1
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Abstract
DNA restriction endonuclease fragment patterns corresponding to both the rbcS and cab multigene families of pea are each shown to segregate as single Mendelian units in the F(2) progeny of two separate crosses. All of the observed variation in each of the multigene families is thus organized on the chromosome in a tightly linked complex. Linkage relationships between both multigene families and an array of morphological and isozyme markers establish the location of the rbcS and cab gene clusters on pea chromosomes 5 and 2, respectively. Our results, which indicate a high level of DNA restriction fragment length polymorphism in pea, suggest sufficient variation to permit the construction of a highly detailed linkage map.
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Affiliation(s)
- N O Polans
- Department of Plant Biology, Carnegie Institution of Washington, 290 Panama Street, Stanford, CA 94305
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2
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Kaufman LS, Watson JC, Thompson WF. Light-regulated changes in DNase I hypersensitive sites in the rRNA genes of Pisum sativum. Proc Natl Acad Sci U S A 2010; 84:1550-4. [PMID: 16578799 PMCID: PMC304473 DOI: 10.1073/pnas.84.6.1550] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have examined the rDNA chromatin of Pisum sativum plants grown with or without exposure to light for the presence of DNase I hypersensitive sites and possible developmental changes in their distribution. Isolated nuclei from pea seedlings were incubated with various concentrations of DNase I. To visualize the hypersensitive sites, DNA purified from these nuclei was restricted and analyzed by gel blot hybridization. We find that several sites exist in both the coding and noncoding regions of rDNA repeating units. Several of the sites in the nontranscribed spacer region are present in the light but are absent in the dark. Conversely, the hypersensitive sites within the mature rRNA coding regions are present in the dark but absent in the light. There are two major length variants of the rRNA genes in P. sativum var. Alaska. The sites in the nontranscribed spacer region that appear during the light treatment occur only in the shorter of these two length variants in this cultivar.
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Affiliation(s)
- L S Kaufman
- Carnegie Institution of Washington, 290 Panama Street, Stanford, CA 94305
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3
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Abstract
We have mapped all the cleavage sites for the restriction endonucleases BstEII, Kpn I, Pst I, Pvu II, Sac I, Sal I, Sma I, and Xho I on the circular chloroplast chromosomes from mung bean and pea. The mung bean chloroplast genome measures 150 kilobase pairs (kb) in length; it includes two identical sequences of 23 kb that contain the ribosomal genes and are arranged as an inverted repeat separated by single-copy regions of 21 and 83 kb. The pea chloroplast genome is only 120 kb in size, has only one set of ribosomal genes, and does not possess any detectable repeated sequences. The mung bean inverted repeat structure is common to all other nonleguminous higher plant chloroplast genomes studied, whereas the pea structure has been found only in the closely related legume Vicia faba. We conclude from these data that loss of one copy of the inverted repeat sequence has occurred only rarely during the evolution of the Angiosperms, and in the case of the legumes after the divergence of the mung bean line from the pea-Vicia line. We present hybridization data indicating that rearrangements that change the linear order of homologous sequences within the chloroplast genome have been quite frequent during the course of legume evolution.
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Affiliation(s)
- J D Palmer
- The Carnegie Institution of Washington, Department of Plant Biology, Stanford, California 94305
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4
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Allen GC, Flores-Vergara MA, Krasynanski S, Kumar S, Thompson WF. A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide. Nat Protoc 2007; 1:2320-5. [PMID: 17406474 DOI: 10.1038/nprot.2006.384] [Citation(s) in RCA: 567] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We describe a modification of the DNA extraction method, in which cetyltrimethylammonium bromide (CTAB) is used to extract nucleic acids from plant tissues. In contrast to the original method, the modified CTAB procedure is faster, omits the selective precipitation and CsCl gradient steps, uses less expensive and toxic reagents, requires only inexpensive laboratory equipment and is more readily adapted to high-throughput DNA extraction. This protocol yields approximately 5-30 microg of total DNA from 200 mg of tissue fresh weight, depending on plant species and tissue source. It can be completed in as little as 5-6 h.
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Affiliation(s)
- G C Allen
- Department of Horticultural Science and Crop Science, 1200 Partners II, Campus Box 7550, 840 Main Campus Drive, North Carolina State University, Raleigh, NC 27606-7550, USA.
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5
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Abstract
Naturally occurring cell loss in the retinal ganglion cell population of one eye can be interrupted by removal of the other eye in newborn rodents. Many of the rescued retinal ganglion cells which project ipsilaterally reside in the nasal retina, that part of the retina normally giving rise to primarily crossed optic axons. Their naturally occurring elimination has been attributed to their hypothesized late neurogenesis and the consequent delayed time of arrival of their axons in the target visual nuclei, thereby placing them at a competitive disadvantage with other, early arriving, optic axons. By combining the technique of tritiated thymidine autoradiography with the retrograde axonal transport of horseradish peroxidase in rats that had been enucleated on the day of birth, we report here that rescued cells in the nasal retina which project ipsilaterally are generated at the same time as their neighbours in the temporal retina. Time of genesis does not distinguish them; consequently, their axons should not differ in their arrival times within the target visual nuclei. Since their only obvious anomaly is one of pathway choice at the optic chiasm, their place of arrival, rather than their time, may ultimately determine their naturally occurring elimination.
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Affiliation(s)
- B. E. Reese
- Neuroscience Research Institute and Department of Psychology, University of California, Santa Barbara, CA 93106, USA
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6
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Abstract
A significant number of studies have detected a post-transcriptional component in the light responses of nuclear genes. As yet there are few in-depth studies of the mechanism(s) involved, and it seems likely some additional examples have been missed. For instance, transcriptional responses have sometimes been inferred on the basis of experiments with translational fusions containing both the promoter and 5' UTR of the test gene, but we now know that elements within the 5' UTR can mediate post-transcriptional light responses. Similarly, because of possible changes in translation rates and protein turnover, the common assumption that mRNA levels directly dictate protein levels is tenuous at best. It is no longer permissible to assume that the biological effect of a gene is a simple function of its transcription. Thus it is likely that with careful experimental design, reports of nuclear-encoded post-transcriptional gene regulation will become increasingly prevalent.
