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  • GENE  (10)
  • RICHTERSIUS-CORONIFER  (5)
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  • 1
    Keywords: gene expression ; BIOLOGY ; EXPRESSION ; CELL ; GENE ; GENE-EXPRESSION ; representational difference analysis ; analysis
    Type of Publication: Book chapter
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  • 2
    Keywords: COMBINATION ; Germany ; TOOL ; GENE ; PROTEIN ; PROTEINS ; METABOLISM ; MOLECULES ; MECHANISM ; mechanisms ; TOLERANCE ; DISCOVERY ; MOLECULE ; WATER ; DAMAGE ; bioinformatics ; MAMMALIAN-CELLS ; STABILITY ; review ; regulation ; HEAT-SHOCK-PROTEIN ; LIFE ; development ; cryopreservation ; BACTERIA ; biotechnology ; STATE ; CHAPERONE ACTIVITY ; WELL ; MILNESIUM-TARDIGRADUM ; RICHTERSIUS-CORONIFER ; ADORYBIOTUS-CORONIFER ; Anhydrobiosis ; ARTEMIA-FRANCISCANA ; Biostabilization ; Cryobanking ; Cryoprotectant ; Cryptobiosis ; DESICCATION TOLERANCE ; FRESH-WATER SPONGE ; SHOCK/ALPHA-CRYSTALLIN PROTEIN ; STRESS-PROTEIN
    Abstract: Certain organisms found across a range of taxa, including bacteria, yeasts, plants and many invertebrates such as nematodes and tardigrades are able to survive almost complete loss of body water. The dry organisms may remain in this state. which is known as anhydrobiosis. for decades without apparent damage. When water again becomes available, they rapidly rehydrate and resume active life. Research in anhydrobiosis has focused mainly on sugar metabolism and stress proteins. Despite the discovery of various molecules which are involved in desiccation and water stress, knowledge of the regulatory network governing the stability of the cellular architecture and the metabolic machinery during dehydration is still fragmentary and not well understood. A combination of transcriptional, proteomic and metabolic approaches with bioinformatics tools can provide a better understanding of gene regulation that underlie the biological functions and physiology related to anhydrobiosis. The development of this concept will raise exciting possibilities and techniques for the preservation and stabilization of biological materials in the dry state. (c) 2009 Elsevier Inc. All rights reserved
    Type of Publication: Journal article published
    PubMed ID: 19472511
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  • 3
    Keywords: EXPRESSION ; TOLERANCE ; CAENORHABDITIS-ELEGANS ; ARABIDOPSIS-THALIANA ; SUPEROXIDE-DISMUTASE ; RICHTERSIUS-CORONIFER ; LIFE-SPAN REGULATION ; VITELLOGENIN GENES ; YOLK PROTEINS ; WATER-STRESS
    Abstract: Tardigrades have fascinated researchers for more than 300 years because of their extraordinary capability to undergo cryptobiosis and survive extreme environmental conditions. However, the survival mechanisms of tardigrades are still poorly understood mainly due to the absence of detailed knowledge about the proteome and genome of these organisms. Our study was intended to provide a basis for the functional characterization of expressed proteins in different states of tardigrades. High-throughput, high-accuracy proteomics in combination with a newly developed tardigrade specific protein database resulted in the identification of more than 3000 proteins in three different states: early embryonic state and adult animals in active and anhydrobiotic state. This comprehensive proteome resource includes protein families such as chaperones, antioxidants, ribosomal proteins, cytoskeletal proteins, transporters, protein channels, nutrient reservoirs, and developmental proteins. A comparative analysis of protein families in the different states was performed by calculating the exponentially modified protein abundance index which classifies proteins in major and minor components. This is the first step to analyzing the proteins involved in early embryonic development, and furthermore proteins which might play an important role in the transition into the anhydrobiotic state.
