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  • 1
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    Origin and Evolution of Laminin Gene Family Diversity (2012)
    Oxford University Press
    Details
    Publication Date: 2012-06-16
    Description: Laminins are a family of multidomain glycoproteins that are important contributors to the structure of metazoan extracellular matrices. To investigate the origin and evolution of the laminin family, we characterized the full complement of laminin-related genes in the genome of the sponge, Amphimedon queenslandica . As a representative of the Demospongiae, a group consistently placed within the earliest diverging branch of animals by molecular phylogenies, Amphimedon is uniquely placed to provide insight into early steps in the evolution of metazoan gene families. Five Amphimedon laminin-related genes possess the conserved molecular features, and most of the domains found in bilaterian laminins, but all display domain architectures distinct from those of the canonical laminin chain types known from model bilaterians. This finding prompted us to perform a comparative genomic analysis of laminins and related genes from a choanoflagellate and diverse metazoans and to conduct phylogenetic analyses using the conserved Laminin N-terminal domain in order to explore the relationships between genes with distinct architectures. Laminin-like genes appear to have originated in the holozoan lineage (choanoflagellates + metazoans + several other unicellular opisthokont taxa), with several laminin domains originating later and appearing only in metazoan (animal) or eumetazoan (placozoans + ctenophores + cnidarians + bilaterians) laminins. Typical bilaterian α, β, and laminin chain forms arose in the eumetazoan stem and another chain type that is conserved in Amphimedon , the cnidarian, Nematostella vectensis , and the echinoderm, Strongylocentrotus purpuratus , appears to have been lost independently from the placozoan, Trichoplax adhaerens , and from multiple bilaterians. Phylogenetic analysis did not clearly reconstruct relationships between the distinct laminin chain types (with the exception of the α chains) but did reveal how several members of the netrin family were generated independently from within the laminin family by duplication and domain shuffling and by domain loss. Together, our results suggest that gene duplication and loss and domain shuffling and loss all played a role in the evolution of the laminin family and contributed to the generation of lineage-specific diversity in the laminin gene complements of extant metazoans.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-12-14
    Description: The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains approximately 16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dehal, Paramvir -- Satou, Yutaka -- Campbell, Robert K -- Chapman, Jarrod -- Degnan, Bernard -- De Tomaso, Anthony -- Davidson, Brad -- Di Gregorio, Anna -- Gelpke, Maarten -- Goodstein, David M -- Harafuji, Naoe -- Hastings, Kenneth E M -- Ho, Isaac -- Hotta, Kohji -- Huang, Wayne -- Kawashima, Takeshi -- Lemaire, Patrick -- Martinez, Diego -- Meinertzhagen, Ian A -- Necula, Simona -- Nonaka, Masaru -- Putnam, Nik -- Rash, Sam -- Saiga, Hidetoshi -- Satake, Masanobu -- Terry, Astrid -- Yamada, Lixy -- Wang, Hong-Gang -- Awazu, Satoko -- Azumi, Kaoru -- Boore, Jeffrey -- Branno, Margherita -- Chin-Bow, Stephen -- DeSantis, Rosaria -- Doyle, Sharon -- Francino, Pilar -- Keys, David N -- Haga, Shinobu -- Hayashi, Hiroko -- Hino, Kyosuke -- Imai, Kaoru S -- Inaba, Kazuo -- Kano, Shungo -- Kobayashi, Kenji -- Kobayashi, Mari -- Lee, Byung-In -- Makabe, Kazuhiro W -- Manohar, Chitra -- Matassi, Giorgio -- Medina, Monica -- Mochizuki, Yasuaki -- Mount, Steve -- Morishita, Tomomi -- Miura, Sachiko -- Nakayama, Akie -- Nishizaka, Satoko -- Nomoto, Hisayo -- Ohta, Fumiko -- Oishi, Kazuko -- Rigoutsos, Isidore -- Sano, Masako -- Sasaki, Akane -- Sasakura, Yasunori -- Shoguchi, Eiichi -- Shin-i, Tadasu -- Spagnuolo, Antoinetta -- Stainier, Didier -- Suzuki, Miho M -- Tassy, Olivier -- Takatori, Naohito -- Tokuoka, Miki -- Yagi, Kasumi -- Yoshizaki, Fumiko -- Wada, Shuichi -- Zhang, Cindy -- Hyatt, P Douglas -- Larimer, Frank -- Detter, Chris -- Doggett, Norman -- Glavina, Tijana -- Hawkins, Trevor -- Richardson, Paul -- Lucas, Susan -- Kohara, Yuji -- Levine, Michael -- Satoh, Nori -- Rokhsar, Daniel S -- HD-37105/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 2002 Dec 13;298(5601):2157-67.