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  • 1
    Electronic Resource
    Electronic Resource
    Enzymatic synthesis of bacteriophage fd viral DNA (1982)
    [s.l.] : Nature Publishing Group
    Nature 296 (1982), S. 828-832 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] An enzyme system with requirements similar to those for replication of phage fd replicative form (RF) DNA in bacteriophage fd-infected cells has been reconstituted with purified fd gene 2 protein, and DNA polymerase III holoenzyme, DNA binding protein I and rep-protein (rep-helicase) of Escherichia ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/296828a0
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    How do electrons get from here to there? (1981)
    [s.l.] : Nature Publishing Group
    Nature 293 (1981), S. 495-495 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] COMPARED to most chemical reactions, electron transfer is a simple process. An electron hops from one chemical site to another, in many cases without significant change in structure. Even so, electron transfer is at the heart of many critical issues in chemistry, physics and biology, and its study ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/293495a0
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    Recognition of two initiation codons for the synthesis of phage fd gene 2 protein (1980)
    Springer
    Molecular genetics and genomics 180 (1980), S. 489-494 
    Details
    ISSN: 1617-4623
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Bacteriophage fd gene 2 protein was specifically labeled with radioactive amino acids and was isolated from membranous cell structures as an apparently homogenous protein. Amino acid sequence analysis revealed that the protein was initiated at two distinct AUG codons close to the ribosome binding site. The two resulting translation products were found to begin with a deformylated methionine residue. Initiation at the first signal was used for 90% of the chains and at the second signal for 10% of the sequenced molecules. The use of one or the other chain start may influence functions of gene 2 protein.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00268051
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    Paper (German National Licenses)
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  • 4
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    Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach (2014)
    BioMed Central
    Details
    Publication Date: 2014-02-08
    Description: Background: Accurate estimation of parameters of biochemical models is required to characterize the dynamics of molecular processes. This problem is intimately linked to identifying the most informative experiments for accomplishing such tasks. While significant progress has been made, effective experimental strategies for parameter identification and for distinguishing among alternative network topologies remain unclear. We approached these questions in an unbiased manner using a unique community-based approach in the context of the DREAM initiative (Dialogue for Reverse Engineering Assessment of Methods). We created an in silico test framework under which participants could probe a network with hidden parameters by requesting a range of experimental assays; results of these experiments were simulated according to a model of network dynamics only partially revealed to participants. Results: We proposed two challenges; in the first, participants were given the topology and underlying biochemical structure of a 9-gene regulatory network and were asked to determine its parameter values. In the second challenge, participants were given an incomplete topology with 11 genes and asked to find three missing links in the model. In both challenges, a budget was provided to buy experimental data generated in silico with the model and mimicking the features of different common experimental techniques, such as microarrays and fluorescence microscopy. Data could be bought at any stage, allowing participants to implement an iterative loop of experiments and computation. Conclusions: A total of 19 teams participated in this competition. The results suggest that the combination of state-of-the-art parameter estimation and a varied set of experimental methods using a few datasets, mostly fluorescence imaging data, can accurately determine parameters of biochemical models of gene regulation. However, the task is considerably more difficult if the gene network topology is not completely defined, as in challenge 2. Importantly, we found that aggregating independent parameter predictions and network topology across submissions creates a solution that can be better than the one from the best-performing submission.
    Electronic ISSN: 1752-0509
    Topics: Biology
    Published by BioMed Central
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  • 5
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    Development of a next-generation NIL library in Arabidopsis thaliana for dissecting complex traits (2013)
    BioMed Central
    Details
    Publication Date: 2013-09-26
    Description: Background: The identification of the loci and specific alleles underlying variation in quantitative traits is an important goal for evolutionary biologists and breeders. Despite major advancements in genomics technology, moving from QTL to causal alleles remains a major challenge in genetics research. Near-isogenic lines are the ideal raw material for QTL validation, refinement of QTL location and, ultimately, gene discovery. Results: In this study, a population of 75 Arabidopsis thaliana near-isogenic lines was developed from an existing recombinant inbred line (RIL) population derived from a cross between physiologically divergent accessions Kas-1 and Tsu-1. First, a novel algorithm was developed to utilize genome-wide marker data in selecting RILs fully isogenic to Kas-1 for a single chromosome. Seven such RILs were used in 2 generations of crossing to Tsu-1 to create BC1 seed. BC1 plants were genotyped with SSR markers so that lines could be selected that carried Kas-1 introgressions, resulting in a population carrying chromosomal introgressions spanning the genome. BC1 lines were genotyped with 48 genome-wide SSRs to identify lines with a targeted Kas-1 introgression and the fewest genomic introgressions elsewhere. 75 such lines were selected and genotyped at an additional 41 SNP loci and another 930 tags using 2b-RAD genotyping by sequencing. The final population carried an average of 1.35 homozygous and 2.49 heterozygous introgressions per line with average introgression sizes of 5.32 and 5.16 Mb, respectively. In a simple case study, we demonstrate the advantage of maintaining heterozygotes in our library whereby fine-mapping efforts are conducted simply by self-pollination. Crossovers in the heterozygous interval during this single selfing generation break the introgression into smaller, homozygous fragments (sub-NILs). Additionally, we utilize a homozygous NIL for validation of a QTL underlying stomatal conductance, a low heritability trait. Conclusions: The present results introduce a new and valuable resource to the Brassicaceae research community that enables rapid fine-mapping of candidate loci in parallel with QTL validation. These attributes along with dense marker coverage and genome-wide chromosomal introgressions make this population an ideal starting point for discovery of genes underlying important complex traits of agricultural and ecological significance.
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
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