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  • 1
    Publication Date: 2014-09-27
    Description: Inspired by the developments of synthetic biology and the need for improved genetic tools to exploit cyanobacteria for the production of renewable bioproducts, we developed a versatile platform for the construction of broad-host-range vector systems. This platform includes the following features: (i) an efficient assembly strategy in which modules released from 3 to 4 donor plasmids or produced by polymerase chain reaction are assembled by isothermal assembly guided by short GC-rich overlap sequences. (ii) A growing library of molecular devices categorized in three major groups: (a) replication and chromosomal integration; (b) antibiotic resistance; (c) functional modules. These modules can be assembled in different combinations to construct a variety of autonomously replicating plasmids and suicide plasmids for gene knockout and knockin. (iii) A web service, the CYANO-VECTOR assembly portal, which was built to organize the various modules, facilitate the in silico construction of plasmids, and encourage the use of this system. This work also resulted in the construction of an improved broad-host-range replicon derived from RSF1010, which replicates in several phylogenetically distinct strains including a new experimental model strain Synechocystis sp. WHSyn, and the characterization of nine antibiotic cassettes, four reporter genes, four promoters, and a ribozyme-based insulator in several diverse cyanobacterial strains.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2000-08-05
    Description: The circadian oscillator of the cyanobacterium Synechococcus elongatus, like those in eukaryotes, is entrained by environmental cues. Inactivation of the gene cikA (circadian input kinase) shortens the circadian period of gene expression rhythms in S. elongatus by approximately 2 hours, changes the phasing of a subset of rhythms, and nearly abolishes resetting of phase by a pulse of darkness. The CikA protein sequence reveals that it is a divergent bacteriophytochrome with characteristic histidine protein kinase motifs and a cryptic response regulator motif. CikA is likely a key component of a pathway that provides environmental input to the circadian oscillator in S. elongatus.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schmitz, O -- Katayama, M -- Williams, S B -- Kondo, T -- Golden, S S -- GM37040/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Aug 4;289(5480):765-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Texas A&M University, College Station, TX 77843-3258, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10926536" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Motifs ; Amino Acid Sequence ; *Bacterial Proteins ; *Biological Clocks/genetics/physiology ; *Circadian Rhythm/genetics/physiology ; Cyanobacteria/genetics/*physiology ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Genes, Reporter ; Luminescent Measurements ; Molecular Sequence Data ; Mutation ; Phenotype ; Protein Kinases/chemistry/*genetics/physiology ; Sequence Alignment
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1997-01-10
    Description: The long-standing supposition that the biological clock cannot function in cells that divide more rapidly than the circadian cycle was investigated. During exponential growth in which the generation time was 10 hours, the profile of bioluminescence from a reporter strain of the cyanobacterium Synechococcus (species PCC 7942) matched a model based on the assumption that cells proliferate exponentially and the bioluminescence of each cell oscillates in a cosine fashion. Some messenger RNAs showed a circadian rhythm in abundance during continuous exponential growth with a doubling time of 5 to 6 hours. Thus, the cyanobacterial circadian clock functions in cells that divide three or more times during one circadian cycle.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kondo, T -- Mori, T -- Lebedeva, N V -- Aoki, S -- Ishiura, M -- Golden, S S -- New York, N.Y. -- Science. 1997 Jan 10;275(5297):224-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-01 Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8985018" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Division ; *Circadian Rhythm ; Cyanobacteria/cytology/genetics/growth & development/*physiology ; Genes, Reporter ; Luciferases/genetics/metabolism ; Luminescence ; Mutation ; Photosynthetic Reaction Center Complex Proteins/genetics ; Photosystem II Protein Complex ; RNA, Bacterial/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Transformation, Bacterial
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 1998-09-04
    Description: Cyanobacteria are the simplest organisms known to have a circadian clock. A circadian clock gene cluster kaiABC was cloned from the cyanobacterium Synechococcus. Nineteen clock mutations were mapped to the three kai genes. Promoter activities upstream of the kaiA and kaiB genes showed circadian rhythms of expression, and both kaiA and kaiBC messenger RNAs displayed circadian cycling. Inactivation of any single kai gene abolished these rhythms and reduced kaiBC-promoter activity. Continuous kaiC overexpression repressed the kaiBC promoter, whereas kaiA overexpression enhanced it. Temporal kaiC overexpression reset the phase of the rhythms. Thus, a negative feedback control of kaiC expression by KaiC generates a circadian oscillation in cyanobacteria, and KaiA sustains the oscillation by enhancing kaiC expression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ishiura, M -- Kutsuna, S -- Aoki, S -- Iwasaki, H -- Andersson, C R -- Tanabe, A -- Golden, S S -- Johnson, C H -- Kondo, T -- MH01179/MH/NIMH NIH HHS/ -- New York, N.Y. -- Science. 1998 Sep 4;281(5382):1519-23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan. ishiura@bio.nagoya-u.ac.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9727980" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*genetics ; Biological Clocks/*genetics ; Circadian Rhythm/*genetics ; Circadian Rhythm Signaling Peptides and Proteins ; Cloning, Molecular ; Cyanobacteria/*genetics/physiology ; Feedback ; *Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Genes, Reporter ; Luminescence ; Models, Biological ; Molecular Sequence Data ; Multigene Family ; Mutation ; Promoter Regions, Genetic ; Recombinant Fusion Proteins ; Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2010-03-20
