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  • American Association for the Advancement of Science (AAAS)  (10)
  • Biodiversity Research  (10)
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  • American Association for the Advancement of Science (AAAS)  (10)
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  • 1
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 327, No. 5968 ( 2010-02-19), p. 1004-1007
    Abstract: Lysine acetylation regulates many eukaryotic cellular processes, but its function in prokaryotes is largely unknown. We demonstrated that central metabolism enzymes in Salmonella were acetylated extensively and differentially in response to different carbon sources, concomitantly with changes in cell growth and metabolic flux. The relative activities of key enzymes controlling the direction of glycolysis versus gluconeogenesis and the branching between citrate cycle and glyoxylate bypass were all regulated by acetylation. This modulation is mainly controlled by a pair of lysine acetyltransferase and deacetylase, whose expressions are coordinated with growth status. Reversible acetylation of metabolic enzymes ensure that cells respond environmental changes via promptly sensing cellular energy status and flexibly altering reaction rates or directions. It represents a metabolic regulatory mechanism conserved from bacteria to mammals.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2010
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  • 2
    Online Resource
    Online Resource
    American Association for the Advancement of Science (AAAS) ; 2017
    In:  Science Vol. 355, No. 6329 ( 2017-03-10)
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 355, No. 6329 ( 2017-03-10)
    Abstract: Perfect matching of an assembled physical sequence to a specified designed sequence is crucial to verify design principles in genome synthesis. We designed and de novo synthesized 536,024–base pair chromosome synV in the “Build-A-Genome China” course. We corrected an initial isolate of synV to perfectly match the designed sequence using integrative cotransformation and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)–mediated editing in 22 steps; synV strains exhibit high fitness under a variety of culture conditions, compared with that of wild-type V strains. A ring synV derivative was constructed, which is fully functional in Saccharomyces cerevisiae under all conditions tested and exhibits lower spore viability during meiosis. Ring synV chromosome can extends Sc2.0 design principles and provides a model with which to study genomic rearrangement, ring chromosome evolution, and human ring chromosome disorders.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2017
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  • 3
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 298, No. 5591 ( 2002-10-04), p. 129-149
    Abstract: Anopheles gambiae is the principal vector of malaria, a disease that afflicts more than 500 million people and causes more than 1 million deaths each year. Tenfold shotgun sequence coverage was obtained from the PEST strain of A. gambiae and assembled into scaffolds that span 278 million base pairs. A total of 91% of the genome was organized in 303 scaffolds; the largest scaffold was 23.1 million base pairs. There was substantial genetic variation within this strain, and the apparent existence of two haplotypes of approximately equal frequency (“dual haplotypes”) in a substantial fraction of the genome likely reflects the outbred nature of the PEST strain. The sequence produced a conservative inference of more than 400,000 single-nucleotide polymorphisms that showed a markedly bimodal density distribution. Analysis of the genome sequence revealed strong evidence for about 14,000 protein-encoding transcripts. Prominent expansions in specific families of proteins likely involved in cell adhesion and immunity were noted. An expressed sequence tag analysis of genes regulated by blood feeding provided insights into the physiological adaptations of a hematophagous insect.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    RVK:
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2002
    detail.hit.zdb_id: 128410-1
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  • 4
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 379, No. 6637 ( 2023-03-17)