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12481130" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Apoptosis ; Base Sequence ; Cellulose/metabolism ; Central Nervous System/physiology ; Ciona intestinalis/anatomy & histology/classification/*genetics/physiology ; Computational Biology ; Endocrine System/physiology ; Gene Dosage ; Gene Duplication ; Genes ; Genes, Homeobox ; *Genome ; Heart/embryology/physiology ; Immunity/genetics ; Molecular Sequence Data ; Multigene Family ; Muscle Proteins/genetics ; Organizers, Embryonic/physiology ; Phylogeny ; Polymorphism, Genetic ; Proteins/genetics/physiology ; *Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Species Specificity ; Thyroid Gland/physiology ; Urochordata/genetics ; Vertebrates/anatomy & histology/classification/genetics/physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Mox homeobox expression in muscle lineage of the gastropod Haliotis asinina : evidence for a conserved role in bilaterian myogenesis (2002)
    Springer
    Details
    Publication Date: 2002-04-01
    Print ISSN: 0949-944X
    Electronic ISSN: 1432-041X
    Topics: Biology
    Published by Springer
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  • 4
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    A sponge allelochemical induces ascidian settlement but inhibits metamorphosis (2002)
    Springer
    Details
    Publication Date: 2002-02-01
    Print ISSN: 0025-3162
    Electronic ISSN: 1432-1793
    Topics: Biology
    Published by Springer
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  • 5
    Electronic Resource
    Electronic Resource
    Highly repetitive DNA sequences provide evidence for a lack of gene flow between two morphological forms of Herdmania momus (Ascidiacea: Stolidobranchia) (1995)
    Springer
    Marine biology 124 (1995), S. 293-299 
    Details
    ISSN: 1432-1793
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The genomic structure of two morphological forms of the pyurid ascidian Herdmania momus — H. momus forma curvata and H. momus forma grandis—are compared using a rapidly evolving highly repetitive element isolated from the genome of H. momus forma curvata. A 663 bp (base pair) Cla I satellite sequence is present only in the genome of H. momus forma curvata, and hence can be used as a form-specific marker. Low-stringency Southern blot analyses, using the Cla I satellite as a probe, revealed that the genomes of H. momus forma grandis and another pyurid ascidian, Pyura stolonifera, do not contain similar sequences to the H. momus forma curvata repetitive element. In addition to this genomic dissimilarity, there are a number of significant reproductive and developmental differences between the two H. momus forms, and interform fertilisation rates are significantly lower than intraform rates. The molecular, reproductive and developmental differences between H. momus forma curvata and H. momus forma grandis indicate the presence of strong barriers to gene flow.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00347133
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  • 6
    Electronic Resource
    Electronic Resource
    Muscle-specific regulation of tropomyosin gene expression and myofibrillogenesis differs among muscle systems examined at metamorphosis of the gastropod Haliotis rufescens (1997)
    Springer
    Development genes and evolution 206 (1997), S. 464-471 
    Details
    ISSN: 1432-041X
    Keywords: Key words Abalone ; Competence ; In situ hybridization ; Larva ; Muscle cell