    Description: Although major progress has been made in uncovering the machinery that underlies individual biological clocks, much less is known about how multiple clocks coordinate their oscillations. We simultaneously tracked cell division events and circadian phases of individual cells of the cyanobacterium Synechococcus elongatus and fit the data to a model to determine when cell cycle progression slows as a function of circadian and cell cycle phases. We infer that cell cycle progression in cyanobacteria slows during a specific circadian interval but is uniform across cell cycle phases. Our model is applicable to the quantification of the coupling between biological oscillators in other organisms.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3118046/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3118046/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Qiong -- Pando, Bernardo F -- Dong, Guogang -- Golden, Susan S -- van Oudenaarden, Alexander -- R01 GM062419/GM/NIGMS NIH HHS/ -- R01 GM062419-05A2/GM/NIGMS NIH HHS/ -- R01 GM062419-06/GM/NIGMS NIH HHS/ -- R01 GM062419-07/GM/NIGMS NIH HHS/ -- R01 GM068957/GM/NIGMS NIH HHS/ -- R01 GM068957-07/GM/NIGMS NIH HHS/ -- R01 GM068957-08/GM/NIGMS NIH HHS/ -- R01-GM062419/GM/NIGMS NIH HHS/ -- R01-GM068957/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Mar 19;327(5972):1522-6. doi: 10.1126/science.1181759.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20299597" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/genetics/metabolism ; *Biological Clocks ; *Cell Cycle ; *Circadian Rhythm ; Circadian Rhythm Signaling Peptides and Proteins/genetics/metabolism ; Computer Simulation ; Light ; Luminescent Proteins/metabolism ; Microscopy, Fluorescence ; Models, Biological ; Monte Carlo Method ; Synechococcus/*cytology/genetics/metabolism/*physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1994-11-18
    Description: A diverse set of circadian clock mutants was isolated in a cyanobacterial strain that carries a bacterial luciferase reporter gene attached to a clock-controlled promoter. Among 150,000 clones of chemically mutagenized bioluminescent cells, 12 mutants were isolated that exhibit a broad spectrum of periods (between 16 and 60 hours), and 5 mutants were found that show a variety of unusual patterns, including arrhythmia. These mutations appear to be clock-specific. Moreover, it was demonstrated that in this cyanobacterium it is possible to clone mutant genes by complementation, which provides a means to genetically dissect the circadian mechanism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kondo, T -- Tsinoremas, N F -- Golden, S S -- Johnson, C H -- Kutsuna, S -- Ishiura, M -- GM37040/GM/NIGMS NIH HHS/ -- MH43836/MH/NIMH NIH HHS/ -- New York, N.Y. -- Science. 1994 Nov 18;266(5188):1233-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Institute for Basic Biology, Okazaki, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7973706" target="_blank"〉PubMed〈/a〉
    Keywords: Circadian Rhythm/*genetics ; Cloning, Molecular ; Cyanobacteria/*genetics/growth & development/physiology ; Darkness ; *Genes, Bacterial ; Genetic Complementation Test ; Light ; Luminescent Measurements ; Mutagenesis ; Mutation ; Temperature
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2011-01-15
    Description: Circadian clocks are self-sustained biological oscillators that can be entrained by environmental cues. Although this phenomenon has been studied in many organisms, the molecular mechanisms of entrainment remain unclear. Three cyanobacterial proteins and adenosine triphosphate (ATP) are sufficient to generate oscillations in phosphorylation in vitro. We show that changes in illumination that induce a phase shift in cultured cyanobacteria also cause changes in the ratio of ATP to adenosine diphosphate (ADP). When these nucleotide changes are simulated in the in vitro oscillator, they cause phase shifts similar to those observed in vivo. Physiological concentrations of ADP inhibit kinase activity in the oscillator, and a mathematical model constrained by data shows that this effect is sufficient to quantitatively explain entrainment of the cyanobacterial circadian clock.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3309039/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3309039/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rust, Michael J -- Golden, Susan S -- O'Shea, Erin K -- GM62419/GM/NIGMS NIH HHS/ -- R01 GM062419/GM/NIGMS NIH HHS/ -- R01 GM062419-08/GM/NIGMS NIH HHS/ -- R01 GM062419-09/GM/NIGMS NIH HHS/ -- R01 GM062419-09S1/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Jan 14;331(6014):220-3. doi: 10.1126/science.1197243.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Center for Systems Biology, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21233390" target="_blank"〉PubMed〈/a〉
    Keywords: ATP Synthetase Complexes/antagonists & inhibitors/metabolism ; Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Bacterial Proteins/antagonists & inhibitors/metabolism ; *Circadian Clocks ; *Circadian Rhythm ; Circadian Rhythm Signaling Peptides and Proteins/antagonists & ; inhibitors/metabolism ; Darkness ; *Energy Metabolism ; *Light ; Models, Biological ; Phosphorylation ; Synechococcus/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2015-06-27