    Abstract: Autoimmune diseases such as ankylosing spondylitis (AS) can be caused by emerging neoantigens that break immune tolerance in humans. Posttranslational modifications (PTMs) have been shown to be a critical mechanism that alters protein structure and function to generate neoantigens and induce subsequent autoimmune responses. Previous studies have confirmed that citrulline-modified peptides are a critical source of neoantigens in rheumatoid arthritis. However, the molecular mechanisms underlying neoantigen formation and pathogenic autoreactive responses for AS are largely unknown. There is an urgent need to develop a systematic approach to profiling the possible PTMs in patients with AS and identifying AS-associated PTMs responsible for autoreactive neoantigen production to better understand the etiology of autoimmune diseases. RATIONALE AS has been suggested to be an autoimmune disease because of its clear correlation with certain major histocompatibility complex (MHC) alleles, including HLA-B27. Neoantigens have been hypothesized to induce an aberrant immune response, leading to pathogenic autoreactive T cell responses and autoantibody generation in AS. Here, we developed a systematic open search approach to identify any possible amino acid residues and derivatives in the proteins that are different from the genomic coding sequences. We then applied this information to identify AS-related neoantigens with PTMs within a possible pool of PTM autoantigens and elucidate the pathogenesis of AS. RESULTS An open search approach was applied to identify any possible amino acid derivatives across the proteome of patients with AS. This approach generated a large set of noncoded amino acids representing the mass differences between the coded amino acids and actual residues. Among these, an amino acid derivative with a delta mass of 72.021 showed the greatest increase in patients with AS and resulted from a PTM called cysteine carboxyethylation. In vitro and in vivo experiments demonstrated that carboxyethylation at a cysteine residue of integrin αIIb [ITGA2B (CD41)] was catalyzed by cystathionine beta synthase (CBS) in a process that required 3-hydroxypropionic acid (3-HPA), a metabolite commonly released from gut microbes. Cysteine carboxyethylation induced the lysosomal degradation of ITGA2B and produced neoantigens that triggered MHC-II–dependent CD4 + T cell responses. Fluorescence polarization and enzyme-linked immunosorbent assay (ELISA) demonstrated that the identified carboxyethylated peptide (ITGA2B-ceC96) specifically interacted with HLA-DRA*01/HLA-DRB1*04 and was associated with autoantibody production and T cell responses in HLA-DRB1*04 patients. Additional in vitro assays showed that the neoantigen ITGA2B-ceC96 correlated with 3-HPA levels but was independent of CBS expression. HLA-DRB1 haplotype, the carboxyethylated peptide, specific autoantibodies, and 3-HPA levels in patients with AS all correlated with one another. 3-HPA–treated and ITGA2B-ceC96–immunized HLA-DR4 transgenic mice developed colitis and vertebral bone erosion. Thus, cysteine carboxyethylation induced by the metabolite 3-HPA generates a neoantigen that appears to be critical for autoimmune responses in patients with AS. CONCLUSION Cysteine carboxyethylation is an in vivo protein modification induced by the metabolite 3-HPA, which is commonly released from gut microbes. Carboxyethylated ITGA2B then induces autoantibody production and autoimmune response in AS. Our work provides a systematic workflow to identify differentially modified proteins that are important for neoantigen production in immune disorders. This approach furthers our understanding of AS pathogenesis and may aid in the development of neoantigen-based diagnosis and treatment for AS and other autoimmune diseases. Metabolite-induced cysteine carboxyethylation provokes HLA-restricted autoimmune responses in ankylosing spondylitis. 3-HPA, which is commonly obtained from food and gut microbes, induces carboxyethylation of cysteine residues in integrin αIIb (ITGA2B). Cysteine carboxyethylation requires CBS, and carboxyethylated ITGA2B (ITGA2B-ceC96) peptides are recruited to the HLA-DR4 complex and thereby stimulate CD4 + T cell responses closely related to AS.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2023
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  • 5
    Online Resource
    Online Resource
    American Association for the Advancement of Science (AAAS) ; 2019
    In:  Science Vol. 364, No. 6446 ( 2019-06-21)
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 364, No. 6446 ( 2019-06-21)
    Abstract: Ruminants are the only extant mammalian group possessing bony (osseous) headgear. We obtained 221 transcriptomes from bovids and cervids and sequenced three genomes representing the only two pecoran lineages that convergently lack headgear. Comparative analyses reveal that bovid horns and cervid antlers share similar gene expression profiles and a common cellular basis developed from neural crest stem cells. The rapid regenerative properties of antler tissue involve exploitation of oncogenetic pathways, and at the same time some tumor suppressor genes are under strong selection in deer. These results provide insights into the evolutionary origin of ruminant headgear as well as mammalian organ regeneration and oncogenesis.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2019
