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  • EXPRESSION  (9)
  • 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: EXPRESSION ; Germany ; CLASSIFICATION ; CDNA ; ENZYMES ; HYBRIDIZATION ; TISSUE ; FAMILY ; primary ; TISSUES ; STAGE ; IN-SITU ; RT-PCR ; IMMUNITY ; HOST-DEFENSE ; in situ hybridization ; DEFENSE ; pathogen ; PATHOGENS ; ECHINATA ; Hydractinia ; HYDROID HYDRACTINIA ; chitin ; allorecognition ; GLYCOSYL HYDROLASES ; periderm
    Abstract: Chitinases are enzymes that degrade chitin, the second most abundant polymer in nature. They are ubiquitous among living organisms where they play a role in development, food-digestion and innate immunity. We have cloned and characterized the first cnidarian chitinase cDNA from the hydroid Hydractinia. The Hydractinia chitinase exhibits a typical secreted family 18 hydrolases primary structure. In situ hybridization and RT-PCR experiments showed that it is exclusively expressed in ectodermal tissues of the animal, only following metamorphosis while undetectable in embryonic and larval stages. Most prominent expression was observed in the stolonal compartment of colonies, structures that are covered by a chitinous periderm. Chitinase mRNA was detected in new branching points along stolons and in hyperplastic stolons indicating a role of the enzyme in pattern formation and allorecognition. It was also expressed in polyps where it was mostly restricted to their basal portion. This expression pattern suggests that HyChitI also fulfills a role in host defense, probably against fungal and nematode pathogens. Endodermal expression of HyChitI has never been observed, suggesting that the enzyme does not participate in food-digestion. (C) 2004 Elsevier Ltd. All rights reserved
    Type of Publication: Journal article published
    PubMed ID: 15236928
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  • 9
    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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  • 10
    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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