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Affiliation(s)
- M E Petracek
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK 74078, USA
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7
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Ascenzi R, Ingram JL, Massel M, Thompson WF, Spiker S, Weissinger AK. The role of cell differentiation state and HMG-I/Y in the expression of transgenes flanked by matrix attachment regions. Transgenic Res 2001; 10:465-70. [PMID: 11708656 DOI: 10.1023/a:1012082602587] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The tobacco nuclear matrix attachment region (MAR), RB7, has been shown to have a much greater effect on transgene expression in cultured cells than in transgenic plants. This is comparable to work in mouse systems showing that MARs have a positive effect on transgene expression in embryonic tissues but not adult tissues. There are several possible explanations for these observations. One is that cell differentiation state and proliferation rate can affect MAR function. We tested this possibility by initiating suspension cell cultures from well-characterized transgenic plants transformed with 35S::GUS with and without flanking MARs and then comparing GUS specific activity in the cell lines to those of the transgenic plants from which the cell lines were derived. If cell differentiation state and proliferation rate do affect MAR function, we would expect the ratio of transgene expression (cell suspensions : plants) to be greater in MAR lines than in control lines. This turned out not to be the case. Thus, it appears that MAR function is not enhanced simply because cells in culture divide rapidly and are not differentiated. Because in animal systems the chromosomal protein HMG-I/Y has been shown to be upregulated in proliferating cells and may have a role in MAR function, we have also examined the levels of the tobacco HMG-I/Y homolog by immunoblotting. The level of this protein does not differ between primary transformant cultured cells (NT-1) and Nicotiana tabacum plants (SR-1). However, a higher molecular weight cross-reacting polypeptide was found in nuclei from the NT-1 cell suspensions but was not detected in SR-1 leaf nuclei or cell suspensions derived from the SR-1 plants.
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Affiliation(s)
- R Ascenzi
- Department of Botany, North Carolina State University, Raleigh 27695-7612, USA
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8
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Persson S, Wyatt SE, Love J, Thompson WF, Robertson D, Boss WF. The Ca(2+) status of the endoplasmic reticulum is altered by induction of calreticulin expression in transgenic plants. Plant Physiol 2001; 126:1092-104. [PMID: 11457960 PMCID: PMC116466 DOI: 10.1104/pp.126.3.1092] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2001] [Revised: 03/14/2001] [Accepted: 04/16/2001] [Indexed: 05/21/2023]
Abstract
To investigate the endoplasmic reticulum (ER) Ca(2+) stores in plant cells, we generated tobacco (Nicotiana tabacum; NT1) suspension cells and Arabidopsis plants with altered levels of calreticulin (CRT), an ER-localized Ca(2+)-binding protein. NT1 cells and Arabidopsis plants were transformed with a maize (Zea mays) CRT gene in both sense and antisense orientations under the control of an Arabidopsis heat shock promoter. ER-enriched membrane fractions from NT1 cells were used to examine how altered expression of CRT affects Ca(2+) uptake and release. We found that a 2.5-fold increase in CRT led to a 2-fold increase in ATP-dependent (45)Ca(2+) accumulation in the ER-enriched fraction compared with heat-shocked wild-type controls. Furthermore, after treatment with the Ca(2+) ionophore ionomycin, ER microsomes from NT1 cells overproducing CRT showed a 2-fold increase in the amount of (45)Ca(2+) released, and a 2- to 3-fold increase in the amount of (45)Ca(2+) retained compared with wild type. These data indicate that altering the production of CRT affects the ER Ca(2+) pool. In addition, CRT transgenic Arabidopsis plants were used to determine if altered CRT levels had any physiological effects. We found that the level of CRT in heat shock-induced CRT transgenic plants correlated positively with the retention of chlorophyll when the plants were transferred from Ca(2+)-containing medium to Ca(2+)-depleted medium. Together these data are consistent with the hypothesis that increasing CRT in the ER increases the ER Ca(2+) stores and thereby enhances the survival of plants grown in low Ca(2+) medium.
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Affiliation(s)
- S Persson
- Dpartment of Botany, North Carolina State University, Raleigh, North Carolina 27695-7612, USA
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9
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Ranvaud R, Thompson WF, Silveira-Moriyama L, Balkwill LL. The speed of pitch resolution in a musical context. J Acoust Soc Am 2001; 109:3021-3030. [PMID: 11425144 DOI: 10.1121/1.1367254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In five experiments, we investigated the speed of pitch resolution in a musical context. In experiments 1-3, listeners were presented an incomplete scale (doh, re, mi, fa, sol, la, ti) and then a probe tone. Listeners were instructed to make a rapid key-press response to probe tones that were relatively proximal in pitch to the last note of the scale (valid trials), and to ignore other probe tones (invalid trials). Reaction times were slower if the pitch of the probe tone was dissonant with the expected pitch (i.e., the completion of the scale, or doh) or if the probe tone was nondiatonic to the key implied by the scale. In experiments 4 and 5, listeners were presented a two-octave incomplete arpeggio, and then a probe tone. In this case, listeners were asked to make a rapid key-press response to probe tones that were relatively distant in pitch from the last note of the arpeggio. Under these conditions, registral direction and pitch proximity were the dominant influences on reaction time. Results are discussed in view of research on auditory attention and models of musical pitch.
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Affiliation(s)
- R Ranvaud
- Departamento de Fisiologia e Biofisíca, Instituto de Ciências Biomédicas, Universidade de São Paulo, SP, Brazil
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10
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Abstract
The "Mozart effect" refers to claims that people perform better on tests of spatial abilities after listening to music composed by Mozart. We examined whether the Mozart effect is a consequence of between-condition differences in arousal and mood. Participants completed a test of spatial abilities after listening to music or sitting in silence. The music was a Mozart sonata (a pleasant and energetic piece) for some participants and an Albinoni adagio (a slow, sad piece) for others. We also measured enjoyment, arousal, and mood. Performance on tbe spatial task was better following the music than the silence condition but only for participants who heard Mozart. The two music selections also induced differential responding on the enjoyment, arousal and mood measures. Moreover, when such differences were held constant by statistical means, the Mozart effect disappeared. These findings provide compelling evidence that the Mozart effect is an artifact of arousal and mood.
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Affiliation(s)
- W F Thompson
- Department of Psychology, Atkinson College, York University, Toronto, Ontario, Canada.
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11
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Abstract
In 3 experiments, the authors examined short-term memory for pitch and duration in unfamiliar tone sequences. Participants were presented a target sequence consisting of 2 tones (Experiment 1) or 7 tones (Experiments 2 and 3) and then a probe tone. Participants indicated whether the probe tone matched 1 of the target tones in both pitch and duration. Error rates were relatively low if the probe tone matched 1 of the target tones or if it differed from target tones in pitch, duration, or both. Error rates were remarkably high, however, if the probe tone combined the pitch of 1 target tone with the duration of a different target tone. The results suggest that illusory conjunctions of these dimensions frequently occur. A mathematical model is presented that accounts for the relative contribution of pitch errors, duration errors, and illusory conjunctions of pitch and duration.