    Type of Publication: Journal article published
    PubMed ID: 23029181
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  • 4
    Keywords: CELLS ; EXPRESSION ; Germany ; CLONING ; GENE ; HYBRIDIZATION ; PROTEIN ; DOMAIN ; IN-SITU ; EVOLUTION ; innate immunity ; LECTIN ; DOMAINS ; in situ hybridization ; Hydractinia ; neuron ; CNIDARIAN ; invertebrate immunity ; TACHYPLEUS-TRIDENTATUS
    Abstract: Tachylectin-related proteins are a recently characterized group of pattern recognition molecules, functioning in the innate immunity of various animals, from the ancient sponges to vertbrates. Tachylectins are characterized by six internal tandem repeats forming beta-propeller domains. We have identified and characterized a tachylectin-related gene in the colonial marine hydroid, Hydractinia echinata. The predicted gene product, termed CTRN, contained an N-terminal signal peptide and had a well-conserved tachylectin-like structure. RT-PCR analyses revealed only post-metamorphic expression while no mRNA was detected during embryonic development or in planula larvae. Exposure of colonies to LPS under conditions known to activate an immune response in Hydractinia did not result in upregulation of the gene. In situ hybridization analysis of metamorphosed animals detected CTRN transcripts only in a small subpopulation of neurons and their precursor cells, localized in a ring-like structure around the mouth of polyps. The same ring-like structure of CTRN expressing neurons was also observed in young polyp buds, predicting the position of the future mouth. This type of expression pattern can hardly be attributed to an immunerelevant gene. Thus, despite high structural similarity to tachylectins, this cnidarian member of this group seems to be an exception to all other tachylectins identified so far as it seems to have no function in cnidarian innate immunity. (c) 2005 Elsevier Ltd. All rights reserved
    Type of Publication: Journal article published
    PubMed ID: 15975655
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  • 5
    Keywords: RECEPTOR ; CELLS ; EXPRESSION ; CELL ; Germany ; human ; PATHWAY ; SYSTEM ; GENE ; GENES ; PROTEIN ; LINES ; ACTIVATION ; MARKER ; T cell ; T cell activation ; T cells ; T-CELL ; T-CELLS ; BINDING ; CELL-LINES ; SIGNAL ; virus ; IDENTIFICATION ; NUMBER ; CELL-LINE ; LINE ; HUMAN-IMMUNODEFICIENCY-VIRUS ; representational difference analysis ; GENE-PRODUCT ; SUBSET ; PRODUCTS ; HIV ; IMMUNODEFICIENCY VIRUS ; NUCLEOCYTOPLASMIC TRANSPORT ; TAP ; 60S RIBOSOMAL-SUBUNITS ; CD83 ; CRM1 ; IMMUNODEFICIENCY-VIRUS REV ; LEPTOMYCIN B ; RAN ; RECEPTOR CRM1 ; RNA export
    Abstract: In metazoans, the nuclear export of bulk mRNAs is mediated by the export receptor TAP, together with its binding partner p15. A number of viral mRNAs, including the unspliced and partially spliced mRNA species of the human immunodeficiency virus (HIV), however, use an alternative export route via the importin beta-related export receptor CRM1. This raises the question of whether a subset of cellular mRNAs might be exported by CRM1 as well. To identify such mRNAs, we performed a systematic screen in different cell lines, using representational difference analyses of cDNA (cDNA-RDA). In HeLa and Cl-4 cells no cellular transcripts could be identified as exported via CRM1. In contrast, we found a number of CRM1-dependent mRNAs in Jurkat T cells, most of which are induced during a T cell response. One of the identified gene products, the dendritic cell marker CD83, was analyzed in detail. CD83 expression depends on a functional CRM1 pathway in activated Jurkat T cells as well as in a heterologous expression system, independent of activation. Our results point to an important role of the CRM1-dependent export pathway for the expression of CD83 and other genes under conditions of T cell activation. (c) 2006 Elsevier Ltd. All rights reserved
    Type of Publication: Journal article published
