We further demonstrate that phosphorylation results in an elevated number of hydrogen bonds at the N terminus of β-amyloid, the region that is critically regulated by a variety of post-translational modifications. Because of the increased lifetime of phosphorylated β-amyloid aggregates, phosphorylation can promote the spreading of β-amyloid in Alzheimer pathogenesis. Our study suggests that regulation of the molecular stability of protein aggregates by post-translational modifications is a crucial factor for disease progression in the brain.

  2. Control of Collagen Triple Helix Stability by Phosphorylation.

    Science.gov (United States)

    Acevedo-Jake, Amanda M; Ngo, Daniel H; Hartgerink, Jeffrey D

    2017-03-10

    The phosphorylation of the collagen triple helix plays an important role in collagen synthesis, assembly, signaling, and immune response, although no reports detailing the effect this modification has on the structure and stability of the triple helix exist. Here we investigate the changes in stability and structure resulting from the phosphorylation of collagen. Additionally, the formation of pairwise interactions between phosphorylated residues and lysine is examined. In all tested cases, phosphorylation increases helix stability. When charged-pair interactions are possible, stabilization via phosphorylation can play a very large role, resulting inasmuch as a 13.0 °C increase in triple helix stability. Two-dimensional NMR and molecular modeling are used to study the local structure of the triple helix. Our results suggest a mechanism of action for phosphorylation in the regulation of collagen and also expand upon our understanding of pairwise amino acid stabilization of the collagen triple helix.

  3. Chemical Approaches to Studying Labile Amino Acid Phosphorylation.

    Science.gov (United States)

    Marmelstein, Alan M; Moreno, Javier; Fiedler, Dorothea

    2017-04-01

    Phosphorylation of serine, threonine, and tyrosine residues is the archetypal posttranslational modification of proteins. While phosphorylation of these residues has become standard textbook knowledge, phosphorylation of other amino acid side chains is underappreciated and minimally characterized by comparison. This disparity is rooted in the relative instability of these chemically distinct amino acid side chain moieties, namely phosphoramidates, acyl phosphates, thiophosphates, and phosphoanhydrides. In the case of the O-phosphorylated amino acids, synthetic constructs were critical to assessing their stability and developing tools for their study. As the chemical biology community has become more aware of these alternative phosphorylation sites, methodology has been developed for the synthesis of well-characterized standards and close mimics of these phosphorylated amino acids as well. In this article, we review the synthetic chemistry that is a prerequisite to progress in this field.

  4. Pharmacologic concentrations of linezolid modify oxidative phosphorylation function and adipocyte secretome

    Directory of Open Access Journals (Sweden)

    Laura Llobet

    2017-10-01

    Full Text Available The oxidative phosphorylation system is important for adipocyte differentiation. Therefore, xenobiotics inhibitors of the oxidative phosphorylation system could affect adipocyte differentiation and adipokine secretion. As adipokines impact the overall health status, these xenobiotics may have wide effects on human health. Some of these xenobiotics are widely used therapeutic drugs, such as ribosomal antibiotics. Because of its similarity to the bacterial one, mitochondrial translation system is an off-target for these compounds. To study the influence of the ribosomal antibiotic linezolid on adipokine production, we analyzed its effects on adipocyte secretome. Linezolid, at therapeutic concentrations, modifies the levels of apolipoprotein E and several adipokines and proteins related with the extracellular matrix. This antibiotic also alters the global methylation status of human adipose tissue-derived stem cells and, therefore, its effects are not limited to the exposure period. Besides their consequences on other tissues, xenobiotics acting on the adipocyte oxidative phosphorylation system alter apolipoprotein E and adipokine production, secondarily contributing to their systemic effects.

  5. Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes, and mitochondria.

    Science.gov (United States)

    Gnad, Florian; Forner, Francesca; Zielinska, Dorota F; Birney, Ewan; Gunawardena, Jeremy; Mann, Matthias

    2010-12-01

    High accuracy mass spectrometry has proven to be a powerful technology for the large scale identification of serine/threonine/tyrosine phosphorylation in the living cell. However, despite many described phosphoproteomes, there has been no comparative study of the extent of phosphorylation and its evolutionary conservation in all domains of life. Here we analyze the results of phosphoproteomics studies performed with the same technology in a diverse set of organisms. For the most ancient organisms, the prokaryotes, only a few hundred proteins have been found to be phosphorylated. Applying the same technology to eukaryotic species resulted in the detection of thousands of phosphorylation events. Evolutionary analysis shows that prokaryotic phosphoproteins are preferentially conserved in all living organisms, whereas-site specific phosphorylation is not. Eukaryotic phosphosites are generally more conserved than their non-phosphorylated counterparts (with similar structural constraints) throughout the eukaryotic domain. Yeast and Caenorhabditis elegans are two exceptions, indicating that the majority of phosphorylation events evolved after the divergence of higher eukaryotes from yeast and reflecting the unusually large number of nematode-specific kinases. Mitochondria present an interesting intermediate link between the prokaryotic and eukaryotic domains. Applying the same technology to this organelle yielded 174 phosphorylation sites mapped to 74 proteins. Thus, the mitochondrial phosphoproteome is similarly sparse as the prokaryotic phosphoproteomes. As expected from the endosymbiotic theory, phosphorylated as well as non-phosphorylated mitochondrial proteins are significantly conserved in prokaryotes. However, mitochondrial phosphorylation sites are not conserved throughout prokaryotes, consistent with the notion that serine/threonine phosphorylation in prokaryotes occurred relatively recently in evolution. Thus, the phosphoproteome reflects major events in the

  6. Synthesis of O-Phosphorylated Oligopeptides Using Phosphoramidite

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Reversible protein phosphorylation is of great importance in the regulation of many cellular processes. Structurally well-defined compounds are needed for the study of the roles of the phospho-proteins in biological processes. In this paper, O-phosphorylated oligopeptides were synthesized using bis-alkyloxy-N,N-dialkylphosphoramidite reacting with the oligopeptide followed by oxidation. Many hydroxyl groups in oligopeptides can be phosphorylated in one step.

  7. Constitutive phosphorylation of Shc proteins in human tumors

    DEFF Research Database (Denmark)

    Pelicci, G; Lanfrancone, L; Salcini, A E

    1995-01-01

    cells. In tumor cells with known TK gene alterations Shc proteins were constitutively phosphorylated and complexed with the activated TK. No constitutive Shc phosphorylation was found in primary cell cultures and normal tissues. In 14 of 27 tumor cell lines with no reported TK alterations, Shc proteins...... activated TKs and that the analysis of Shc phosphorylation allow the identification of tumors with constitutive TK activation....

  8. A New Intermolecular Phosphoryl Transfer between Serine and Histidine Residues

    Institute of Scientific and Technical Information of China (English)

    SU,Yu-Qian; NIU,Ming-Yu; CAO,Shu-Xia; ZHANG,Jian-Chen; QU,Ling-Bo; LIAO,Xin-Cheng; ZHAO,Yu-Fen

    2004-01-01

    @@ Phosphoryl transfer constitutes one of the most important reactions in functionalized molecules, bioorganic chemistry and biochemistry.[1] The transformations are involved in diverse processes, such as activated state change of phosphorus, DNA/RNA synthesis, energy metabolism and signal transduction. So, phosphoryl transfer reaction which can be performed by either intramolecular or intermolecular phosphorylation and dephosphorylation mechanism has been investigated by many scientists in wide fields.

  9. Improved Matrix Uncertainty Selector

    CERN Document Server

    Rosenbaum, Mathieu

    2011-01-01

    We consider the regression model with observation error in the design: y=X\\theta* + e, Z=X+N. Here the random vector y in R^n and the random n*p matrix Z are observed, the n*p matrix X is unknown, N is an n*p random noise matrix, e in R^n is a random noise vector, and \\theta* is a vector of unknown parameters to be estimated. We consider the setting where the dimension p can be much larger than the sample size n and \\theta* is sparse. Because of the presence of the noise matrix N, the commonly used Lasso and Dantzig selector are unstable. An alternative procedure called the Matrix Uncertainty (MU) selector has been proposed in Rosenbaum and Tsybakov (2010) in order to account for the noise. The properties of the MU selector have been studied in Rosenbaum and Tsybakov (2010) for sparse \\theta* under the assumption that the noise matrix N is deterministic and its values are small. In this paper, we propose a modification of the MU selector when N is a random matrix with zero-mean entries having the variances th...

  10. A Crystallographic Snapshot of Tyrosine Trans-phosphorylation in Action

    Energy Technology Data Exchange (ETDEWEB)

    Chen, H.; Xu, C; Ma, J; Eliseenkova, A; Li, W; Pollock, P; Pitteloud, N; Miller, W; Neubert, T; Mohammadi, M

    2008-01-01

    Tyrosine trans-phosphorylation is a key event in receptor tyrosine kinase signaling, yet, the structural basis for this process has eluded definition. Here, we present the crystal structure of the FGF receptor 2 kinases caught in the act of trans-phosphorylation of Y769, the major C-terminal phosphorylation site. The structure reveals that enzyme- and substrate-acting kinases engage each other through elaborate and specific interactions not only in the immediate vicinity of Y769 and the enzyme active site, but also in regions that are as much of 18 {angstrom} away from D626, the catalytic base in the enzyme active site. These interactions lead to an unprecedented level of specificity and precision during the trans-phosphorylation on Y769. Time-resolved mass spectrometry analysis supports the observed mechanism of trans-phosphorylation. Our data provide a molecular framework for understanding the mechanism of action of Kallmann syndrome mutations and the order of trans-phosphorylation reactions in FGFRs. We propose that the salient mechanistic features of Y769 trans-phosphorylation are applicable to trans-phosphorylation of the equivalent major phosphorylation sites in many other RTKs.

  11. Elementary matrix theory

    CERN Document Server

    Eves, Howard

    1980-01-01

    The usefulness of matrix theory as a tool in disciplines ranging from quantum mechanics to psychometrics is widely recognized, and courses in matrix theory are increasingly a standard part of the undergraduate curriculum.This outstanding text offers an unusual introduction to matrix theory at the undergraduate level. Unlike most texts dealing with the topic, which tend to remain on an abstract level, Dr. Eves' book employs a concrete elementary approach, avoiding abstraction until the final chapter. This practical method renders the text especially accessible to students of physics, engineeri

  12. Rheocasting Al matrix composites

    Energy Technology Data Exchange (ETDEWEB)

    Girot, F.A.; Albingre, L.; Quenisset, J.M.; Naslain, R.

    1987-11-01

    A development status account is given for the rheocasting method of Al-alloy matrix/SiC-whisker composites, which involves the incorporation and homogeneous distribution of 8-15 vol pct of whiskers through the stirring of the semisolid matrix melt while retaining sufficient fluidity for casting. Both 1-, 3-, and 6-mm fibers of Nicalon SiC and and SiC whisker reinforcements have been experimentally investigated, with attention to the characterization of the resulting microstructures and the effects of fiber-matrix interactions. A thin silica layer is found at the whisker surface. 7 references.

  13. Mueller matrix differential decomposition.

    Science.gov (United States)

    Ortega-Quijano, Noé; Arce-Diego, José Luis

    2011-05-15

    We present a Mueller matrix decomposition based on the differential formulation of the Mueller calculus. The differential Mueller matrix is obtained from the macroscopic matrix through an eigenanalysis. It is subsequently resolved into the complete set of 16 differential matrices that correspond to the basic types of optical behavior for depolarizing anisotropic media. The method is successfully applied to the polarimetric analysis of several samples. The differential parameters enable one to perform an exhaustive characterization of anisotropy and depolarization. This decomposition is particularly appropriate for studying media in which several polarization effects take place simultaneously. © 2011 Optical Society of America

  14. Tyrosine-phosphorylated Galectin-3 Protein Is Resistant to Prostate-specific Antigen (PSA) Cleavage*

    Science.gov (United States)

    Balan, Vitaly; Nangia-Makker, Pratima; Kho, Dhong Hyo; Wang, Yi; Raz, Avraham

    2012-01-01

    Galectin-3 is a chimeric carbohydrate-binding protein, which interacts with cell surface carbohydrate-containing molecules and extracellular matrix glycoproteins and has been implicated in various biological processes such as cell growth, angiogenesis, motility, and metastasis. It is expressed in a wide range of tumor cells and is associated with tumor progression. The functions of galectin-3 are dependent on its localization and post-translational modifications such as cleavage and phosphorylation. Recently, we showed that galectin-3 Tyr-107 is phosphorylated by c-Abl; concomitantly, it was also shown that galectin-3 can be cleaved at this site by prostate-specific antigen (PSA), a chymotrypsin-like serine protease, after Tyr-107, resulting in loss of galectin-3 multivalency while preserving its carbohydrate binding activity. Galectin-3 is largely a monomer in solution but may form a homodimer by self-association through its carbohydrate recognition domain, whereas, in the presence of a ligand, galectin-3 polymerizes up to pentamers utilizing its N-terminal domain. Oligomerization is a unique feature of secreted galectin-3, which allows its function by forming ordered galectin-glycan structures, i.e. lattices, on the cell surface or through direct engagement of specific cell surface glycoconjugates by traditional ligand-receptor binding. We questioned whether Tyr-107 phosphorylation by c-Abl affects galectin-3 cleavage by PSA. The data suggest a role for galectin-3 in prostate cells associated with increased activity of c-Abl kinase and loss of phosphatase and tensin homologue deleted on chromosome 10 (PTEN) activity. In addition, the ratio of phosphorylated/dephosphorylated galectin-3 might be used as a complementary value to that of PSA for prognosis of prostate cancer and a novel therapeutic target for the treatment of prostate cancer. PMID:22232548

  15. Pesticide-Exposure Matrix

    Science.gov (United States)

    The "Pesticide-exposure Matrix" was developed to help epidemiologists and other researchers identify the active ingredients to which people were likely exposed when their homes and gardens were treated for pests in past years.

  16. Matrix theory of gravitation

    CERN Document Server

    Koehler, Wolfgang

    2011-01-01

    A new classical theory of gravitation within the framework of general relativity is presented. It is based on a matrix formulation of four-dimensional Riemann-spaces and uses no artificial fields or adjustable parameters. The geometrical stress-energy tensor is derived from a matrix-trace Lagrangian, which is not equivalent to the curvature scalar R. To enable a direct comparison with the Einstein-theory a tetrad formalism is utilized, which shows similarities to teleparallel gravitation theories, but uses complex tetrads. Matrix theory might solve a 27-year-old, fundamental problem of those theories (sec. 4.1). For the standard test cases (PPN scheme, Schwarzschild-solution) no differences to the Einstein-theory are found. However, the matrix theory exhibits novel, interesting vacuum solutions.

  17. Matrix comparison, Part 2

    DEFF Research Database (Denmark)

    Schneider, Jesper Wiborg; Borlund, Pia

    2007-01-01

    The present two-part article introduces matrix comparison as a formal means for evaluation purposes in informetric studies such as cocitation analysis. In the first part, the motivation behind introducing matrix comparison to informetric studies, as well as two important issues influencing...... such comparisons, matrix generation, and the composition of proximity measures, are introduced and discussed. In this second part, the authors introduce and thoroughly demonstrate two related matrix comparison techniques the Mantel test and Procrustes analysis, respectively. These techniques can compare...... important. Alternatively, or as a supplement, Procrustes analysis compares the actual ordination results without investigating the underlying proximity measures, by matching two configurations of the same objects in a multidimensional space. An advantage of the Procrustes analysis though, is the graphical...

  18. A grammar inference approach for predicting kinase specific phosphorylation sites.

    Science.gov (United States)

    Datta, Sutapa; Mukhopadhyay, Subhasis

    2015-01-01

    Kinase mediated phosphorylation site detection is the key mechanism of post translational mechanism that plays an important role in regulating various cellular processes and phenotypes. Many diseases, like cancer are related with the signaling defects which are associated with protein phosphorylation. Characterizing the protein kinases and their substrates enhances our ability to understand the mechanism of protein phosphorylation and extends our knowledge of signaling network; thereby helping us to treat such diseases. Experimental methods for predicting phosphorylation sites are labour intensive and expensive. Also, manifold increase of protein sequences in the databanks over the years necessitates the improvement of high speed and accurate computational methods for predicting phosphorylation sites in protein sequences. Till date, a number of computational methods have been proposed by various researchers in predicting phosphorylation sites, but there remains much scope of improvement. In this communication, we present a simple and novel method based on Grammatical Inference (GI) approach to automate the prediction of kinase specific phosphorylation sites. In this regard, we have used a popular GI algorithm Alergia to infer Deterministic Stochastic Finite State Automata (DSFA) which equally represents the regular grammar corresponding to the phosphorylation sites. Extensive experiments on several datasets generated by us reveal that, our inferred grammar successfully predicts phosphorylation sites in a kinase specific manner. It performs significantly better when compared with the other existing phosphorylation site prediction methods. We have also compared our inferred DSFA with two other GI inference algorithms. The DSFA generated by our method performs superior which indicates that our method is robust and has a potential for predicting the phosphorylation sites in a kinase specific manner.

  19. The Matrix Organization Revisited

    DEFF Research Database (Denmark)

    Gattiker, Urs E.; Ulhøi, John Parm

    1999-01-01

    This paper gives a short overview of matrix structure and technology management. It outlines some of the characteristics and also points out that many organizations may actualy be hybrids (i.e. mix several ways of organizing to allocate resorces effectively).......This paper gives a short overview of matrix structure and technology management. It outlines some of the characteristics and also points out that many organizations may actualy be hybrids (i.e. mix several ways of organizing to allocate resorces effectively)....

  20. Optical Coherency Matrix Tomography

    Science.gov (United States)

    2015-10-19

    optics has been studied theoretically11, but has not been demonstrated experimentally heretofore. Even in the simplest case of two binary DoFs6 (e.g...coherency matrix G spanning these DoFs. This optical coherency matrix has not been measured in its entirety to date—even in the simplest case of two...dense coding, etc. CREOL, The College of Optics & Photonics, University of Central Florida, Orlando , Florida 32816, USA. Correspondence and requests

  1. Matrix fractional systems

    Science.gov (United States)

    Tenreiro Machado, J. A.

    2015-08-01

    This paper addresses the matrix representation of dynamical systems in the perspective of fractional calculus. Fractional elements and fractional systems are interpreted under the light of the classical Cole-Cole, Davidson-Cole, and Havriliak-Negami heuristic models. Numerical simulations for an electrical circuit enlighten the results for matrix based models and high fractional orders. The conclusions clarify the distinction between fractional elements and fractional systems.

  2. Hacking the Matrix.

    Science.gov (United States)

    Czerwinski, Michael; Spence, Jason R

    2017-01-05

    Recently in Nature, Gjorevski et al. (2016) describe a fully defined synthetic hydrogel that mimics the extracellular matrix to support in vitro growth of intestinal stem cells and organoids. The hydrogel allows exquisite control over the chemical and physical in vitro niche and enables identification of regulatory properties of the matrix. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. The Matrix Organization Revisited

    DEFF Research Database (Denmark)

    Gattiker, Urs E.; Ulhøi, John Parm

    1999-01-01

    This paper gives a short overview of matrix structure and technology management. It outlines some of the characteristics and also points out that many organizations may actualy be hybrids (i.e. mix several ways of organizing to allocate resorces effectively).......This paper gives a short overview of matrix structure and technology management. It outlines some of the characteristics and also points out that many organizations may actualy be hybrids (i.e. mix several ways of organizing to allocate resorces effectively)....

  4. The in vivo phosphorylation sites of rat brain dynamin I

    DEFF Research Database (Denmark)

    Graham, Mark E; Anggono, Victor; Bache, Nicolai

    2007-01-01

    tail splice variant dynIxa and was not hierarchical. Co-purified, (32)P-labeled dynIII was phosphorylated at Ser(759), Ser(763), and Ser(853). Ser(853) is homologous to Ser(851) in dynIxa. The results identify all major and several minor phosphorylation sites in dynI and provide the first measure...

  5. Phosphorylation of proteins during human myometrial contractions: A phosphoproteomic approach.

    Science.gov (United States)

    Hudson, Claire A; López Bernal, Andrés

    2017-01-22

    Phasic myometrial contractility is a key component of human parturition and the contractions are driven by reversible phosphorylation of myosin light chains catalyzed by the calcium (Ca(2+))-dependent enzyme myosin light chain kinase (MYLK). Other yet unknown phosphorylation or de-phosphorylation events may contribute to myometrial contraction and relaxation. In this study we have performed a global phosphoproteomic analysis of human myometrial tissue using tandem mass tagging to detect changes in the phosphorylation status of individual myometrial proteins during spontaneous and oxytocin-driven phasic contractions. We were able to detect 22 individual phosphopeptides whose relative ratio changed (fold > 2 or contraction. The most significant changes in phosphorylation were to MYLK on serine 1760, a site associated with reductions in calmodulin binding and subsequent kinase activity. Phosphorylated MYLK (ser1760) increased significantly during spontaneous (9.83 ± 3.27 fold, P contractions and we were able to validate these data using immunoblotting. Pathway analysis suggested additional proteins involved in calcium signalling, cGMP-PRKG signalling, adrenergic signalling and oxytocin signalling were also phosphorylated during contractions. This study demonstrates that a global phosphoproteomic analysis of myometrial tissue is a sensitive approach to detect changes in the phosphorylation of proteins during myometrial contractions, and provides a platform for further validation of these changes and for identification of their functional significance.

  6. Intermolecular Phosphoryl Transfer Between Serine and Histidine Residues

    Institute of Scientific and Technical Information of China (English)

    Yu Qian SU; Ming Yu NIU; Shu Xia CAO; Jian Chen ZHANG; Yu Fen ZHAO

    2004-01-01

    A novel intermolecular phosphoryl transfer from O-trimethylsilyl-N-(O, O-diisopropyl) phosphoryl serine trimethylsilyl ester to N, N'-bis(trimethylsilyl) histidine trimethylsilyl ester was studied through electrospray ionization mass spectrometry (ESI-MS). It was proposed that the transfer reaction went through penta-coordinated phosphorus intermediate.

  7. Phosphorylation of the Epstein-Barr virus nuclear antigen 2

    DEFF Research Database (Denmark)

    Grässer, F A; Göttel, S; Haiss, P

    1992-01-01

    A major in vivo phosphorylation site of the Epstein-Barr virus nuclear antigen 2 (EBNA-2) was found to be localized at the C-terminus of the protein. In vitro phosphorylation studies using casein kinase 1 (CK-1) and casein kinase 2 (CK-2) revealed that EBNA-2 is a substrate for CK-2, but not for CK...

  8. Phosphorylation of the Goodpasture antigen by type A protein kinases.

    Science.gov (United States)

    Revert, F; Penadés, J R; Plana, M; Bernal, D; Johansson, C; Itarte, E; Cervera, J; Wieslander, J; Quinones, S; Saus, J

    1995-06-02

    Collagen IV is the major component of basement membranes. The human alpha 3 chain of collagen IV contains an antigenic domain called the Goodpasture antigen that is the target for the circulating immunopathogenic antibodies present in patients with Goodpasture syndrome. Characteristically, the gene region encoding the Goodpasture antigen generates multiple alternative products that retain the antigen amino-terminal region with a five-residue motif (KRGDS). The serine therein appears to be the major in vitro cAMP-dependent protein kinase phosphorylation site in the isolated antigen and can be phosphorylated in vitro by two protein kinases of approximately 50 and 41 kDa associated with human kidney plasma membrane, suggesting that it can also be phosphorylated in vivo. Consistent with this, the Goodpasture antigen is isolated from human kidney in phosphorylated and non-phosphorylated forms and only the non-phosphorylated form is susceptible to phosphorylation in vitro. Since this motif is exclusive to the human alpha 3(IV) chain and includes the RGD cell adhesion motif, its phosphorylation might play a role in pathogenesis and influence cell attachment to basement membrane.

  9. Exploring the diversity of protein modifications: special bacterial phosphorylation systems

    DEFF Research Database (Denmark)

    Mijakovic, Ivan; Grangeasse, Christophe; Turgay, Kürşad

    2016-01-01

    that has been most thoroughly investigated. Unlike in eukarya, a large diversity of enzyme families has been shown to phosphorylate and dephosphorylate proteins on various amino acids with different chemical properties in bacteria. In this review, after a brief overview of the known bacterial...... phosphorylation systems, we focus on more recently discovered and less widely known kinases and phosphatases. Namely, we describe in detail tyrosine- and arginine-phosphorylation together with some examples of unusual serine-phosphorylation systems and discuss their potential role and function in bacterial...... physiology, and regulatory networks. Investigating these unusual bacterial kinase and phosphatases is not only important to understand their role in bacterial physiology but will help to generally understand the full potential and evolution of protein phosphorylation for signal transduction, protein...

  10. Systematic inference of functional phosphorylation events in yeast metabolism

    DEFF Research Database (Denmark)

    Chen, Yu; Wang, Yonghong; Nielsen, Jens

    2017-01-01

    Motivation: Protein phosphorylation is a post-translational modification that affects proteins by changing their structure and conformation in a rapid and reversible way, and it is an important mechanism for metabolic regulation in cells. Phosphoproteomics enables high-throughput identification...... of phosphorylation events on metabolic enzymes, but identifying functional phosphorylation events still requires more detailed biochemical characterization. Therefore, development of computational methods for investigating unknown functions of a large number of phosphorylation events identified by phosphoproteomics...... has received increased attention.Results: We developed a mathematical framework that describes the relationship between phosphorylation level of a metabolic enzyme and the corresponding flux through the enzyme. Using this framework, it is possible to quantitatively estimate contribution...

  11. Phosphorylation of the Epstein-Barr virus nuclear antigen 2

    DEFF Research Database (Denmark)

    Grässer, F A; Göttel, S; Haiss, P

    1992-01-01

    A major in vivo phosphorylation site of the Epstein-Barr virus nuclear antigen 2 (EBNA-2) was found to be localized at the C-terminus of the protein. In vitro phosphorylation studies using casein kinase 1 (CK-1) and casein kinase 2 (CK-2) revealed that EBNA-2 is a substrate for CK-2, but not for CK......-1. The CK-2 specific phosphorylation site was localized in the 140 C-terminal amino acids using a recombinant trpE-C-terminal fusion protein. In a similar experiment, the 58 N-terminal amino acids expressed as a recombinant trpE-fusion protein were not phosphorylated. Phosphorylation of a synthetic...

  12. Sequential phosphorylation of GRASP65 during mitotic Golgi disassembly

    Directory of Open Access Journals (Sweden)

    Danming Tang

    2012-09-01

    GRASP65 phosphorylation during mitosis and dephosphorylation after mitosis are required for Golgi disassembly and reassembly during the cell cycle. At least eight phosphorylation sites on GRASP65 have been identified, but whether they are modified in a coordinated fashion during mitosis is so far unknown. In this study, we raised phospho-specific antibodies that recognize phosphorylated T220/T224, S277 and S376 residues of GRASP65, respectively. Biochemical analysis showed that cdc2 phosphorylates all three sites, while plk1 enhances the phosphorylation. Microscopic studies using these antibodies for double and triple labeling demonstrate sequential phosphorylation and dephosphorylation during the cell cycle. S277 and S376 are phosphorylated from late G2 phase through metaphase until telophase when the new Golgi is reassembled. T220/224 is not modified until prophase, but is highly modified from prometaphase to anaphase. In metaphase, phospho-T220/224 signal localizes on both Golgi haze and mitotic Golgi clusters that represent dispersed Golgi vesicles and Golgi remnants, respectively, while phospho-S277 and S376 labeling is more concentrated on mitotic Golgi clusters. Expression of a phosphorylation-resistant GRASP65 mutant T220A/T224A inhibited mitotic Golgi fragmentation to a much larger extent than the expression of the S277A and S376A mutants. In cytokinesis, T220/224 dephosphorylation occurs prior to that of S277, but after S376. This study provides evidence that GRASP65 is sequentially phosphorylated and dephosphorylated during mitosis at different sites to orchestrate Golgi disassembly and reassembly during cell division, with phosphorylation of the T220/224 site being most critical in the process.

  13. Matrix Information Geometry

    CERN Document Server

    Bhatia, Rajendra

    2013-01-01

    This book is an outcome of the Indo-French Workshop on Matrix Information Geometries (MIG): Applications in Sensor and Cognitive Systems Engineering, which was held in Ecole Polytechnique and Thales Research and Technology Center, Palaiseau, France, in February 23-25, 2011. The workshop was generously funded by the Indo-French Centre for the Promotion of Advanced Research (IFCPAR).  During the event, 22 renowned invited french or indian speakers gave lectures on their areas of expertise within the field of matrix analysis or processing. From these talks, a total of 17 original contribution or state-of-the-art chapters have been assembled in this volume. All articles were thoroughly peer-reviewed and improved, according to the suggestions of the international referees. The 17 contributions presented  are organized in three parts: (1) State-of-the-art surveys & original matrix theory work, (2) Advanced matrix theory for radar processing, and (3) Matrix-based signal processing applications.  

