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  • 1
    Electronic Resource
    Electronic Resource
    Berkeley, Calif. : Berkeley Electronic Press (now: De Gruyter)
    Statistical applications in genetics and molecular biology 6.2007, 1, art5 
    ISSN: 1544-6115
    Source: Berkeley Electronic Press Academic Journals
    Topics: Biology
    Notes: Multi-color optical mapping is a new technique being developed to obtain detailed physical maps (indicating relative positions of various recognition sites) of DNA molecules. We consider a study design in which the data consist of noisy observations of multiple copies of a DNA molecule marked with colors at recognition sites. The primary goal is to estimate a physical map. A secondary goal is to estimate error rates associated with the experiment, which are potentially useful for analysis and refinement of the biochemical steps in the mapping procedure. We propose statistical models for various sources of error and use maximum likelihood estimation (MLE) to construct a physical map and estimate error rates. To overcome difficulties arising in the maximization process, a latent-variable Markov chain version of the model is proposed, and the EM algorithm is used for maximization. In addition, a simulated annealing procedure is applied to maximize the profile likelihood over the discrete space of sequences of colors. We apply the methods to simulated data on the bacteriophage lambda genome.
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  • 2
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 98 (1994), S. 4736-4741 
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 98 (1994), S. 3094-3098 
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 93 (1989), S. 8271-8275 
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Journal of comparative physiology 144 (1981), S. 277-286 
    ISSN: 1432-1351
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary Males of the fireflyPteroptyx cribellata of Papua New Guinea luminesce spontaneously in two principal modes: a regular one-per-second display flash (Fig. 1 A) and an irregular flicker of 3–10 peaks per second (Fig. 1B). In free run rhythmic display flashing by intact, restrained individuals, serial correlation analysis of interflash duration in successive cycles indicates that the variability of the brain-to-lantern excitation delay is negligible in comparison with the variability of the endogenous timing process (Figs. 6, 7). It is therefore possible to use the duration of the flash-to-flash interval of the intact firefly as a measure of endogenous pacemaker timing behavior. It is deduced that the cycling of the pacemaker is continuous, does not require that the animal see his own flash or even that he flash (Fig. 2 A), shows intercycle independence (Fig. 5) and may phase-shift its rhythm spontaneously upon occasion (Fig. 2C). Pacemaker period is normally distributed (Fig. 3), is not correlated with flash intensity, and appears to shorten slightly if a flash is skipped (Table 3). The occurrence of spontaneous flash skipping is taken to indicate that the timing process that measures pacemaker period can cycle independently of its usual triggering of the flash-excitation message to the lantern.
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  • 6
    ISSN: 1432-0983
    Keywords: C. reinhardii chloroplast DNA ; Orientation isomers ; Inverted repeat ; Recombination
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Two orientations of the Chlamydomonas reinhardii chloroplast (ct) genome are shown to be produced by recombination within the inverted repeat (IR) sequences that separate the two single copy (SC) regions. SC region 1 is bounded on its two ends by EeoRI restriction endonuclease fragments of 3.2 and 4.7 kilobase pairs (kb) (Rochaix 1978). The 3.2 kb EeoRI fragment overlaps a 51.3 kb BglII fragment spanning one of the 19.7 kb IR sequences, and the 4.7 kb EcoRI fragment overlaps a 42.1 kb BglII fragment spanning the other 19.7 kb IR sequence. We have shown by hybridization analysis that the 3.2 kb fragment also overlaps a BgIII fragment with a predicted size of 52.3 kb, and that the 4.7 kb fragment also overlaps a BglII fragment of a predicted size of 41.1 kb. The second set of BglII fragments are isomers produced by recombination localized to the IR region. The two isomers are present in approximately equimolar ratio. Knowledge of the isomeric composition of the C. reinhardii ctDNA is essential for establishing a correlation between genetic and physical maps of the ct genome.