    PubMed ID: 16580684
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  • 6
    Keywords: EXPRESSION ; PROTECTION ; tumor ; COMBINATION ; Germany ; CDNA ; GENE ; GENE-EXPRESSION ; GENES ; GENOME ; HYBRIDIZATION ; microarray ; transcription ; HEART ; TIME ; INJURIES ; MECHANISM ; REPERFUSION ; RAT ; INTERVENTION ; gene expression ; DIFFERENCE ; arteries ; POLYMERASE-CHAIN-REACTION ; NETHERLANDS ; CHAIN-REACTION ; ARTERY ; myocardium ; ISCHEMIA-REPERFUSION INJURY ; INJURY ; ALPHA MESSENGER-RNA ; CARDIAC MYOCYTE ; CONFERS RESISTANCE ; E-SELECTIN GENE ; INFARCTION ; MATRIX-METALLOPROTEINASE ACTIVITY ; preconditioning ; REPERFUSION INJURY ; representational difference analysis ; TRISTETRAPROLIN
    Abstract: Myocardial ischemic preconditioning (IPC) is a potent endogenous mechanism of cardioprotection against ischemia-reperfusion injury. In this study we focused on the second phase of IPC as the most interesting in terms of therapeutic implementations. We aimed at the detection of genes, which are differentially expressed at 16 h after reperfusion. Preconditioning of canine myocardium was initiated by 5 min occlusion of the left anterior descending coronary artery with subsequent reperfusion. cDNA representational difference analysis in combination with microarray hybridization and reverse transcription polymerase chain reaction were used to reveal the changes in gene expression in canine hearts. We found that functionally related genes for tristetraproline (TTP), selectin E, matrix metalloproteinase 9, and tumor necrosis factor-a were highly upregulated at the late phase of IPC. The upregulation of TTP gene at the late phase of IPC, reported here for the first time, may represent a cardioprotective mechanism, which could be a promising perspective in clinical interventions against ischemia-reperfusion injuries of the heart. (C) 2003 Federation of European Biochemical Societies. Published by Elsevier Science B.V. All rights reserved
    Type of Publication: Journal article published
    PubMed ID: 12860385
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  • 7
    Keywords: CELLS ; EXPRESSION ; CELL ; Germany ; human ; COMMON ; SYSTEM ; GENE ; PROTEIN ; PROTEINS ; MOLECULAR CHARACTERIZATION ; FAMILY ; PROTEIN FAMILIES ; PROTEIN FAMILY ; CYCLE ; NERVOUS-SYSTEM ; HUMANS ; EVOLUTION ; LOCALIZATION ; STEM-CELLS ; NETHERLANDS ; OF-FUNCTION ; ORIGIN ; PATTERN ; CIRCADIAN OUTPUT ; ECHINATA ; FMR1 ; FMRP ; FXR ; FXR2 ; Hydractinia ; HYDROID HYDRACTINIA ; hydrozoa ; LIFE-CYCLE ; NEURONS ; RIBOSOMES ; RNA-BINDING ; RNA-BINDING PROTEIN ; TRANSLATION
    Abstract: The fragile X mental retardation syndrome in humans is caused by a mutational loss of function of the fragile X mental retardation gene 1 (FMR1). FMR1 is an RNA-binding protein, involved in the development and function of the nervous system. Despite of its medical significance, the evolutionary origin of FMR1 has been unclear. Here, we report the molecular characterization of HyFMR1, an FMR1 orthologue, from the cnidarian hydroid Hydractinia echinata. Cnidarians are the most basal metazoans possessing neurons. HyFMR1 is expressed throughout the life cycle of Hydractinia. Its expression pattern correlates to the position of neurons and their precursor stem cells in the animal. Our data indicate that the origin of the fraxile X related (FXR) protein family dates back at least to the common ancestor of cnidarians and bilaterians. The lack of FXR proteins in other invertebrates may have been due to gene loss in particular lineages. (C) 2004 Elsevier B.V. All rights reserved
    Type of Publication: Journal article published
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  • 8
    Keywords: CELLS ; EXPRESSION ; DISTINCT ; GENE ; GENES ; PROTEIN ; PROTEINS ; FAMILY ; DOMAIN ; IDENTIFICATION ; EVOLUTION ; CLUSTER ; Hydractinia ; function ; CNIDARIAN ; HYDRA ; CATALYTIC DOMAIN ; HATCHING ENZYME ; MEPRIN ; ORYZIAS-LATIPES ; PROCOLLAGEN C-PROTEINASE ; ZINC-ENDOPEPTIDASE