  14. Phosphoryl functionalized mesoporous silica for uranium adsorption

    Science.gov (United States)

    Xue, Guo; Yurun, Feng; Li, Ma; Dezhi, Gao; Jie, Jing; Jincheng, Yu; Haibin, Sun; Hongyu, Gong; Yujun, Zhang

    2017-04-01

    Phosphoryl functionalized mesoporous silica (TBP-SBA-15) was synthesized by modified mesoporous silica with γ-amino propyl triethoxy silane and tributyl phosphate. The obtained samples were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), small angle X-ray diffraction (SAXRD), thermo-gravimetric/differential thermalanalyzer (TG/DTA), N2 adsorption-desorption (BET) and Fourier transform infrared spectroscopy (FT-IR) techniques. Results showed that TBP-SBA-15 had large surface areas with ordered channel structure. Moreover, the effects of adsorption time, sorbent dose, solution pH, initial uranium concentration and temperature on the uranium adsorption behaviors were investigated. TBP-SBA-15 showed a high uranium adsorption capacity in a broad range of pH values. The U(VI) adsorption rate of TBP-SBA-15 was fast and nearly achieved completion in 10 min with the sorbent dose of 1 g/L. The U(VI) adsorption of TBP-SBA-15 followed the pseudo-second-order kinetic model and Freundlich isotherm model, indicating that the process was belonged to chemical adsorption. Furthermore, the thermodynamic parameters (ΔG0, ΔH0 and ΔS0) confirmed that the adsorption process was endothermic and spontaneous.

  15. Variation in the composition of corals, fishes, sponges, echinoderms, ascidians, molluscs, foraminifera and macroalgae across a pronounced in-to-offshore environmental gradient in the Jakarta Bay-Thousand Islands coral reef complex.

    Science.gov (United States)

    Cleary, D F R; Polónia, A R M; Renema, W; Hoeksema, B W; Rachello-Dolmen, P G; Moolenbeek, R G; Budiyanto, A; Yahmantoro; Tuti, Y; Giyanto; Draisma, S G A; Prud'homme van Reine, W F; Hariyanto, R; Gittenberger, A; Rikoh, M S; de Voogd, N J

    2016-09-30

    Substrate cover, water quality parameters and assemblages of corals, fishes, sponges, echinoderms, ascidians, molluscs, benthic foraminifera and macroalgae were sampled across a pronounced environmental gradient in the Jakarta Bay-Thousand Islands reef complex. Inshore sites mainly consisted of sand, rubble and turf algae with elevated temperature, dissolved oxygen, pH and chlorophyll concentrations and depauperate assemblages of all taxa. Live coral cover was very low inshore and mainly consisted of sparse massive coral heads and a few encrusting species. Faunal assemblages were more speciose and compositionally distinct mid- and offshore compared to inshore. There were, however, small-scale differences among taxa. Certain midshore sites, for example, housed assemblages resembling those typical of the inshore environment but this differed depending on the taxon. Substrate, water quality and spatial variables together explained from 31% (molluscs) to 72% (foraminifera) of the variation in composition. In general, satellite-derived parameters outperformed locally measured parameters.

  16. Ceramic Matrix Composites .

    Directory of Open Access Journals (Sweden)

    J. Mukerji

    1993-10-01

    Full Text Available The present state of the knowledge of ceramic-matrix composites have been reviewed. The fracture toughness of present structural ceramics are not enough to permit design of high performance machines with ceramic parts. They also fail by catastrophic brittle fracture. It is generally believed that further improvement of fracture toughness is only possible by making composites of ceramics with ceramic fibre, particulate or platelets. Only ceramic-matrix composites capable of working above 1000 degree centigrade has been dealt with keeping reinforced plastics and metal-reinforced ceramics outside the purview. The author has discussed the basic mechanisms of toughening and fabrication of composites and the difficulties involved. Properties of available fibres and whiskers have been given. The best results obtained so far have been indicated. The limitations of improvement in properties of ceramic-matrix composites have been discussed.

  17. Matrix interdiction problem

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Feng [Los Alamos National Laboratory; Kasiviswanathan, Shiva [Los Alamos National Laboratory

    2010-01-01

    In the matrix interdiction problem, a real-valued matrix and an integer k is given. The objective is to remove k columns such that the sum over all rows of the maximum entry in each row is minimized. This combinatorial problem is closely related to bipartite network interdiction problem which can be applied to prioritize the border checkpoints in order to minimize the probability that an adversary can successfully cross the border. After introducing the matrix interdiction problem, we will prove the problem is NP-hard, and even NP-hard to approximate with an additive n{gamma} factor for a fixed constant {gamma}. We also present an algorithm for this problem that achieves a factor of (n-k) mUltiplicative approximation ratio.

  18. Extracellular matrix structure.

    Science.gov (United States)

    Theocharis, Achilleas D; Skandalis, Spyros S; Gialeli, Chrysostomi; Karamanos, Nikos K

    2016-02-01

    Extracellular matrix (ECM) is a non-cellular three-dimensional macromolecular network composed of collagens, proteoglycans/glycosaminoglycans, elastin, fibronectin, laminins, and several other glycoproteins. Matrix components bind each other as well as cell adhesion receptors forming a complex network into which cells reside in all tissues and organs. Cell surface receptors transduce signals into cells from ECM, which regulate diverse cellular functions, such as survival, growth, migration, and differentiation, and are vital for maintaining normal homeostasis. ECM is a highly dynamic structural network that continuously undergoes remodeling mediated by several matrix-degrading enzymes during normal and pathological conditions. Deregulation of ECM composition and structure is associated with the development and progression of several pathologic conditions. This article emphasizes in the complex ECM structure as to provide a better understanding of its dynamic structural and functional multipotency. Where relevant, the implication of the various families of ECM macromolecules in health and disease is also presented.

  19. Finite Temperature Matrix Theory

    CERN Document Server

    Meana, M L; Peñalba, J P; Meana, Marco Laucelli; Peñalba, Jesús Puente

    1998-01-01

    We present the way the Lorentz invariant canonical partition function for Matrix Theory as a light-cone formulation of M-theory can be computed. We explicitly show how when the eleventh dimension is decompactified, the N=1 eleven dimensional SUGRA partition function appears. From this particular analysis we also clarify the question about the discernibility problem when making statistics with supergravitons (the N! problem) in Matrix black hole configurations. We also provide a high temperature expansion which captures some structure of the canonical partition function when interactions amongst D-particles are on. The connection with the semi-classical computations thermalizing the open superstrings attached to a D-particle is also clarified through a Born-Oppenheimer approximation. Some ideas about how Matrix Theory would describe the complementary degrees of freedom of the massless content of eleven dimensional SUGRA are also discussed.

  20. Matrixed business support comparison study.

    Energy Technology Data Exchange (ETDEWEB)

    Parsons, Josh D.

    2004-11-01

    The Matrixed Business Support Comparison Study reviewed the current matrixed Chief Financial Officer (CFO) division staff models at Sandia National Laboratories. There were two primary drivers of this analysis: (1) the increasing number of financial staff matrixed to mission customers and (2) the desire to further understand the matrix process and the opportunities and challenges it creates.

  1. IIB Matrix Model

    CERN Document Server

    Aoki, H; Kawai, H; Kitazawa, Y; Tada, T; Tsuchiya, A

    1999-01-01

    We review our proposal for a constructive definition of superstring, type IIB matrix model. The IIB matrix model is a manifestly covariant model for space-time and matter which possesses N=2 supersymmetry in ten dimensions. We refine our arguments to reproduce string perturbation theory based on the loop equations. We emphasize that the space-time is dynamically determined from the eigenvalue distributions of the matrices. We also explain how matter, gauge fields and gravitation appear as fluctuations around dynamically determined space-time.

  2. Little IIB Matrix Model

    CERN Document Server

    Kitazawa, Y; Saito, O; Kitazawa, Yoshihisa; Mizoguchi, Shun'ya; Saito, Osamu

    2006-01-01

    We study the zero-dimensional reduced model of D=6 pure super Yang-Mills theory and argue that the large N limit describes the (2,0) Little String Theory. The one-loop effective action shows that the force exerted between two diagonal blocks of matrices behaves as 1/r^4, implying a six-dimensional spacetime. We also observe that it is due to non-gravitational interactions. We construct wave functions and vertex operators which realize the D=6, (2,0) tensor representation. We also comment on other "little" analogues of the IIB matrix model and Matrix Theory with less supercharges.

  3. Elementary matrix algebra

    CERN Document Server

    Hohn, Franz E

    2012-01-01

    This complete and coherent exposition, complemented by numerous illustrative examples, offers readers a text that can teach by itself. Fully rigorous in its treatment, it offers a mathematically sound sequencing of topics. The work starts with the most basic laws of matrix algebra and progresses to the sweep-out process for obtaining the complete solution of any given system of linear equations - homogeneous or nonhomogeneous - and the role of matrix algebra in the presentation of useful geometric ideas, techniques, and terminology.Other subjects include the complete treatment of the structur

  4. Rheocasting Al Matrix Composites

    Science.gov (United States)

    Girot, F. A.; Albingre, L.; Quenisset, J. M.; Naslain, R.

    1987-11-01

    Aluminum alloy matrix composites reinforced by SiC short fibers (or whiskers) can be prepared by rheocasting, a process which consists of the incorporation and homogeneous distribution of the reinforcement by stirring within a semi-solid alloy. Using this technique, composites containing fiber volume fractions in the range of 8-15%, have been obtained for various fibers lengths (i.e., 1 mm, 3 mm and 6 mm for SiC fibers). This paper attempts to delineate the best compocasting conditions for aluminum matrix composites reinforced by short SiC (e.g Nicalon) or SiC whiskers (e.g., Tokamax) and characterize the resulting microstructures.

  5. Reduced Google matrix

    CERN Document Server

    Frahm, K M

    2016-01-01

    Using parallels with the quantum scattering theory, developed for processes in nuclear and mesoscopic physics and quantum chaos, we construct a reduced Google matrix $G_R$ which describes the properties and interactions of a certain subset of selected nodes belonging to a much larger directed network. The matrix $G_R$ takes into account effective interactions between subset nodes by all their indirect links via the whole network. We argue that this approach gives new possibilities to analyze effective interactions in a group of nodes embedded in a large directed networks. Possible efficient numerical methods for the practical computation of $G_R$ are also described.

  6. Density matrix perturbation theory.

    Science.gov (United States)

    Niklasson, Anders M N; Challacombe, Matt

    2004-05-14

    An orbital-free quantum perturbation theory is proposed. It gives the response of the density matrix upon variation of the Hamiltonian by quadratically convergent recursions based on perturbed projections. The technique allows treatment of embedded quantum subsystems with a computational cost scaling linearly with the size of the perturbed region, O(N(pert.)), and as O(1) with the total system size. The method allows efficient high order perturbation expansions, as demonstrated with an example involving a 10th order expansion. Density matrix analogs of Wigner's 2n+1 rule are also presented.

  7. Complex matrix model duality

    Energy Technology Data Exchange (ETDEWEB)

    Brown, T.W.

    2010-11-15

    The same complex matrix model calculates both tachyon scattering for the c=1 non-critical string at the self-dual radius and certain correlation functions of half-BPS operators in N=4 super- Yang-Mills. It is dual to another complex matrix model where the couplings of the first model are encoded in the Kontsevich-like variables of the second. The duality between the theories is mirrored by the duality of their Feynman diagrams. Analogously to the Hermitian Kontsevich- Penner model, the correlation functions of the second model can be written as sums over discrete points in subspaces of the moduli space of punctured Riemann surfaces. (orig.)

  8. Compressive stress induces dephosphorylation of the myosin regulatory light chain via RhoA phosphorylation by the adenylyl cyclase/protein kinase A signaling pathway.

    Directory of Open Access Journals (Sweden)

    Kenji Takemoto

    Full Text Available Mechanical stress that arises due to deformation of the extracellular matrix (ECM either stretches or compresses cells. The cellular response to stretching has been actively studied. For example, stretching induces phosphorylation of the myosin regulatory light chain (MRLC via the RhoA/RhoA-associated protein kinase (ROCK pathway, resulting in increased cellular tension. In contrast, the effects of compressive stress on cellular functions are not fully resolved. The mechanisms for sensing and differentially responding to stretching and compressive stress are not known. To address these questions, we investigated whether phosphorylation levels of MRLC were affected by compressive stress. Contrary to the response in stretching cells, MRLC was dephosphorylated 5 min after cells were subjected to compressive stress. Compressive loading induced activation of myosin phosphatase mediated via the dephosphorylation of myosin phosphatase targeting subunit 1 (Thr853. Because myosin phosphatase targeting subunit 1 (Thr853 is phosphorylated only by ROCK, compressive loading may have induced inactivation of ROCK. However, GTP-bound RhoA (active form increased in response to compressive stress. The compression-induced activation of RhoA and inactivation of its effector ROCK are contradictory. This inconsistency was due to phosphorylation of RhoA (Ser188 that reduced affinity of RhoA to ROCK. Treatment with the inhibitor of protein kinase A that phosphorylates RhoA (Ser188 induced suppression of compression-stimulated MRLC dephosphorylation. Incidentally, stretching induced phosphorylation of MRLC, but did not affect phosphorylation levels of RhoA (Ser188. Together, our results suggest that RhoA phosphorylation is an important process for MRLC dephosphorylation by compressive loading, and for distinguishing between stretching and compressing cells.

  9. Expression and phosphorylation of neurofilament protein in different neuronal tissues

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The neurofilament proteins (NFPs) from different neuronal tissues including Alzheimer and Huntington disease gray matter, rat brain gray, white matter and spinal cord were separated biochemically into two major fractions. A systematic investigation on the distribution, expression and phosphorylation of NFPs in those fractions was undertaken in the present study. It was found that only non-phosphorylated NF-H and NF-M, but not NF-L subunit were detected in Alzheimer brain gray matter high speed supernatant, whereas all neurofilament subunits including non-phosphorylated and phosphorylated were measured in high speed pellet fraction of the same tissue. The hyperphosphorylation of NF-H and NF-M in Alzheimer brain was shown by phosphorylation dependent monoclonal antibodies SMI31 and SMI34. This hyperphosphorylation was confirmed by non-phosphorylation dependent antibody SMI32 with dephosphosphorylation of the samples. Furthermore, an increased amount of NF-H, NH-M and NF-L, detected by SMI33 and NR4 respectively, was also observed in Alzheimer samples, in which the elevation in NF-L was significant. A significantly different immunoblot patterns in distribution, expression and phosphorylation were determined in various position of the neural system and alternative fractions. To our best knowledge, this is the first data shown definite abnormality of NFPs in Alzheimer disease. The information obtained in the present study will be extremely valuable in further study of the proteins both in physiological and pathological conditions.

  10. Phosphorylation sites of Arabidopsis MAP Kinase Substrate 1 (MKS1)

    DEFF Research Database (Denmark)

    Caspersen, M.B.; Qiu, J.-L.; Zhang, X.

    2007-01-01

    The Arabidopsis MAP kinase 4 (MPK4) substrate MKS1 was expressed in Escherichia coli and purified, full-length, 6x histidine (His)-tagged MKS1 was phosphorylated in vitro by hemagglutinin (HA)-tagged MPK4 immuno-precipitated from plants. MKS1 phosphorylation was initially verified by electrophore......The Arabidopsis MAP kinase 4 (MPK4) substrate MKS1 was expressed in Escherichia coli and purified, full-length, 6x histidine (His)-tagged MKS1 was phosphorylated in vitro by hemagglutinin (HA)-tagged MPK4 immuno-precipitated from plants. MKS1 phosphorylation was initially verified...... phosphopeptide detection. As MAP kinases generally phosphorylate serine or threonine followed by proline (Ser/Thr-Pro), theoretical masses of potentially phosphorylated peptides were calculated and mass spectrometric peaks matching these masses were fragmented and searched for a neutral-loss signal...... at approximately 98 Da indicative of phosphorylation. Additionally, mass spectrometric peaks present in the MPK4-treated MKS1, but not in the control peptide map of untreated MKS1, were fragmented. Fragmentation spectra were subjected to a MASCOT database search which identified three of the twelve Ser-Pro serine...

  11. Phosphorylation of ribosomal protein S6 mediates compensatory renal hypertrophy

    Science.gov (United States)

    Xu, Jinxian; Chen, Jianchun; Dong, Zheng; Meyuhas, Oded; Chen, Jian-Kang

    2014-01-01

    The molecular mechanism underlying renal hypertrophy and progressive nephron damage remains poorly understood. Here we generated congenic ribosomal protein S6 (rpS6) knockin mice expressing non-phosphorylatable rpS6 and found that uninephrectomy-induced renal hypertrophy was significantly blunted in these knockin mice. Uninephrectomy-induced increases in cyclin D1 and decreases in cyclin E in the remaining kidney were attenuated in the knockin mice compared to their wild-type littermates. Uninephrectomy induced rpS6 phosphorylation in the wild type mice; however, no rpS6 phosphorylation was detected in uninephrectomized or sham-operated knockin mice. Nonetheless, uninephrectomy stimulated comparable 4E-BP1 phosphorylation in both knockin and wild type mice, indicating that mTORC1 was still activated in the knockin mice. Moreover, the mTORC1 inhibitor rapamycin prevented both rpS6 and 4E-BP1 phosphorylation, significantly blunted uninephrectomy-induced renal hypertrophy in wild type mice, but did not prevent residual renal hypertrophy despite inhibiting 4E-BP1 phosphorylation in uninephrectomized knockin mice. Thus, both genetic and pharmacological approaches unequivocally demonstrate that phosphorylated rpS6 is a downstream effector of the mTORC1-S6K1 signaling pathway mediating renal hypertrophy. Hence, rpS6 phosphorylation facilitates the increase in cyclin D1 and decrease in cyclin E1 that underlie the hypertrophic nature of uninephrectomy-induced kidney growth. PMID:25229342

  12. Cytochrome C is tyrosine 97 phosphorylated by neuroprotective insulin treatment.

    Directory of Open Access Journals (Sweden)

    Thomas H Sanderson

    Full Text Available Recent advancements in isolation techniques for cytochrome c (Cytc have allowed us to discover post-translational modifications of this protein. We previously identified two distinct tyrosine phosphorylated residues on Cytc in mammalian liver and heart that alter its electron transfer kinetics and the ability to induce apoptosis. Here we investigated the phosphorylation status of Cytc in ischemic brain and sought to determine if insulin-induced neuroprotection and inhibition of Cytc release was associated with phosphorylation of Cytc. Using an animal model of global brain ischemia, we found a ∼50% decrease in neuronal death in the CA1 hippocampal region with post-ischemic insulin administration. This insulin-mediated increase in neuronal survival was associated with inhibition of Cytc release at 24 hours of reperfusion. To investigate possible changes in the phosphorylation state of Cytc we first isolated the protein from ischemic pig brain and brain that was treated with insulin. Ischemic brains demonstrated no detectable tyrosine phosphorylation. In contrast Cytc isolated from brains treated with insulin showed robust phosphorylation of Cytc, and the phosphorylation site was unambiguously identified as Tyr97 by immobilized metal affinity chromatography/nano-liquid chromatography/electrospray ionization mass spectrometry. We next confirmed these results in rats by in vivo application of insulin in the absence or presence of global brain ischemia and determined that Cytc Tyr97-phosphorylation is strongly induced under both conditions but cannot be detected in untreated controls. These data suggest a mechanism whereby Cytc is targeted for phosphorylation by insulin signaling, which may prevent its release from the mitochondria and the induction of apoptosis.

  13. Acute exercise modifies titin phosphorylation and increases cardiac myofilament stiffness

    Directory of Open Access Journals (Sweden)

    Anna Eliane Müller

    2014-11-01

    Full Text Available Titin-based myofilament stiffness is largely modulated by phosphorylation of its elastic I-band regions N2-Bus (decreases passive stiffness, PT and PEVK (increases PT. Here, we tested the hypothesis that acute exercise changes titin phosphorylation and modifies myofilament stiffness. Adult rats were exercised on a treadmill for 15min, untrained animals served as controls. Titin phosphorylation was determined by Western blot analysis using phosphospecific antibodies to Ser4099 and Ser4010 in the N2-Bus region (PKG and PKA-dependent. respectively, and to Ser11878 and Ser 12022 in the PEVK region (PKCα and CaMKIIδ-dependent, respectively. Passive tension was determined by step-wise stretching of isolated skinned cardiomyocytes to sarcomere length ranging from 1.9-2.4µm and showed a significantly increased PT from exercised samples, compared to controls. In cardiac samples titin N2-Bus phosphorylation was significantly decreased by 40% at Ser4099, however, no significant changes were observed at Ser4010. PEVK phosphorylation at Ser11878 was significantly increased, which is probably mediated by the observed exercise-induced increase in PKCα activity. Interestingly, relative phosphorylation of Ser12022 was substantially decreased in the exercised samples. Surprisingly, in skeletal samples from acutely exercised animals we detected a significant decrease in PEVK phosphorylation at Ser11878 and an increase in Ser12022 phosphorylation; however, PKCα activity remained unchanged. In summary, our data show that a single exercise bout of 15 min affects titin domain phosphorylation and titin-based myocyte stiffness with obviously divergent effects in cardiac and skeletal muscle tissues. The observed changes in titin stiffness could play an important role in adapting the passive and active properties of the myocardium and the skeletal muscle to increased physical activity.

  14. PKC isoforms interact with and phosphorylate DNMT1

    Directory of Open Access Journals (Sweden)

    Pradhan Sriharsa

    2011-05-01

    Full Text Available Abstract Background DNA methyltransferase 1 (DNMT1 has been shown to be phosphorylated on multiple serine and threonine residues, based on cell type and physiological conditions. Although recent studies have suggested that protein kinase C (PKC may be involved, the individual contribution of PKC isoforms in their ability to phosphorylate DNMT1 remains unknown. The PKC family consists of at least 12 isoforms that possess distinct differences in structure, substrate requirement, expression and localization. Results Here we show that PKCα, βI, βII, δ, γ, η, ζ and μ preferentially phosphorylate the N-terminal domain of human DNMT1. No such phosphorylation of DNMT1 was observed with PKCε. Using PKCζ as a prototype model, we also found that PKC physically interacts with and phosphorylates DNMT1. In vitro phosphorylation assays conducted with recombinant fragments of DNMT1 showed that PKCζ preferentially phosphorylated the N-terminal region of DNMT1. The interaction of PKCζ with DNMT1 was confirmed by GST pull-down and co-immunoprecipitation experiments. Co-localization experiments by fluorescent microscopy further showed that endogenous PKCζ and DNMT1 were present in the same molecular complex. Endogenous PKCζ activity was also detected when DNMT1 was immunoprecipitated from HEK-293 cells. Overexpression of both PKCζ and DNMT1 in HEK-293 cells, but not of either alone, reduced the methylation status of genes distributed across the genome. Moreover, in vitro phosphorylation of DNMT1 by PKCζ reduced its methytransferase activity. Conclusions Our results indicate that phosphorylation of human DNMT1 by PKC is isoform-specific and provides the first evidence of cooperation between PKCζ and DNMT1 in the control of the DNA methylation patterns of the genome.

  15. Rosamines targeting the cancer oxidative phosphorylation pathway.

    Directory of Open Access Journals (Sweden)

    Siang Hui Lim

    Full Text Available Reprogramming of energy metabolism is pivotal to cancer, so mitochondria are potential targets for anticancer therapy. A prior study has demonstrated the anti-proliferative activity of a new class of mitochondria-targeting rosamines. This present study describes in vitro cytotoxicity of second-generation rosamine analogs, their mode of action, and their in vivo efficacies in a tumor allografted mouse model. Here, we showed that these compounds exhibited potent cytotoxicity (average IC50<0.5 µM, inhibited Complex II and ATP synthase activities of the mitochondrial oxidative phosphorylation pathway and induced loss of mitochondrial transmembrane potential. A NCI-60 cell lines screen further indicated that rosamine analogs 4 and 5 exhibited potent antiproliferative effects with Log10GI50 = -7 (GI50 = 0.1 µM and were more effective against a colorectal cancer sub-panel than other cell lines. Preliminary in vivo studies on 4T1 murine breast cancer-bearing female BALB/c mice indicated that treatment with analog 5 in a single dosing of 5 mg/kg or a schedule dosing of 3 mg/kg once every 2 days for 6 times (q2d×6 exhibited only minimal induction of tumor growth delay. Our results suggest that rosamine analogs may be further developed as mitochondrial targeting agents. Without a doubt proper strategies need to be devised to enhance tumor uptake of rosamines, i.e. by integration to carrier molecules for better therapeutic outcome.

  16. Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns

    DEFF Research Database (Denmark)

    Larsen, Martin Røssel; Thingholm, Tine E; Jensen, Ole N

    2005-01-01

    Reversible phosphorylation of proteins regulates the majority of all cellular processes, e.g. proliferation, differentiation, and apoptosis. A fundamental understanding of these biological processes at the molecular level requires characterization of the phosphorylated proteins. Phosphorylation i...

  17. Dynamic Matrix Rank

    DEFF Research Database (Denmark)

    Frandsen, Gudmund Skovbjerg; Frandsen, Peter Frands

    2009-01-01

    We consider maintaining information about the rank of a matrix under changes of the entries. For n×n matrices, we show an upper bound of O(n1.575) arithmetic operations and a lower bound of Ω(n) arithmetic operations per element change. The upper bound is valid when changing up to O(n0.575) entri...... closed fields. The upper bound for element updates uses fast rectangular matrix multiplication, and the lower bound involves further development of an earlier technique for proving lower bounds for dynamic computation of rational functions.......We consider maintaining information about the rank of a matrix under changes of the entries. For n×n matrices, we show an upper bound of O(n1.575) arithmetic operations and a lower bound of Ω(n) arithmetic operations per element change. The upper bound is valid when changing up to O(n0.575) entries...... in a single column of the matrix. We also give an algorithm that maintains the rank using O(n2) arithmetic operations per rank one update. These bounds appear to be the first nontrivial bounds for the problem. The upper bounds are valid for arbitrary fields, whereas the lower bound is valid for algebraically...

  18. Empirical codon substitution matrix

    Directory of Open Access Journals (Sweden)

    Gonnet Gaston H

    2005-06-01

    Full Text Available Abstract Background Codon substitution probabilities are used in many types of molecular evolution studies such as determining Ka/Ks ratios, creating ancestral DNA sequences or aligning coding DNA. Until the recent dramatic increase in genomic data enabled construction of empirical matrices, researchers relied on parameterized models of codon evolution. Here we present the first empirical codon substitution matrix entirely built from alignments of coding sequences from vertebrate DNA and thus provide an alternative to parameterized models of codon evolution. Results A set of 17,502 alignments of orthologous sequences from five vertebrate genomes yielded 8.3 million aligned codons from which the number of substitutions between codons were counted. From this data, both a probability matrix and a matrix of similarity scores were computed. They are 64 × 64 matrices describing the substitutions between all codons. Substitutions from sense codons to stop codons are not considered, resulting in block diagonal matrices consisting of 61 × 61 entries for the sense codons and 3 × 3 entries for the stop codons. Conclusion The amount of genomic data currently available allowed for the construction of an empirical codon substitution matrix. However, more sequence data is still needed to construct matrices from different subsets of DNA, specific to kingdoms, evolutionary distance or different amount of synonymous change. Codon mutation matrices have advantages for alignments up to medium evolutionary distances and for usages that require DNA such as ancestral reconstruction of DNA sequences and the calculation of Ka/Ks ratios.

  19. Matrix Embedded Organic Synthesis

    Science.gov (United States)

    Kamakolanu, U. G.; Freund, F. T.

    2016-05-01

    In the matrix of minerals such as olivine, a redox reaction of the low-z elements occurs. Oxygen is oxidized to the peroxy state while the low-Z-elements become chemically reduced. We assign them a formula [CxHyOzNiSj]n- and call them proto-organics.