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  • 6
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 354, No. 6318 ( 2016-12-16), p. 1414-1419
    Abstract: Improving the platinum (Pt) mass activity for the oxygen reduction reaction (ORR) requires optimization of both the specific activity and the electrochemically active surface area (ECSA). We found that solution-synthesized Pt/NiO core/shell nanowires can be converted into PtNi alloy nanowires through a thermal annealing process and then transformed into jagged Pt nanowires via electrochemical dealloying. The jagged nanowires exhibit an ECSA of 118 square meters per gram of Pt and a specific activity of 11.5 milliamperes per square centimeter for ORR (at 0.9 volts versus reversible hydrogen electrode), yielding a mass activity of 13.6 amperes per milligram of Pt, nearly double previously reported best values. Reactive molecular dynamics simulations suggest that highly stressed, undercoordinated rhombus-rich surface configurations of the jagged nanowires enhance ORR activity versus more relaxed surfaces.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    RVK:
    RVK:
    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2016
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  • 7
    Online Resource
    Online Resource
    American Association for the Advancement of Science (AAAS) ; 2023
    In:  Science Vol. 379, No. 6629 ( 2023-01-20), p. 288-294
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 379, No. 6629 ( 2023-01-20), p. 288-294
    Abstract: Stabilizing perovskite crystal structure and mitigating lithium ion diffusion enhance the performance of perovskite solar modules.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    RVK:
    RVK:
    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2023
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  • 8
    Online Resource
    Online Resource
    American Association for the Advancement of Science (AAAS) ; 2021
    In:  Science Vol. 372, No. 6545 ( 2021-05-28), p. 948-952
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 372, No. 6545 ( 2021-05-28), p. 948-952
    Abstract: Quantum walks are the quantum mechanical analog of classical random walks and an extremely powerful tool in quantum simulations, quantum search algorithms, and even for universal quantum computing. In our work, we have designed and fabricated an 8-by-8 two-dimensional square superconducting qubit array composed of 62 functional qubits. We used this device to demonstrate high-fidelity single- and two-particle quantum walks. Furthermore, with the high programmability of the quantum processor, we implemented a Mach-Zehnder interferometer where the quantum walker coherently traverses in two paths before interfering and exiting. By tuning the disorders on the evolution paths, we observed interference fringes with single and double walkers. Our work is a milestone in the field, bringing future larger-scale quantum applications closer to realization for noisy intermediate-scale quantum processors.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    RVK:
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2021
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  • 9
    Online Resource
    Online Resource
    American Association for the Advancement of Science (AAAS) ; 2022
    In:  Science Vol. 378, No. 6623 ( 2022-12-02)
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 378, No. 6623 ( 2022-12-02)
    Abstract: Cell-cell communication through direct contact is pervasive in multicellular organisms and is essential in many fundamental biological processes. The ability to experimentally track such cell-cell communication signaling could substantially advance our understanding of diverse biological processes from embryogenesis to tumorigenesis. The existing technologies are not suitable to monitor and trace cell-cell contact for long-term in vivo studies, because many biological processes such as embryogenesis, tumorigenesis, and tissue regeneration develop over time after the initial cell-cell contact. RATIONALE The Notch pathway transmits signaling through direct cell-cell contact in many cellular processes during development and homeostasis. In the canonical Notch pathway, upon cell contact, the Notch ligand on one cell binds to the Notch receptor on another cell to trigger a signaling pathway that leads to transcription activation of particular genes. To understand the dynamic in vivo cell-cell communications over time, we developed an intercellular genetic approach using the synthetic Notch pathway (synNotch) that converts a cellular contact event into a controllable transcriptional program. We engineered in mice an artificial Notch ligand, a membrane-tethered green fluorescent protein (GFP), into one cell type (the sender cell) and