    Abstract: Astacin-like metalloproteases are ubiquitous in the animal kingdom but their phylogenetic relationships and ancient functions within the Metazoa are unclear. We have cloned and characterized four astacin-like cDNAs from the marine hydroid Hydractinia echinata and performed a database search for related genes in the draft genome sequence of the sea anemone Nematostella vectensis. These sequences and those of higher animals' astacins were subjected to phylogenetic analysis revealing five clusters within the Eumetazoa. The bone morphogenetic protein-1/tolloid-like astacins were represented in all eumetazoan phyla studied. The meprins were only found in vertebrates and cnidarians. Two clusters were taxon-specific, and one cluster represented astacins, which probably evolved after the split of the Cnidaria. Interestingly, grouping of astacins according to the protease catalytic domain alone resulted in clusters of proteins with similar overall domain architecture. The Hydractinia astacins were expressed in distinct cells during metamorphosis and some also during wound healing. Previously characterized cnidarian astacins also act during development. Based on our phylogeny, however, we propose that the developmental function of most of them is not homologous to the developmental function assigned to higher animals' astacins
    Type of Publication: Journal article published
    PubMed ID: 16509900
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  • 9
    Keywords: IONIZING-RADIATION ; Germany ; MODEL ; INFORMATION ; GENE ; GENES ; DNA ; TOLERANCE ; SEQUENCE ; SEQUENCES ; WATER ; IDENTIFICATION ; CHROMATIN ; HEAT-SHOCK ; STRESS ; genetics ; DAMAGE ; DATABASE ; CAENORHABDITIS-ELEGANS ; assembly ; TRANSLATION ; EXPRESSED SEQUENCE TAGS ; transcriptome ; CONTROLLED TUMOR PROTEIN ; radiation tolerance ; Genetic ; MILNESIUM-TARDIGRADUM ; RICHTERSIUS-CORONIFER ; ADORYBIOTUS-CORONIFER ; DESICCATION TOLERANCE ; Species ; CONTRIBUTE ; EST ; ACID-BINDING PROTEINS ; FREEZE TOLERANCE ; POLYPEDILUM-VANDERPLANKI ; Sequence information
    Abstract: Background: The phenomenon of desiccation tolerance, also called anhydrobiosis, involves the ability of an organism to survive the loss of almost all cellular water without sustaining irreversible damage. Although there are several physiological, morphological and ecological studies on tardigrades, only limited DNA sequence information is available. Therefore, we explored the transcriptome in the active and anhydrobiotic state of the tardigrade Milnesium tardigradum which has extraordinary tolerance to desiccation and freezing. In this study, we present the first overview of the transcriptome of M. tardigradum and its response to desiccation and discuss potential parallels to stress responses in other organisms. Results: We sequenced a total of 9984 expressed sequence tags (ESTs) from two cDNA libraries from the eutardigrade M. tardigradum in its active and inactive, anhydrobiotic (tun) stage. Assembly of these ESTs resulted in 3283 putative unique transcripts, whereof similar to 50% showed significant sequence similarity to known genes. The resulting unigenes were functionally annotated using the Gene Ontology (GO) vocabulary. A GO term enrichment analysis revealed several GOs that were significantly underrepresented in the inactive stage. Furthermore we compared the putative unigenes of M. tardigradum with ESTs from two other eutardigrade species that are available from public sequence databases, namely Richtersius coronifer and Hypsibius dujardini. The processed sequences of the three tardigrade species revealed similar functional content and the M. tardigradum dataset contained additional sequences from tardigrades not present in the other two. Conclusions: This study describes novel sequence data from the tardigrade M. tardigradum, which significantly