  20. Simvastatin Ameliorates Matrix Stiffness-Mediated Endothelial Monolayer Disruption.

    Science.gov (United States)

    Lampi, Marsha C; Faber, Courtney J; Huynh, John; Bordeleau, Francois; Zanotelli, Matthew R; Reinhart-King, Cynthia A

    2016-01-01

    Arterial stiffening accompanies both aging and atherosclerosis, and age-related stiffening of the arterial intima increases RhoA activity and cell contractility contributing to increased endothelium permeability. Notably, statins are 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase inhibitors whose pleiotropic effects include disrupting small GTPase activity; therefore, we hypothesized the statin simvastatin could be used to attenuate RhoA activity and inhibit the deleterious effects of increased age-related matrix stiffness on endothelial barrier function. Using polyacrylamide gels with stiffnesses of 2.5, 5, and 10 kPa to mimic the physiological stiffness of young and aged arteries, endothelial cells were grown to confluence and treated with simvastatin. Our data indicate that RhoA and phosphorylated myosin light chain activity increase with matrix stiffness but are attenuated when treated with the statin. Increases in cell contractility, cell-cell junction size, and indirect measurements of intercellular tension that increase with matrix stiffness, and are correlated with matrix stiffness-dependent increases in monolayer permeability, also decrease with statin treatment. Furthermore, we report that simvastatin increases activated Rac1 levels that contribute to endothelial barrier enhancing cytoskeletal reorganization. Simvastatin, which is prescribed clinically due to its ability to lower cholesterol, alters the endothelial cell response to increased matrix stiffness to restore endothelial monolayer barrier function, and therefore, presents a possible therapeutic intervention to prevent atherogenesis initiated by age-related arterial stiffening.

  1. Simvastatin Ameliorates Matrix Stiffness-Mediated Endothelial Monolayer Disruption.

    Directory of Open Access Journals (Sweden)

    Marsha C Lampi

    Full Text Available Arterial stiffening accompanies both aging and atherosclerosis, and age-related stiffening of the arterial intima increases RhoA activity and cell contractility contributing to increased endothelium permeability. Notably, statins are 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA reductase inhibitors whose pleiotropic effects include disrupting small GTPase activity; therefore, we hypothesized the statin simvastatin could be used to attenuate RhoA activity and inhibit the deleterious effects of increased age-related matrix stiffness on endothelial barrier function. Using polyacrylamide gels with stiffnesses of 2.5, 5, and 10 kPa to mimic the physiological stiffness of young and aged arteries, endothelial cells were grown to confluence and treated with simvastatin. Our data indicate that RhoA and phosphorylated myosin light chain activity increase with matrix stiffness but are attenuated when treated with the statin. Increases in cell contractility, cell-cell junction size, and indirect measurements of intercellular tension that increase with matrix stiffness, and are correlated with matrix stiffness-dependent increases in monolayer permeability, also decrease with statin treatment. Furthermore, we report that simvastatin increases activated Rac1 levels that contribute to endothelial barrier enhancing cytoskeletal reorganization. Simvastatin, which is prescribed clinically due to its ability to lower cholesterol, alters the endothelial cell response to increased matrix stiffness to restore endothelial monolayer barrier function, and therefore, presents a possible therapeutic intervention to prevent atherogenesis initiated by age-related arterial stiffening.

  2. Prostate Cell Specific Regulation of Androgen Receptor Phosphorylation In Vivo

    Science.gov (United States)

    2006-11-01

    analysis indicates that the screen is preferentially isolating proteins with a known role in gene transcription and we are currently assessing the phosphorylation- dependence of the putative AR interacting proteins .

  3. The Synthesis of a Series of Phosphoryl Coumarins

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Different hydroxy substituted coumarins were successfully phosphorylated with diisopropylphophite (DIPPH) by the Atherton-Todd reaction in 76-89% yields. Moreover, the reaction activities of different hydroxys of the coumarins in the Atherton-Todd reaction were studied.

  4. Phosphorylation: The Molecular Switch of Double-Strand Break Repair

    Directory of Open Access Journals (Sweden)

    K. C. Summers

    2011-01-01

    Full Text Available Repair of double-stranded breaks (DSBs is vital to maintaining genomic stability. In mammalian cells, DSBs are resolved in one of the following complex repair pathways: nonhomologous end-joining (NHEJ, homologous recombination (HR, or the inclusive DNA damage response (DDR. These repair pathways rely on factors that utilize reversible phosphorylation of proteins as molecular switches to regulate DNA repair. Many of these molecular switches overlap and play key roles in multiple pathways. For example, the NHEJ pathway and the DDR both utilize DNA-PK phosphorylation, whereas the HR pathway mediates repair with phosphorylation of RPA2, BRCA1, and BRCA2. Also, the DDR pathway utilizes the kinases ATM and ATR, as well as the phosphorylation of H2AX and MDC1. Together, these molecular switches regulate repair of DSBs by aiding in DSB recognition, pathway initiation, recruitment of repair factors, and the maintenance of repair mechanisms.

  5. Phosphorylation of the viral coat protein regulates RNA virus infection

    Directory of Open Access Journals (Sweden)

    Hoover HS

    2016-11-01

    Full Text Available Haley S Hoover, C Cheng Kao Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA Abstract: Coat proteins (CPs are the most abundant protein produced during a viral infection. CPs have been shown to regulate the infection processes of RNA viruses, including RNA replication and gene expression. The numerous activities of the CP in infection are likely to require regulation, possibly through posttranslational modifications. Protein posttranslational modifications are involved in signal transduction, expanding and regulating protein function, and responding to changes in the environment. Accumulating evidence suggests that phosphorylation of viral CPs is involved in the regulation of the viral infection process from enabling virion disassembly to regulation of viral protein synthesis and replication. CP phosphorylation also affects viral trafficking and virion assembly. This review focuses on the regulatory roles that phosphorylation of CPs has in the life cycle of viruses with RNA genomes. Keywords: viral capsid protein, posttranslational modification, phosphorylation, protein–RNA interaction

  6. A Green Synthesis of Diisopropyl Phosphoryl Amino Acid

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    In this paper, we report that diisopropyl phosphoryl amino acid could be prepared with reasonable yields under solvent-free condition by adding amino acid to the mixture of diisopropyl phosphite and N-chlorodiisopropylamine.

  7. Tau Phosphorylation by GSK3 in Different Conditions

    Science.gov (United States)

    Avila, Jesús; León-Espinosa, Gonzalo; García, Esther; García-Escudero, Vega; Hernández, Félix; DeFelipe, Javier

    2012-01-01

    Almost a 20% of the residues of tau protein are phosphorylatable amino acids: serine, threonine, and tyrosine. In this paper we comment on the consequences for tau of being a phosphoprotein. We will focus on serine/threonine phosphorylation. It will be discussed that, depending on the modified residue in tau molecule, phosphorylation could be protective, in processes like hibernation, or toxic like in development of those diseases known as tauopathies, which are characterized by an hyperphosphorylation and aggregation of tau. PMID:22675648

  8. Fission yeast Rad52 phosphorylation restrains error prone recombination pathways.

    Directory of Open Access Journals (Sweden)

    Angela Bellini

    Full Text Available Rad52 is a key protein in homologous recombination (HR, a DNA repair pathway dedicated to double strand breaks and recovery of blocked or collapsed replication forks. Rad52 allows Rad51 loading on single strand DNA, an event required for strand invasion and D-loop formation. In addition, Rad52 functions also in Rad51 independent pathways because of its ability to promote single strand annealing (SSA that leads to loss of genetic material and to promote D-loops formation that are cleaved by Mus81 endonuclease. We have previously reported that fission yeast Rad52 is phosphorylated in a Sty1 dependent manner upon oxidative stress and in cells where the early step of HR is impaired because of lack of Rad51. Here we show that Rad52 is also constitutively phosphorylated in mus81 null cells and that Sty1 partially impinges on such phosphorylation. As upon oxidative stress, the Rad52 phosphorylation in rad51 and mus81 null cells appears to be independent of Tel1, Rad3 and Cdc2. Most importantly, we show that mutating serine 365 to glycine (S365G in Rad52 leads to loss of the constitutive Rad52 phosphorylation observed in cells lacking Rad51 and to partial loss of Rad52 phosphorylation in cells lacking Mus81. Contrariwise, phosphorylation of Rad52-S365G protein is not affected upon oxidative stress. These results indicate that different Rad52 residues are phosphorylated in a Sty1 dependent manner in response to these distinct situations. Analysis of spontaneous HR at direct repeats shows that mutating serine 365 leads to an increase in spontaneous deletion-type recombinants issued from mitotic recombination that are Mus81 dependent. In addition, the recombination rate in the rad52-S365G mutant is further increased by hydroxyurea, a drug to which mutant cells are sensitive.

  9. Identification of Phosphorylation Sites Regulating sst3 Somatostatin Receptor Trafficking.

    Science.gov (United States)

    Lehmann, Andreas; Kliewer, Andrea; Günther, Thomas; Nagel, Falko; Schulz, Stefan

    2016-06-01

    The human somatostatin receptor 3 (sst3) is expressed in about 50% of all neuroendocrine tumors and hence a promising target for multireceptor somatostatin analogs. The sst3 receptor is unique among ssts in that it exhibits a very long intracellular C-terminal tail containing a huge number of potential phosphate acceptor sites. Consequently, our knowledge about the functional role of the C-terminal tail in sst3 receptor regulation is very limited. Here, we have generated a series of phosphorylation-deficient mutants that enabled us to determine crucial sites for its agonist-induced β-arrestin mobilization, internalization, and down-regulation. Based on this information, we generated phosphosite-specific antibodies for C-terminal Ser(337)/Thr(341), Thr(348), and Ser(361) that enabled us to investigate the temporal patterns of sst3 phosphorylation and dephosphorylation. We found that the endogenous ligand somatostatin induced a rapid and robust phosphorylation that was completely blocked by the sst3 antagonist NVP-ACQ090. The stable somatostatin analogs pasireotide and octreotide promoted clearly less phosphorylation compared with somatostatin. We also show that sst3 phosphorylation occurred within seconds to minutes, whereas dephosphorylation of the sst3 receptor occurred at a considerable slower rate. In addition, we also identified G protein-coupled receptor kinases 2 and 3 and protein phosphatase 1α and 1β as key regulators of sst3 phosphorylation and dephosphorylation, respectively. Thus, we here define the C-terminal phosphorylation motif of the human sst3 receptor that regulates its agonist-promoted phosphorylation, β-arrestin recruitment, and internalization of this clinically relevant receptor.

  10. Sequencing of phosphopeptides sulfonated by 4-sulfophenyl isothiocyanate using post-source decay matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

    Institute of Scientific and Technical Information of China (English)

    TANG Jianguang; WANG Yongjun; ZHANG Hainan; WANG Chunyu; HU Zhiping; XUE Zhigang; XIA Kun; SHI Xiaoliu

    2006-01-01

    Phosphorylation/dephosphorylation is probably the most common and important reversible post-translational modificaion of proteins. Analyzing the functional effects of phosphorylation is helpful for understanding the biological functions of proteins. Identification of the phosphorylation sites of phosphorylated protein is a prerequisite for research on phosphorylation. In this work, an effective and simple method of identification of protein phosphorylation sites has been developed. Phosphopeptides were selectively enriched with immobilized metal affinity chromatography (IMAC) and subsequently chemically modified by 4-sulfophenyl isothiocyanate, and then the chemically modified phosphopeptides were sequenced with post-source decay (PSD) matrix-assisted laser desorption/ionization (MALDI)time-of-flight mass spectrometry for detecting phosphorylation sites. The charge of derivatization by 4-sulfophenyl isothiocyanate introduces a negative sulfonic acid group at the N-terminus of a peptide, and enables the selective detection of only a single series of C-terminal y-type ions. This chemically assisted method greatly simplifies the extremely complex pattern of PSD fragment ions and makes the PSD spectra more easier to be interpreted. The phosphorylation sites of a synthesized model phosphopeptide and human c-myc protein have been successfully identified by this method.Phosphorylation/dephosphorylation is probably the most common and important reversible post-translational modificaion of proteins. Analyzing the functional effects of phosphorylation is helpful for understanding the biological functions of proteins. Identification of the phosphorylation sites of phosphorylated protein is a prerequisite for research on phosphorylation. In this work, an effective and simple method of identification of protein phosphorylation sites has been developed. Phosphopeptides were selectively enriched with immobilized metal affinity chromatography (IMAC) and subsequently chemically

  11. Role of 20-kDa amelogenin (P148) phosphorylation in calcium phosphate formation in vitro.

    Science.gov (United States)

    Kwak, Seo-Young; Wiedemann-Bidlack, Felicitas B; Beniash, Elia; Yamakoshi, Yasuo; Simmer, James P; Litman, Amy; Margolis, Henry C

    2009-07-10

    The potential role of amelogenin phosphorylation in enamel formation is elucidated through in vitro mineralization studies. Studies focused on the native 20-kDa porcine amelogenin proteolytic cleavage product P148 that is prominent in developing enamel. Experimental conditions supported spontaneous calcium phosphate precipitation with the initial formation of amorphous calcium phosphate (ACP). In the absence of protein, ACP was found to undergo relatively rapid transformation to randomly oriented plate-like apatitic crystals. In the presence of non-phosphorylated recombinant full-length amelogenin, rP172, a longer induction period was observed during which relatively small ACP nanoparticles were transiently stabilized. In the presence of rP172, these nanoparticles were found to align to form linear needle-like particles that subsequently transformed and organized into parallel arrays of apatitic needle-like crystals. In sharp contrast to these findings, P148, with a single phosphate group on serine 16, was found to inhibit calcium phosphate precipitation and stabilize ACP formation for more than 1 day. Additional studies using non-phosphorylated recombinant (rP147) and partially dephosphorylated forms of P148 (dephoso-P148) showed that the single phosphate group in P148 was responsible for the profound effect on mineral formation in vitro. The present study has provided, for the first time, evidence suggesting that the native proteolytic cleavage product P148 may have an important functional role in regulating mineralization during enamel formation by preventing unwanted mineral formation within the enamel matrix during the secretory stage of amelogenesis. Results obtained have also provided new insights into the functional role of the highly conserved hydrophilic C terminus found in full-length amelogenin.

  12. Protein phosphorylation and its role in archaeal signal transduction.

    Science.gov (United States)

    Esser, Dominik; Hoffmann, Lena; Pham, Trong Khoa; Bräsen, Christopher; Qiu, Wen; Wright, Phillip C; Albers, Sonja-Verena; Siebers, Bettina

    2016-09-01

    Reversible protein phosphorylation is the main mechanism of signal transduction that enables cells to rapidly respond to environmental changes by controlling the functional properties of proteins in response to external stimuli. However, whereas signal transduction is well studied in Eukaryotes and Bacteria, the knowledge in Archaea is still rather scarce. Archaea are special with regard to protein phosphorylation, due to the fact that the two best studied phyla, the Euryarchaeota and Crenarchaeaota, seem to exhibit fundamental differences in regulatory systems. Euryarchaeota (e.g. halophiles, methanogens, thermophiles), like Bacteria and Eukaryotes, rely on bacterial-type two-component signal transduction systems (phosphorylation on His and Asp), as well as on the protein phosphorylation on Ser, Thr and Tyr by Hanks-type protein kinases. Instead, Crenarchaeota (e.g. acidophiles and (hyper)thermophiles) only depend on Hanks-type protein phosphorylation. In this review, the current knowledge of reversible protein phosphorylation in Archaea is presented. It combines results from identified phosphoproteins, biochemical characterization of protein kinases and protein phosphatases as well as target enzymes and first insights into archaeal signal transduction by biochemical, genetic and polyomic studies.

  13. PHOSPHORYLATED TAU: TOXIC, PROTECTIVE, OR NONE OF THE ABOVE

    Science.gov (United States)

    Castellani, Rudy J.; Nunomura, Akihiko; Lee, Hyoung-gon; Perry, George; Smith, Mark A.

    2009-01-01

    Identification of phosphorylated tau as the major protein component of neurofibrillary tangles (NFTs) led to the concept that phosphorylated tau was inherently toxic and, as such, intimately involved in Alzheimer’s disease (AD) pathogenesis. While superficially logical, this construct ignores a number of key findings in AD, including i) that NFTs are encountered in viable neurons until late stage disease; ii) that NFTs persist within the neuronal cytoplasm for decades; iii) that NFTs are encountered, sometimes in significant numbers, in cognitively intact elderly; and iv) that neurons with NFTs contain normal content and structure of microtubules. Experimental data in transgenic animal models has further demonstrated that NFTs accumulate in neurons in spite of tau suppression and behavior normalization. These data call into question the inherent toxicity of phosphorylated tau, seemingly leaving the only viable hypothesis of the ad hoc “toxic intermediate” phosphorylated tau concept. However, since we also know that phosphorylated tau sequesters redox active heavy metals and protects against oxidative stress, here we suggest that phosphorylated tau serves a protective role against cellular toxicity. PMID:18688087

  14. Structural basis for Mep2 ammonium transceptor activation by phosphorylation.

    Science.gov (United States)

    van den Berg, Bert; Chembath, Anupama; Jefferies, Damien; Basle, Arnaud; Khalid, Syma; Rutherford, Julian C

    2016-04-18

    Mep2 proteins are fungal transceptors that play an important role as ammonium sensors in fungal development. Mep2 activity is tightly regulated by phosphorylation, but how this is achieved at the molecular level is not clear. Here we report X-ray crystal structures of the Mep2 orthologues from Saccharomyces cerevisiae and Candida albicans and show that under nitrogen-sufficient conditions the transporters are not phosphorylated and present in closed, inactive conformations. Relative to the open bacterial ammonium transporters, non-phosphorylated Mep2 exhibits shifts in cytoplasmic loops and the C-terminal region (CTR) to occlude the cytoplasmic exit of the channel and to interact with His2 of the twin-His motif. The phosphorylation site in the CTR is solvent accessible and located in a negatively charged pocket ∼30 Å away from the channel exit. The crystal structure of phosphorylation-mimicking Mep2 variants from C. albicans show large conformational changes in a conserved and functionally important region of the CTR. The results allow us to propose a model for regulation of eukaryotic ammonium transport by phosphorylation.

  15. Protein phosphorylation in isolated hepatocytes of septic and endotoxemic rats

    Energy Technology Data Exchange (ETDEWEB)

    Deaciuc, I.V.; Spitzer, J.A. (Louisiana State Univ. Medical Center, New Orleans (USA))

    1989-11-01

    The purpose of this study was to investigate possible alterations induced by sepsis and endotoxicosis in the late phase of Ca2+-dependent signaling in rat liver. Hepatocytes isolated from septic or chronically endotoxin (ET)-treated rats were labeled with (32P)H3PO4 and stimulated with various agents. Proteins were resolved by one-dimensional polyacrylamide gel electrophoresis and autoradiographed. Vasopressin (VP)- and phenylephrine (PE)-induced responses were attenuated in both septic and ET-treated rats for cytosolic and membrane proteins compared with their respective controls. Glucagon and 12-O-myristate phorbol-13-acetate (TPA) affected only the phosphorylation of membrane proteins. Glucagon-induced changes in the phosphorylation of membrane proteins were affected by both sepsis and endotoxicosis, whereas TPA-stimulated phosphorylation was lowered only in endotoxicosis. Response to the Ca2+ ionophore A23187 was depressed in septic rats for cytosolic proteins. The phosphorylation of two cytosolic proteins, i.e., 93 and 61 kDa (previously identified as glycogen phosphorylase and pyruvate kinase, respectively), in response to VP, PE, and A23187 was severely impaired by endotoxicosis and sepsis. TPA did not affect the phosphorylation state of these two proteins. The results show that sepsis and endotoxicosis produce perturbations of the phosphorylation step in Ca2+ transmembrane signaling. Such changes can explain alterations of glycogenolysis and gluconeogenesis associated with sepsis and endotoxicosis.

  16. Neuromedin B receptors regulate EGF receptor tyrosine phosphorylation in lung cancer cells

    Science.gov (United States)

    Moody, Terry W.; Berna, Marc J.; Mantey, Samuel; Sancho, Veronica; Ridnour, Lisa; Wink, David A.; Chan, Daniel; Giaccone, Giuseppe; Jensen, Robert T.

    2014-01-01

    Neuromedin B (NMB), a member of the bombesin family of peptides, is an autocrine growth factor for many lung cancer cells. The present study investigated the ability of NMB to cause transactivation of the epidermal growth factor (EGF) receptor in lung cancer cells. By Western blot, addition of NMB or related peptides to NCI-H1299 human non-small cell lung cancer (NSCLC) cells, caused phosphorylation of Tyr1068 of the EGF receptor. The signal was amplified using NCI-H1299 cells stably transected with NMB receptors. The transactivation of the EGF receptor or the tyrosine phosphorylation of ERK caused by NMB-like peptides was inhibited by AG1478 or gefitinib (tyrosine kinase inhibitors) and NMB receptor antagonist PD168368 but not the GRP receptor antagonist, BW2258U89. The transactivation of the EGF receptor caused by NMB-like peptides was inhibited by GM6001 (matrix metalloprotease inhibitor), PP2 (Src inhibitor), or transforming growth factor (TGF)α antibody. The transactivation of the EGF receptor and the increase in reactive oxygen species caused by NMB-like peptides was inhibited by N-acetylcysteine (NAC) or Tiron. Gefitinib inhibited the proliferation of NCI-H1299 cells and its sensitivity was increased by the addition of PD168368. The results indicate that the NMB receptor regulates EGF receptor transactivation by a mechanism dependent on Src as well as metalloprotease activation and generation of reactive oxygen species. PMID:20388507

  17. Matrix string theory

    Science.gov (United States)

    Dijkgraaf, Robbert; Verlinde, Erik; Verlinde, Herman

    1997-02-01

    Via compactification on a circle, the matrix mode] of M-theory proposed by Banks et a]. suggests a concrete identification between the large N limit of two-dimensional N = 8 supersymmetric Yang-Mills theory and type IIA string theory. In this paper we collect evidence that supports this identification. We explicitly identify the perturbative string states and their interactions, and describe the appearance of D-particle and D-membrane states.

  18. Matrix string theory

    Energy Technology Data Exchange (ETDEWEB)

    Dijkgraaf, R. [Amsterdam Univ. (Netherlands). Dept. of Mathematics; Verlinde, E. [TH-Division, CERN, CH-1211 Geneva 23 (Switzerland)]|[Institute for Theoretical Physics, Universtity of Utrecht, 3508 TA Utrecht (Netherlands); Verlinde, H. [Institute for Theoretical Physics, University of Amsterdam, 1018 XE Amsterdam (Netherlands)

    1997-09-01

    Via compactification on a circle, the matrix model of M-theory proposed by Banks et al. suggests a concrete identification between the large N limit of two-dimensional N=8 supersymmetric Yang-Mills theory and type IIA string theory. In this paper we collect evidence that supports this identification. We explicitly identify the perturbative string states and their interactions, and describe the appearance of D-particle and D-membrane states. (orig.).

  19. Matrix String Theory

    CERN Document Server

    Dijkgraaf, R; Verlinde, Herman L

    1997-01-01

    Via compactification on a circle, the matrix model of M-theory proposed by Banks et al suggests a concrete identification between the large N limit of two-dimensional N=8 supersymmetric Yang-Mills theory and type IIA string theory. In this paper we collect evidence that supports this identification. We explicitly identify the perturbative string states and their interactions, and describe the appearance of D-particle and D-membrane states.

  20. Holomorphic matrix integrals

    CERN Document Server

    Felder, G; Felder, Giovanni; Riser, Roman

    2004-01-01

    We study a class of holomorphic matrix models. The integrals are taken over middle dimensional cycles in the space of complex square matrices. As the size of the matrices tends to infinity, the distribution of eigenvalues is given by a measure with support on a collection of arcs in the complex planes. We show that the arcs are level sets of the imaginary part of a hyperelliptic integral connecting branch points.

  1. Matrix groups for undergraduates

    CERN Document Server

    Tapp, Kristopher

    2016-01-01

    Matrix groups touch an enormous spectrum of the mathematical arena. This textbook brings them into the undergraduate curriculum. It makes an excellent one-semester course for students familiar with linear and abstract algebra and prepares them for a graduate course on Lie groups. Matrix Groups for Undergraduates is concrete and example-driven, with geometric motivation and rigorous proofs. The story begins and ends with the rotations of a globe. In between, the author combines rigor and intuition to describe the basic objects of Lie theory: Lie algebras, matrix exponentiation, Lie brackets, maximal tori, homogeneous spaces, and roots. This second edition includes two new chapters that allow for an easier transition to the general theory of Lie groups. From reviews of the First Edition: This book could be used as an excellent textbook for a one semester course at university and it will prepare students for a graduate course on Lie groups, Lie algebras, etc. … The book combines an intuitive style of writing w...

  2. Metal matrix Composites

    Directory of Open Access Journals (Sweden)

    Pradeep K. Rohatgi

    1993-10-01

    Full Text Available This paper reviews the world wide upsurge in metal matrix composite research and development activities with particular emphasis on cast metal-matrix particulate composites. Extensive applications of cast aluminium alloy MMCs in day-to-day use in transportation as well as durable good industries are expected to advance rapidly in the next decade. The potential for extensive application of cast composites is very large in India, especially in the areas of transportation, energy and electromechanical machinery; the extensive use of composites can lead to large savings in materials and energy, and in several instances, reduce environmental pollution. It is important that engineering education and short-term courses be organized to bring MMCs to the attention of students and engineering industry leaders. India already has excellent infrastructure for development of composites, and has a long track record of world class research in cast metal matrix particulate composites. It is now necessary to catalyze prototype and regular production of selected composite components, and get them used in different sectors, especially railways, cars, trucks, buses, scooters and other electromechanical machinery. This will require suitable policies backed up by funding to bring together the first rate talent in cast composites which already exists in India, to form viable development groups followed by setting up of production plants involving the process engineering capability already available within the country. On the longer term, cast composites should be developed for use in energy generation equipment, electronic packaging aerospace systems, and smart structures.

  3. Thr175-phosphorylated tau induces pathologic fibril formation via GSK3β-mediated phosphorylation of Thr231 in vitro.

    Science.gov (United States)

    Moszczynski, Alexander J; Gohar, May; Volkening, Kathryn; Leystra-Lantz, Cheryl; Strong, Wendy; Strong, Michael J

    2015-03-01

    We have previously shown that amyotrophic lateral sclerosis with cognitive impairment can be characterized by pathologic inclusions of microtubule-associated protein tau (tau) phosphorylated at Thr(175) (pThr(175)) in association with GSK3β activation. We have now examined whether pThr(175) induces GSK3β activation and whether this leads to pathologic fibril formation through Thr(231) phosphorylation. Seventy-two hours after transfection of Neuro2A cells with pseudophosphorylated green fluorescent protein-tagged 2N4R tau (Thr(175)Asp), phosphorylated kinase glycogen synthase kinase 3 beta (active GSK3β) levels were significantly increased as was pathologic fibril formation and cell death. Treatment with each of 4 GSK3β inhibitors or small hairpin RNA knockdown of GSK3β abolished fibril formation and prevented cell death. Inhibition of Thr(231) phosphorylation (Thr(231)Ala) prevented pathologic tau fibril formation, regardless of Thr(175) state, whereas Thr(231)Asp (pseudophosphorylated at Thr(231)) developed pathologic tau fibrils. Ser(235) mutations did not affect fibril formation, indicating an unprimed mechanism of Thr(231) phosphorylation. These findings suggest a mechanism of tau pathology by which pThr(175) induces GSK3β phosphorylation of Thr(231) leading to fibril formation, indicating a potential therapeutic avenue for amyotrophic lateral sclerosis with cognitive impairment. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. Structural Basis for Inactivation of the Human Pyruvate Dehydrogenase Complex by Phosphorylation: Role of Disordered Phosphorylation Loops

    Energy Technology Data Exchange (ETDEWEB)

    Kato, Masato; Wynn, R. Max; Chuang, Jacinta L.; Tso, Shih-Chia; Machius, Mischa; Li, Jun; Chuang, David T. (UTSMC)

    2009-09-11

    We report the crystal structures of the phosporylated pyruvate dehydrogenase (E1p) component of the human pyruvate dehydrogenase complex (PDC). The complete phosphorylation at Ser264-{alpha} (site 1) of a variant E1p protein was achieved using robust pyruvate dehydrogenase kinase 4 free of the PDC core. We show that unlike its unmodified counterpart, the presence of a phosphoryl group at Ser264-{alpha} prevents the cofactor thiamine diphosphate-induced ordering of the two loops carrying the three phosphorylation sites. The disordering of these phosphorylation loops is caused by a previously unrecognized steric clash between the phosphoryl group at site 1 and a nearby Ser266-{alpha}, which nullifies a hydrogen-bonding network essential for maintaining the loop conformations. The disordered phosphorylation loops impede the binding of lipoyl domains of the PDC core to E1p, negating the reductive acetylation step. This results in the disruption of the substrate channeling in the PDC, leading to the inactivation of this catalytic machine.