    Description: Organisms are adapted to the relentless cycles of day and night, because they evolved timekeeping systems called circadian clocks, which regulate biological activities with ~24-hour rhythms. The clock of cyanobacteria is driven by a three-protein oscillator composed of KaiA, KaiB, and KaiC, which together generate a circadian rhythm of KaiC phosphorylation. We show that KaiB flips between two distinct three-dimensional folds, and its rare transition to an active state provides a time delay that is required to match the timing of the oscillator to that of Earth's rotation. Once KaiB switches folds, it binds phosphorylated KaiC and captures KaiA, which initiates a phase transition of the circadian cycle, and it regulates components of the clock-output pathway, which provides the link that joins the timekeeping and signaling functions of the oscillator.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4506712/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4506712/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chang, Yong-Gang -- Cohen, Susan E -- Phong, Connie -- Myers, William K -- Kim, Yong-Ick -- Tseng, Roger -- Lin, Jenny -- Zhang, Li -- Boyd, Joseph S -- Lee, Yvonne -- Kang, Shannon -- Lee, David -- Li, Sheng -- Britt, R David -- Rust, Michael J -- Golden, Susan S -- LiWang, Andy -- AI081982/AI/NIAID NIH HHS/ -- AI101436/AI/NIAID NIH HHS/ -- GM062419/GM/NIGMS NIH HHS/ -- GM100116/GM/NIGMS NIH HHS/ -- GM107521/GM/NIGMS NIH HHS/ -- R01 GM062419/GM/NIGMS NIH HHS/ -- R01 GM100116/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2015 Jul 17;349(6245):324-8. doi: 10.1126/science.1260031. Epub 2015 Jun 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Natural Sciences, University of California, Merced, CA 95343, USA. ; Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA. ; Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA. ; Department of Chemistry, University of California, Davis, CA 95616, USA. ; School of Natural Sciences, University of California, Merced, CA 95343, USA. Quantitative and Systems Biology, University of California, Merced, CA 95343, USA. ; Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA. ; Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA. ; Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA. Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA. ; School of Natural Sciences, University of California, Merced, CA 95343, USA. Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA. Quantitative and Systems Biology, University of California, Merced, CA 95343, USA. Chemistry and Chemical Biology, University of California, Merced, CA 95343, USA. Health Sciences Research Institute, University of California, Merced, CA 95343, USA. aliwang@ucmerced.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26113641" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/genetics/*metabolism ; *Circadian Rhythm ; Circadian Rhythm Signaling Peptides and Proteins/*chemistry/genetics/*metabolism ; Phosphorylation ; Protein Folding ; Protein Structure, Secondary ; Synechococcus/metabolism/*physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1985-09-13
    Description: A psbA gene encoding the target of photosystem II herbicide inhibition, the 32,000-dalton thylakoid membrane protein, has been cloned from a mutant of Anacystis nidulans R2, which is resistant to 3-(3,4-dichlorophenyl)-1,1-dimethylurea-(diuron). A cloned DNA fragment from within the coding region of this gene transforms wild-type cells to herbicide resistance, proving that mutation within psbA is responsible for that phenotype. The mutation consists of a single nucleotide change that replaces serine at position 264 of the wild-type protein with alanine in that of the diuron-resistant mutant.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Golden, S S -- Haselkorn, R -- New York, N.Y. -- Science. 1985 Sep 13;229(4718):1104-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3929379" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Cyanobacteria/*genetics ; Diuron ; Drug Resistance ; Electrophoresis, Polyacrylamide Gel ; *Herbicides ; Membrane Proteins/genetics ; Molecular Weight ; *Mutation ; Phenotype
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
    ISSN: 1432-072X
    Keywords: Key words CheY ; Cyanobacteria ; LysR ; OmpR ; Response regulator
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We designed a strategy to isolate and characterize response regulator genes from the cyanobacterium Synechococcus sp. strain PCC 7942 based on the premise that cyanobacterial response regulators would bear strong similarity to their counterparts from other eubacteria. Two response regulator genes, srrA and srrB, were isolated from Synechococcus and found to encode proteins similar to the OmpR subclass of response regulators. Disruption of either gene by insertional mutagenesis did not produce an obvious phenotype and did not affect the accumulation of psbAII mRNA under high-light conditions, indicating that these gene products are not involved in mediating the well characterized standard- to high-light transition response of photosystem II genes in this cyanobacterium. Analysis of the chromosomal region adjacent to srrA revealed the presence of another presumptive transcriptional activator gene. This gene, named lrrA, belongs to the lysR family. Attempts to disrupt lrrA or an adjacent ORF (orfG) were not successful, suggesting that these genes are important for the growth of Synechococcus.
    Type of Medium: Electronic Resource
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