contributes to the available tardigrade sequence data and will help to establish this extraordinary tardigrade as a model for studying anhydrobiosis. Functional comparison of active and anhydrobiotic tardigrades revealed a differential distribution of Gene Ontology terms associated with chromatin structure and the translation machinery, which are underrepresented in the inactive animals. These findings imply a widespread metabolic response of the animals on dehydration. The collective tardigrade transcriptome data will serve as a reference for further studies and support the identification and characterization of genes involved in the anhydrobiotic response
    Type of Publication: Journal article published
    PubMed ID: 20226016
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  • 10
    Keywords: EXPRESSION ; Germany ; MODEL ; INFORMATION ; SYSTEM ; GENE ; GENE-EXPRESSION ; GENOME ; PROTEIN ; PROTEINS ; RESOLUTION ; MECHANISM ; FAMILY ; DOMAIN ; mechanisms ; TOLERANCE ; CYCLE ; SEQUENCE ; IDENTIFICATION ; gene expression ; HEAT-SHOCK ; mass spectrometry ; SPECTROMETRY ; DATABASE ; MASS-SPECTROMETRY ; PROJECT ; PROTEOMICS ; PROTEIN IDENTIFICATION ; ARABIDOPSIS-THALIANA ; HIGH-RESOLUTION ; ANNOTATION ; SCIENCE ; LIFE ; MOLECULAR-MECHANISMS ; GLUTATHIONE S-TRANSFERASES ; Genetic ; protein extraction ; MILNESIUM-TARDIGRADUM ; RICHTERSIUS-CORONIFER ; ARTEMIA-FRANCISCANA ; DESICCATION TOLERANCE ; EST ; Sequence information ; Molecular mechanisms ; BRINE SHRIMP ; TREHALOSE
    Abstract: Background: Tardigrades are small, multicellular invertebrates which are able to survive times of unfavourable environmental conditions using their well-known capability to undergo cryptobiosis at any stage of their life cycle. Milnesium tardigradum has become a powerful model system for the analysis of cryptobiosis. While some genetic information is already available for Milnesium tardigradum the proteome is still to be discovered. Principal Findings: Here we present to the best of our knowledge the first comprehensive study of Milnesium tardigradum on the protein level. To establish a proteome reference map we developed optimized protocols for protein extraction from tardigrades in the active state and for separation of proteins by high resolution two-dimensional gel electrophoresis. Since only limited sequence information of M. tardigradum on the genome and gene expression level is available to date in public databases we initiated in parallel a tardigrade EST sequencing project to allow for protein identification by electrospray ionization tandem mass spectrometry. 271 out of 606 analyzed protein spots could be identified by searching against the publicly available NCBInr database as well as our newly established tardigrade protein database corresponding to 144 unique proteins. Another 150 spots could be identified in the tardigrade clustered EST database corresponding to 36 unique contigs and ESTs. Proteins with annotated function were further categorized in more detail by their molecular function, biological process and cellular component. For the proteins of unknown function more information could be obtained by performing a protein domain annotation analysis. Our results include proteins like protein member of different heat shock protein families and LEA group 3, which might play important roles in surviving extreme conditions. Conclusions: The proteome reference map of Milnesium tardigradum provides the basis for further studies in order to identify and characterize the biochemical mechanisms of tolerance to extreme desiccation. The optimized proteomics workflow will enable application of sensitive quantification techniques to detect differences in protein expression, which are characteristic of the active and anhydrobiotic states of tardigrades
    Type of Publication: Journal article published
    PubMed ID: 20224743
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