  5. PP2A(Cdc55) Phosphatase Imposes Ordered Cell-Cycle Phosphorylation by Opposing Threonine Phosphorylation.

    Science.gov (United States)

    Godfrey, Molly; Touati, Sandra A; Kataria, Meghna; Jones, Andrew; Snijders, Ambrosius P; Uhlmann, Frank

    2017-02-02

    In the quantitative model of cell-cycle control, progression from G1 through S phase and into mitosis is ordered by thresholds of increasing cyclin-dependent kinase (Cdk) activity. How such thresholds are read out by substrates that respond with the correct phosphorylation timing is not known. Here, using the budding yeast model, we show that the abundant PP2A(Cdc55) phosphatase counteracts Cdk phosphorylation during interphase and delays phosphorylation of late Cdk substrates. PP2A(Cdc55) specifically counteracts phosphorylation on threonine residues, and consequently, we find that threonine-directed phosphorylation occurs late in the cell cycle. Furthermore, the late phosphorylation of a model substrate, Ndd1, depends on threonine identity of its Cdk target sites. Our results support a model in which Cdk-counteracting phosphatases contribute to cell-cycle ordering by imposing Cdk thresholds. They also unveil a regulatory principle based on the phosphoacceptor amino acid, which is likely to apply to signaling pathways beyond cell-cycle control. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  6. Matrix Theory of Small Oscillations

    Science.gov (United States)

    Chavda, L. K.

    1978-01-01

    A complete matrix formulation of the theory of small oscillations is presented. Simple analytic solutions involving matrix functions are found which clearly exhibit the transients, the damping factors, the Breit-Wigner form for resonances, etc. (BB)

  7. Matrix Completions and Chordal Graphs

    Institute of Scientific and Technical Information of China (English)

    Kenneth John HARRISON

    2003-01-01

    In a matrix-completion problem the aim is to specifiy the missing entries of a matrix inorder to produce a matrix with particular properties. In this paper we survey results concerning matrix-completion problems where we look for completions of various types for partial matrices supported ona given pattern. We see that thc existence of completions of the required type often depends on thechordal properties of graphs associated with the pattern.

  8. Protein kinase Ciota promotes nicotine-induced migration and invasion of cancer cells via phosphorylation of micro- and m-calpains.

    Science.gov (United States)

    Xu, Lijun; Deng, Xingming

    2006-02-17

    Nicotine is a major component in cigarette smoke that activates the growth-promoting pathways to facilitate the development of lung cancer. However, it is not clear whether nicotine affects cell motility to facilitate tumor metastasis. Here we discovered that nicotine potently induces phosphorylation of both mu- and m-calpains via activation of protein kinase Ciota (PKCiota), which is associated with accelerated migration and invasion of human lung cancer cells. Purified PKCiota directly phosphorylates mu- and m-calpains in vitro. Overexpression of PKCiota results in increased phosphorylation of both mu- and m-calpains in vivo. Nicotine also induces activation of c-Src, which is a known PKCiota upstream kinase. Treatment of cells with the alpha(7) nicotinic acetylcholine receptor inhibitor alpha-bungarotoxin can block nicotine-induced calpain phosphorylation with suppression of calpain activity, wound healing, cell migration, and invasion, indicating that nicotine-induced calpain phosphorylation occurs, at least in part, through a signaling pathway involving the upstream alpha(7) nicotinic acetylcholine receptor. Intriguingly, depletion of PKCiota by RNA interference suppresses nicotine-induced calpain phosphorylation, calpain activity, cell migration, and invasion, indicating that PKCiota is a necessary component in nicotine-mediated cell motility signaling. Importantly, nicotine potently induces secretion of mu- and m-calpains from lung cancer cells into culture medium, which may have potential to cleave substrates in the extracellular matrix. These findings reveal a novel role for PKCiota as a nicotine-activated, physiological calpain kinase that directly phosphorylates and activates calpains, leading to enhanced migration and invasion of human lung cancer cells.

  9. Phosphorylation of ribosomal protein S6 mediates compensatory renal hypertrophy.

    Science.gov (United States)

    Xu, Jinxian; Chen, Jianchun; Dong, Zheng; Meyuhas, Oded; Chen, Jian-Kang

    2015-03-01

    The molecular mechanism underlying renal hypertrophy and progressive nephron damage remains poorly understood. Here we generated congenic ribosomal protein S6 (rpS6) knock-in mice expressing nonphosphorylatable rpS6 and found that uninephrectomy-induced renal hypertrophy was significantly blunted in these knock-in mice. Uninephrectomy-induced increases in cyclin D1 and decreases in cyclin E in the remaining kidney were attenuated in the knock-in mice compared with their wild-type littermates. Uninephrectomy induced rpS6 phosphorylation in the wild-type mice; however, no rpS6 phosphorylation was detected in uninephrectomized or sham-operated knock-in mice. Nonetheless, uninephrectomy stimulated comparable 4E-BP1 phosphorylation in both knock-in and wild-type mice, indicating that mTORC1 was still activated in the knock-in mice. Moreover, the mTORC1 inhibitor rapamycin prevented both rpS6 and 4E-BP1 phosphorylation, significantly blunted uninephrectomy-induced renal hypertrophy in wild-type mice, but did not prevent residual renal hypertrophy despite inhibiting 4E-BP1 phosphorylation in uninephrectomized knock-in mice. Thus, both genetic and pharmacological approaches unequivocally demonstrate that phosphorylated rpS6 is a downstream effector of the mTORC1-S6K1 signaling pathway mediating renal hypertrophy. Hence, rpS6 phosphorylation facilitates the increase in cyclin D1 and decrease in cyclin E1 that underlie the hypertrophic nature of uninephrectomy-induced kidney growth.

  10. Tyrosine phosphorylation of NEDD4 activates its ubiquitin ligase activity.

    Science.gov (United States)

    Persaud, Avinash; Alberts, Philipp; Mari, Sara; Tong, Jiefei; Murchie, Ryan; Maspero, Elena; Safi, Frozan; Moran, Michael F; Polo, Simona; Rotin, Daniela

    2014-10-07

    Ligand binding to the receptor tyrosine kinase fibroblast growth factor (FGF) receptor 1 (FGFR1) causes dimerization and activation by transphosphorylation of tyrosine residues in the kinase domain. FGFR1 is ubiquitylated by the E3 ligase NEDD4 (also known as NEDD4-1), which promotes FGFR1 internalization and degradation. Although phosphorylation of FGFR1 is required for NEDD4-dependent endocytosis, NEDD4 directly binds to a nonphosphorylated region of FGFR1. We found that activation of FGFR1 led to activation of c-Src kinase-dependent tyrosine phosphorylation of NEDD4, enhancing the ubiquitin ligase activity of NEDD4. Using mass spectrometry, we identified several FGF-dependent phosphorylated tyrosines in NEDD4, including Tyr(43) in the C2 domain and Tyr(585) in the HECT domain. Mutating these tyrosines to phenylalanine to prevent phosphorylation inhibited FGF-dependent NEDD4 activity and FGFR1 endocytosis and enhanced cell proliferation. Mutating the tyrosines to glutamic acid to mimic phosphorylation enhanced NEDD4 activity. Moreover, the NEDD4 C2 domain bound the HECT domain, and the presence of phosphomimetic mutations inhibited this interaction, suggesting that phosphorylation of NEDD4 relieves an inhibitory intra- or intermolecular interaction. Accordingly, activation of FGFR1 was not required for activation of NEDD4 that lacked its C2 domain. Activation of c-Src by epidermal growth factor (EGF) also promoted tyrosine phosphorylation and enhanced the activity of NEDD4. Thus, we identified a feedback mechanism by which receptor tyrosine kinases promote catalytic activation of NEDD4 and that may represent a mechanism of receptor crosstalk.

  11. Phosphorylation of ATPase subunits of the 26S proteasome.

    Science.gov (United States)

    Mason, G G; Murray, R Z; Pappin, D; Rivett, A J

    1998-07-01

    The 26S proteasome complex plays a major role in the non-lysosomal degradation of intracellular proteins. Purified 26S proteasomes give a pattern of more than 40 spots on 2D-PAGE gels. The positions of subunits have been identified by mass spectrometry of tryptic peptides and by immunoblotting with subunit-specific antipeptide antibodies. Two-dimensional polyacrylamide gel electrophoresis of proteasomes immunoprecipitated from [32P]phosphate-labelled human embryo lung L-132 cells revealed the presence of at least three major phosphorylated polypeptides among the regulatory subunits as well as the C8 and C9 components of the core 20S proteasome. Comparison with the positions of the regulatory polypeptides revealed a minor phosphorylated form to be S7 (MSS1). Antibodies against S4, S6 (TBP7) and S12 (MOV34) all cross-reacted at the position of major phosphorylated polypeptides suggesting that several of the ATPase subunits may be phosphorylated. The phosphorylation of S4 was confirmed by double immunoprecipitation experiments in which 26S proteasomes were immunoprecipitated as above and dissociated and then S4 was immunoprecipitated with subunit-specific antibodies. Antibodies against the non-ATPase subunit S10, which has been suggested by others to be phosphorylated, did not coincide with the position of a phosphorylated polypeptide. Some differences were observed in the 2D-PAGE pattern of proteasomes immunoprecipitated from cultured cells compared to purified rat liver 26S proteasomes suggesting possible differences in subunit compositions of 26S proteasomes.

  12. Actin Tyrosine-53-Phosphorylation in Neuronal Maturation and Synaptic Plasticity.

    Science.gov (United States)

    Bertling, Enni; Englund, Jonas; Minkeviciene, Rimante; Koskinen, Mikko; Segerstråle, Mikael; Castrén, Eero; Taira, Tomi; Hotulainen, Pirta

    2016-05-11

    Rapid reorganization and stabilization of the actin cytoskeleton in dendritic spines enables cellular processes underlying learning, such as long-term potentiation (LTP). Dendritic spines are enriched in exceptionally short and dynamic actin filaments, but the studies so far have not revealed the molecular mechanisms underlying the high actin dynamics in dendritic spines. Here, we show that actin in dendritic spines is dynamically phosphorylated at tyrosine-53 (Y53) in rat hippocampal and cortical neurons. Our findings show that actin phosphorylation increases the turnover rate of actin filaments and promotes the short-term dynamics of dendritic spines. During neuronal maturation, actin phosphorylation peaks at the first weeks of morphogenesis, when dendritic spines form, and the amount of Y53-phosphorylated actin decreases when spines mature and stabilize. Induction of LTP transiently increases the amount of phosphorylated actin and LTP induction is deficient in neurons expressing mutant actin that mimics phosphorylation. Actin phosphorylation provides a molecular mechanism to maintain the high actin dynamics in dendritic spines during neuronal development and to induce fast reorganization of the actin cytoskeleton in synaptic plasticity. In turn, dephosphorylation of actin is required for the stabilization of actin filaments that is necessary for proper dendritic spine maturation and LTP maintenance. Dendritic spines are small protrusions from neuronal dendrites where the postsynaptic components of most excitatory synapses reside. Precise control of dendritic spine morphology and density is critical for normal brain function. Accordingly, aberrant spine morphology is linked to many neurological diseases. The actin cytoskeleton is a structural element underlying the proper morphology of dendritic spines. Therefore, defects in the regulation of the actin cytoskeleton in neurons have been implicated in neurological diseases. Here, we revealed a novel mechanism for

  13. THE GENERALIZED POLARIZATION SCATTERING MATRIX

    Science.gov (United States)

    the Least Square Best Estimate of the Generalized Polarization matrix from a set of measurements is then developed. It is shown that the Faraday...matrix data. It is then shown that the Least Square Best Estimate of the orientation angle of a symmetric target is also determinable from Faraday rotation contaminated short pulse monostatic polarization matrix data.

  14. The cellulose resource matrix.

    Science.gov (United States)

    Keijsers, Edwin R P; Yılmaz, Gülden; van Dam, Jan E G

    2013-03-01

    The emerging biobased economy is causing shifts from mineral fossil oil based resources towards renewable resources. Because of market mechanisms, current and new industries utilising renewable commodities, will attempt to secure their supply of resources. Cellulose is among these commodities, where large scale competition can be expected and already is observed for the traditional industries such as the paper industry. Cellulose and lignocellulosic raw materials (like wood and non-wood fibre crops) are being utilised in many industrial sectors. Due to the initiated transition towards biobased economy, these raw materials are intensively investigated also for new applications such as 2nd generation biofuels and 'green' chemicals and materials production (Clark, 2007; Lange, 2007; Petrus & Noordermeer, 2006; Ragauskas et al., 2006; Regalbuto, 2009). As lignocellulosic raw materials are available in variable quantities and qualities, unnecessary competition can be avoided via the choice of suitable raw materials for a target application. For example, utilisation of cellulose as carbohydrate source for ethanol production (Kabir Kazi et al., 2010) avoids the discussed competition with easier digestible carbohydrates (sugars, starch) deprived from the food supply chain. Also for cellulose use as a biopolymer several different competing markets can be distinguished. It is clear that these applications and markets will be influenced by large volume shifts. The world will have to reckon with the increase of competition and feedstock shortage (land use/biodiversity) (van Dam, de Klerk-Engels, Struik, & Rabbinge, 2005). It is of interest - in the context of sustainable development of the bioeconomy - to categorize the already available and emerging lignocellulosic resources in a matrix structure. When composing such "cellulose resource matrix" attention should be given to the quality aspects as well as to the available quantities and practical possibilities of processing the

  15. Matrix string partition function

    CERN Document Server

    Kostov, Ivan K; Kostov, Ivan K.; Vanhove, Pierre

    1998-01-01

    We evaluate quasiclassically the Ramond partition function of Euclidean D=10 U(N) super Yang-Mills theory reduced to a two-dimensional torus. The result can be interpreted in terms of free strings wrapping the space-time torus, as expected from the point of view of Matrix string theory. We demonstrate that, when extrapolated to the ultraviolet limit (small area of the torus), the quasiclassical expressions reproduce exactly the recently obtained expression for the partition of the completely reduced SYM theory, including the overall numerical factor. This is an evidence that our quasiclassical calculation might be exact.

  16. Matrix vector analysis

    CERN Document Server

    Eisenman, Richard L

    2005-01-01

    This outstanding text and reference applies matrix ideas to vector methods, using physical ideas to illustrate and motivate mathematical concepts but employing a mathematical continuity of development rather than a physical approach. The author, who taught at the U.S. Air Force Academy, dispenses with the artificial barrier between vectors and matrices--and more generally, between pure and applied mathematics.Motivated examples introduce each idea, with interpretations of physical, algebraic, and geometric contexts, in addition to generalizations to theorems that reflect the essential structur

  17. Random matrix theory

    CERN Document Server

    Deift, Percy

    2009-01-01

    This book features a unified derivation of the mathematical theory of the three classical types of invariant random matrix ensembles-orthogonal, unitary, and symplectic. The authors follow the approach of Tracy and Widom, but the exposition here contains a substantial amount of additional material, in particular, facts from functional analysis and the theory of Pfaffians. The main result in the book is a proof of universality for orthogonal and symplectic ensembles corresponding to generalized Gaussian type weights following the authors' prior work. New, quantitative error estimates are derive

  18. Supported Molecular Matrix Electrophoresis.

    Science.gov (United States)

    Matsuno, Yu-Ki; Kameyama, Akihiko

    2015-01-01

    Mucins are difficult to separate using conventional gel electrophoresis methods such as SDS-PAGE and agarose gel electrophoresis, owing to their large size and heterogeneity. On the other hand, cellulose acetate membrane electrophoresis can separate these molecules, but is not compatible with glycan analysis. Here, we describe a novel membrane electrophoresis technique, termed "supported molecular matrix electrophoresis" (SMME), in which a porous polyvinylidene difluoride (PVDF) membrane filter is used to achieve separation. This description includes the separation, visualization, and glycan analysis of mucins with the SMME technique.

  19. Matrix algebra for linear models

    CERN Document Server

    Gruber, Marvin H J

    2013-01-01

    Matrix methods have evolved from a tool for expressing statistical problems to an indispensable part of the development, understanding, and use of various types of complex statistical analyses. This evolution has made matrix methods a vital part of statistical education. Traditionally, matrix methods are taught in courses on everything from regression analysis to stochastic processes, thus creating a fractured view of the topic. Matrix Algebra for Linear Models offers readers a unique, unified view of matrix analysis theory (where and when necessary), methods, and their applications. Written f

  20. Cellular Functions Regulated by Phosphorylation of EGFR on Tyr845

    Directory of Open Access Journals (Sweden)

    Ken-ichi Sato

    2013-05-01

    Full Text Available The Src gene product (Src and the epidermal growth factor receptor (EGFR are prototypes of oncogene products and function primarily as a cytoplasmic non-receptor tyrosine kinase and a transmembrane receptor tyrosine kinase, respectively. The identification of Src and EGFR, and the subsequent extensive investigations of these proteins have long provided cutting edge research in cancer and other molecular and cellular biological studies. In 1995, we reported that the human epidermoid carcinoma cells, A431, contain a small fraction of Src and EGFR in which these two kinase were in physical association with each other, and that Src phosphorylates EGFR on tyrosine 845 (Y845 in the Src-EGFR complex. Y845 of EGFR is located in the activation segment of the kinase domain, where many protein kinases contain kinase-activating autophosphorylation sites (e.g., cAMP-dependent protein kinase, Src family kinases, transmembrane receptor type tyrosine kinases or trans-phosphorylation sites (e.g., cyclin-dependent protein kinase, mitogen-activated protein kinase, Akt protein kinase. A number of studies have demonstrated that Y845 phosphorylation serves an important role in cancer as well as normal cells. Here we compile the experimental facts involving Src phosphorylation of EGFR on Y845, by which cell proliferation, cell cycle control, mitochondrial regulation of cell metabolism, gamete activation and other cellular functions are regulated. We also discuss the physiological relevance, as well as structural insights of the Y845 phosphorylation.

  1. Determining in vivo phosphorylation sites using mass spectrometry.

    Science.gov (United States)

    Breitkopf, Susanne B; Asara, John M

    2012-04-01

    Phosphorylation is the most studied protein post-translational modification (PTM) in biological systems, since it controls cell growth, proliferation, survival, and other processes. High-resolution/high mass accuracy mass spectrometers are used to identify protein phosphorylation sites due to their speed, sensitivity, selectivity, and throughput. The protocols described here focus on two common strategies: (1) identifying phosphorylation sites from individual proteins and small protein complexes, and (2) identifying global phosphorylation sites from whole-cell and tissue extracts. For the first, endogenous or epitope-tagged proteins are typically immunopurified from cell lysates, purified via gel electrophoresis or precipitation, and enzymatically digested into peptides. Samples can be optionally enriched for phosphopeptides using immobilized metal affinity chromatography (IMAC) or titanium dioxide (TiO(2)) and then analyzed by microcapillary liquid chromatography/tandem mass spectrometry (LC-MS/MS). Global phosphorylation site analyses that capture pSer/pThr/pTyr sites from biological sources sites are more resource and time consuming and involve digesting the whole-cell lysate, followed by peptide fractionation by strong cation-exchange chromatography, phosphopeptide enrichment by IMAC or TiO(2), and LC-MS/MS. Alternatively, the protein lysate can be fractionated by SDS-PAGE, followed by digestion, phosphopeptide enrichment, and LC-MS/MS. One can also immunoprecipitate only phosphotyrosine peptides using a pTyr antibody followed by LC-MS/MS.

  2. Phosphorylation of actopaxin regulates cell spreading and migration

    Science.gov (United States)

    Clarke, Dominic M.; Brown, Michael C.; LaLonde, David P.; Turner, Christopher E.

    2004-01-01

    Actopaxin is an actin and paxillin binding protein that localizes to focal adhesions. It regulates cell spreading and is phosphorylated during mitosis. Herein, we identify a role for actopaxin phosphorylation in cell spreading and migration. Stable clones of U2OS cells expressing actopaxin wild-type (WT), nonphosphorylatable, and phosphomimetic mutants were developed to evaluate actopaxin function. All proteins targeted to focal adhesions, however the nonphosphorylatable mutant inhibited spreading whereas the phosphomimetic mutant cells spread more efficiently than WT cells. Endogenous and WT actopaxin, but not the nonphosphorylatable mutant, were phosphorylated in vivo during cell adhesion/spreading. Expression of the nonphosphorylatable actopaxin mutant significantly reduced cell migration, whereas expression of the phosphomimetic increased cell migration in scrape wound and Boyden chamber migration assays. In vitro kinase assays demonstrate that extracellular signal-regulated protein kinase phosphorylates actopaxin, and treatment of U2OS cells with the MEK1 inhibitor UO126 inhibited adhesion-induced phosphorylation of actopaxin and also inhibited cell migration. PMID:15353548

  3. Tau phosphorylation affects its axonal transport and degradation

    Science.gov (United States)

    Rodríguez-Martín, Teresa; Cuchillo-Ibáñez, Inmaculada; Noble, Wendy; Nyenya, Fanon; Anderton, Brian H.; Hanger, Diane P.

    2013-01-01

    Phosphorylated forms of microtubule-associated protein tau accumulate in neurofibrillary tangles in Alzheimer's disease. To investigate the effects of specific phosphorylated tau residues on its function, wild type or phosphomutant tau was expressed in cells. Elevated tau phosphorylation decreased its microtubule binding and bundling, and increased the number of motile tau particles, without affecting axonal transport kinetics. In contrast, reducing tau phosphorylation enhanced the amount of tau bound to microtubules and inhibited axonal transport of tau. To determine whether differential tau clearance is responsible for the increase in phosphomimic tau, we inhibited autophagy in neurons which resulted in a 3-fold accumulation of phosphomimic tau compared with wild type tau, and endogenous tau was unaffected. In autophagy-deficient mouse embryonic fibroblasts, but not in neurons, proteasomal degradation of phosphomutant tau was also reduced compared with wild type tau. Therefore, autophagic and proteasomal pathways are involved in tau degradation, with autophagy appearing to be the primary route for clearing phosphorylated tau in neurons. Defective autophagy might contribute to the accumulaton of tau in neurodegenerative diseases. PMID:23601672

  4. Neurofilament subunit (NFL) head domain phosphorylation regulates axonal transport of neurofilaments.

    LENUS (Irish Health Repository)

    Yates, Darran M

    2009-04-01

    Neurofilaments are the intermediate filaments of neurons and are synthesised in neuronal cell bodies and then transported through axons. Neurofilament light chain (NFL) is a principal component of neurofilaments, and phosphorylation of NFL head domain is believed to regulate the assembly of neurofilaments. However, the role that NFL phosphorylation has on transport of neurofilaments is poorly understood. To address this issue, we monitored axonal transport of phosphorylation mutants of NFL. We mutated four known phosphorylation sites in NFL head domain to either preclude phosphorylation, or mimic permanent phosphorylation. Mutation to preclude phosphorylation had no effect on transport but mutation of three sites to mimic permanent phosphorylation inhibited transport. Mutation of all four sites together to mimic permanent phosphorylation proved especially potent at inhibiting transport and also disrupted neurofilament assembly. Our results suggest that NFL head domain phosphorylation is a regulator of neurofilament axonal transport.

  5. BRD4 Phosphorylation Regulates HPV E2-Mediated Viral Transcription, Origin Replication, and Cellular MMP-9 Expression

    Directory of Open Access Journals (Sweden)

    Shwu-Yuan Wu

    2016-08-01

    Full Text Available Post-translational modification can modulate protein conformation and alter binding partner recruitment within gene regulatory regions. Here, we report that bromodomain-containing protein 4 (BRD4, a transcription co-factor and chromatin regulator, uses a phosphorylation-induced switch mechanism to recruit E2 protein encoded by cancer-associated human papillomavirus (HPV to viral early gene and cellular matrix metalloproteinase-9 (MMP-9 promoters. Enhanced MMP-9 expression, induced upon keratinocyte differentiation, occurs via BRD4-dependent recruitment of active AP-1 and NF-κB to their target sequences. This is triggered by replacement of AP-1 family members JunB and JunD by c-Jun and by re-localization of NF-κB from the cytoplasm to the nucleus. In addition, BRD4 phosphorylation is critical for E2- and origin-dependent HPV DNA replication. A class of phospho-BRD4-targeting compounds, distinct from the BET bromodomain inhibitors, effectively blocks BRD4 phosphorylation-specific functions in transcription and factor recruitment.

  6. Extracellular Matrix Proteins

    Directory of Open Access Journals (Sweden)

    Linda Christian Carrijo-Carvalho

    2012-01-01

    Full Text Available Lipocalin family members have been implicated in development, regeneration, and pathological processes, but their roles are unclear. Interestingly, these proteins are found abundant in the venom of the Lonomia obliqua caterpillar. Lipocalins are β-barrel proteins, which have three conserved motifs in their amino acid sequence. One of these motifs was shown to be a sequence signature involved in cell modulation. The aim of this study is to investigate the effects of a synthetic peptide comprising the lipocalin sequence motif in fibroblasts. This peptide suppressed caspase 3 activity and upregulated Bcl-2 and Ki-67, but did not interfere with GPCR calcium mobilization. Fibroblast responses also involved increased expression of proinflammatory mediators. Increase of extracellular matrix proteins, such as collagen, fibronectin, and tenascin, was observed. Increase in collagen content was also observed in vivo. Results indicate that modulation effects displayed by lipocalins through this sequence motif involve cell survival, extracellular matrix remodeling, and cytokine signaling. Such effects can be related to the lipocalin roles in disease, development, and tissue repair.

  7. Rat1p maintains RNA polymerase II CTD phosphorylation balance

    DEFF Research Database (Denmark)

    Jimeno-González, Silvia; Schmid, Manfred; Malagon, Francisco

    2014-01-01

    In S. cerevisiae, the 5'-3' exonuclease Rat1p partakes in transcription termination. Although Rat1p-mediated RNA degradation has been suggested to play a role for this activity, the exact mechanisms by which Rat1p helps release RNA polymerase II (RNAPII) from the DNA template are poorly understood....... Here we describe a function of Rat1p in regulating phosphorylation levels of the C-terminal domain (CTD) of the largest RNAPII subunit, Rpb1p, during transcription elongation. The rat1-1 mutant exhibits highly elevated levels of CTD phosphorylation as well as RNAPII distribution and transcription...... termination defects. These phenotypes are all rescued by overexpression of the CTD phosphatase Fcp1p, suggesting a functional relationship between the absence of Rat1p activity, elevated CTD phosphorylation, and transcription defects. We also demonstrate that rat1-1 cells display increased RNAPII...

  8. Identification and quantitation of signal molecule-dependent protein phosphorylation

    KAUST Repository

    Groen, Arnoud J.

    2013-09-03

    Phosphoproteomics is a fast-growing field that aims at characterizing phosphorylated proteins in a cell or a tissue at a given time. Phosphorylation of proteins is an important regulatory mechanism in many cellular processes. Gel-free phosphoproteome technique involving enrichment of phosphopeptide coupled with mass spectrometry has proven to be invaluable to detect and characterize phosphorylated proteins. In this chapter, a gel-free quantitative approach involving 15N metabolic labelling in combination with phosphopeptide enrichment by titanium dioxide (TiO2) and their identification by MS is described. This workflow can be used to gain insights into the role of signalling molecules such as cyclic nucleotides on regulatory networks through the identification and quantification of responsive phospho(proteins). © Springer Science+Business Media New York 2013.

  9. Exploring the intramolecular phosphorylation sites in human Chk2

    DEFF Research Database (Denmark)

    Olsen, Birgitte B; Larsen, Martin R; Boldyreff, Brigitte;

    2008-01-01

    A comparative biochemical analysis was performed using recombinant human protein kinase Chk2 (checkpoint kinase 2) expressed in bacteria and insect cells. Dephosphorylated, inactive, recombinant human Chk2 could be reactivated in a concentration-dependent manner. Despite distinct time....... Mass spectrometric analyses of human recombinant Chk2 isolated from bacteria and insect cells showed distinct differences. The number of phosphorylated residues in human recombinant Chk2 isolated from bacteria was 16, whereas in the case of the recombinant human Chk2 from insect cells it was 8. Except...... for phosphorylated amino acid T378 which was not found in the Chk2 isolated from bacteria, all other phosphorylated residues identified in human Chk2 from insect cells were present also in Chk2 from bacteria....