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Affiliation(s)
- W F Thompson
- Department of Psychology, Atkinson Faculty of Liberal and Professional Studies, York University, Toronto, Ontario, Canada.
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12
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Hansen ER, Petracek ME, Dickey LF, Thompson WF. The 5' end of the pea ferredoxin-1 mRNA mediates rapid and reversible light-directed changes in translation in tobacco. Plant Physiol 2001; 125:770-8. [PMID: 11161034 PMCID: PMC64878 DOI: 10.1104/pp.125.2.770] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2000] [Revised: 07/12/2000] [Accepted: 10/02/2000] [Indexed: 05/20/2023]
Abstract
Ferredoxin-1 (Fed-1) mRNA contains an internal light response element (iLRE) that destabilizes mRNA when light-grown plants are placed in darkness. mRNAs containing this element dissociate from polyribosomes in the leaves of transgenic tobacco (Nicotiana tabacum) plants transferred to the dark for 2 d. Here, we report in vivo labeling experiments with a chloramphenicol acetyl transferase mRNA fused to the Fed-1 iLRE. Our data indicate that the Fed-1 iLRE mediates a rapid decline in translational efficiency and that iLRE-containing mRNAs dissociate from polyribosomes within 20 min after plants are transferred to darkness. Both events occur before the decline in mRNA abundance, and polyribosome association is rapidly reversible if plants are re-illuminated. These observations support a model in which Fed-1 mRNA in illuminated leaves is stabilized by its association with polyribosomes, and/or by translation. In darkness a large portion of the mRNA dissociates from polyribosomes and is subsequently degraded. We also show that a significant portion of total tobacco leaf mRNA is shifted from polyribosomal to non-polyribosomal fractions after 20 min in the dark, indicating that translation of other mRNAs is also rapidly down-regulated in response to darkness. This class includes some, but not all, cytoplasmic mRNAs encoding proteins involved in photosynthesis.
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Affiliation(s)
- E R Hansen
- Department of Botany, North Carolina State University, Raleigh, North Carolina 27695, USA
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13
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Abstract
In 3 experiments, the authors examined short-term memory for pitch and duration in unfamiliar tone sequences. Participants were presented a target sequence consisting of 2 tones (Experiment 1) or 7 tones (Experiments 2 and 3) and then a probe tone. Participants indicated whether the probe tone matched 1 of the target tones in both pitch and duration. Error rates were relatively low if the probe tone matched 1 of the target tones or if it differed from target tones in pitch, duration, or both. Error rates were remarkably high, however, if the probe tone combined the pitch of 1 target tone with the duration of a different target tone. The results suggest that illusory conjunctions of these dimensions frequently occur. A mathematical model is presented that accounts for the relative contribution of pitch errors, duration errors, and illusory conjunctions of pitch and duration.
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Affiliation(s)
- W F Thompson
- Department of Psychology, Atkinson Faculty of Liberal and Professional Studies, York University, Toronto, Ontario, Canada.
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14
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Ling J, Wells DR, Tanguay RL, Dickey LF, Thompson WF, Gallie DR. Heat shock protein HSP101 binds to the Fed-1 internal light regulator y element and mediates its high translational activity. Plant Cell 2000; 12:1213-27. [PMID: 10899985 PMCID: PMC149060 DOI: 10.1105/tpc.12.7.1213] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2000] [Accepted: 05/01/2000] [Indexed: 05/20/2023]
Abstract
The internal light-regulatory element (iLRE) of ferredoxin (Fed-1) mRNA, comprising the 5' leader and at least the first 13 codons of the open reading frame, controls transcript abundance after illumination of the plant in a translation-dependent manner. We have characterized the RNA binding activities associated with the Fed-1 iLRE and have identified one activity as the heat shock protein HSP101, a protein shown to bind the 5' leader of tobacco mosaic virus. HSP101 was sufficient and necessary to mediate a high level of translational activity from a Fed-1 iLRE-containing mRNA in yeast. Moreover, the Fed-1 iLRE substantially enhanced translation of reporter mRNAs in plant protoplasts expressing HSP101. Expression of HSP101 was subject to developmental regulation in leaves in that expression was highest in young leaves. These data suggest that Fed-1 mRNA may use the HSP101 regulatory mechanism as a means of ensuring a high level of translation required for the light-mediated regulation of Fed-1 mRNA stability.
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Affiliation(s)
- J Ling
- Department of Biochemistry, University of California, Riverside 92521-0129, USA
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15
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Abstract
In four experiments, we examined the effects of exposure to unfamiliar tone sequences on melodic expectancy and memory. In Experiment 1, 30 unfamiliar tone sequences (target sequences) were presented to listeners three times each in random order (exposure phase), and listeners recorded the number of notes in each sequence. Listeners were then presented target and novel sequences and rated how well the final note continued the pattern of notes that preceded it. Novel sequences were identical to target sequences, except for the final note. Ratings were significantly higher for target sequences than for novel sequences, illustrating the influence of exposure on melodic expectancy. Experiment 2 confirmed that without exposure to target sequences, ratings were equivalent for target and novel sequences. In Experiment 3, new listeners were assessed for explicit memory for target sequences following the exposure phase. Recognition of target sequences was above chance, but unrelated to expectancy judgments in Experiment 1. Experiment 4 replicated the exposure effect, using a modified experiment design, and confirmed that the effect is not dependent on explicit memory for sequences. We discuss the idea that melodic expectancies are influenced by implicit memory for recently heard melodic patterns.
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Affiliation(s)
- W F Thompson
- Department of Psychology, Atkinson College, York University, Toronto, Ontario, Canada.
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16
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Abstract
Matrix attachment regions (MARs) are operationally defined as DNA elements that bind specifically to the nuclear matrix in vitro. It is possible, although unproven, that they also mediate binding of chromatin to the nuclear matrix in vivo and alter the topology of the genome in interphase nuclei. When MARs are positioned on either side of a transgene their presence usually results in higher and more stable expression in transgenic plants or cell lines, most likely by minimizing gene silencing. Our review explores current data and presents several plausible models to explain MAR effects on transgene expression.
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Affiliation(s)
- G C Allen
- Department of Botany, North Carolina State University, Raleigh 27695, USA.