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  • 7
    ISSN: 1432-0983
    Keywords: Chlamydomonas reinhardtii ; Chlorophyll synthesis ; Trans-splicing ; Chloroplast genes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Chloroplast DNA deletions in the unicellular green alga Chlamydomonas reinhardtii localize two novel chloroplast gene functions. One of these, tscA, is required in trans for splicing, in trans, of the first and second, but not the second and third, exons of the RNA of the chloroplast gene psaA. Previously, no chloroplast genes were known to be required in trans for the splicing of chloroplast RNA. The other chloroplast gene function is required for light-independent reduction of protochlorophyllide, a key step in the algal pathway of chlorophyll biosynthesis. Both functions reside in the same 4 kbp region of chloroplast DNA.
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  • 8
    ISSN: 1573-5028
    Keywords: Agrobacterium tumefaciens ; C4 photosynthesis ; Flaveria ; regeneration ; ribulose bisphosphate carboxylase/oxygenase ; transformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We report the successful transformation, via Agrobacterium tumefaciens infection, and regeneration of two species of the genus Flaveria: F. brownii and F. palmeri. We document the expression of a C3 plant gene, an abundantly expressed ribulose 1,5-bisphosphate carboxylase/oxygenase small subunit gene isolated from petunia, in these C4 plants. The organ-specific expression of this petunia gene in Flaveria brownii is qualitatively identical to its endogenous pattern of expression.
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  • 9
    ISSN: 1617-4623
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Proteins from chloroplast and cytoplasmic ribosomes of Chlamydomonas reinhardi were mapped by a two-dimensional gel electrophoresis system which also permitted their molecular weights to be determined. Estimates of the numbers of proteins in the ribosomal subunits are: small chloroplast, 22; small cytoplasmic, 26; large chloroplast, 26; large cytoplasmic, 39. Two pairs of proteins of the small subunits and four pairs of the large subunits had similar electrophoretic mobilities in both dimensions.
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  • 10
    ISSN: 1617-4623
    Keywords: Chloroplast ; Cytochromes ; Gabaculine Heme ; Heme attachment
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Chlamydomonas reinhardtii uses two c-type cytochromes for photosynthetic electron transfer: the thylakoid membrane-bound cytochrome f of the cytochrome b6f complex and the soluble cytochrome c6. Previously, a class of photosynthesis-minus, acetate-requiring mutants was identified which were deficient in both c-type cytochromes, and biochemical analyses of cytochrome c6 biosynthesis in these strains indicated that they were each blocked at the step of heme attachment to apocytochrome c6. In order to demonstrate that the deficiency in cytochrome f results from the same biochemical and genetic defect, cytochrome f biosynthesis was examined in the 136 mutant (a representative of this phenotypic class) and in spontaneous suppressor strains derived from 136. Pulse-radio-labeling experiments show that B6 synthesizes a form of cytochrome f that is rapidly degraded in vivo. This polypeptide is membrane associated and migrates with an electrophoretic mobility identical to that of standard apocytochrome f produced in vitro but slightly greater than that of standard holocytochrome f produced in vivo by wild-type cells. These findings suggest that the B6 strain is unable to convert apocytochrome f to holocytochrome f and that apocytochrome f is unstable in vivo. In the suppressed strains, accumulation of both holocytochrome f and holocytochrome c6 is restored. One suppressor mutation (strain B6R) displays uniparental inheritance whereas another (B6T3) displays Mendelian inheritance. In both cases, the three phenotypes, photosynthesis-plus, b6f + and cyt c6 + co-segregate in genetic crosses. This study therefore confirms that the dual cyt b6f/cytc6 − deficiency in B6 results from a single mutation that affects a step in holocytochrome formation that is common to the biosynthetic pathways of both plastidic c-type cytochromes. The study also confirms that pre-apocytochrome f synthesis, processing and association with the membrane is not dependent on heme attachment. Synthesis of cytochrome f does, however, appear to be dependent on heme availability. In cells depleted of tetrapyrrole pathway intermediates by gabaculine treatment, cytochrome f synthesis was significantly reduced. Since gabaculine treatment did not affect the stability of cytochrome f nor the accumulation of cytochrome f-encoding transcripts, the reduction is attributed to post-transcriptional regulation of preapocytochrome f synthesis via a pathway that is sensitive to the availability of heme or a tetrapyrrole pathway intermediate.
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