  10. Ca/calmodulin-dependent phosphorylation of endocytic scaffold ITSN1

    Directory of Open Access Journals (Sweden)

    Morderer D. Ye.

    2014-01-01

    Full Text Available ITSN1 is an endocytic scaffold protein with a prominent function in synaptic transmission. It is known that Ca signaling is crucial for the regulation of synaptic proteins functioning. Aim. Checking the possibility of Ca/calmodulin-dependent phosphorylation of ITSN1. Methods. Affinity chromatography, in vitro kinase reaction, Western blotting, gel staining with fluorescent stains. Results. We show that the fraction of calmodulin-binding proteins is able to phosphorylate the recombinant fragments encoding the coiled-coil region and the SH3 domain-containing region of ITSN1 in the presence of Ca ions and calmodulin. Conclusions. The coiled-coil region and the SH3 domain-containing region of ITSN1 undergo Ca/calmodulin-dependent phosphorylation in vitro, suggesting a possible regulation of ITSN1 by Ca signaling.

  11. Regulatory Phosphorylation of Ikaros by Bruton's Tyrosine Kinase

    Science.gov (United States)

    Zhang, Jian; Ishkhanian, Rita; Uckun, Fatih M.

    2013-01-01

    Diminished Ikaros function has been implicated in the pathogenesis of acute lymphoblastic leukemia (ALL), the most common form of childhood cancer. Therefore, a stringent regulation of Ikaros is of paramount importance for normal lymphocyte ontogeny. Here we provide genetic and biochemical evidence for a previously unknown function of Bruton's tyrosine kinase (BTK) as a partner and posttranslational regulator of Ikaros, a zinc finger-containing DNA-binding protein that plays a pivotal role in immune homeostasis. We demonstrate that BTK phosphorylates Ikaros at unique phosphorylation sites S214 and S215 in the close vicinity of its zinc finger 4 (ZF4) within the DNA binding domain, thereby augmenting its nuclear localization and sequence-specific DNA binding activity. Our results further demonstrate that BTK-induced activating phosphorylation is critical for the optimal transcription factor function of Ikaros. PMID:23977012

  12. Regulatory phosphorylation of Ikaros by Bruton's tyrosine kinase.

    Directory of Open Access Journals (Sweden)

    Hong Ma

    Full Text Available Diminished Ikaros function has been implicated in the pathogenesis of acute lymphoblastic leukemia (ALL, the most common form of childhood cancer. Therefore, a stringent regulation of Ikaros is of paramount importance for normal lymphocyte ontogeny. Here we provide genetic and biochemical evidence for a previously unknown function of Bruton's tyrosine kinase (BTK as a partner and posttranslational regulator of Ikaros, a zinc finger-containing DNA-binding protein that plays a pivotal role in immune homeostasis. We demonstrate that BTK phosphorylates Ikaros at unique phosphorylation sites S214 and S215 in the close vicinity of its zinc finger 4 (ZF4 within the DNA binding domain, thereby augmenting its nuclear localization and sequence-specific DNA binding activity. Our results further demonstrate that BTK-induced activating phosphorylation is critical for the optimal transcription factor function of Ikaros.

  13. Crystal Structure of a Phosphorylation-coupled Saccharide Transporter

    Energy Technology Data Exchange (ETDEWEB)

    Y Cao; X Jin; E Levin; H Huang; Y Zong; W Hendrickson; J Javitch; K Rajashankar; M Zhou; et al.

    2011-12-31

    Saccharides have a central role in the nutrition of all living organisms. Whereas several saccharide uptake systems are shared between the different phylogenetic kingdoms, the phosphoenolpyruvate-dependent phosphotransferase system exists almost exclusively in bacteria. This multi-component system includes an integral membrane protein EIIC that transports saccharides and assists in their phosphorylation. Here we present the crystal structure of an EIIC from Bacillus cereus that transports diacetylchitobiose. The EIIC is a homodimer, with an expansive interface formed between the amino-terminal halves of the two protomers. The carboxy-terminal half of each protomer has a large binding pocket that contains a diacetylchitobiose, which is occluded from both sides of the membrane with its site of phosphorylation near the conserved His250 and Glu334 residues. The structure shows the architecture of this important class of transporters, identifies the determinants of substrate binding and phosphorylation, and provides a framework for understanding the mechanism of sugar translocation.

  14. Surface-phosphorylated copolymer promotes direct bone bonding.

    Science.gov (United States)

    Gopalakrishnanchettiyar, Sailaja S; Mohanty, Mira; Kumary, Thrikkovil V; Valappil, Mohanan P; Parameshwaran, Ramesh; Varma, Harikrishna K

    2009-10-01

    The bone bonding potential of surface-phosphorylated poly (2-hydroxyethyl methacrylate-co-methyl methacrylate) [poly (HEMA-co-MMA)] has been investigated and compared with commercially available poly (methyl methacrylate) bone cement (CMW1 radiopaque, Depuy; Johnson & Johnson, Blackpool, Lancashire, England, United Kingdom) as control. Poly (HEMA-co-MMA) is synthesized by free radical-initiated copolymerization and surface functionalized by phosphorylation. The X-ray photoelectron spectroscopy confirms the presence of surface-bound phosphate groups on poly (HEMA-co-MMA). The surface-phosphorylated poly (HEMA-co-MMA) promotes in vitro biomineralization, cell viability, cell adhesion, and expression of bone-specific markers such as osteocalcin and alkaline phosphatase. The bone implantation study performed in rabbits as per ISO 10993-6; 1994 (E) shows that surface-phosphorylated poly (HEMA-co-MMA) elicits bone bonding and new bone formation. New woven bone trabeculae are formed at the defect site of surface-phosphorylated poly (HEMA-co-MMA) within 1 week, while for control sample, inflammatory cells--predominantly, macrophages, fibroblasts, and fibrocytes--are present at the cortical margins around the defect. The 4 and 12 weeks postimplantation results show that the major part of the defects around the surface-phosphorylated poly (HEMA-co-MMA) implant is bridged with new woven bone, with significant remodeling (evident from resorption bays) along both the margins of the defect, but for control implants, the defects are only partially closed, with slight remodeling along the margins, but most of them are separated by fibrous tissue.

  15. Phosphorylated DegU Manipulates Cell Fate Differentiation in the Bacillus subtilis Biofilm

    Science.gov (United States)

    Marlow, Victoria L.; Porter, Michael; Hobley, Laura; Kiley, Taryn B.; Swedlow, Jason R.; Davidson, Fordyce A.

    2014-01-01

    Cell differentiation is ubiquitous and facilitates division of labor and development. Bacteria are capable of multicellular behaviors that benefit the bacterial community as a whole. A striking example of bacterial differentiation occurs throughout the formation of a biofilm. During Bacillus subtilis biofilm formation, a subpopulation of cells differentiates into a specialized population that synthesizes the exopolysaccharide and the TasA amyloid components of the extracellular matrix. The differentiation process is indirectly controlled by the transcription factor Spo0A that facilitates transcription of the eps and tapA (tasA) operons. DegU is a transcription factor involved in regulating biofilm formation. Here, using a combination of genetics and live single-cell cytological techniques, we define the mechanism of biofilm inhibition at high levels of phosphorylated DegU (DegU∼P) by showing that transcription from the eps and tapA promoter regions is inhibited. Data demonstrating that this is not a direct regulatory event are presented. We demonstrate that DegU∼P controls the frequency with which cells activate transcription from the operons needed for matrix biosynthesis in favor of an off state. Subsequent experimental analysis led us to conclude that DegU∼P functions to increase the level of Spo0A∼P, driving cell fate differentiation toward the terminal developmental process of sporulation. PMID:24123822

  16. Phosphorylation site dynamics of early T-cell receptor signaling

    DEFF Research Database (Denmark)

    Chylek, Lily A; Akimov, Vyacheslav; Dengjel, Jörn

    2014-01-01

    a systems-level understanding of how these components cooperate to control signaling dynamics, especially during the crucial first seconds of stimulation. Here, we used quantitative proteomics to characterize reshaping of the T-cell phosphoproteome in response to TCR/CD28 co-stimulation, and found...... that diverse dynamic patterns emerge within seconds. We detected phosphorylation dynamics as early as 5 s and observed widespread regulation of key TCR signaling proteins by 30 s. Development of a computational model pointed to the presence of novel regulatory mechanisms controlling phosphorylation of sites...

  17. The phosphorylation pattern of bovine heart complex I subunits

    DEFF Research Database (Denmark)

    Palmisano, Giuseppe; Sardanelli, Anna Maria; Signorile, Anna;

    2007-01-01

    The phosphoproteome of bovine heart complex I of the respiratory chain has been analysed with a procedure based on nondenaturing gel electrophoretic separation of complex I from small quantities of mitochondria samples, in-gel digestion, in combination with phosphopeptide enrichment by titanium...... dioxide and MS. The results, complemented by analyses of purified samples of complex I, showed phosphorylation of five subunits of the complex, 42 kDa (human gene NDUFA10), ESSS, B14.5a (human gene NDUFA7), B14.5b (human gene NDUFC2) and B16.6 (GRIM-19). MS also revealed the presence of phosphorylated...

  18. Kinase-specific prediction of protein phosphorylation sites

    DEFF Research Database (Denmark)

    Miller, Martin Lee; Blom, Nikolaj

    2009-01-01

    -substrate specificity. Here, we briefly describe the available resources for predicting kinase-specific phosphorylation from sequence properties. We address the strengths and weaknesses of these resources, which are based on methods ranging from simple consensus patterns to more advanced machine-learning algorithms....... Furthermore, a protocol for the use of the artificial neural network based predictors, NetPhos and NetPhosK, is provided. Finally, we point to possible developments with the intention of providing the community with improved and additional phosphorylation predictors for large-scale modeling of cellular...... signaling networks....

  19. Chemical phosphorylation of deoxyribonucleosides and thermolytic DNA oligonucleotides.

    Science.gov (United States)

    Ausín, Cristina; Grajkowski, Andrzej; Cieślak, Jacek; Beaucage, Serge L

    2006-10-01

    The phosphorylating reagent bis[S-(4,4'-dimethoxytrityl)-2-mercaptoethyl]-N,N-diisopropylphosphoramidite is prepared in three steps from commercial methyl thioglycolate and diisopropylphosphoramidous dichloride. The phosphorylating reagent has been used successfully in the solid-phase synthesis of deoxyribonucleoside 5'-/3'-phosphate or -thiophosphate monoesters and oligonucleotide 5'-phosphate/-thiophosphate monoesters. Bis[S-(4,4'-dimethoxytrityl)-2-mercaptoethyl]-N,N-diisopropylphosphoramidite has also been employed in the construction of a thermolytic dinucleotide prodrug model to evaluate the ability of the reagent to produce thermosentive oligonucleotide prodrugs under mild temperature conditions ( approximately 25 degrees C) for potential therapeutic applications.

  20. Matrix Quantization of Turbulence

    CERN Document Server

    Floratos, Emmanuel

    2011-01-01

    Based on our recent work on Quantum Nambu Mechanics $\\cite{af2}$, we provide an explicit quantization of the Lorenz chaotic attractor through the introduction of Non-commutative phase space coordinates as Hermitian $ N \\times N $ matrices in $ R^{3}$. For the volume preserving part, they satisfy the commutation relations induced by one of the two Nambu Hamiltonians, the second one generating a unique time evolution. Dissipation is incorporated quantum mechanically in a self-consistent way having the correct classical limit without the introduction of external degrees of freedom. Due to its volume phase space contraction it violates the quantum commutation relations. We demonstrate that the Heisenberg-Nambu evolution equations for the Matrix Lorenz system develop fast decoherence to N independent Lorenz attractors. On the other hand there is a weak dissipation regime, where the quantum mechanical properties of the volume preserving non-dissipative sector survive for long times.

  1. Matrix Graph Grammars

    CERN Document Server

    Velasco, Pedro Pablo Perez

    2008-01-01

    This book objective is to develop an algebraization of graph grammars. Equivalently, we study graph dynamics. From the point of view of a computer scientist, graph grammars are a natural generalization of Chomsky grammars for which a purely algebraic approach does not exist up to now. A Chomsky (or string) grammar is, roughly speaking, a precise description of a formal language (which in essence is a set of strings). On a more discrete mathematical style, it can be said that graph grammars -- Matrix Graph Grammars in particular -- study dynamics of graphs. Ideally, this algebraization would enforce our understanding of grammars in general, providing new analysis techniques and generalizations of concepts, problems and results known so far.

  2. Matrix anticirculant calculus

    Science.gov (United States)

    Dimiev, Stancho; Stoev, Peter; Stoilova, Stanislava

    2013-12-01

    The notion of anticirculant is ordinary of interest for specialists of general algebra (to see for instance [1]). In this paper we develop some aspects of anticirculants in real function theory. Denoting by X≔x0+jx1+⋯+jmxm, xk∈R, m+1 = 2n, and jk is the k-th degree of the matrix j = (0100...00010...00001...0..................-1000...0), we study the functional anticirculants f(X)≔f0(x0,x1,...,xm)+jf1(x0,x1,...,xm)+⋯+jm-1fm-1(x0,x1,...,xm)+jmfm(x0,x1,...,xm), where fk(x0,x1,...,xm) are smooth functions of 2n real variables. A continuation for complex function theory will appear.

  3. Light cone matrix product

    Energy Technology Data Exchange (ETDEWEB)

    Hastings, Matthew B [Los Alamos National Laboratory

    2009-01-01

    We show how to combine the light-cone and matrix product algorithms to simulate quantum systems far from equilibrium for long times. For the case of the XXZ spin chain at {Delta} = 0.5, we simulate to a time of {approx} 22.5. While part of the long simulation time is due to the use of the light-cone method, we also describe a modification of the infinite time-evolving bond decimation algorithm with improved numerical stability, and we describe how to incorporate symmetry into this algorithm. While statistical sampling error means that we are not yet able to make a definite statement, the behavior of the simulation at long times indicates the appearance of either 'revivals' in the order parameter as predicted by Hastings and Levitov (e-print arXiv:0806.4283) or of a distinct shoulder in the decay of the order parameter.

  4. Matrix membranes and integrability

    Energy Technology Data Exchange (ETDEWEB)

    Zachos, C. [Argonne National Lab., IL (United States); Fairlie, D. [University of Durham (United Kingdom). Dept. of Mathematical Sciences; Curtright, T. [University of Miami, Coral Gables, FL (United States). Dept. of Physics

    1997-06-01

    This is a pedagogical digest of results reported in Curtright, Fairlie, {ampersand} Zachos 1997, and an explicit implementation of Euler`s construction for the solution of the Poisson Bracket dual Nahm equation. But it does not cover 9 and 10-dimensional systems, and subsequent progress on them Fairlie 1997. Cubic interactions are considered in 3 and 7 space dimensions, respectively, for bosonic membranes in Poisson Bracket form. Their symmetries and vacuum configurations are explored. Their associated first order equations are transformed to Nahm`s equations, and are hence seen to be integrable, for the 3-dimensional case, by virtue of the explicit Lax pair provided. Most constructions introduced also apply to matrix commutator or Moyal Bracket analogs.

  5. Discrimination between acid and alkali-labile phosphorylated residues on Immobilon: phosphorylation studies of nucleoside diphosphate kinase

    DEFF Research Database (Denmark)

    Biondi, R M; Walz, K; Issinger, O G

    1996-01-01

    to deplete phosphate from membranes incubated successively under acid and basic conditions. The technique was applied to the study of nucleoside diphosphate kinase (NDP kinase) phosphorylation. In this enzyme, autophosphorylation of active site histidine is an accepted intermediate step in the catalytic...... phosphate transfer activity of nucleoside diphosphate kinase (NDP kinase). Nonetheless, a significant degree of autophosphorylation on other residues has been reported by several laboratories, and the hypothesis has been advanced that this nonhistidine phosphorylation may play an important role in NDP...... of phosphoserine after strong acid hydrolysis of the histidine autophosphorylated enzyme is in fact a nonenzymatic transphosphorylation from phosphohistidine due to the harsh acid treatment. This methodology was also applied to in vivo phosphorylation studies of C. albicans NDP kinase. We believe...

  6. Phosphorylation status of 72 kDa MMP-2 determines its structure and activity in response to peroxynitrite.

    Directory of Open Access Journals (Sweden)

    Anna Laura Jacob-Ferreira

    Full Text Available Matrix metalloproteinase-2 (MMP-2 is a key intra- and extra-cellular protease which contributes to several oxidative stress related pathologies. A molecular understanding of 72 kDa MMP-2 activity, directly mediated by S-glutathiolation of its cysteine residues in the presence of peroxynitrite (ONOO(- and by phosphorylation of its serine and threonine residues, is essential to develop new generation inhibitors of intracellular MMP-2. Within its propeptide and collagen binding domains there is an interesting juxtaposition of predicted phosphorylation sites with nearby cysteine residues which form disulfide bonds. However, the combined effect of these two post-translational modifications on MMP-2 activity has not been studied. The activity of human recombinant 72 kDa MMP-2 (hrMMP-2 following in vitro treatments was measured by troponin I proteolysis assay and a kinetic activity assay using a fluorogenic peptide substrate. ONOO(- treatment in the presence of 30 µM glutathione resulted in concentration-dependent changes in MMP-2 activity, with 0.1-1 µM increasing up to twofold and 100 µM attenuating its activity. Dephosphorylation of MMP-2 with alkaline phosphatase markedly increased its activity by sevenfold, either with or without ONOO(-. Dephosphorylation of MMP-2 also affected the conformational structure of the enzyme as revealed by circular dichroism studies, suggesting an increase in the proportion of α-helices and a decrease in β-strands compared to the phosphorylated form of MMP-2. These results suggest that ONOO(- activation (at low µM and inactivation (at high µM of 72 kDa MMP-2, in the presence or absence of glutathione, is also influenced by its phosphorylation status. These insights into the role of post-translational modifications in the structure and activity of 72 kDa MMP-2 will aid in the development of inhibitors specifically targeting intracellular MMP-2.

  7. Spherical membranes in Matrix theory

    CERN Document Server

    Kabat, D; Kabat, Daniel; Taylor, Washington

    1998-01-01

    We consider membranes of spherical topology in uncompactified Matrix theory. In general for large membranes Matrix theory reproduces the classical membrane dynamics up to 1/N corrections; for certain simple membrane configurations, the equations of motion agree exactly at finite N. We derive a general formula for the one-loop Matrix potential between two finite-sized objects at large separations. Applied to a graviton interacting with a round spherical membrane, we show that the Matrix potential agrees with the naive supergravity potential for large N, but differs at subleading orders in N. The result is quite general: we prove a pair of theorems showing that for large N, after removing the effects of gravitational radiation, the one-loop potential between classical Matrix configurations agrees with the long-distance potential expected from supergravity. As a spherical membrane shrinks, it eventually becomes a black hole. This provides a natural framework to study Schwarzschild black holes in Matrix theory.

  8. Elucidation of O-Phosphoryl and N-Phosphoryl Amino Acids by Electrospray Ionization Tandem Mass Spectrometry

    Institute of Scientific and Technical Information of China (English)

    ZHANG,Jian-Chen(张建臣); CAO,Shu-Xiaa(曹书霞); XU,Juna(徐军); LIAO,Xin-Cheng(廖新成); ZHAO,Yu-Fen(赵玉芬)

    2004-01-01

    Mass spectroscopic characteristics of phosphoryl amino acids were studied in detail by positive and negative electrospray ionization mass spectrometry (ESI-MS) in conjunction with tandem mass spectrometry (MS/MS). Besides N-diisopropyloxyphosphoryl amino acids (N-DIPP-AA), O-phospho- and O-diisopropyloxyphosphoryl amino acids (O-DIPP-AA) were studied and compared to N-DIPP-AA. The fragmentation pathways of [M+H]+, [M+Na]+ and [M-H]- ions of phosphoryl amino acids were summarized. In addition to several similar patterns,each of them showed its characteristic fragmention.

  9. MG63 osteoblast-like cells exhibit different behavior when grown on electrospun collagen matrix versus electrospun gelatin matrix.

    Directory of Open Access Journals (Sweden)

    Shiao-Wen Tsai

    Full Text Available Electrospinning is a simple and efficient method of fabricating a non-woven polymeric nanofiber matrix. However, using fluorinated alcohols as a solvent for the electrospinning of proteins often results in protein denaturation. TEM and circular dichroism analysis indicated a massive loss of triple-helical collagen from an electrospun collagen (EC matrix, and the random coils were similar to those found in gelatin. Nevertheless, from mechanical testing we found the Young's modulus and ultimate tensile stresses of EC matrices were significantly higher than electrospun gelatin (EG matrices because matrix stiffness can affect many cell behaviors such as cell adhesion, proliferation and differentiation. We hypothesize that the difference of matrix stiffness between EC and EG will affect intracellular signaling through the mechano-transducers Rho kinase (ROCK and focal adhesion kinase (FAK and subsequently regulates the osteogenic phenotype of MG63 osteoblast-like cells. From the results, we found there was no significant difference between the EC and EG matrices with respect to either cell attachment or proliferation rate. However, the gene expression levels of OPN, type I collagen, ALP, and OCN were significantly higher in MG63 osteoblast-like cells grown on the EC than in those grown on the EG. In addition, the phosphorylation levels of Y397-FAK, ERK1/2, BSP, and OPN proteins, as well as ALP activity, were also higher on the EC than on the EG. We further inhibited ROCK activation with Y27632 during differentiation to investigate its effects on matrix-mediated osteogenic differentiation. Results showed the extent of mineralization was decreased with inhibition after induction. Moreover, there is no significant difference between EC and EG. From the results of the protein levels of phosphorylated Y397-FAK, ERK1/2, BSP and OPN, ALP activity and mineral deposition, we speculate that the mechanism that influences the osteogenic differentiation of MG63

  10. Linearized supergravity from Matrix theory

    CERN Document Server

    Kabat, D; Kabat, Daniel; Taylor, Washington

    1998-01-01

    We show that the linearized supergravity potential between two objects arising from the exchange of quanta with zero longitudinal momentum is reproduced to all orders in 1/r by terms in the one-loop Matrix theory potential. The essential ingredient in the proof is the identification of the Matrix theory quantities corresponding to moments of the stress tensor and membrane current. We also point out that finite-N Matrix theory violates the Equivalence Principle.

  11. Lectures on Matrix Field Theory

    Science.gov (United States)

    Ydri, Badis

    The subject of matrix field theory involves matrix models, noncommutative geometry, fuzzy physics and noncommutative field theory and their interplay. In these lectures, a lot of emphasis is placed on the matrix formulation of noncommutative and fuzzy spaces, and on the non-perturbative treatment of the corresponding field theories. In particular, the phase structure of noncommutative $\\phi^4$ theory is treated in great detail, and an introduction to noncommutative gauge theory is given.

  12. Matrix elements of unstable states

    CERN Document Server

    Bernard, V; Meißner, U -G; Rusetsky, A

    2012-01-01

    Using the language of non-relativistic effective Lagrangians, we formulate a systematic framework for the calculation of resonance matrix elements in lattice QCD. The generalization of the L\\"uscher-Lellouch formula for these matrix elements is derived. We further discuss in detail the procedure of the analytic continuation of the resonance matrix elements into the complex energy plane and investigate the infinite-volume limit.

  13. Enhancing an R-matrix

    CERN Document Server

    MacKaay, M A

    1996-01-01

    In order to construct a representation of the tangle category one needs an enhanced R-matrix. In this paper we define a sufficient and necessary condition for enhancement that can be checked easily for any R-matrix. If the R-matrix can be enhanced, we also show how to construct the additional data that define the enhancement. As a direct consequence we find a sufficient condition for the construction of a knot invariant.

  14. Matrix Models and Gravitational Corrections

    CERN Document Server

    Dijkgraaf, R; Temurhan, M; Dijkgraaf, Robbert; Sinkovics, Annamaria; Temurhan, Mine

    2002-01-01

    We provide evidence of the relation between supersymmetric gauge theories and matrix models beyond the planar limit. We compute gravitational R^2 couplings in gauge theories perturbatively, by summing genus one matrix model diagrams. These diagrams give the leading 1/N^2 corrections in the large N limit of the matrix model and can be related to twist field correlators in a collective conformal field theory. In the case of softly broken SU(N) N=2 super Yang-Mills theories, we find that these exact solutions of the matrix models agree with results obtained by topological field theory methods.

  15. A matrix model for WZW

    Energy Technology Data Exchange (ETDEWEB)

    Dorey, Nick [Department of Applied Mathematics and Theoretical Physics, University of Cambridge,Wilberforce Road, Cambridge, CB3 OWA (United Kingdom); Tong, David [Department of Applied Mathematics and Theoretical Physics, University of Cambridge,Wilberforce Road, Cambridge, CB3 OWA (United Kingdom); Department of Theoretical Physics, TIFR,Homi Bhabha Road, Mumbai 400 005 (India); Stanford Institute for Theoretical Physics,Via Pueblo, Stanford, CA 94305 (United States); Turner, Carl [Department of Applied Mathematics and Theoretical Physics, University of Cambridge,Wilberforce Road, Cambridge, CB3 OWA (United Kingdom)

    2016-08-01

    We study a U(N) gauged matrix quantum mechanics which, in the large N limit, is closely related to the chiral WZW conformal field theory. This manifests itself in two ways. First, we construct the left-moving Kac-Moody algebra from matrix degrees of freedom. Secondly, we compute the partition function of the matrix model in terms of Schur and Kostka polynomials and show that, in the large N limit, it coincides with the partition function of the WZW model. This same matrix model was recently shown to describe non-Abelian quantum Hall states and the relationship to the WZW model can be understood in this framework.

  16. A Matrix Model for WZW

    CERN Document Server

    Dorey, Nick; Turner, Carl

    2016-01-01

    We study a U(N) gauged matrix quantum mechanics which, in the large N limit, is closely related to the chiral WZW conformal field theory. This manifests itself in two ways. First, we construct the left-moving Kac-Moody algebra from matrix degrees of freedom. Secondly, we compute the partition function of the matrix model in terms of Schur and Kostka polynomials and show that, in the large $N$ limit, it coincides with the partition function of the WZW model. This same matrix model was recently shown to describe non-Abelian quantum Hall states and the relationship to the WZW model can be understood in this framework.

  17. Phytophthora infestans specific phosphorylation patterns and new putative control targets.

    Science.gov (United States)

    Frades, Itziar; Andreasson, Erik

    2016-04-01

    In this study we applied biomathematical searches of gene regulatory mechanisms to learn more about oomycete biology and to identify new putative targets for pesticides or biological control against Phytophthora infestans. First, oomycete phylum-specific phosphorylation motifs were found by discriminative n-gram analysis. We found 11.600 P. infestans specific n-grams, mapping 642 phosphoproteins. The most abundant group among these related to phosphatidylinositol metabolism. Due to the large number of possible targets found and our hypothesis that multi-level control is a sign of usefulness as targets for intervention, we identified overlapping targets with a second screen. This was performed to identify proteins dually regulated by small RNA and phosphorylation. We found 164 proteins to be regulated by both sRNA and phosphorylation and the dominating functions where phosphatidylinositol signalling/metabolism, endocytosis, and autophagy. Furthermore we performed a similar regulatory study and discriminative n-gram analysis of proteins with no clear orthologs in other species and proteins that are known to be unique to P. infestans such as the RxLR effectors, Crinkler (CRN) proteins and elicitins. We identified CRN proteins with specific phospho-motifs present in all life stages. PITG_12626, PITG_14042 and PITG_23175 are CRN proteins that have species-specific phosphorylation motifs and are subject to dual regulation.

  18. Construction and Analysis of N-phosphoryl Peptide Libraries

    Institute of Scientific and Technical Information of China (English)

    Shu Xia CAO; Jian Chen ZHANG; Ming Yu NIU; Kui LU; Xin Cheng LIAO; Yu Fen ZHAO

    2004-01-01

    N-Phosphoryl peptide libraries were constructed by transformation from homo-oligopeptide libraries, which was synthesized by self-assembly of amino acids with the assistance of phosphorus oxychloride. Electrospray ionization mass spectrometry (ESI-MS) was used to monitor the reaction.