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17
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Abstract
We show that the tightly regulated tetracycline-sensitive Top10 promoter system (Weinmann et al. Plant J. 1994, 5, 559-569) is functional in Arabidopsis thaliana. A pure breeding A. thaliana line (JL-tTA/8) was generated which expressed a chimeric fusion of the tetracycline repressor and the activation domain of Herpes simplex virus (tTA), from a single transgenic locus. Plants from this line were crossed with transgenics carrying the ER-targeted green fluorescent protein coding sequence (mGFP5) under control of the Top10 promoter sequence. Progeny from this cross displayed ER-targeted GFP fluorescence throughout the plant, indicating that the tTA-Top10 promoter interaction was functional in A. thaliana. GFP expression was repressed by 100 ng ml-1 tetracycline, an order of magnitude lower than the concentration used previously to repress expression in Nicotiana tabacum. Moreover, the level of GFP expression was controlled by varying the concentration of tetracycline in the medium, allowing a titred regulation of transgenic activity that was previously unavailable in A. thaliana. The kinetics of GFP activity were determined following de-repression of the Top10:mGFP5 transgene, with a visible ER-targeted GFP signal appearing from 24 to 48 h after de-repression.
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Affiliation(s)
- J Love
- Department of Botany, North Carolina State University, Raleigh, NC 27695-7612, USA.
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18
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Abstract
Ferredoxin-1 (Fed-1) mRNA is poorly translated in dark-treated tobacco (Nicotiana tabacum) leaves, resulting in destabilization of Fed-1 mRNA and a differential light/dark accumulation of the mRNA. Insertion of nonsense codons within the Fed-1 coding sequence disrupts the light regulation of Fed-1 mRNA abundance. Here we show that the nonsense codon effect results primarily from lowering the Fed-1 mRNA stability in light-treated leaf tissue and in rapidly growing tobacco cell cultures, but not in dark-treated leaf tissue. These results suggest that nonsense codons trigger a decay pathway distinct from that seen for Fed-1 mRNA in the dark. We propose that nonsense-mediated decay of nonsense-containing Fed-1 mRNA occurs in light-treated leaves and in non-photosynthetic tobacco culture cells where Fed-1 mRNA is being actively translated.
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Affiliation(s)
- M E Petracek
- Department of Botany, North Carolina State University, Raleigh, NC 27695, USA.
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19
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Fitzmaurice WP, Nguyen LV, Wernsman EA, Thompson WF, Conkling MA. Transposon tagging of the sulfur gene of tobacco using engineered maize Ac/Ds elements. Genetics 1999; 153:1919-28. [PMID: 10581296 PMCID: PMC1460851 DOI: 10.1093/genetics/153.4.1919] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Sulfur gene of tobacco is nuclearly encoded. A Su allele at this locus acts as a dominant semilethal mutation and causes reduced accumulation of chlorophyll, resulting in a yellow color in the plant. An engineered transposon tagging system, based upon the maize element Ac/Ds, was used to mutate the gene. High frequency of transposon excision from the Su locus produced variegated sectors. Plants regenerated from the variegated sector exhibited a similar variegated phenotype. Genetic analyses showed that the variegation was always associated with the transposase construct and the transposon was linked to the Su locus. Sequences surrounding the transposon were isolated, and five revertant sectors possessed typical direct repeats following Ds excisions. These genetic and molecular data are consistent with the tagging of the Su allele by the transposon.
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Affiliation(s)
- W P Fitzmaurice
- Department of Botany, North Carolina State University, Raleigh, North Carolina 27695, USA.
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20
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Michalowski SM, Allen GC, Hall GE, Thompson WF, Spiker S. Characterization of randomly-obtained matrix attachment regions (MARs) from higher plants. Biochemistry 1999; 38:12795-804. [PMID: 10504249 DOI: 10.1021/bi991142c] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Matrix attachment regions (MARs) can be operationally defined as DNA fragments that bind to the nuclear matrix. We have created a library of randomly obtained MARs from tobacco (Nicotiana tobacum) by cloning DNA fragments that co-isolate with nuclear matrixes prepared by a method involving lithium diiodosalicylate. The interactions of several of the cloned MARs with nuclear matrixes were tested by an in vitro binding assay in which genomic DNA was used as competitor. Based on this assay, the MARs were classified as strong, medium, and weak binders. Examples of each of the binding classes were further studied by in vitro binding using self- and cross-competition. Estimates of dissociation constants for several MARs ranged from 6 to 11 nM and correlated inversely with binding strength. The number of binding sites per matrix for several MARs ranged from 4 x 10(5) to 9 x 10(5) and correlated directly with binding strength. We conclude that binding strength, as we have measured it, is a function of both numbers of binding sites and affinity for the sites. The tobacco MARs were sequenced and analyzed for overall AT content, for distribution of AT-rich regions, and for the abundance of several MAR-related motifs. Previously identified MAR motifs correlate to various degrees with binding strength. Notably, the Drosophila topoisomerase II motif does not correlate with binding strength of the tobacco MARs. A newly identified motif, the "90%AT Box," correlates better with binding strength than any of the previously identified motifs we investigated.
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Affiliation(s)
- S M Michalowski
- Department of Genetics and Department of Botany, North Carolina State University, Raleigh, North Carolina 27695, USA
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21
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Petracek ME, Dickey LF, Nguyen TT, Gatz C, Sowinski DA, Allen GC, Thompson WF. Ferredoxin-1 mRNA is destabilized by changes in photosynthetic electron transport. Proc Natl Acad Sci U S A 1998; 95:9009-13. [PMID: 9671795 PMCID: PMC21193 DOI: 10.1073/pnas.95.15.9009] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/1998] [Indexed: 02/08/2023] Open
Abstract
In transgenic tobacco, pea Ferredoxin-1 (Fed-1) mRNA accumulates rapidly in response to photosynthesis even when the transgene is driven by a constitutive promoter. To investigate the role of photosynthesis on Fed-1 mRNA stability, we used the tetracycline repressible Top10 promoter system to specifically shut off transcription of the Fed-1 transgene. The Fed-1 mRNA has a half-life of approximately 2.4 hr in the light and a half-life of only 1.2 hr in the dark or in the presence of the photosynthetic electron transport inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU). These data indicate that cessation of photosynthesis, either by darkness or DCMU results in a destabilization of the Fed-1 mRNA. Furthermore, the Fed-1 mRNA half-life is reduced immediately upon transfer to darkness, suggesting that Fed-1 mRNA destabilization is a primary response to photosynthesis rather than a secondary response to long-term dark adaptation. Finally, the two different methods for efficient tetracycline delivery reported here generally should be useful for half-life measurements of other mRNAs in whole plants.
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Affiliation(s)
- M E Petracek
- Department of Botany, North Carolina State University, Raleigh, NC 27695, USA.