an artificial receptor in which the extracellular and intracellular domains of Notch were replaced with an anti-GFP nanobody and the tetracycline transactivator, respectively, into another cell type (the receiver cell). Contact between the sender and receiver cells triggered synNotch signaling that activated the downstream transcriptional programs in the receiver cell in vivo. To reveal the ongoing cell-cell contact, as reflected by synNotch activation in a receiver cell after direct contact with a sender cell, we used a tet-off system to express detectable reporters. To trace cell contact history, we used the Cre-loxP system to genetically fate map receiver cells, along with their progenies, permanently after cell contact. RESULTS In the intercellular genetic system, we demonstrated that endothelial cells (receiver cells) in the developing heart were genetically labeled after contact with neighboring cardiomyocytes (sender cells). The endothelial cells that had contact with cardiomyocytes in early embryogenesis were permanently tagged with the genetic reporter. Their progenies migrated into liver and subsequently formed a substantial portion of the vasculature there, suggesting that part of the liver vasculature originates from the developing heart during embryogenesis. Application of these synNotch mice in tumorigenesis revealed the contact history between tumor cells (sender cells) and endothelial cells (receiver cells) during tumor growth and revealed that tumor vessels not only expanded within the tumor but also outgrew into the periphery of the tumor and had strong angiogenic properties. Upon contacting tumor cells, these endothelial cells gained properties in angiogenic, migratory, and inflammatory responses. Additionally, we generated mice for Cre-induced synNotch ligand or receptor expression, enabling broadly applicable approaches for genetic labeling of cell-cell contact and study of cell contact signaling in vivo. Engineering both the synNotch ligand and receptor, as well as different genetic readouts, in one mouse, we demonstrated simultaneous yet distinct recording of not only ongoing cell-cell contact but also historical cell-cell contact. CONCLUSION Our work provides a genetic system for recording cell-cell contact and cell contact history in vivo. The implications of our findings are that endothelial cells in the developing heart migrate and contribute to the liver vasculature, whereas endothelial cells in tumors not only expand within the tumor but also grow outward into the boundary-adjacent normal tissue with robust angiogenesis. The suite of new synNotch mouse lines provides a toolbox for genetic labeling and tracing of contacts between any cell type, offering a useful approach for studying dynamic in vivo cell-cell communications and the resulting cell fate plasticity in diverse life science fields. Monitoring of cell-cell contact in the heart. ( A ) Whole-mount fluorescence image of a mouse embryo showing that cardiomyocytes and endothelial cells express the synNotch ligand (green) and the synNotch receptor (purple). ( B to D ) Whole-mount images of synNotch neonatal hearts shown in green (B), blue (C), and red (D) fluorescence channels. Present and past cell contact signaling are displayed by blue and red fluorescence, respectively.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    RVK:
    RVK:
    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2022
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  • 10
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 296, No. 5573 ( 2002-05-31), p. 1661-1671
    Abstract: The high degree of similarity between the mouse and human genomes is demonstrated through analysis of the sequence of mouse chromosome 16 (Mmu 16), which was obtained as part of a whole-genome shotgun assembly of the mouse genome. The mouse genome is about 10% smaller than the human genome, owing to a lower repetitive DNA content. Comparison of the structure and protein-coding potential of Mmu 16 with that of the homologous segments of the human genome identifies regions of conserved synteny with human chromosomes (Hsa) 3, 8, 12, 16, 21, and 22. Gene content and order are highly conserved between Mmu 16 and the syntenic blocks of the human genome. Of the 731 predicted genes on Mmu 16, 509 align with orthologs on the corresponding portions of the human genome, 44 are likely paralogous to these genes, and 164 genes have homologs elsewhere in the human genome; there are 14 genes for which we could find no human counterpart.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    RVK:
    RVK:
    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2002
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    detail.hit.zdb_id: 2066996-3
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    SSG: 11
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