  19. A mathematical model of phosphorylation AKT in Acute Myeloid Leukemia

    Energy Technology Data Exchange (ETDEWEB)

    Adi, Y. A., E-mail: yudi.adi@math.uad.ac.id [Department of Mathematic Faculty of MIPA Universitas Ahmad Dahlan (Indonesia); Department of Mathematic Faculty of MIPA Universitas Gadjah Mada (Indonesia); Kusumo, F. A.; Aryati, L. [Department of Mathematic Faculty of MIPA Universitas Gadjah Mada (Indonesia); Hardianti, M. S. [Department of Internal Medicine, Faculty of Medicine, Universitas Gadjah Mada (Indonesia)

    2016-04-06

    In this paper we consider a mathematical model of PI3K/AKT signaling pathways in phosphorylation AKT. PI3K/AKT pathway is an important mediator of cytokine signaling implicated in regulation of hematopoiesis. Constitutive activation of PI3K/AKT signaling pathway has been observed in Acute Meyloid Leukemia (AML) it caused by the mutation of Fms-like Tyrosine Kinase 3 in internal tandem duplication (FLT3-ITD), the most common molecular abnormality associated with AML. Depending upon its phosphorylation status, protein interaction, substrate availability, and localization, AKT can phosphorylate or inhibite numerous substrates in its downstream pathways that promote protein synthesis, survival, proliferation, and metabolism. Firstly, we present a mass action ordinary differential equation model describing AKT double phosphorylation (AKTpp) in a system with 11 equations. Finally, under the asumtion enzyme catalyst constant and steady state equilibrium, we reduce the system in 4 equation included Michaelis Menten constant. Simulation result suggested that a high concentration of PI3K and/or a low concentration of phospatase increased AKTpp activation. This result also indicates that PI3K is a potential target theraphy in AML.

  20. Genetic defects in the oxidative phosphorylation (OXPHOS) system.

    NARCIS (Netherlands)

    Janssen, R.J.R.J.; Heuvel, L.P.W.J. van den; Smeitink, J.A.M.

    2004-01-01

    The oxidative phosphorylation (OXPHOS) system consists of five multiprotein complexes and two mobile electron carriers embedded in the lipid bilayer of the mitochondrial inner membrane. With the exception of complex II and the mobile carriers, the other parts of the OXPHOS system are under dual gene

  1. Plk phosphorylation regulates the microtubule-stabilizing protein TCTP.

    Science.gov (United States)

    Yarm, Frederic R

    2002-09-01

    The mitotic polo-like kinases have been implicated in the formation and function of bipolar spindles on the basis of their respective localizations and mutant phenotypes. To date, this putative regulation has been limited to a kinesin-like motor protein, a centrosomal structural protein, and two microtubule-associated proteins (MAPs). In this study, another spindle-regulating protein, the mammalian non-MAP microtubule-binding and -stabilizing protein, the translationally controlled tumor protein (TCTP), was identified as a putative Plk-interacting clone by a two-hybrid screen. Plk phosphorylates TCTP on two serine residues in vitro and cofractionates with the majority of kinase activity toward TCTP in mitotic cell lysates. In addition, these sites were demonstrated to be phosphorylated in vivo. Overexpression of a Plk phosphorylation site-deficient mutant of TCTP induced a dramatic increase in the number of multinucleate cells, rounded cells with condensed ball-like nuclei, and cells undergoing cell death, similar to both the reported anti-Plk antibody microinjection and the low-concentration taxol treatment phenotypes. These results suggest that phosphorylation decreases the microtubule-stabilizing activity of TCTP and promotes the increase in microtubule dynamics that occurs after metaphase.

  2. Spatial separation of Plk1 phosphorylation and activity

    Directory of Open Access Journals (Sweden)

    Wytse eBruinsma

    2015-06-01

    Full Text Available Polo-like kinase 1 (Plk1 is one of the major kinases controlling mitosis and cell division. Plk1 is first recruited to the centrosome in S phase, then appears on the kinetochores in late G2 and at the end of mitosis it translocates to the central spindle. Activation of Plk1 requires phosphorylation of T210 by Aurora A, an event that critically depends on the co-factor Bora. However, conflicting reports exist as to where Plk1 is first activated. Phosphorylation of T210 is first observed at the centrosomes, but kinase activity seems to be restricted to the nucleus in the earlier phases of G2. Here we demonstrate that Plk1 activity manifests itself first in the nucleus using a nuclear FRET-based biosensor for Plk1 activity. However, we find that Bora is restricted to the cytoplasm and that Plk1 is phosphorylated on T210 at the centrosomes. Our data demonstrate that while Plk1 activation occurs on centrosomes, downstream target phosphorylation by Plk1 first occurs in the nucleus. We discuss several explanations for this surprising separation of activation and function.

  3. Histone 3 s10 phosphorylation: "caught in the R loop!".

    Science.gov (United States)

    Skourti-Stathaki, Konstantina; Proudfoot, Nicholas J

    2013-11-21

    In this issue of Molecular Cell, Castellano-Pozo et al. (2013) describe a connection between R loop structures and histone 3 S10 phosphorylation (H3S10P), a mark of chromatin compaction. Their results constitute a significant advance in our understanding of the role of R loops in genomic instability.

  4. Annealing properties of potato starches with different degrees of phosphorylation

    DEFF Research Database (Denmark)

    Muhrbeck, Per; Svensson, E

    1996-01-01

    Changes in the gelatinization temperature interval and gelatinization enthalpy with annealing time at 50 degrees C were followed for a number of potato starch samples, with different degrees of phosphorylation, using differential scanning calorimetry. The gelatinization temperature increased with...... and crystalline structure of amylopectin helices. (C) 1997 Elsevier Science Ltd....

  5. Genetic defects in the oxidative phosphorylation (OXPHOS) system.

    NARCIS (Netherlands)

    Janssen, R.J.R.J.; Heuvel, L.P.W.J. van den; Smeitink, J.A.M.

    2004-01-01

    The oxidative phosphorylation (OXPHOS) system consists of five multiprotein complexes and two mobile electron carriers embedded in the lipid bilayer of the mitochondrial inner membrane. With the exception of complex II and the mobile carriers, the other parts of the OXPHOS system are under dual

  6. Animation Model to Conceptualize ATP Generation: A Mitochondrial Oxidative Phosphorylation

    Science.gov (United States)

    Jena, Ananta Kumar

    2015-01-01

    Adenosine triphosphate (ATP) is the molecular unit of intracellular energy and it is the product of oxidative phosphorylation of cellular respiration uses in cellular processes. The study explores the growth of the misconception levels amongst the learners and evaluates the effectiveness of animation model over traditional methods. The data…

  7. Enteric GFAP expression and phosphorylation in Parkinson's disease

    NARCIS (Netherlands)

    Clairembault, Thomas; Kamphuis, W.; Leclair-Visonneau, Laurène; Rolli-Derkinderen, Malvyne; Coron, Emmanuel; Neunlist, Michel; Hol, Elly M; Derkinderen, Pascal

    2014-01-01

    Enteric glial cells (EGCs) are in many respects similar to astrocytes of the central nervous system and express similar proteins including glial fibrillary acidic protein (GFAP). Changes in GFAP expression and/or phosphorylation have been reported during brain damage or central nervous system degene

  8. Phosphorylation of as1-casein is regulated by different genes

    NARCIS (Netherlands)

    Bijl, E.; Valenberg, van H.J.F.; Huppertz, T.; Hooijdonk, van A.C.M.; Bovenhuis, H.

    2014-01-01

    Casein phosphorylation is a posttranslational modification catalyzed by kinase enzymes that attach phosphate groups to specific AA in the protein sequence. This modification is one of the key factors responsible for the stabilization of calcium phosphate nanoclusters in casein micelles and for the i

  9. Eph-mediated tyrosine phosphorylation of citron kinase controls abscission

    Science.gov (United States)

    Jungas, Thomas; Perchey, Renaud T.; Fawal, Mohamad; Callot, Caroline; Froment, Carine; Burlet-Schiltz, Odile; Besson, Arnaud

    2016-01-01

    Cytokinesis is the last step of cell division, culminating in the physical separation of daughter cells at the end of mitosis. Cytokinesis is a tightly regulated process that until recently was mostly viewed as a cell-autonomous event. Here, we investigated the role of Ephrin/Eph signaling, a well-known local cell-to-cell communication pathway, in cell division. We show that activation of Eph signaling in vitro leads to multinucleation and polyploidy, and we demonstrate that this is caused by alteration of the ultimate step of cytokinesis, abscission. Control of abscission requires Eph kinase activity, and Src and citron kinase (CitK) are downstream effectors in the Eph-induced signal transduction cascade. CitK is phosphorylated on tyrosines in neural progenitors in vivo, and Src kinase directly phosphorylates CitK. We have identified the specific tyrosine residues of CitK that are phosphorylated and show that tyrosine phosphorylation of CitK impairs cytokinesis. Finally, we show that, similar to CitK, Ephrin/Eph signaling controls neuronal ploidy in the developing neocortex. Our study indicates that CitK integrates intracellular and extracellular signals provided by the local environment to coordinate completion of cytokinesis. PMID:27551053

  10. Circadian KaiC phosphorylation: a multi-layer network.

    Directory of Open Access Journals (Sweden)

    Congxin Li

    2009-11-01

    Full Text Available Circadian KaiC phosphorylation in cyanobacteria reconstituted in vitro recently initiates a series of studies experimentally and theoretically to explore its mechanism. In this paper, we report a dynamic diversity in hexameric KaiC phosphoforms using a multi-layer reaction network based on the nonequivalence of the dual phosphorylation sites (S431 and T432 in each KaiC subunit. These diverse oscillatory profiles can generate a kaleidoscopic phase modulation pattern probably responsible for the genome-wide transcription rhythms directly and/or indirectly in cyanobacteria. Particularly, our model reveals that a single KaiC hexamer is an energy-based, phosphorylation-dependent and self-regulated circadian oscillator modulated by KaiA and KaiB. We suggest that T432 is the main regulator for the oscillation amplitude, while S431 is the major phase regulator. S431 and T432 coordinately control the phosphorylation period. Robustness of the Kai network was examined by mixing samples in different phases, and varying protein concentrations and temperature. Similar results were obtained regardless of the deterministic or stochastic method employed. Therefore, the dynamic diversities and robustness of Kai oscillator make it a qualified core pacemaker that controls the cellular processes in cyanobacteria pervasively and accurately.

  11. ACTH, cyclic nucleotides, and brain protein phosphorylation in vitro

    NARCIS (Netherlands)

    Zwiers, H; Veldhuis, H D; Schotman, P; Gispen, W H

    1976-01-01

    Endogenous phosphorylation of proteins from rat brain synaptosomal plasma membranes was studied in vitro. Cyclic AMP (cAMP) markedly stimulated(32)P incorporation in three protein bands with molecular weights of 75,000, 57,000, and 54,000, respectively. The effect of the behaviorally active peptide

  12. The phosphatase calcineurin regulates pathological TDP-43 phosphorylation.

    Science.gov (United States)

    Liachko, Nicole F; Saxton, Aleen D; McMillan, Pamela J; Strovas, Timothy J; Currey, Heather N; Taylor, Laura M; Wheeler, Jeanna M; Oblak, Adrian L; Ghetti, Bernardino; Montine, Thomas J; Keene, C Dirk; Raskind, Murray A; Bird, Thomas D; Kraemer, Brian C

    2016-10-01

    Detergent insoluble inclusions of TDP-43 protein are hallmarks of the neuropathology in over 90 % of amyotrophic lateral sclerosis (ALS) cases and approximately half of frontotemporal dementia (FTLD-TDP) cases. In TDP-43 proteinopathy disorders, lesions containing aggregated TDP-43 protein are extensively post-translationally modified, with phosphorylated TDP-43 (pTDP) being the most consistent and robust marker of pathological TDP-43 deposition. Abnormally phosphorylated TDP-43 has been hypothesized to mediate TDP-43 toxicity in many neurodegenerative disease models. To date, several different kinases have been implicated in the genesis of pTDP, but no phosphatases have been shown to reverse pathological TDP-43 phosphorylation. We have identified the phosphatase calcineurin as an enzyme binding to and catalyzing the removal of pathological C-terminal phosphorylation of TDP-43 in vitro. In C. elegans models of TDP-43 proteinopathy, genetic elimination of calcineurin results in accumulation of excess pTDP, exacerbated motor dysfunction, and accelerated neurodegenerative changes. In cultured human cells, treatment with FK506 (tacrolimus), a calcineurin inhibitor, results in accumulation of pTDP species. Lastly, calcineurin co-localizes with pTDP in degenerating areas of the central nervous system in subjects with FTLD-TDP and ALS. Taken together, these findings suggest calcineurin acts on pTDP as a phosphatase in neurons. Furthermore, patient treatment with calcineurin inhibitors may have unappreciated adverse neuropathological consequences.

  13. Studies on the synthesis of phosphorylated and alanylated cytokinins.

    NARCIS (Netherlands)

    Shadid, B.

    1990-01-01

    New approaches are described in this thesis towards the syntheses of phosphorylated and alanylated cytokinins.In chapter 1 a general picture of the stucture of cytokinins, their occurence in nature, their biological synthesis, their effects on plants and their chemical synthesis is described.A liter

  14. Stem rust spores elicit rapid RPG1 phosphorylation

    Science.gov (United States)

    Stem rust threatens cereal production worldwide. Understanding the mechanism by which durable resistance genes, such as Rpg1, function is critical. We show that the RPG1 protein is phosphorylated within 5 min by exposure to spores from avirulent but not virulent races of stem rust. Transgenic mutant...

  15. One-Pot Synthesis of N-Phosphoryl Amino Acids

    Institute of Scientific and Technical Information of China (English)

    GUO Xin; FU Hua; LIN Chang-Xue; ZHAO Yu-Fen

    2003-01-01

    @@ Phosphoramidates have been considered as an important class of rationally designed therapeutics especially asoligonucleotide analogs employed as antisene and antigene agents. [1] N-Phosphoryl amino acids are of biological andpharmaceutical interest, [2] and can be used as the building blocks in synthesis of polypeptides. [3

  16. Mechanism of Ribonuclease III Catalytic Regulation by Serine Phosphorylation

    Science.gov (United States)

    Gone, Swapna; Alfonso-Prieto, Mercedes; Paudyal, Samridhdi; Nicholson, Allen W.

    2016-05-01

    Ribonuclease III (RNase III) is a conserved, gene-regulatory bacterial endonuclease that cleaves double-helical structures in diverse coding and noncoding RNAs. RNase III is subject to multiple levels of control, reflective of its global regulatory functions. Escherichia coli (Ec) RNase III catalytic activity is known to increase during bacteriophage T7 infection, reflecting the expression of the phage-encoded protein kinase, T7PK. However, the mechanism of catalytic enhancement is unknown. This study shows that Ec-RNase III is phosphorylated on serine in vitro by purified T7PK, and identifies the targets as Ser33 and Ser34 in the N-terminal catalytic domain. Kinetic experiments reveal a 5-fold increase in kcat and a 1.4-fold decrease in Km following phosphorylation, providing a 7.4–fold increase in catalytic efficiency. Phosphorylation does not change the rate of substrate cleavage under single-turnover conditions, indicating that phosphorylation enhances product release, which also is the rate-limiting step in the steady-state. Molecular dynamics simulations provide a mechanism for facilitated product release, in which the Ser33 phosphomonoester forms a salt bridge with the Arg95 guanidinium group, thereby weakening RNase III engagement of product. The simulations also show why glutamic acid substitution at either serine does not confer enhancement, thus underscoring the specific requirement for a phosphomonoester.

  17. A mathematical model of phosphorylation AKT in Acute Myeloid Leukemia

    Science.gov (United States)

    Adi, Y. A.; Kusumo, F. A.; Aryati, L.; Hardianti, M. S.

    2016-04-01

    In this paper we consider a mathematical model of PI3K/AKT signaling pathways in phosphorylation AKT. PI3K/AKT pathway is an important mediator of cytokine signaling implicated in regulation of hematopoiesis. Constitutive activation of PI3K/AKT signaling pathway has been observed in Acute Meyloid Leukemia (AML) it caused by the mutation of Fms-like Tyrosine Kinase 3 in internal tandem duplication (FLT3-ITD), the most common molecular abnormality associated with AML. Depending upon its phosphorylation status, protein interaction, substrate availability, and localization, AKT can phosphorylate or inhibite numerous substrates in its downstream pathways that promote protein synthesis, survival, proliferation, and metabolism. Firstly, we present a mass action ordinary differential equation model describing AKT double phosphorylation (AKTpp) in a system with 11 equations. Finally, under the asumtion enzyme catalyst constant and steady state equilibrium, we reduce the system in 4 equation included Michaelis Menten constant. Simulation result suggested that a high concentration of PI3K and/or a low concentration of phospatase increased AKTpp activation. This result also indicates that PI3K is a potential target theraphy in AML.

  18. Decoding the phosphorylation code in Hedgehog signal transduction

    Institute of Scientific and Technical Information of China (English)

    Yongbin Chen; Jin Jiang

    2013-01-01

    Hedgehog (Hh) signaling plays pivotal roles in embryonic development and adult tissue homeostasis,and its deregulation leads to numerous human disorders including cancer.Binding of Hh to Patched (Ptc),a twelve-transmembrane protein,alleviates its inhibition of Smoothened (Smo),a seven-transmembrane protein related to G-proteincoupled receptors (GPCRs),leading to Smo phosphorylation and activation.Smo acts through intracellular signaling complexes to convert the latent transcription factor Cubitus interruptus (Ci)/Gli from a truncated repressor to a fulllength activator,leading to derepression/activation of Hh target genes.Increasing evidence suggests that phosphorylation participates in almost every step in the signal relay from Smo to Ci/Gli,and that differential phosphorylation of several key pathway components may be crucial for translating the Hh morphogen gradient into graded pathway activities.In this review,we focus on the multifaceted roles that phosphorylation plays in Hh signal transduction,and discuss the conservation and difference between Drosophila and mammalian Hh signaling mechanisms.

  19. Phosphoproteomics of collagen receptor networks reveals SHP-2 phosphorylation downstream of wild-type DDR2 and its lung cancer mutants.

    Science.gov (United States)

    Iwai, Leo K; Payne, Leo S; Luczynski, Maciej T; Chang, Francis; Xu, Huifang; Clinton, Ryan W; Paul, Angela; Esposito, Edward A; Gridley, Scott; Leitinger, Birgit; Naegle, Kristen M; Huang, Paul H

    2013-09-15

    Collagen is an important extracellular matrix component that directs many fundamental cellular processes including differentiation, proliferation and motility. The signalling networks driving these processes are propagated by collagen receptors such as the β1 integrins and the DDRs (discoidin domain receptors). To gain an insight into the molecular mechanisms of collagen receptor signalling, we have performed a quantitative analysis of the phosphorylation networks downstream of collagen activation of integrins and DDR2. Temporal analysis over seven time points identified 424 phosphorylated proteins. Distinct DDR2 tyrosine phosphorylation sites displayed unique temporal activation profiles in agreement with in vitro kinase data. Multiple clustering analysis of the phosphoproteomic data revealed several DDR2 candidate downstream signalling nodes, including SHP-2 (Src homology 2 domain-containing protein tyrosine phosphatase 2), NCK1 (non-catalytic region of tyrosine kinase adaptor protein 1), LYN, SHIP-2 [SH2 (Src homology 2)-domain-containing inositol phosphatase 2], PIK3C2A (phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2α) and PLCL2 (phospholipase C-like 2). Biochemical validation showed that SHP-2 tyrosine phosphorylation is dependent on DDR2 kinase activity. Targeted proteomic profiling of a panel of lung SCC (squamous cell carcinoma) DDR2 mutants demonstrated that SHP-2 is tyrosine-phosphorylated by the L63V and G505S mutants. In contrast, the I638F kinase domain mutant exhibited diminished DDR2 and SHP-2 tyrosine phosphorylation levels which have an inverse relationship with clonogenic potential. Taken together, the results of the present study indicate that SHP-2 is a key signalling node downstream of the DDR2 receptor which may have therapeutic implications in a subset of DDR2 mutations recently uncovered in genome-wide lung SCC sequencing screens.

  20. Bioinformatics Study of Cancer-Related Mutations within p53 Phosphorylation Site Motifs

    Directory of Open Access Journals (Sweden)

    Xiaona Ji

    2014-07-01

    Full Text Available p53 protein has about thirty phosphorylation sites located at the N- and C-termini and in the core domain. The phosphorylation sites are relatively less mutated than other residues in p53. To understand why and how p53 phosphorylation sites are rarely mutated in human cancer, using a bioinformatics approaches, we examined the phosphorylation site and its nearby flanking residues, focusing on the consensus phosphorylation motif pattern, amino-acid correlations within the phosphorylation motifs, the propensity of structural disorder of the phosphorylation motifs, and cancer mutations observed within the phosphorylation motifs. Many p53 phosphorylation sites are targets for several kinases. The phosphorylation sites match 17 consensus sequence motifs out of the 29 classified. In addition to proline, which is common in kinase specificity-determining sites, we found high propensity of acidic residues to be adjacent to phosphorylation sites. Analysis of human cancer mutations in the phosphorylation motifs revealed that motifs with adjacent acidic residues generally have fewer mutations, in contrast to phosphorylation sites near proline residues. p53 phosphorylation motifs are mostly disordered. However, human cancer mutations within phosphorylation motifs tend to decrease the disorder propensity. Our results suggest that combination of acidic residues Asp and Glu with phosphorylation sites provide charge redundancy which may safe guard against loss-of-function mutations, and that the natively disordered nature of p53 phosphorylation motifs may help reduce mutational damage. Our results further suggest that engineering acidic amino acids adjacent to potential phosphorylation sites could be a p53 gene therapy strategy.

  1. Extended Matrix Variate Hypergeometric Functions and Matrix Variate Distributions

    Directory of Open Access Journals (Sweden)

    Daya K. Nagar

    2015-01-01

    Full Text Available Hypergeometric functions of matrix arguments occur frequently in multivariate statistical analysis. In this paper, we define and study extended forms of Gauss and confluent hypergeometric functions of matrix arguments and show that they occur naturally in statistical distribution theory.

  2. Extracellular matrix mineralization in periodontal tissues: Noncollagenous matrix proteins, enzymes, and relationship to hypophosphatasia and X-linked hypophosphatemia.

    Science.gov (United States)

    McKee, Marc D; Hoac, Betty; Addison, William N; Barros, Nilana M T; Millán, José L; Chaussain, Catherine

    2013-10-01

    As broadly demonstrated for the formation of a functional skeleton, proper mineralization of periodontal alveolar bone and teeth - where calcium phosphate crystals are deposited and grow within an extracellular matrix - is essential for dental function. Mineralization defects in tooth dentin and cementum of the periodontium invariably lead to a weak (soft or brittle) dentition in which teeth become loose and prone to infection and are lost prematurely. Mineralization of the extremities of periodontal ligament fibers (Sharpey's fibers) where they insert into tooth cementum and alveolar bone is also essential for the function of the tooth-suspensory apparatus in occlusion and mastication. Molecular determinants of mineralization in these tissues include mineral ion concentrations (phosphate and calcium), pyrophosphate, small integrin-binding ligand N-linked glycoproteins and matrix vesicles. Amongst the enzymes important in regulating these mineralization determinants, two are discussed at length here, with clinical examples given, namely tissue-nonspecific alkaline phosphatase and phosphate-regulating gene with homologies to endopeptidases on the X chromosome. Inactivating mutations in these enzymes in humans and in mouse models lead to the soft bones and teeth characteristic of hypophosphatasia and X-linked hypophosphatemia, respectively, where the levels of local and systemic circulating mineralization determinants are perturbed. In X-linked hypophosphatemia, in addition to renal phosphate wasting causing low circulating phosphate levels, phosphorylated mineralization-regulating small integrin-binding ligand N-linked glycoproteins, such as matrix extracellular phosphoglycoprotein and osteopontin, and the phosphorylated peptides proteolytically released from them, such as the acidic serine- and aspartate-rich-motif peptide, may accumulate locally to impair mineralization in this disease.

  3. PR65A phosphorylation regulates PP2A complex signaling.

    Directory of Open Access Journals (Sweden)

    Kumar Kotlo

    Full Text Available Serine-threonine Protein phosphatase 2 A (PP2A, a member of the PPP family of phosphatases, regulates a variety of essential cellular processes, including cell-cycling, DNA replication, transcription, translation, and secondary signaling pathways. In the heart, increased PP2A activity/signaling has been linked to cardiac remodeling, contractile dysfunction and, in failure, arrythmogenicity. The core PP2A complex is a hetero-trimeric holoenzyme consisting of a 36 kDa catalytic subunit (PP2Ac; a regulatory scaffold subunit of 65 kDa (PR65A or PP2Aa; and one of at least 18 associated variable regulatory proteins (B subunits classified into 3 families. In the present study, three in vivo sites of phosphorylation in cardiac PR65A are identified (S303, T268, S314. Using HEK cells transfected with recombinant forms of PR65A with phosphomimetic (P-PR65A and non-phosphorylated (N-PR65A amino acid substitutions at these sites, these phosphorylations were shown to inhibit the interaction of PR65A with PP2Ac and PP2A holoenzyme signaling. Forty-seven phospho-proteins were increased in abundance in HEK cells transfected with P-PR65A versus N-PR65A by phospho-protein profiling using 2D-DIGE analysis on phospho-enriched whole cell protein extracts. Among these proteins were elongation factor 1α (EF1A, elongation factor 2, heat shock protein 60 (HSP60, NADPH-dehydrogenase 1 alpha sub complex, annexin A, and PR65A. Compared to controls, failing hearts from the Dahl rat had less phosphorylated PR65A protein abundance and increased PP2A activity. Thus, PR65A phosphorylation is an in vivo mechanism for regulation of the PP2A signaling complex and increased PP2A activity in heart failure.

  4. A redox-regulated tyrosine phosphorylation cascade in rat spermatozoa.

    Science.gov (United States)

    Lewis, B; Aitken, R J

    2001-01-01

    Rat spermatozoa from both the caput and cauda epididymidis were shown to generate superoxide anion (O2-.) both spontaneously and following stimulation with NAD(P)H. Caput spermatozoa gave a significantly greater O2- response to NADPH stimulation than caudal cells, whereas in both cell types the responses to exogenous NADPH and NADH were approximately equivalent. Analysis of H2O2 production revealed that this oxidant was generated only by caudal epididymal cells and only in these cells did the stimulation of reactive oxygen species (ROS) production with NADPH lead to an increase in tyrosine phosphorylation. Stimulation of ROS production with NADPH increased intracellular cyclic adenosine monophosphate (cAMP) levels in both caput and caudal epididymal cells, but only in caudal cells did cAMP stimulate tyrosine phosphorylation, in keeping with the NADPH results. On the basis of these findings we propose that tyrosine phosphorylation in rat spermatozoa is driven by ROS acting via 2 different but complementary mechanisms; O2-. stimulates tyrosine kinase activity indirectly through the elevation of intracellular cAMP while H2O2 acts directly on the kinase/phosphatase system, stimulating the former and inhibiting the latter. Zinc was examined as a potential regulator of this signal transduction cascade and was shown to suppress tyrosine phosphorylation in caput cells but to promote this activity in caudal spermatozoa, possibly through an inhibitory effect on tyrosine phosphatase activity. These results reveal the maturation of a redox-regulated, cAMP-mediated, signal transduction cascade during epididymal transit in the rat that is sensitive to zinc and plays a key role in the control of tyrosine phosphorylation events associated with capacitation.

  5. Disruption of GluA2 phosphorylation potentiates stress responsivity.

    Science.gov (United States)

    Ellis, Alexandra S; Fosnocht, Anne Q; Lucerne, Kelsey E; Briand, Lisa A

    2017-08-30

    Cocaine addiction is characterized by persistent craving and addicts frequently relapse even after long periods of abstinence. Exposure to stress can precipitate relapse in humans and rodents. Stress and drug use can lead to common alterations in synaptic plasticity and these commonalities may contribute to the ability of stress to elicit relapse. These common changes in synaptic plasticity are mediated, in part, by alterations in the trafficking and stabilization of AMPA receptors. Exposure to both cocaine and stress can lead to alterations in protein kinase C-mediated phosphorylation of GluA2 AMPA subunits and thus alter the trafficking of GluA2-containing AMPARs. However, it is not clear what role AMPAR trafficking plays in the interactions between stress and cocaine. The current study utilized a mouse with a point mutation within the GluA2 subunit c-terminus resulting in a disruption of PKC-mediated GluA2 phosphorylation to examine stress responsivity. Although no differences were seen in the response to a forced swim stress in naïve mice, GluA2 K882A knock-in mice exhibited an increased stress response following cocaine self-administration. Furthermore, we demonstrated that disrupting GluA2 phosphorylation increases vulnerability to stress-induced reinstatement of both cocaine seeking and cocaine-conditioned reward. Finally, GluA2 K882A knock-in mice exhibit an increased vulnerability to social defeat as indicated by increased social avoidance. Taken together these results indicate that disrupting GluA2 phosphorylation leads to increased responsivity to acute stress following cocaine exposure and increased vulnerability to chronic stress. These results highlight the GluA2 phosphorylation site as a novel target for the stress-related disorders. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Phosphorylation of the chromatin binding domain of KSHV LANA.