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22
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Kjemtrup S, Sampson KS, Peele CG, Nguyen LV, Conkling MA, Thompson WF, Robertson D. Gene silencing from plant DNA carried by a Geminivirus. Plant J 1998; 14:91-100. [PMID: 15494056 DOI: 10.1046/j.1365-313x.1998.00101.x] [Citation(s) in RCA: 127] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The geminivirus tomato golden mosaic virus (TGMV) replicates in nuclei and expresses genes from high copy number DNA episomes. The authors used TGMV as a vector to determine whether episomal DNA can cause silencing of homologous, chromosomal genes. Two markers were used to asses silencing: (1) the sulfur allele (su) of magnesium chelatase, an enzyme required for chlorophyll formation; and (2) the firefly luciferase gene (luc). Various portions of both marker genes were inserted into TGMV in place of the coat protein open-reading frame and the constructs were introduced into intact plants using particle bombardment. When TGMV vectors carrying fragments of su (TGMV::su) were introduced into leaves of wild type Nicotiana benthamiana, circular, yellow spots with an area of several hundred cells formed after 3-5 days. Systemic movement of TGMV::su subsequently produced varigated leaf and stem tissue. Fragments that caused silencing included a 786 bp 5' fragment of the 1392 bp su cDNA in sense and anti-sense orientation, and a 403 bp 3' fragment. TGMV::su-induced silencing was propogated through tissue culture, along with the viral episome, but was not retained through meiosis. Systemic downregulation of a constitutively expresse luciferase transgene in plants was achieved following infection with TGMV vectors carrying a 623 bp portion of luc in sense or anti-sense orientation. These results establish that homologous DNA sequences localized in nuclear episomes can modulate the expression of active chromosomal genes.
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Affiliation(s)
- S Kjemtrup
- Department of Botany, North Carolina State University, Raleigh, NC 27695, USA
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Dickey LF, Petracek ME, Nguyen TT, Hansen ER, Thompson WF. Light regulation of Fed-1 mRNA requires an element in the 5' untranslated region and correlates with differential polyribosome association. Plant Cell 1998; 10:475-84. [PMID: 9501119 PMCID: PMC143995 DOI: 10.1105/tpc.10.3.475] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Light regulation of Fed-1 mRNA abundance in the leaves of green plants is primarily a post-transcriptional process. Previously, we have shown that the Fed-1 mRNA light response requires an open reading frame, indicating that the light regulation of the mRNA depends on its concurrent translation. We now show that light-induced increases in Fed-1 mRNA abundance are associated with increases in polyribosome association that require both a functional AUG and a normal Fed-1 translational start context. We also present evidence that light regulation of Fed-1 mRNA levels requires more than efficient translation per se. Substitution of the efficiently translated tobacco mosaic virus Omega 5' untranslated region resulted in a loss of Fed-1 light regulation. In addition, we identified a CAT T repeat element located near the 5' terminus of the Fed-1 5' untranslated region that is essential for light regulation. We introduced two different mutations in the CAT T repeat element, but only one of these substitutions blocked the normal light effect on polyribosome association, whereas both altered dark-induced Fed-1 mRNA disappearance. The element may thus be important for Fed-1 mRNA stability rather than polyribosome loading. We propose a model in which Fed-1 mRNA is relatively stable when it is associated with polyribosomes in illuminated plants but in darkness is not polyribosome associated and is thus rapidly degraded by a process involving the CAT T repeat element.
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Affiliation(s)
- L F Dickey
- Department of Botany, North Carolina State University, Raleigh, North Carolina 27695-7612, USA.
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Petracek ME, Dickey LF, Huber SC, Thompson WF. Light-regulated changes in abundance and polyribosome association of ferredoxin mRNA are dependent on photosynthesis. Plant Cell 1997; 9:2291-300. [PMID: 9437868 PMCID: PMC157075 DOI: 10.1105/tpc.9.12.2291] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In transgenic tobacco plants containing a pea ferredoxin transcribed region (Fed-1) driven by the cauliflower mosaic virus 35S promoter (P35S), light acts at a post-transcriptional level to control the abundance of Fed-1 mRNA in green leaves. To determine whether the light signal for this response involves photosynthesis, we treated transgenic seedlings with or without 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), an inhibitor of photosynthetic electron transport. DCMU prevented the normal light response by blocking reaccumulation of Fed-1 transcripts when dark-adapted green plants were returned to the light. In contrast, reaccumulation of light-harvesting complex B (Lhcb) transcripts was unaffected by DCMU treatment. Because Fed-1 light regulation requires translation, we also examined polyribosome profiles. We found that Fed-1 transcripts accumulated on polyribosomes in the light but were found primarily in non-polyribosomal fractions in dark-adapted plants or in illuminated plants exposed to lower than normal light intensity or treated with DCMU. Surprisingly, although Lhcb mRNA abundance was not affected by DCMU, its polyribosomal loading pattern was altered in much the same way as was that of Fed-1 mRNA. In contrast, DCMU had no effect on either the abundance or the polyribosome profiles of endogenous histone H1 or transgenic P35S::CAT transcripts. Thus, our results are consistent with the hypothesis that a process coupled to photosynthesis affects the polyribosome loading of a subset of cytoplasmic mRNAs.
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Affiliation(s)
- M E Petracek
- Department of Botany, North Carolina State University, Raleigh 27695, USA
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25
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Thompson WF, Cuddy LL, Plaus C. Expectancies generated by melodic intervals: evaluation of principles of melodic implication in a melody-completion task. Percept Psychophys 1997; 59:1069-76. [PMID: 9360479 DOI: 10.3758/bf03205521] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Bottom-up principles of melodic implication (Narmour, 1990) were evaluated in a melody-completion task. One hundred subjects (50 low training; 50 high training in music) were presented each of eight melodic intervals. For each interval, the subjects were asked to compose a short melody on a piano keyboard, treating the interval provided as the first two notes of the melody. For each melody, the first response--the note immediately following the initial interval--was analyzed. Multinomial log linear analyses were conducted to assess the extent to which responses could be predicted by Narmour's (1990, 1992) bottom-up principles. Support was found for all of Narmour's principles, and two additional predictors based on implied tonal structure. Responses of low- and high-training groups were similar.