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The spatial and temporal association of muscle-specific tropomyosin gene expression, and myofibril assembly and degradation during metamorphosis is analyzed in the gastropod mollusc, Haliotis rufescens. Metamorphosis of the planktonic larva to the benthic juvenile includes rearrangement and atrophy of specific larval muscles, and biogenesis of the new juvenile muscle system. The major muscle of the larva – the larval retractor muscle – reorganizes at metamorphosis, with two suites of cells having different fates. The ventral cells degenerate, while the dorsal cells become part of the developing juvenile mantle musculature. Prior to these changes in myofibrillar structure, tropomyosin mRNA prevalence declines until undetectable in the ventral cells, while increasing markedly in the dorsal cells. In the foot muscle and right shell muscle, tropomyosin mRNA levels remain relatively stable, even though myofibril content increases. In a population of median mesoderm cells destined to form de novo the major muscle of the juvenile and adult (the columellar muscle), tropomyosin expression is initiated at 45 h after induction of metamorphosis. Myofibrillar filamentous actin is not detected in these cells until about 7 days later. Given that patterns of tropomyosin mRNA accumulation in relation to myofibril assembly and disassembly differ significantly among the four major muscle systems examined, we suggest that different regulatory mechanisms, probably operating at both transcriptional and post-transcriptional levels, control the biogenesis and atrophy of different larval and postlarval muscles at metamorphosis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004270050076
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  • 7
    Electronic Resource
    Electronic Resource
    Induction of metamorphosis with potassium ions requires development of competence and an anterior signalling centre in the ascidian Herdmania momus (1997)
    Springer
    Development genes and evolution 206 (1997), S. 370-376 
    Details
    ISSN: 1432-041X
    Keywords: Key words Ascidian ; Competence ; Metamorphosis ; Settlement ; Urochordate
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Increased K+ concentration in seawater induces metamorphosis in the ascidian Herdmania momus. Larvae cultivated at 24°C exhibit highest rates of metamorphosis when treated with 40 mM KCl-elevated seawater at 21°C. At 24°C, H. momus larvae develop competence to respond to KCl-seawater and initiate metamorphosis approximately 3 h after hatching. Larval trunks and tails separated from the anterior papillae region, but maintained in a common tunic at a distance of greater than 60 μm, do not undergo metamorphosis when treated with KCl-seawater; normal muscle degradation does not occur in separated tails while ampullae develop from papillae-containing anterior fragments. Normal programmed degradation of myofibrils occurs when posterior fragments are fused to papillae-containing anterior fragments. These data indicate that H. momus settlement and metamorphosis only occurs when larvae have attained competence, and suggest that an anterior signalling centre is stimulated to release a factor that induces metamorphosis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004270050066
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  • 8
    Electronic Resource
    Electronic Resource
    Retinoic acid perturbs Otx gene expression in the ascidian pharynx (2000)
    Springer
    Development genes and evolution 210 (2000), S. 129-139 
    Details
    ISSN: 1432-041X
    Keywords: Key words Ascidian ; Chordate evolution ; Herdmania curvata ; Otx ; Retinoic acid ; Pharynx
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  In vertebrate embryos, ectopic application of all-trans retinoic acid (RA) alters the expression of Otx genes in the developing midbrain. In conjunction with RA-induced misexpression of other regulatory genes this leads to a loss of anterior CNS. In the ascidian Herdmania curvata, RA primarily inhibits the development of the juvenile pharynx. An ascidian Otx gene, Hec-Otx, is expressed largely in this tissue, associated stomodeal structures and the anterior endostyle of the juvenile. Treatment with 10–6 M RA reduces Hec-Otx mRNA levels in the juvenile to about 12% of normal and is correlated closely with the loss of pharyngeal structures. During embryogenesis the expression of Hec-Otx becomes restricted to cell lineages fated to give rise to the anterior-most nervous system and the stomodeal component of the primordial pharynx. In hatched larvae Hec-Otx transcripts are detected only in the sensory (brain) vesicle. RA reduces Hec-Otx expression in the tailbud stomodeal pharynx primordium/anterior nervous system cell line but not in the larval sensory vesicle, suggesting that RA regulation of Hec-Otx expression is restricted to pharyngeal tissues throughout embryonic and postlarval development. RA does not affect expression of Hec-Pax2/5/8, which is normally expressed within the developing nervous system immediately posterior to Hec-Otx at the tailbud stage, lending support to the proposition that RA does not impact CNS axial patterning. These data combined with those from other chordates suggest that RA regulation of Otx expression in the anterior nerve cord and pharynx is a primitive chordate feature which has been maintained predominantly in pharyngeal tissues in the ascidian.