    Directory of Open Access Journals (Sweden)

    Crystal Woodard

    Full Text Available The Kaposi sarcoma associated herpesvirus (KSHV latency associated nuclear antigen (LANA is expressed in all KSHV associated malignancies and is essential for maintenance of KSHV genomes in infected cells. To identify kinases that are potentially capable of modifying LANA, in vitro phosphorylation assays were performed using an Epstein Barr virus plus LANA protein microarray and 268 human kinases purified in active form from yeast. Interestingly, of the Epstein-Barr virus proteins on the array, the EBNA1 protein had the most similar kinase profile to LANA. We focused on nuclear kinases and on the N-terminus of LANA (amino acids 1-329 that contains the LANA chromatin binding domain. Sixty-three nuclear kinases phosphorylated the LANA N-terminus. Twenty-four nuclear kinases phosphorylated a peptide covering the LANA chromatin binding domain (amino acids 3-21. Alanine mutations of serine 10 and threonine 14 abolish or severely diminish chromatin and histone binding by LANA. However, conversion of these residues to the phosphomimetic glutamic acid restored histone binding suggesting that phosphorylation of serine 10 and threonine 14 may modulate LANA function. Serine 10 and threonine 14 were validated as substrates of casein kinase 1, PIM1, GSK-3 and RSK3 kinases. Short-term treatment of transfected cells with inhibitors of these kinases found that only RSK inhibition reduced LANA interaction with endogenous histone H2B. Extended treatment of PEL cell cultures with RSK inhibitor caused a decrease in LANA protein levels associated with p21 induction and a loss of PEL cell viability. The data indicate that RSK phosphorylation affects both LANA accumulation and function.

  7. Phosphorylation regulates NCC stability and transporter activity in vivo.

    Science.gov (United States)

    Yang, Sung-Sen; Fang, Yu-Wei; Tseng, Min-Hua; Chu, Pei-Yi; Yu, I-Shing; Wu, Han-Chung; Lin, Shu-Wha; Chau, Tom; Uchida, Shinichi; Sasaki, Sei; Lin, Yuh-Feng; Sytwu, Huey-Kang; Lin, Shih-Hua

    2013-10-01

    A T60M mutation in the thiazide-sensitive sodium chloride cotransporter (NCC) is common in patients with Gitelman's syndrome (GS). This mutation prevents Ste20-related proline and alanine-rich kinase (SPAK)/oxidative stress responsive kinase-1 (OSR1)-mediated phosphorylation of NCC and alters NCC transporter activity in vitro. Here, we examined the physiologic effects of NCC phosphorylation in vivo using a novel Ncc T58M (human T60M) knock-in mouse model. Ncc(T58M/T58M) mice exhibited typical features of GS with a blunted response to thiazide diuretics. Despite expressing normal levels of Ncc mRNA, these mice had lower levels of total Ncc and p-Ncc protein that did not change with a low-salt diet that increased p-Spak. In contrast to wild-type Ncc, which localized to the apical membrane of distal convoluted tubule cells, T58M Ncc localized primarily to the cytosolic region and caused an increase in late distal convoluted tubule volume. In MDCK cells, exogenous expression of phosphorylation-defective NCC mutants reduced total protein expression levels and membrane stability. Furthermore, our analysis found diminished total urine NCC excretion in a cohort of GS patients with homozygous NCC T60M mutations. When Wnk4(D561A/+) mice, a model of pseudohypoaldosteronism type II expressing an activated Spak/Osr1-Ncc, were crossed with Ncc(T58M/T58M) mice, total Ncc and p-Ncc protein levels decreased and the GS phenotype persisted over the hypertensive phenotype. Overall, these data suggest that SPAK-mediated phosphorylation of NCC at T60 regulates NCC stability and function, and defective phosphorylation at this residue corrects the phenotype of pseudohypoaldosteronism type II.

  8. Proteomic analysis of tyrosine phosphorylation during human liver transplantation

    Directory of Open Access Journals (Sweden)

    Boutros Tarek

    2007-01-01

    Full Text Available Abstract Background Ischemia-reperfusion (I/R causes a dramatic reprogramming of cell metabolism during liver transplantation and can be linked to an alteration of the phosphorylation level of several cellular proteins. Over the past two decades, it became clear that tyrosine phosphorylation plays a pivotal role in a variety of important signalling pathways and was linked to a wide spectrum of diseases. Functional profiling of the tyrosine phosphoproteome during liver transplantation is therefore of great biological significance and is likely to lead to the identification of novel targets for drug discovery and provide a basis for novel therapeutic strategies. Results Using liver biopsies collected during the early phases of organ procurement and transplantation, we aimed at characterizing the global patterns of tyrosine phosphorylation during hepatic I/R. A proteomic approach, based on the purification of tyrosine phosphorylated proteins followed by their identification using mass spectrometry, allowed us to identify Nck-1, a SH2/SH3 adaptor, as a potential regulator of I/R injury. Using immunoblot, cell fractionation and immunohistochemistry, we demonstrate that Nck-1 phosphorylation, expression and localization were affected in liver tissue upon I/R. In addition, mass spectrometry identification of Nck-1 binding partners during the course of the transplantation also suggested a dynamic interaction between Nck-1 and actin during I/R. Conclusion Taken together, our data suggest that Nck-1 may play a role in I/R-induced actin reorganization, which was previously reported to be detrimental for the hepatocytes of the transplanted graft. Nck-1 could therefore represent a target of choice for the design of new organ preservation strategies, which could consequently help to reduce post-reperfusion liver damages and improve transplantation outcomes.

  9. Matrix Product Operators, Matrix Product States, and ab initio Density Matrix Renormalization Group algorithms

    CERN Document Server

    Chan, Garnet Kin-Lic; Nakatani, Naoki; Li, Zhendong; White, Steven R

    2016-01-01

    Current descriptions of the ab initio DMRG algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab-initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational par...

  10. Phosphorylation of acidic ribosomal proteins from rabbit reticulocytes by a ribosome-associated casein kinase

    DEFF Research Database (Denmark)

    Issinger, O G

    1977-01-01

    Two acidic proteins from 80-S ribosomes were isolated and purified to homogeneity. The purified acidic proteins could be phosphorylated by casein kinase using [gamma-32P]ATP and [gamma-32P]GTP as a phosphoryl donor. The proteins became phosphorylated in situ, too. Sodium dodecyl sulfate polyacryl......Two acidic proteins from 80-S ribosomes were isolated and purified to homogeneity. The purified acidic proteins could be phosphorylated by casein kinase using [gamma-32P]ATP and [gamma-32P]GTP as a phosphoryl donor. The proteins became phosphorylated in situ, too. Sodium dodecyl sulfate...

  11. Ceramic matrix composite article and process of fabricating a ceramic matrix composite article

    Science.gov (United States)

    Cairo, Ronald Robert; DiMascio, Paul Stephen; Parolini, Jason Robert

    2016-01-12

    A ceramic matrix composite article and a process of fabricating a ceramic matrix composite are disclosed. The ceramic matrix composite article includes a matrix distribution pattern formed by a manifold and ceramic matrix composite plies laid up on the matrix distribution pattern, includes the manifold, or a combination thereof. The manifold includes one or more matrix distribution channels operably connected to a delivery interface, the delivery interface configured for providing matrix material to one or more of the ceramic matrix composite plies. The process includes providing the manifold, forming the matrix distribution pattern by transporting the matrix material through the manifold, and contacting the ceramic matrix composite plies with the matrix material.

  12. Matrix stiffness-mediated effects on stemness characteristics occurring in HCC cells.

    Science.gov (United States)

    You, Yang; Zheng, Qiongdan; Dong, Yinying; Xie, Xiaoying; Wang, Yaohui; Wu, Sifan; Zhang, Lan; Wang, Yingcong; Xue, Tongchun; Wang, Zhiming; Chen, Rongxin; Wang, Yanhong; Cui, Jiefeng; Ren, Zhenggang

    2016-05-31

    Matrix stiffness as an important physical attribute of extracellular matrix exerts significant impacts on biological behaviors of cancer cells such as growth, proliferation, motility, metabolism and invasion. However, its influence on cancer stemness still remains elusive. Here, we explore whether matrix stiffness-mediated effects on stemness characteristics occur in HCC cells. As the substrate stiffness increased, HCC cells exhibited high proportion of cells with CD133(+)/EpCAM(+), high expression levels of CD133, EpCAM, Nanog and SOX2, greater self-renewing ability and oxaliplatin resistance. Simultaneously, their phosphorylation levels of Akt and mTOR, as well as p-4E-BP and SOX2 expressions were also obviously upregulated. Conversely, knockdown of integrin β1 partially attenuated higher stiffness-mediated stemness characteristics in HCC cells, and reversed the phosphorylation levels of Akt and mTOR, and expressions of p-4E-BP and SOX2, suggesting that integrin β1 may deliver higher stiffness signal into HCC cells and activate mTOR signaling pathway. Additionally, mTOR inhibitor suppressed the mTOR phosphorylation level and expression levels of p-4E-BP and SOX2 in HCC cells grown on higher stiffness substrate, as well as depressed their stemness properties significantly, favoring a regulating role of mTOR signaling pathway in matrix stiffness-mediated effects on stemness. In summary, matrix stiffness may be involved in the process of stemness regulation via activating integrin β1/Akt/mTOR/SOX2 signaling pathway. To the best of our knowledge, this study first reveals a novel regulating pathway to direct the stemness characteristics in HCC cells.

  13. The effect of stromelysin-1 (MMP-3) on non-collagenous extracellular matrix proteins of demineralized dentin and the adhesive properties of restorative resins.

    Science.gov (United States)

    Boukpessi, T; Menashi, S; Camoin, L; Tencate, J M; Goldberg, M; Chaussain-Miller, C

    2008-11-01

    Dentin non-collagenous matrix components (NCPs) are structural proteins involved in the formation, the architecture and the mineralization of the extracellular matrix (ECM). We investigated here how recombinant metalloproteinase stromelysin-1, also termed MMP-3, initiates the release of ECM molecules from artificially demineralized human dentin. Analysis of the supernatants by Western blotting reveals that MMP-3 extracts PGs (decorin, biglycan), and also a series of phosphorylated proteins: dentin sialoprotein (DSP), osteopontin (OPN), bone sialoprotein (BSP) and MEPE, but neither dentin matrix protein-1 (DMP1), another member of the SIBLING family, nor osteocalcin (OC), a non-phosphorylated matrix molecule. After treatment of dentin surfaces by MMP-3, scanning electron microscope (SEM) examination of resin replica shows an increased penetration of the resin into the dentin tubules when compared to surfaces only treated by demineralizing solutions. This preclinical investigation suggests that MMP-3 may be used to improve the adhesive properties of restorative materials.

  14. Matrix Theory of pp Waves

    CERN Document Server

    Michelson, J

    2004-01-01

    The Matrix Theory that has been proposed for various pp wave backgrounds is discussed. Particular emphasis is on the existence of novel nontrivial supersymmetric solutions of the Matrix Theory. These correspond to branes of various shapes (ellipsoidal, paraboloidal, and possibly hyperboloidal) that are unexpected from previous studies of branes in pp wave geometries.

  15. How to Study a Matrix

    Science.gov (United States)

    Jairam, Dharmananda; Kiewra, Kenneth A.; Kauffman, Douglas F.; Zhao, Ruomeng

    2012-01-01

    This study investigated how best to study a matrix. Fifty-three participants studied a matrix topically (1 column at a time), categorically (1 row at a time), or in a unified way (all at once). Results revealed that categorical and unified study produced higher: (a) performance on relationship and fact tests, (b) study material satisfaction, and…

  16. Machining of Metal Matrix Composites

    CERN Document Server

    2012-01-01

    Machining of Metal Matrix Composites provides the fundamentals and recent advances in the study of machining of metal matrix composites (MMCs). Each chapter is written by an international expert in this important field of research. Machining of Metal Matrix Composites gives the reader information on machining of MMCs with a special emphasis on aluminium matrix composites. Chapter 1 provides the mechanics and modelling of chip formation for traditional machining processes. Chapter 2 is dedicated to surface integrity when machining MMCs. Chapter 3 describes the machinability aspects of MMCs. Chapter 4 contains information on traditional machining processes and Chapter 5 is dedicated to the grinding of MMCs. Chapter 6 describes the dry cutting of MMCs with SiC particulate reinforcement. Finally, Chapter 7 is dedicated to computational methods and optimization in the machining of MMCs. Machining of Metal Matrix Composites can serve as a useful reference for academics, manufacturing and materials researchers, manu...

  17. Matrix Model Approach to Cosmology

    CERN Document Server

    Chaney, A; Stern, A

    2015-01-01

    We perform a systematic search for rotationally invariant cosmological solutions to matrix models, or more specifically the bosonic sector of Lorentzian IKKT-type matrix models, in dimensions $d$ less than ten, specifically $d=3$ and $d=5$. After taking a continuum (or commutative) limit they yield $d-1$ dimensional space-time surfaces, with an attached Poisson structure, which can be associated with closed, open or static cosmologies. For $d=3$, we obtain recursion relations from which it is possible to generate rotationally invariant matrix solutions which yield open universes in the continuum limit. Specific examples of matrix solutions have also been found which are associated with closed and static two-dimensional space-times in the continuum limit. The solutions provide for a matrix resolution of cosmological singularities. The commutative limit reveals other desirable features, such as a solution describing a smooth transition from an initial inflation to a noninflationary era. Many of the $d=3$ soluti...

  18. Matrix convolution operators on groups

    CERN Document Server

    Chu, Cho-Ho

    2008-01-01

    In the last decade, convolution operators of matrix functions have received unusual attention due to their diverse applications. This monograph presents some new developments in the spectral theory of these operators. The setting is the Lp spaces of matrix-valued functions on locally compact groups. The focus is on the spectra and eigenspaces of convolution operators on these spaces, defined by matrix-valued measures. Among various spectral results, the L2-spectrum of such an operator is completely determined and as an application, the spectrum of a discrete Laplacian on a homogeneous graph is computed using this result. The contractivity properties of matrix convolution semigroups are studied and applications to harmonic functions on Lie groups and Riemannian symmetric spaces are discussed. An interesting feature is the presence of Jordan algebraic structures in matrix-harmonic functions.

  19. Mitochondrial diaphorases as NAD+ donors to segments of the citric acid cycle that support substrate-level phosphorylation yielding ATP during respiratory inhibition

    Science.gov (United States)

    Kiss, Gergely; Konrad, Csaba; Pour-Ghaz, Issa; Mansour, Josef J.; Németh, Beáta; Starkov, Anatoly A.; Adam-Vizi, Vera; Chinopoulos, Christos

    2014-01-01

    Substrate-level phosphorylation mediated by succinyl-CoA ligase in the mitochondrial matrix produces high-energy phosphates in the absence of oxidative phosphorylation. Furthermore, when the electron transport chain is dysfunctional, provision of succinyl-CoA by the α-ketoglutarate dehydrogenase complex (KGDHC) is crucial for maintaining the function of succinyl-CoA ligase yielding ATP, preventing the adenine nucleotide translocase from reversing. We addressed the source of the NAD+ supply for KGDHC under anoxic conditions and inhibition of complex I. Using pharmacologic tools and specific substrates and by examining tissues from pigeon liver exhibiting no diaphorase activity, we showed that mitochondrial diaphorases in the mouse liver contribute up to 81% to the NAD+ pool during respiratory inhibition. Under these conditions, KGDHC's function, essential for the provision of succinyl-CoA to succinyl-CoA ligase, is supported by NAD+ derived from diaphorases. Through this process, diaphorases contribute to the maintenance of substrate-level phosphorylation during respiratory inhibition, which is manifested in the forward operation of adenine nucleotide translocase. Finally, we show that reoxidation of the reducible substrates for the diaphorases is mediated by complex III of the respiratory chain.—Kiss, G., Konrad, C., Pour-Ghaz, I., Mansour, J. J., Németh, B., Starkov, A. A., Adam-Vizi, V., Chinopoulos, C. Mitochondrial diaphorases as NAD+ donors to segments of the citric acid cycle that support substrate-level phosphorylation yielding ATP during respiratory inhibition. PMID:24391134

  20. Molecular mechanism of APC/C activation by mitotic phosphorylation.

    Science.gov (United States)

    Zhang, Suyang; Chang, Leifu; Alfieri, Claudio; Zhang, Ziguo; Yang, Jing; Maslen, Sarah; Skehel, Mark; Barford, David

    2016-05-12

    In eukaryotes, the anaphase-promoting complex (APC/C, also known as the cyclosome) regulates the ubiquitin-dependent proteolysis of specific cell-cycle proteins to coordinate chromosome segregation in mitosis and entry into the G1 phase. The catalytic activity of the APC/C and its ability to specify the destruction of particular proteins at different phases of the cell cycle are controlled by its interaction with two structurally related coactivator subunits, Cdc20 and Cdh1. Coactivators recognize substrate degrons, and enhance the affinity of the APC/C for its cognate E2 (refs 4-6). During mitosis, cyclin-dependent kinase (Cdk) and polo-like kinase (Plk) control Cdc20- and Cdh1-mediated activation of the APC/C. Hyperphosphorylation of APC/C subunits, notably Apc1 and Apc3, is required for Cdc20 to activate the APC/C, whereas phosphorylation of Cdh1 prevents its association with the APC/C. Since both coactivators associate with the APC/C through their common C-box and Ile-Arg tail motifs, the mechanism underlying this differential regulation is unclear, as is the role of specific APC/C phosphorylation sites. Here, using cryo-electron microscopy and biochemical analysis, we define the molecular basis of how phosphorylation of human APC/C allows for its control by Cdc20. An auto-inhibitory segment of Apc1 acts as a molecular switch that in apo unphosphorylated APC/C interacts with the C-box binding site and obstructs engagement of Cdc20. Phosphorylation of the auto-inhibitory segment displaces it from the C-box-binding site. Efficient phosphorylation of the auto-inhibitory segment, and thus relief of auto-inhibition, requires the recruitment of Cdk-cyclin in complex with a Cdk regulatory subunit (Cks) to a hyperphosphorylated loop of Apc3. We also find that the small-molecule inhibitor, tosyl-l-arginine methyl ester, preferentially suppresses APC/C(Cdc20) rather than APC/C(Cdh1), and interacts with the binding sites of both the C-box and Ile-Arg tail motifs. Our

  1. HSP20 phosphorylation and airway smooth muscle relaxation

    Directory of Open Access Journals (Sweden)

    Mariam Ba

    2009-06-01

    Full Text Available Mariam Ba1, Cherie A Singer1, Manoj Tyagi2, Colleen Brophy3, Josh E Baker4, Christine Cremo4, Andrew Halayko5, William T Gerthoffer21Department of Pharmacology, University of Nevada School of Medicine, Reno, NV, USA; 2Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL, USA; 3Harrington Department of Biochemistry, Arizona State University, Tempe, AZ, USA; 4Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA; 5Departments of Physiology and Internal Medicine, University of Manitoba, Winnipeg, MB, CanadaAbstract: HSP20 (HSPB6 is a small heat shock protein expressed in smooth muscles that is hypothesized to inhibit contraction when phosphorylated by cAMP-dependent protein kinase. To investigate this hypothesis in airway smooth muscle (ASM we showed that HSP20 was constitutively expressed as well as being inducible in cultured hASM cells by treatment with 1 µM isoproterenol or 10 µM salmeterol. In contrast, a mixture of proinflammatory mediators (interleukin-1β, tumor necrosis factor α, and interferon γ inhibited expression of HSP20 by about 50% in 48 hours. To determine whether phosphorylation of HSP20 is sufficient to induce relaxation, canine tracheal smooth muscle was treated with a cell permeant phosphopeptide that mimics the phosphorylation of HSP20. The HSP20 phosphopeptide antagonized carbacholinduced contraction by 60% with no change in myosin light chain phosphorylation. Recombinant full length HSP20 inhibited skeletal actin binding to smooth muscle myosin subfragment 1 (S1, and recombinant cell permeant TAT-HSP20 S16D mutant reduced F-actin filaments in cultured hASM cells. Carbachol stimulation of canine tracheal smooth muscle tissue caused redistribution of HSP20 from large macromolecular complexes (200–500 kDa to smaller complexes (<60 kDa. The results are consistent with HSP20 expression and macromolecular structure being dynamically regulated in airway

  2. Phosphorylation of rat aquaporin-4 at Ser(111) is not required for channel gating

    DEFF Research Database (Denmark)

    Assentoft, Mette; Kaptan, Shreyas; Fenton, Robert A

    2013-01-01

    of a phosphorylation of AQP4.Ser(111) recorded no phosphorylation-induced change in water permeability. A phospho-specific antibody, exclusively recognizing AQP4 when phosphorylated on Ser(111) , failed to detect phosphorylation in cell lysate of rat brain stimulated by conditions proposed to induce phosphorylation...... is therefore of therapeutic interest. Phosphorylation of some aquaporins has been proposed to regulate their water permeability via gating of the channel itself. Protein kinase (PK)-dependent phosphorylation of Ser(111) has been reported to increase the water permeability of AQP4 expressed in an astrocytic...... cell line. This possibility was, however, questioned based on the crystal structure of the human AQP4. Our study aimed to resolve if Ser(111) was indeed a site involved in phosphorylation-mediated gating of AQP4. The water permeability of AQP4-expressing Xenopus oocytes was not altered by a range...

  3. The Self-catalytic Esterification Reaction of O-Phosphoryl Serine Derivative

    Institute of Scientific and Technical Information of China (English)

    Jin Tang DU; Yan Mei LI; Zhong Zhou CHEN; Shi Zhong LUO; Yu Fen ZHAO

    2005-01-01

    O-Phosphoryl serine derivative can perform self-catalytic esterification reaction in the mixture of CH3OH and CHCl3 at the room temperature. The phosphoryl group participation was the key step of the esterification. This type of reactions were proposed through an intermediate of mixed phosphoric-carboxylic anhydride that might provide a clue to the function of the phosphoryl group in the phosphorylated enzymes and in the prebiotic synthesis of protein.

  4. Phospho.ELM: A database of experimentally verified phosphorylation sites in eukaryotic proteins

    DEFF Research Database (Denmark)

    Diella, F.; Cameron, S.; Gemund, C.

    2004-01-01

    need for an accurate database dedicated to phosphorylation to provide easily retrievable information on phosphoproteins. Description: Phospho. ELM http://phospho.elm.eu.org is a new resource containing experimentally verified phosphorylation sites manually curated from the literature and is developed...... to be phosphorylated by cellular kinases. Additional annotation includes literature references, subcellular compartment, tissue distribution, and information about the signaling pathways involved as well as links to the molecular interaction database MINT. Phospho. ELM version 2.0 contains 1703 phosphorylation site...

  5. Dynamic phosphorylation patterns of RNA polymerase II CTD during transcription.

    Science.gov (United States)

    Heidemann, Martin; Hintermair, Corinna; Voß, Kirsten; Eick, Dirk

    2013-01-01

    The eukaryotic RNA polymerase II (RNAPII) catalyzes the transcription of all protein encoding genes and is also responsible for the generation of small regulatory RNAs. RNAPII has evolved a unique domain composed of heptapeptide repeats with the consensus sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 at the C-terminus (CTD) of its largest subunit (Rpb1). Dynamic phosphorylation patterns of serine residues in CTD during gene transcription coordinate the recruitment of factors to the elongating RNAPII and to the nascent transcript. Recent studies identified threonine 4 and tyrosine 1 as new CTD modifications and thereby expanded the "CTD code". In this review, we focus on CTD phosphorylation and its function in the RNAPII transcription cycle. We also discuss in detail the limitations of the phosphospecific CTD antibodies, which are used in all studies. This article is part of a Special Issue entitled: RNA Polymerase II Transcript Elongation.

  6. Oxygen sensing requires mitochondrial ROS but not oxidative phosphorylation.

    Science.gov (United States)

    Brunelle, Joslyn K; Bell, Eric L; Quesada, Nancy M; Vercauteren, Kristel; Tiranti, Valeria; Zeviani, Massimo; Scarpulla, Richard C; Chandel, Navdeep S

    2005-06-01

    Mammalian cells detect decreases in oxygen concentrations to activate a variety of responses that help cells adapt to low oxygen levels (hypoxia). One such response is stabilization of the protein HIF-1 alpha, a component of the transcription factor HIF-1. Here we show that a small interfering RNA (siRNA) against the Rieske iron-sulfur protein of mitochondrial complex III prevents the hypoxic stabilization of HIF-1 alpha protein. Fibroblasts from a patient with Leigh's syndrome, which display residual levels of electron transport activity and are incompetent in oxidative phosphorylation, stabilize HIF-1 alpha during hypoxia. The expression of glutathione peroxidase or catalase, but not superoxide dismutase 1 or 2, prevents the hypoxic stabilization of HIF-1 alpha. These findings provide genetic evidence that oxygen sensing is dependent on mitochondrial-generated reactive oxygen species (ROS) but independent of oxidative phosphorylation.

  7. Random-coil chemical shifts of phosphorylated amino acids

    Energy Technology Data Exchange (ETDEWEB)

    Bienkiewicz, Ewa A.; Lumb, Kevin J. [Colorado State University, Department of Biochemistry and Molecular Biology (United States)

    1999-11-15

    The {sup 1}H, {sup 13}C, {sup 15}N and {sup 31} P random-coil chemical shifts and phosphate pK{sub a} values of the phosphorylated amino acids pSer, pThr and pTyr in the protected peptide Ac-Gly-Gly-X-Gly-Gly-NH{sub 2} have been obtained in water at 25 deg. C over the pH range 2 to 9. Analysis of ROESY spectra indicates that the peptides are unstructured. Phosphorylation induces changes in random-coil chemical shifts, some of which are comparable to those caused by secondary structure formation, and are therefore significant in structural analyses based on the chemical shift.

  8. GABAB receptor phosphorylation regulates KCTD12-induced K+ current desensitization

    DEFF Research Database (Denmark)

    Adelfinger, L; Turecek, R; Ivankova, K

    2014-01-01

    released from the G-protein. Receptor-activated K+ currents desensitize in the sustained presence of agonist to avoid excessive effects on neuronal activity. Desensitization of K+ currents integrates distinct mechanistic underpinnings. GABAB receptor activity reduces protein kinase-A activity, which...... reduces phosphorylation of serine-892 in GABAB2 and promotes receptor degradation. This form of desensitization operates on the time scale of several minutes to hours. A faster form of desensitization is induced by the auxiliary subunit KCTD12, which interferes with channel activation by binding to the G......-protein βγ subunits. Here we show that the two mechanisms of desensitization influence each other. Serine-892 phosphorylation in heterologous cells rearranges KCTD12 at the receptor and slows KCTD12-induced desensitization. Likewise, protein kinase-A activation in hippocampal neurons slows fast...

  9. ERK phosphorylation regulates sleep and plasticity in Drosophila.

    Directory of Open Access Journals (Sweden)

    William M Vanderheyden

    Full Text Available Given the relationship between sleep and plasticity, we examined the role of Extracellular signal-regulated kinase (ERK in regulating baseline sleep, and modulating the response to waking experience. Both sleep deprivation and social enrichment increase ERK phosphorylation in wild-type flies. The effects of both sleep deprivation and social enrichment on structural plasticity in the LNvs can be recapitulated by expressing an active version of ERK (UAS-ERK(SEM pan-neuronally in the adult fly using GeneSwitch (Gsw Gsw-elav-GAL4. Conversely, disrupting ERK reduces sleep and prevents both the behavioral and structural plasticity normally induced by social enrichment. Finally, using transgenic flies carrying a cAMP response Element (CRE-luciferase reporter we show that activating ERK enhances CRE-Luc activity while disrupting ERK reduces it. These data suggest that ERK phosphorylation is an important mediator in transducing waking experience into sleep.

  10. Reactions of. cap alpha. -phosphorylated carbonyl compounds with amino alcohols

    Energy Technology Data Exchange (ETDEWEB)

    Moskva, V.V.; Sitdikova, T.Sh.; Zykova, T.V.; Alparova, M.V.; Shagvaleev, F.Sh.