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Affiliation(s)
- W F Thompson
- Department of Psychology, Atkinson College, York University, ON, Canada
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26
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Thompson WF, Beven AF, Wells B, Shaw PJ. Sites of rDNA transcription are widely dispersed through the nucleolus in Pisum sativum and can comprise single genes. Plant J 1997; 12:571-81. [PMID: 9351243 DOI: 10.1046/j.1365-313x.1997.00571.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Incorporation by RNA polymerases of BrUTP into both plant root tissue and isolated plant nuclei as a method for localization of the sites of transcription has been used. In this paper pea root tissue was used, and under the conditions employed, nearly all the incorporation occurs in the nucleolus, and thus must be catalysed by RNA polymerase I. Immunofluorescence and confocal microscopy shows that incorporation occurs in a pattern consisting of many small foci distributed widely through the dense fibrillar component of the nucleoli. Immunogold labelling using silver-enhanced Nanogold probe at the electron microscopic level confirms the sites of transcription as small foci approximately 200 nm in diameter. Simultaneous fluorescence in situ hybridization with a probe to the external transcribed spacer (ETS) region of the pre-rRNA shows that the structures revealed by this probe and the BrUTP immunofluorescence labelling are very similar. A probe to the transcribed portion of the rDNA (18S) also shows a good correlation to the sites of BrUTP incorporation within the nucleolus. On the other hand a probe to the non-transcribed intergenic spacer region (NTS) shows very little coincidence with the sites of BrUTP incorporation, and double fluorescence in situ labelling with both 18S and NTS probes confirms this difference in localization. These results suggest that most BrUTP foci correspond to single transcribed genes.
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Affiliation(s)
- W F Thompson
- Department of Cell Biology, John Innes Centre, Colney, Norwich, UK
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27
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Frances S, Thompson WF. The dark-adaptation response of the de-etiolated pea mutant lip1 is modulated by external signals and endogenous programs. Plant Physiol 1997; 115:23-8. [PMID: 9306689 PMCID: PMC158456 DOI: 10.1104/pp.115.1.23] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The lip1 mutant of pea (Pisum sativum L.) exhibits a de-etiolated phenotype. When grown in darkness, lip1 plants have several characteristics normally associated only with light-grown plants. Young wild-type (WT) seedlings accumulate high levels of transcripts from plastid-related genes (such as those encoding chlorophyll a/b-binding proteins, ferredoxin, and the small subunit of Rubisco) only in the light. In contrast, regardless of the light conditions under which the plants are grown, young mutant seedlings accumulate transcript levels equal to or greater than those seen in light-grown WT seedlings of the same age. Under some conditions, light-grown lip1 seedlings failed to respond to dark treatment. The largest response to darkness observed in the mutant occurred when older seedlings were first grown under low-light conditions before transfer to darkness. The mutant's inability to respond to darkness is not due to a gross disturbance in the circadian clock. We conclude that environmental signals (light) and endogenous programs (developmental and circadian) regulate gene expression in both WT and mutant plants. However, mutant seedlings exhibit a developmentally regulated and exaggerated response to light. In addition, the effect of the mutation may be greatest during a brief period early in development.
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Affiliation(s)
- S Frances
- Department of Genetics, North Carolina State University, Raleigh 27695, USA
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Tanzer MM, Thompson WF, Law MD, Wernsman EA, Uknes S. Characterization of Post-Transcriptionally Suppressed Transgene Expression That Confers Resistance to Tobacco Etch Virus Infection in Tobacco. Plant Cell 1997; 9:1411-1423. [PMID: 12237389 PMCID: PMC157007 DOI: 10.1105/tpc.9.8.1411] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Tobacco lines expressing transgenes that encode tobacco etch virus (TEV) coat protein (CP) mRNA with or without nonsense codons give rise to TEV-resistant tissues that have reduced levels of TEV CP mRNA while maintaining high levels of transgene transcriptional activity. Two phenotypes for virus resistance in the lines containing the transgene have been described: immune (no virus infection) and recovery (initial systemic symptoms followed by gradual recovery over several weeks). Here, we show that at early times in development, immune lines are susceptible to TEV infection and accumulate full-length CP mRNA. Therefore, immune lines also exhibit meiotic resetting, as is seen in the recovery lines, providing molecular evidence for a common mechanism of gene silencing and virus resistance in both cases. We also investigated the characteristics of two sets of low molecular weight RNAs that appear only in silenced tissue. One set has nearly intact 5[prime] ends, lacks poly(A) tails, and is associated with polyribosomes; the second set contains the 3[prime] end of the mRNA. Treating silenced leaf tissue with cycloheximide resulted in decreased levels of full-length mRNA and an increase in the levels of the low molecular weight RNAs, supporting a cytoplasmic decay mechanism that does not require ongoing translation. Surprisingly, mRNA from the transgene containing nonsense codons was associated with more ribosomes than expected, possibly resulting from translation from a start codon downstream of the introduced translational stop codons. We present a hypothesis for transgene/viral RNA degradation in which RNA degradation occurs in the cytoplasm while in association with polyribosomes.
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Affiliation(s)
- M. M. Tanzer
- Department of Botany, North Carolina State University, Raleigh, North Carolina 27695-7612
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29
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Abstract
The effect of music performance on perceived key movement was examined. Listeners judged key movement in sequences presented without performance expression (mechanical) in Experiment 1 and with performance expression in Experiment 2. Modulation distance varied. Judgments corresponded to predictions based on the cycle of fifths and toroidal models of key relatedness, with the highest correspondence for performed versions with the toroidal model. In Experiment 3, listeners compared mechanical sequences with either performed sequences or modifications of performed sequences. Modifications preserved expressive differences between chords, but not between voices. Predictions from Experiments 1 and 2 held only for performed sequences, suggesting that differences between voices are informative of key movement. Experiment 4 confirmed that modifications did not disrupt musicality. Analyses of performances further suggested a link between performance expression and key.
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Affiliation(s)
- W F Thompson
- Department of Psychology, Atkinson College, York University, North York, Ontario, Canada
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30
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Abstract
The effect of music performance on perceived key movement was examined. Listeners judged key movement in sequences presented without performance expression (mechanical) in Experiment 1 and with performance expression in Experiment 2. Modulation distance varied. Judgments corresponded to predictions based on the cycle of fifths and toroidal models of key relatedness, with the highest correspondence for performed versions with the toroidal model. In Experiment 3, listeners compared mechanical sequences with either performed sequences or modifications of performed sequences. Modifications preserved expressive differences between chords, but not between voices. Predictions from Experiments 1 and 2 held only for performed sequences, suggesting that differences between voices are informative of key movement. Experiment 4 confirmed that modifications did not disrupt musicality. Analyses of performances further suggested a link between performance expression and key.