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004270050019
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  • 9
    Electronic Resource
    Electronic Resource
    Neuroectodermal and endodermal expression of the ascidian Cdx gene is separated by metamorphosis (2000)
    Springer
    Development genes and evolution 210 (2000), S. 212-216 
    Details
    ISSN: 1432-041X
    Keywords: Key words Chordate evolution ; Heterochrony Urochordate
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Ascidians are a group of invertebrate chordates that exhibit a biphasic life history, with chordate-specific structures developing during embryogenesis (dorsal neural tube and notochord) and metamorphosis (pharyngeal gill slits and endostyle). Here we characterize the expression of a caudal/Cdx gene homologue, Hec-Cdx, from the ascidian Herdmania curvata. Vertebrate Cdx genes are expressed at gastrulation and in the posterior of the developing neural tube and endoderm. Hec-Cdx expression is initiated at the earliest stages of gastrulation, with peaks in RNA abundance occurring first during neurulation and tailbud extension and then in 3- to 5-day-old juveniles. Hec-Cdx is expressed in a pair of cells in the anterior lip of the blastopore in the late gastrula which form the most posterior portion of the neural plate. During tailbud formation expression is maintained in and solely restricted to these cells. During metamorphosis expression is localized to the intestine of the juvenile. These data, along with data for the H. curvata Otx gene, suggest that the evolution of the novel ascidian biphasic body plan was not accompanied by a deployment of these genes into new pathways but by a temporal separation of tissue-specific expression.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004270050306
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  • 10
    Electronic Resource
    Electronic Resource
    Transport and metabolism of glucose and arabinose in Bifidobacterium breve (1993)
    Springer
    Archives of microbiology 160 (1993), S. 144-151 
    Details
    ISSN: 1432-072X
    Keywords: Bifidobacterium breve ; Phosphorylation- ; Phosphoenolpyruvate: phosphotransferase system ; Fermentation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Glucose was required for the transport of arabinose into Bifidobacterium breve. The non-metabolisable glucose analogue 2-deoxy-d-glucose (2-DG) did not facilitate assimilation of arabinose. Studies using d-[U-14C]-labelled arabinose showed that it was fermented to pyruvate, formate, lactate and acetate, whereas the principal metabolic products of d-[U-14C]-labelled glucose were acetate and formate. In contrast to glucose, arabinose was not incorporated into cellular macromolecules. A variety of metabolic inhibitors and inhibitors of sugar transport (proton ionophores, metal ionophores, compounds associated with electron transport) were used to investigate the mechanisms of sugar uptake. Only NaF, an inhibitor of substrate level phosphorylation, and 2-DG inhibited glucose assimilation. 2-DG had no effect on arabinose uptake, but NaF was stimulatory. High levels of phosphorylation of glucose and 2-DG by PEP and to a lesser degree, ATP were seen in phosphoenolpyruvate: phosphotransferase (PEP:PTS) assays. These data together with strong inhibition of glucose uptake by NaF suggest a role for phosphorylation in the transport process. Arabinose uptake in B. breve was not directly dependent on phosphorylation or any other energy-linked form of transport but may be assimilated by glucose-dependent facilitated diffusion.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00288717
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