    1986-10-20

    2-Aminoethanol reacts with carbonyl compounds with the formation, depending on the structure of the latter, either of a mixture of azomethines and oxazolidines, or of only azomethines. In the development of investigations on the reactivity of ..cap alpha..-phosphorylated carbonyl compounds the authors studied the reactions of a number of amino alcohols with phosphorylated acetaldehyde and acetone. In both cases they observed the formation of compounds of enamine structure, oxazolidines and azomethines were not observed. By means of NMR spectroscopy they established clearly the formation of the E-isomeric products. The /sup 1/H, /sup 31/P, and /sup 13/C NMR spectra were recorded on a WP-80 spectrometer. Chemical shifts of protons and /sup 13/C nuclei are given relative to TMS, and phosphorus nuclei relative to orthophosphoric acid.

  11. Detection of Echinoderm Microtubule Associated Protein Like 4-Anaplastic Lymphoma Kinase Fusion Genes in Non-small Cell Lung Cancer Clinical Samples by a Real-time Quantitative Reverse Transcription Polymerase Chain Reaction Method.

    Science.gov (United States)

    Zhao, Jing; Zhao, Jin-Yin; Chen, Zhi-Xia; Zhong, Wei; Li, Long-Yun; Liu, Li-Cheng; Hu, Xiao-Xu; Chen, Wei-Jun; Wang, Meng-Zhao

    2016-12-20

    Objective To establish a real-time quantitative reverse transcription polymerase chain reaction assay (qRT-PCR) for the rapid, sensitive, and specific detection of echinoderm microtubule associated protein like 4-anaplastic lymphoma kinase (EML4-ALK) fusion genes in non-small cell lung cancer. Methods The specific primers for the four variants of EML4-ALK fusion genes (V1, V2, V3a, and V3b) and Taqman fluorescence probes for the detection of the target sequences were carefully designed by the Primer Premier 5.0 software. Then, using pseudovirus containing EML4-ALK fusion genes variants (V1, V2, V3a, and V3b) as the study objects, we further analyzed the lower limit, sensitivity, and specificity of this method. Finally, 50 clinical samples, including 3 ALK-fluorescence in situ hybridization (FISH) positive specimens, were collected and used to detect EML4-ALK fusion genes using this method. Results The lower limit of this method for the detection of EML4-ALK fusion genes was 10 copies/μl if no interference of background RNA existed. Regarding the method's sensitivity, the detection resolution was as high as 1% and 0.5% in the background of 500 and 5000 copies/μl wild-type ALK gene, respectively. Regarding the method's specificity, no non-specific amplification was found when it was used to detect EML4-ALK fusion genes in leukocyte and plasma RNA samples from healthy volunteers. Among the 50 clinical samples, 47 ALK-FISH negative samples were also negative. Among 3 ALK-FISH positive samples, 2 cases were detected positive using this method, but another was not detected because of the failure of RNA extraction. Conclusion The proposed qRT-PCR assay for the detection of EML4-ALK fusion genes is rapid, simple, sensitive, and specific, which is deserved to be validated and widely used in clinical settings.

  12. Manufacturing Titanium Metal Matrix Composites by Consolidating Matrix Coated Fibres

    Institute of Scientific and Technical Information of China (English)

    Hua-Xin PENG

    2005-01-01

    Titanium metal matrix composites (TiMMCs) reinforced by continuous silicon carbide fibres are being developed for aerospace applications. TiMMCs manufactured by the consolidation of matrix-coated fibre (MCF) method offer optimum properties because of the resulting uniform fibre distribution, minimum fibre damage and fibre volume fraction control. In this paper, the consolidation of Ti-6Al-4V matrix-coated SiC fibres during vacuum hot pressing has been investigated. Experiments were carried out on multi-ply MCFs under vacuum hot pressing (VHP). In contrast to most of existing studies, the fibre arrangement has been carefully controlled either in square or hexagonal arraysthroughout the consolidated sample. This has enabled the dynamic consolidation behaviour of MCFs to be demonstrated by eliminating the fibre re-arrangement during the VHP process. The microstructural evolution of the matrix coating was reported and the deformation mechanisms involved were discussed.

  13. Structure of a bacterial enzyme regulated by phosphorylation, isocitrate dehydrogenase.

    OpenAIRE

    1989-01-01

    The structure of isocitrate dehydrogenase [threo-DS-isocitrate: NADP+ oxidoreductase (decarboxylating), EC 1.1.1.42] from Escherichia coli has been solved and refined at 2.5 A resolution and is topologically different from that of any other dehydrogenase. This enzyme, a dimer of identical 416-residue subunits, is inactivated by phosphorylation at Ser-113, which lies at the edge of an interdomain pocket that also contains many residues conserved between isocitrate dehydrogenase and isopropylma...

  14. Snapshot of a phosphorylated substrate intermediate by kinetic crystallography

    OpenAIRE

    Käck, Helena; Gibson, Katharine J.; Lindqvist, Ylva; Schneider, Gunter

    1998-01-01

    The ATP-dependent enzyme dethiobiotin synthetase from Escherichia coli catalyses the formation of dethiobiotin from CO2 and 7,8-diaminopelargonic acid. The reaction is initiated by the formation of a carbamate and proceeds through a phosphorylated intermediate, a mixed carbamic phosphoric anhydride. Here, we report the crystal structures at 1.9- and 1.6-Å resolution, respectively, of the enzyme–MgATP–diaminopelargonic acid and enzyme–MgADP–carbamic–phosphoric acid anhydride complexes, observe...

  15. Regulation of PCNA Function by Tyrosine Phosphorylation in Prostate Cancer

    Science.gov (United States)

    2012-10-01

    prostate cancer. 15. SUBJECT TERMS PCNA, Tyrosine Phosphorylation, Prostate Cancer 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT...directed peptide is a rational strategy to target proliferation-competent PCNA, limitations associated with peptides as a therapeutic agent, particularly...radical prostatectomy: Where have we been? Where are we going? Urol Oncol 2007;25:11–8. 2. Moldovan GL, Pfander B, Jentsch S. PCNA, the maestro of the

  16. New pole placement algorithm - Polynomial matrix approach

    Science.gov (United States)

    Shafai, B.; Keel, L. H.

    1990-01-01

    A simple and direct pole-placement algorithm is introduced for dynamical systems having a block companion matrix A. The algorithm utilizes well-established properties of matrix polynomials. Pole placement is achieved by appropriately assigning coefficient matrices of the corresponding matrix polynomial. This involves only matrix additions and multiplications without requiring matrix inversion. A numerical example is given for the purpose of illustration.

  17. High temperature polymer matrix composites

    Science.gov (United States)

    Serafini, Tito T. (Editor)

    1987-01-01

    These are the proceedings of the High Temperature Polymer Matrix Composites Conference held at the NASA Lewis Research Center on March 16 to 18, 1983. The purpose of the conference is to provide scientists and engineers working in the field of high temperature polymer matrix composites an opportunity to review, exchange, and assess the latest developments in this rapidly expanding area of materials technology. Technical papers are presented in the following areas: (1) matrix development; (2) adhesive development; (3) Characterization; (4) environmental effects; and (5) applications.

  18. Matrix Elements for Hylleraas CI

    Science.gov (United States)

    Harris, Frank E.

    The limitation to at most a single interelectron distance in individual configurations of a Hylleraas-type multiconfiguration wave function restricts significantly the types of integrals occurring in matrix elements for energy calculations, but even then if the formulation is not handled efficiently the angular parts of these integrals escalate to create expressions of great complexity. This presentation reviews ways in which the angular-momentum calculus can be employed to systematize and simplify the matrix element formulas, particularly those for the kinetic-energy matrix elements.

  19. Large-scale analysis of phosphorylation site occupancy in eukaryotic proteins

    DEFF Research Database (Denmark)

    Rao, R Shyama Prasad; Møller, Ian Max

    2012-01-01

    maximum randomness. An analysis of phosphorylation motifs indicated that just 40 motifs and a much lower number of associated kinases might account for nearly 50% of the known phosphorylations in eukaryotic proteins. Our results provide a broad picture of the phosphorylation sites in eukaryotic proteins....

  20. Effect of some organic solvents on oxidative phosphorylation in rat liver mitochondria

    DEFF Research Database (Denmark)

    Syed, Muzeeb; Skonberg, Christian; Hansen, Steen Honoré

    2013-01-01

    The effect of acetone, acetonitrile, dimethyl sulfoxide (DMSO), ethanol and methanol on oxidative phosphorylation (ATP synthesis) in rat liver mitochondria has been studied. All the organic solvents inhibited the oxidative phosphorylation in a concentration dependent manner, but with differences...... on oxidative phosphorylation in mitochondria should therefore include the use of relevant concentrations of the organic solvent in order to validate the contribution....

  1. Absolute Phosphorylation Stoichiometry Analysis by Motif-Targeting Quantitative Mass Spectrometry.

    Science.gov (United States)

    Tsai, Chia-Feng; Ku, Wei-Chi; Chen, Yu-Ju; Ishihama, Yasushi

    2017-01-01

    Direct measurement of site-specific phosphorylation stoichiometry can unambiguously distinguish whether the degree of phosphorylation is regulated by upstream kinase/phosphatase activity or by transcriptional regulation to alter protein expression level. Here, we describe a motif-targeting quantitative proteomic approach that integrates dephosphorylation, isotope tag labeling, and enzymatic kinase reaction for large-scale phosphorylation stoichiometry measurement of the human proteome.

  2. Roles of “junk phosphorylation” in modulating biomolecular association of phosphorylated proteins?

    DEFF Research Database (Denmark)

    Tan, Chris Soon Heng; Jørgensen, Claus; Linding, Rune

    2010-01-01

    Protein phosphorylation dynamically regulates cellular activities in response to environmental cues. Sequence conservation analysis of recent proteome-wide phosphorylation data revealed that many previously unidentified phosphorylation sites are not well-conserved leading to the proposal that man...... evolutionary approaches to interpret physiological important sites....

  3. Detection of tyrosine phosphorylated proteins in trichinella spiralis L1 larvae

    Directory of Open Access Journals (Sweden)

    Allegretti S.

    2001-06-01

    Full Text Available Western-blotting analysis showed the presence of tyrosine phosphorylated proteins in crude extracts of T. spiralis larvae and these phosphorylated proteins were located by immunofluorescence on the striations of the larval cuticle. The patterns of phosphorylated proteins were modified when larvae were incubated with bile.

  4. NetPhosYeast: prediction of protein phosphorylation sites in yeast

    DEFF Research Database (Denmark)

    Ingrell, C.R.; Miller, Martin Lee; Jensen, O.N.

    2007-01-01

    We here present a neural network-based method for the prediction of protein phosphorylation sites in yeast-an important model organism for basic research. Existing protein phosphorylation site predictors are primarily based on mammalian data and show reduced sensitivity on yeast phosphorylation s...

  5. Spatial proximity statistics suggest a regulatory role of protein phosphorylation on compound binding.

    Science.gov (United States)

    Korkuć, Paula; Walther, Dirk

    2016-05-01

    Phosphorylation is an important post-translational modification that regulates protein function by the attachment of negatively charged phosphate groups to phosphorylatable amino acid residues. As a mode of action, an influence of phosphorylation on the binding of compounds to proteins has been discussed and described for a number of proteins in the literature. However, a systematic statistical survey probing for enriched phosphorylation sites close to compound binding sites in support of this notion and with properly chosen random reference distributions has not been presented yet. Using high-resolution protein structures from the Protein Data Bank including their co-crystallized non-covalently bound compounds and experimentally determined phosphorylation sites, we analyzed the pairwise distance distributions of phosphorylation and compound binding sites on protein surfaces. We found that phosphorylation sites are indeed located at significantly closer distances to compounds than expected by chance holding true specifically also for the subset of compound binding sites serving as catalytic sites of metabolic reactions. This tendency was particularly evident when treating phosphorylation sites as collective sets supporting the relevance of phosphorylation hotspots. Interestingly, phosphorylation sites were found to be closer to negatively charged than to positively charged compounds suggesting a stronger modulation of the binding of negatively charged compounds in dependence on phosphorylation status than on positively charged compounds. The enrichment of phosphorylation sites near compound binding sites confirms a regulatory role of phosphorylation in compound binding and provides a solid statistical basis for the literature-reported selected events.

  6. Phosphorylation of the Na+,K+-ATPase and the H+,K+-ATPase

    DEFF Research Database (Denmark)

    Poulsen, Hanne; Morth, Jens Preben; Jensen, Jan Egebjerg;

    2010-01-01

    Phosphorylation is a widely used, reversible means of regulating enzymatic activity. Among the important phosphorylation targets are the Na(+),K(+)- and H(+),K(+)-ATPases that pump ions against their chemical gradients to uphold ionic concentration differences over the plasma membrane. The two...... as supported by electrophysiological results presented here. We further review the other proposed pump phosphorylations....

  7. Synaptic Activation of Ribosomal Protein S6 Phosphorylation Occurs Locally in Activated Dendritic Domains

    Science.gov (United States)

    Pirbhoy, Patricia Salgado; Farris, Shannon; Steward, Oswald

    2016-01-01

    Previous studies have shown that induction of long-term potentiation (LTP) induces phosphorylation of ribosomal protein S6 (rpS6) in postsynaptic neurons, but the functional significance of rpS6 phosphorylation is poorly understood. Here, we show that synaptic stimulation that induces perforant path LTP triggers phosphorylation of rpS6 (p-rpS6)…

  8. Coilin phosphorylation mediates interaction with SMN and SmB'.

    Science.gov (United States)

    Toyota, Cory G; Davis, Misty D; Cosman, Angela M; Hebert, Michael D

    2010-04-01

    Cajal bodies (CBs) are subnuclear domains that participate in spliceosomal small nuclear ribonucleoprotein (snRNP) biogenesis and play a part in the assembly of the spliceosomal complex. The CB marker protein, coilin, interacts with survival of motor neuron (SMN) and Sm proteins. Several coilin phosphoresidues have been identified by mass spectrometric analysis. Phosphorylation of coilin affects its self-interaction and localization in the nucleus. We hypothesize that coilin phosphorylation also impacts its binding to SMN and Sm proteins. In vitro binding studies with a C-terminal fragment of coilin and corresponding phosphomimics show that SMN binds preferentially to dephosphorylated analogs and that SmB' binds preferentially to phosphomimetic constructs. Bacterially expressed full-length coilin binds more SMN and SmB' than does the C-terminal fragment. Co-immunoprecipitation and phosphatase experiments show that SMN also binds dephosphorylated coilin in vivo. These data show that phosphorylation of coilin influences interaction with its target proteins and, thus, may be significant in managing the flow of snRNPs through the CB.

  9. Coilin phosphorylation mediates interaction with SMN and SmB′

    Science.gov (United States)

    Toyota, Cory G.; Davis, Misty D.; Cosman, Angela M.; Hebert, Michael D.

    2010-01-01

    Cajal bodies (CBs) are subnuclear domains that participate in spliceosomal small nuclear ribonucleoprotein (snRNP) biogenesis and play a part in the assembly of the spliceosomal complex. The CB marker protein, coilin, interacts with survival of motor neuron (SMN) and Sm proteins. Several coilin phosphoresidues have been identified by mass spectrometric analysis. Phosphorylation of coilin affects its self-interaction and localization in the nucleus. We hypothesize that coilin phosphorylation also impacts its binding to SMN and Sm proteins. In vitro binding studies with a C-terminal fragment of coilin and corresponding phosphomimics show that SMN binds preferentially to dephosphorylated analogs and that SmB′ binds preferentially to phosphomimetic constructs. Bacterially expressed full-length coilin binds more SMN and SmB′ than does the C-terminal fragment. Co-immunoprecipitation and phosphatase experiments show that SMN also binds dephosphorylated coilin in vivo. These data show that phosphorylation of coilin influences interaction with its target proteins and, thus, may be significant in managing the flow of snRNPs through the CB. PMID:19997741

  10. Glucose phosphorylation is required for Mycobacterium tuberculosis persistence in mice.

    Directory of Open Access Journals (Sweden)

    Joeli Marrero

    2013-01-01

    Full Text Available Mycobacterium tuberculosis (Mtb is thought to preferentially rely on fatty acid metabolism to both establish and maintain chronic infections. Its metabolic network, however, allows efficient co-catabolism of multiple carbon substrates. To gain insight into the importance of carbohydrate substrates for Mtb pathogenesis we evaluated the role of glucose phosphorylation, the first reaction in glycolysis. We discovered that Mtb expresses two functional glucokinases. Mtb required the polyphosphate glucokinase PPGK for normal growth on glucose, while its second glucokinase GLKA was dispensable. (13C-based metabolomic profiling revealed that both enzymes are capable of incorporating glucose into Mtb's central carbon metabolism, with PPGK serving as dominant glucokinase in wild type (wt Mtb. When both glucokinase genes, ppgK and glkA, were deleted from its genome, Mtb was unable to use external glucose as substrate for growth or metabolism. Characterization of the glucokinase mutants in mouse infections demonstrated that glucose phosphorylation is dispensable for establishing infection in mice. Surprisingly, however, the glucokinase double mutant failed to persist normally in lungs, which suggests that Mtb has access to glucose in vivo and relies on glucose phosphorylation to survive during chronic mouse infections.

  11. Phosphorylation of Intrinsically Disordered Regions in Remorin Proteins

    Directory of Open Access Journals (Sweden)

    Macarena eMarín

    2012-05-01

    Full Text Available Plant-specific remorin proteins reside in subdomains of plasma membranes, originally termed membrane rafts. They probably facilitate cellular signal transduction by direct interaction with signalling proteins such as receptor-like kinases (RLKs and may dynamically modulate their lateral segregation within plasma membranes. Recent evidence suggests such functions of remorins during plant-microbe interactions and innate immune responses, where differential phosphorylation of some of these proteins has been described to be dependent on the perception of the microbe-associated molecular pattern (MAMP flg22 and the presence of the NBS-LRR resistance protein RPM1. A number of specifically phosphorylated residues in their highly variable and intrinsically disordered N-terminal regions have been identified. Sequence diversity of these evolutionary distinct domains suggests that remorins may serve a wide range of biological functions. Here, we describe patterns and features of intrinsic disorder in remorin protein and discuss possible functional implications of phosphorylation within these rapidly evolving domains.

  12. TTBK2: A Tau Protein Kinase beyond Tau Phosphorylation

    Directory of Open Access Journals (Sweden)

    Jung-Chi Liao

    2015-01-01

    Full Text Available Tau tubulin kinase 2 (TTBK2 is a kinase known to phosphorylate tau and tubulin. It has recently drawn much attention due to its involvement in multiple important cellular processes. Here, we review the current understanding of TTBK2, including its sequence, structure, binding sites, phosphorylation substrates, and cellular processes involved. TTBK2 possesses a casein kinase 1 (CK1 kinase domain followed by a ~900 amino acid segment, potentially responsible for its localization and substrate recruitment. It is known to bind to CEP164, a centriolar protein, and EB1, a microtubule plus-end tracking protein. In addition to autophosphorylation, known phosphorylation substrates of TTBK2 include tau, tubulin, CEP164, CEP97, and TDP-43, a neurodegeneration-associated protein. Mutations of TTBK2 are associated with spinocerebellar ataxia type 11. In addition, TTBK2 is essential for regulating the growth of axonemal microtubules in ciliogenesis. It also plays roles in resistance of cancer target therapies and in regulating glucose and GABA transport. Reported sites of TTBK2 localization include the centriole/basal body, the midbody, and possibly the mitotic spindles. Together, TTBK2 is a multifunctional kinase involved in important cellular processes and demands augmented efforts in investigating its functions.

  13. Raf activation is regulated by tyrosine 510 phosphorylation in Drosophila.

    Directory of Open Access Journals (Sweden)

    Fan Xia

    2008-05-01

    Full Text Available The proto-oncoprotein Raf is pivotal for mitogen-activated protein kinase (MAPK signaling, and its aberrant activation has been implicated in multiple human cancers. However, the precise molecular mechanism of Raf activation, especially for B-Raf, remains unresolved. By genetic and biochemical studies, we demonstrate that phosphorylation of tyrosine 510 is essential for activation of Drosophila Raf (Draf, which is an ortholog of mammalian B-Raf. Y510 of Draf is phosphorylated by the c-src homolog Src64B. Acidic substitution of Y510 promotes and phenylalanine substitution impairs Draf activation without affecting its enzymatic activity, suggesting that Y510 plays a purely regulatory role. We further show that Y510 regulates Draf activation by affecting the autoinhibitory interaction between the N- and C-terminal fragments of the protein. Finally, we show that Src64B is required for Draf activation in several developmental processes. Together, these results suggest a novel mechanism of Raf activation via Src-mediated tyrosine phosphorylation. Since Y510 is a conserved residue in the kinase domain of all Raf proteins, this mechanism is likely evolutionarily conserved.

  14. Rat1p maintains RNA polymerase II CTD phosphorylation balance

    Science.gov (United States)

    Jimeno-González, Silvia; Schmid, Manfred; Malagon, Francisco; Haaning, Line Lindegaard; Jensen, Torben Heick

    2014-01-01

    In S. cerevisiae, the 5′-3′ exonuclease Rat1p partakes in transcription termination. Although Rat1p-mediated RNA degradation has been suggested to play a role for this activity, the exact mechanisms by which Rat1p helps release RNA polymerase II (RNAPII) from the DNA template are poorly understood. Here we describe a function of Rat1p in regulating phosphorylation levels of the C-terminal domain (CTD) of the largest RNAPII subunit, Rpb1p, during transcription elongation. The rat1-1 mutant exhibits highly elevated levels of CTD phosphorylation as well as RNAPII distribution and transcription termination defects. These phenotypes are all rescued by overexpression of the CTD phosphatase Fcp1p, suggesting a functional relationship between the absence of Rat1p activity, elevated CTD phosphorylation, and transcription defects. We also demonstrate that rat1-1 cells display increased RNAPII transcription kinetics, a feature that may contribute to the cellular phenotypes of the mutant. Consistently, the rat1-1 allele is synthetic lethal with the rpb1-E1103G mutation, causing increased RNAPII speed, and is suppressed by the rpb2-10 mutation, causing slowed transcription. Thus, Rat1p plays more complex roles in controlling transcription than previously thought. PMID:24501251

  15. Catalytic constants enable the emergence of bistability in dual phosphorylation.

    Science.gov (United States)

    Conradi, Carsten; Mincheva, Maya

    2014-06-06

    Dual phosphorylation of proteins is a principal component of intracellular signalling. Bistability is considered an important property of such systems and its origin is not yet completely understood. Theoretical studies have established parameter values for multistationarity and bistability for many types of proteins. However, up to now no formal criterion linking multistationarity and bistability to the parameter values characterizing dual phosphorylation has been established. Deciding whether an unclassified protein has the capacity for bistability, therefore requires careful numerical studies. Here, we present two general algebraic conditions in the form of inequalities. The first employs the catalytic constants, and if satisfied guarantees multistationarity (and hence the potential for bistability). The second involves the catalytic and Michaelis constants, and if satisfied guarantees uniqueness of steady states (and hence absence of bistability). Our method also allows for the direct computation of the total concentration values such that multistationarity occurs. Applying our results yields insights into the emergence of bistability in the ERK-MEK-MKP system that previously required a delicate numerical effort. Our algebraic conditions present a practical way to determine the capacity for bistability and hence will be a useful tool for examining the origin of bistability in many models containing dual phosphorylation.

  16. Extracellular matrix structure and nano-mechanics determine megakaryocyte function.

    Science.gov (United States)

    Malara, Alessandro; Gruppi, Cristian; Pallotta, Isabella; Spedden, Elise; Tenni, Ruggero; Raspanti, Mario; Kaplan, David; Tira, Maria Enrica; Staii, Cristian; Balduini, Alessandra

    2011-10-20

    Cell interactions with matrices via specific receptors control many functions, with chemistry, physics, and membrane elasticity as fundamental elements of the processes involved. Little is known about how biochemical and biophysical processes integrate to generate force and, ultimately, to regulate hemopoiesis into the bone marrow-matrix environment. To address this hypothesis, in this work we focus on the regulation of MK development by type I collagen. By atomic force microscopy analysis, we demonstrate that the tensile strength of fibrils in type I collagen structure is a fundamental requirement to regulate cytoskeleton contractility of human MKs through the activation of integrin-α2β1-dependent Rho-ROCK pathway and MLC-2 phosphorylation. Most importantly, this mechanism seemed to mediate MK migration, fibronectin assembly, and platelet formation. On the contrary, a decrease in mechanical tension caused by N-acetylation of lysine side chains in type I collagen completely reverted these processes by preventing fibrillogenesis.

  17. Astaxanthin reduces matrix metalloproteinase expression in human chondrocytes.

    Science.gov (United States)

    Chen, Wei-Ping; Xiong, Yan; Shi, Yong-Xiang; Hu, Peng-Fei; Bao, Jia-Peng; Wu, Li-Dong

    2014-03-01

    Astaxanthin is a red carotenoid pigment which exerts multiple biological activities. However, little is known about the effects of astaxanthin on matrix metalloproteinases (MMPs) in OA. The present study investigated the effects of astaxanthin on MMPs in human chondrocytes. Human chondrocytes were pretreated with astaxanthin at 1, 10 or 50μM, then, cells were stimulated with IL-1β (10ng/ml) for 24h. MMP-1, MMP-3 and MMP-13 were observed. We found that astaxanthin reduced the expression of MMP-1, MMP-3 and MMP-13 as well as the phosphorylation of two mitogen-activated protein kinases (MAPK) (p38 and ERK1/2) in IL-1β-stimulated chondrocytes. Astaxanthin also blocked the IκB-α degradation. These results suggest that astaxanthin may be beneficial in the treatment of OA.

  18. Determination of sites of U50,488H-promoted phosphorylation of the mouse κ opioid receptor (KOPR): disconnect between KOPR phosphorylation and internalization.

    Science.gov (United States)

    Chen, Chongguang; Chiu, Yi-Ting; Wu, Wenman; Huang, Peng; Mann, Anika; Schulz, Stefan; Liu-Chen, Lee-Yuan

    2016-02-15

    Phosphorylation sites of KOPR (κ opioid receptor) following treatment with the selective agonist U50,488H {(-)(trans)-3,4-dichloro-N-methyl-N-[2-(1-pyrrolidiny)cyclo-hexyl]benzeneacetamide} were identified after affinity purification, SDS/PAGE, in-gel digestion with Glu-C and HPLC-MS/MS. Single- and double-phosphorylated peptides were identified containing phosphorylated Ser(356), Thr(357), Thr(363) and Ser(369) in the C-terminal domain. Antibodies were generated against three phosphopeptides containing pSer(356)/pThr(357), pThr(363) and pSer(369) respectively, and affinity-purified antibodies were found to be highly specific for phospho-KOPR. U50,488H markedly enhanced staining of the KOPR by pThr(363)-, pSer(369)- and pSer(356)/pThr(357)-specific antibodies in immunoblotting, which was blocked by the selective KOPR antagonist norbinaltorphimine. Ser(369) phosphorylation affected Thr(363) phosphorylation and vice versa, and Thr(363) or Ser(369) phosphorylation was important for Ser(356)/Thr(357) phosphorylation, revealing a phosphorylation hierarchy. U50,488H, but not etorphine, promoted robust KOPR internalization, although both were full agonists. U50,488H induced higher degrees of phosphorylation than etorphine at Ser(356)/Thr(357), Thr(363) and Ser(369) as determined by immunoblotting. Using SILAC (stable isotope labelling by amino acids in cell culture) and HPLC-MS/MS, we found that, compared with control (C), U50,488H (U) and etorphine (E) KOPR promoted single phosphorylation primarily at Thr(363) and Ser(369) with U/E ratios of 2.5 and 2 respectively. Both induced double phosphorylation at Thr(363)+Ser(369) and Thr(357)+Ser(369) with U/E ratios of 3.3 and 3.4 respectively. Only U50,488H induced triple phosphorylation at Ser(356)+Thr(357)+Ser(369). An unphosphorylated KOPR-(354-372) fragment containing all of the phosphorylation sites was detected with a C/E/U ratio of 1/0.7/0.4, indicating that ∼60% and ∼30% of the mouse KOPR are phosphorylated

  19. Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms

    Science.gov (United States)

    Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R.

    2016-07-01

    Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.

  20. Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms.

    Science.gov (United States)

    Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R

    2016-07-01

    Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.