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Affiliation(s)
- W F Thompson
- Department of Psychology, Atkinson College, York University, North York, Ontario, Canada
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31
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Allen GC, Hall G, Michalowski S, Newman W, Spiker S, Weissinger AK, Thompson WF. High-level transgene expression in plant cells: effects of a strong scaffold attachment region from tobacco. Plant Cell 1996; 8:899-913. [PMID: 8672887 PMCID: PMC161147 DOI: 10.1105/tpc.8.5.899] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
We have previously shown that yeast scaffold attachment regions (SARs) flanking a chimeric beta-glucuronidase (GUS) reporter gene increased per-copy expression levels by 24-fold in tobacco suspension cell lines stably transformed by microprojectile bombardment. In this study, we examined the effect of a DNA fragment originally identified in a tobacco genomic clone by its activity in an in vitro binding assay. The tobacco SAR has much greater scaffold binding affinity than does the yeast SAR, and tobacco cell lines stably transformed with constructs containing the tobacco SAR accumulated greater than fivefold more GUS enzyme activity than did lines transformed with the yeast SAR construct. Relative to the control construct, flanking the GUS gene with plant SARs increased overall expression per transgene copy by almost 140-fold. In transient expression assays, the same construct increased expression only approximately threefold relative to a control without SARs, indicating that the full SAR effect requires integration into chromosomal DNA. GUS activity in individual stable transformants was not simply proportional to transgene copy number, and the SAR effect was maximal in cell lines with fewer than approximately 10 transgene copies per tobacco genome. Lines with significantly higher copy numbers showed greatly greatly reduced expression relative to the low-copy-number lines. Our results indicate that strong SARs flanking a transgene greatly increases expression without eliminating variation between transformants. We propose that SARs dramatically reduce the severity or likelihood of homology-dependent gene silencing in cells with small numbers of transgenes but do not prevent silencing of transgenes present in many copies.
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Affiliation(s)
- G C Allen
- Department of Botany, North Carolina State University, Raleigh 27695, USA
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Allen GC, Hall G, Michalowski S, Newman W, Spiker S, Weissinger AK, Thompson WF. High-level transgene expression in plant cells: effects of a strong scaffold attachment region from tobacco. Plant Cell 1996. [PMID: 8672887 DOI: 10.2307/3870291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We have previously shown that yeast scaffold attachment regions (SARs) flanking a chimeric beta-glucuronidase (GUS) reporter gene increased per-copy expression levels by 24-fold in tobacco suspension cell lines stably transformed by microprojectile bombardment. In this study, we examined the effect of a DNA fragment originally identified in a tobacco genomic clone by its activity in an in vitro binding assay. The tobacco SAR has much greater scaffold binding affinity than does the yeast SAR, and tobacco cell lines stably transformed with constructs containing the tobacco SAR accumulated greater than fivefold more GUS enzyme activity than did lines transformed with the yeast SAR construct. Relative to the control construct, flanking the GUS gene with plant SARs increased overall expression per transgene copy by almost 140-fold. In transient expression assays, the same construct increased expression only approximately threefold relative to a control without SARs, indicating that the full SAR effect requires integration into chromosomal DNA. GUS activity in individual stable transformants was not simply proportional to transgene copy number, and the SAR effect was maximal in cell lines with fewer than approximately 10 transgene copies per tobacco genome. Lines with significantly higher copy numbers showed greatly greatly reduced expression relative to the low-copy-number lines. Our results indicate that strong SARs flanking a transgene greatly increases expression without eliminating variation between transformants. We propose that SARs dramatically reduce the severity or likelihood of homology-dependent gene silencing in cells with small numbers of transgenes but do not prevent silencing of transgenes present in many copies.
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Affiliation(s)
- G C Allen
- Department of Botany, North Carolina State University, Raleigh 27695, USA
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33
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Affiliation(s)
- S. Spiker
- Department of Genetics (S.S.) and Department of Botany (W.F.T.), North Carolina State University, Raleigh, North Carolina 27695
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34
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Bovy A, Van den Berg C, De Vrieze G, Thompson WF, Weisbeek P, Smeekens S. Light-regulated expression of the Arabidopsis thaliana ferredoxin gene requires sequences upstream and downstream of the transcription initiation site. Plant Mol Biol 1995; 27:27-39. [PMID: 7865794 DOI: 10.1007/bf00019176] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The effect of light on the expression of the Arabidopsis thaliana ferredoxin gene (fedA) was studied in mature tobacco plants. In light-treated leaves of tobacco plants transformed with a full-length ferredoxin gene, fedA-specific mRNA levels were more than twenty fold higher than in dark-treated controls. This indicates that all components for regulation of the Arabidopsis ferredoxin gene are present in tobacco. To identify light-regulatory elements in the fedA gene, we have tested a set of chimeric genes containing various parts of the fedA gene for light-dependent expression in mature tobacco plants. A fedA promoter-GUS fusion gene was not light-responsive, indicating that the 5'-upstream promoter region is not sufficient for light regulation. Fusion genes in which different transcribed regions of the fedA gene were expressed from the CaMV 35S promoter showed only limited light regulation, if any at all. This indicates that, like the fedA upstream region, the region downstream of the transcription start site is also not sufficient for full light regulation. The combined results suggest that for full light-regulated expression of the fedA gene, both the promoter region and sequences downstream of the transcription start site are required.
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MESH Headings
- Arabidopsis/genetics
- Arabidopsis/radiation effects
- Base Sequence
- DNA, Plant/genetics
- DNA, Recombinant/genetics
- Ferredoxins/genetics
- Gene Expression Regulation, Plant
- Genes, Plant/genetics
- Light
- Molecular Sequence Data
- Pisum sativum/genetics
- Plants, Genetically Modified
- Plants, Toxic
- Promoter Regions, Genetic/genetics
- RNA, Messenger/analysis
- Regulatory Sequences, Nucleic Acid/genetics
- Nicotiana/genetics
- Transcription, Genetic/genetics
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Affiliation(s)
- A Bovy
- Department of Molecular Cell Biology, University of Utrecht, Netherlands
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35
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White MJ, Kaufman LS, Horwitz BA, Briggs WR, Thompson WF. Individual Members of the Cab Gene Family Differ Widely in Fluence Response. Plant Physiol 1995; 107:161-165. [PMID: 12228352 PMCID: PMC161179 DOI: 10.1104/pp.107.1.161] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Chlorophyll a/b-binding protein genes (Cab genes) can be extremely sensitive to light. Transcript accumulation following a red light pulse increases with fluence over 8 orders of magnitude (L.S. Kaufman, W.F. Thompson, W.R. Briggs [1984] Science 226: 1447-1449). We have constructed fluence-response curves for individual Cab genes. At least two Cab genes (Cab-8 and AB96) show a very low fluence response to a single red light pulse. In contrast, two other Cab genes (AB80 and AB66) fail to produce detectable transcript following a single pulse of either red or blue light but are expressed in continuous red light. Thus, very low fluence responses and high irradiance responses occur in the same gene family.
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Affiliation(s)
- M. J. White
- Department of Biology, Saint Mary's University, Halifax, Nova Scotia, B3H 3C3 Canada (M.J.W.)
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36
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Thompson WF. Sensitivity to combinations of musical parameters: pitch with duration, and pitch pattern with durational pattern. Percept Psychophys 1994; 56:363-74. [PMID: 7971136 DOI: 10.3758/bf03209770] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In four experiments, listeners' sensitivity to combinations of pitch and duration was investigated. Experiments 1-3 involved "textures" of notes, which were created by repeatedly sounding one of two notes (e.g., C4 quarter note; D4 eighth note), so that each note had an equal chance of occurring at any point within a texture. Experiment 1 showed that if a texture change was effected by introducing a pitch or duration that was not in the initial texture, the change was perceived by both attentive and distracted listeners. If a texture change was effected by combining the pitch of one note with the duration of the other note in the initial texture, and vice versa, it was perceived only if the listeners were attentive. Sensitivity to pitch/duration combinations was poorer when the pitch difference between component notes of textures was increased (Experiment 2), but it was better when the difference in duration between component notes was increased (Experiment 3). In Experiment 4, listeners' sensitivity to combinations of pitch pattern and durational pattern in brief sequences was examined. Listeners were sensitive to the manner in which parameter patterns were combined when they were attentive, but not when they were distracted. The results are discussed in view of feature-integration theory and its application to music cognition.
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Affiliation(s)
- W F Thompson
- Department of Psychology, Atkinson College, York University, ON, Canada
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37
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Abstract
Ferredoxin I (Fed-1) mRNA abundance is modulated by an internal light regulatory element that includes sequences both 5' and 3' of the translational initiation site. To test the hypothesis that the light response mediated by this element might be coupled to translation, we transformed tobacco plants with gene constructs blocked in translational initiation or elongation. Here, we report that such mutations abolish the light response in vivo. A nonsense mutation could be rescued by restoring the open reading frame with a different sequence, even when the new codon caused an amino acid substitution. Our data establish that the light response requires a translatable reading frame and thus provide strong circumstantial evidence for post-transcriptional modulation of Fed-1 mRNA levels. The Fed-1 system is presently the only higher plant example of a developmentally regulated change in mRNA abundance that requires translation of the affected mRNA.
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Affiliation(s)
- L F Dickey
- Department of Botany, North Carolina State University, Raleigh 27695
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38
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Quail PH, Briggs WR, Chory J, Hangarter RP, Harberd NP, Kendrick RE, Koornneef M, Parks B, Sharrock RA, Schafer E, Thompson WF, Whitelam GC. Spotlight on Phytochrome Nomenclature. Plant Cell 1994; 6:468-471. [PMID: 12244245 PMCID: PMC160449 DOI: 10.1105/tpc.6.4.468] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
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Abstract
The present study determined the temporal and spatial patterns of genesis for neurons of different sizes in the retinal ganglion cell layer of the ferret. Fetal ferrets were exposed to tritiated thymidine on embryonic days E-22 through E-36. One to 3 months after birth, they were perfused and their retinae dissected, and autoradiographs were prepared from resin-embedded sections throughout the entire flattened retinal ganglion cell layer. Soma size differences in conjunction with separate retrograde labeling and calbindin immunocytochemical studies were used as criteria for identifying different retinal ganglion cell subtypes in juvenile and adult ferrets. Neurons of different sizes in the ganglion cell layer were generated at different stages during development. Medium sized cells were generated primarily between E-22 and E-26; the largest cells were generated between E-24 and E-29; small cells were generated between E-26 and E-32; and very small cells were generated between E-29 and E-36. The former three groups were interpreted to be three subtypes of retinal ganglion cells, while the latter group was interpreted to be displaced amacrine cells. This temporal order of the genesis of ganglion cell classes is consistent with the spatial ordering of their fibers in the mature optic chiasm and tract, and it is consistent with the developmental change in decussation pattern recently shown in the optic pathway of embryonic ferrets. The spatial pattern of genesis suggests that ganglion cells of a particular class are added to the ganglion cell layer in a centroperipheral fashion initiated in the dorsocentral retina nasal to the area centralis. No evidence was found for a wave of ganglion cell addition that proceeded in a spiralling pattern around the area centralis, as has been reported in the cat.
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Affiliation(s)
- B E Reese
- Neuroscience Research Institute, University of California at Santa Barbara 93106-5060
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40
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Falconet D, Godon C, White MJ, Thompson WF. Sequence of Lhcb3*1, a gene encoding a Photosystem II chlorophyll a/b-binding protein in Pisum. Biochim Biophys Acta 1993; 1173:333-6. [PMID: 8318543 DOI: 10.1016/0167-4781(93)90133-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We have cloned and sequenced a pea Lhcb3 gene, encoding a Photosystem II chlorophyll a/b-binding protein. Sequence analysis indicates that the gene contains two introns and predicts a polypeptide of 265 amino acids. The predicted polypeptide sequence is highly homologous to the polypeptide sequences deduced from Lhcb3 genes previously characterized in tomato and barley.
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Affiliation(s)
- D Falconet
- Laboratoire de Biologie Moléculaire Végétale, URA 1128, Université Paris Sud, Orsay, France
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41
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Allen GC, Hall GE, Childs LC, Weissinger AK, Spiker S, Thompson WF. Scaffold attachment regions increase reporter gene expression in stably transformed plant cells. Plant Cell 1993; 5:603-13. [PMID: 8329896 PMCID: PMC160298 DOI: 10.1105/tpc.5.6.603] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The yeast ARS-1 element contains a scaffold attachment region (SAR) that we have previously shown can bind to plant nuclear scaffolds in vitro. To test effects on expression, constructs in which a chimeric beta-glucuronidase (GUS) gene was flanked by this element were delivered into tobacco suspension cells by microprojectile bombardment. In stably transformed cell lines, GUS activity averaged 12-fold higher (24-fold on a gene copy basis) for a construct containing two flanking SARs than for a control construct lacking SARs. Expression levels were not proportional to gene copy number, as would have been predicted if the element simply reduced position effect variation. Instead, the element appeared to reduce an inhibitory effect on expression in certain transformants containing multiple gene copies. The effect on expression appears to require chromosomal integration, because SAR constructs were only twofold more active than the controls in transient assays.
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Affiliation(s)
- G C Allen
- Department of Botany, North Carolina State University, Raleigh 27695
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42
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Abstract
Perceptual relationships between four-voice harmonic sequences and single voices were examined in three experiments. In Experiment 1, listeners rated the extent to which single voices were musically consistent with harmonic sequences. When harmonic sequences did not change key, judgments were influenced by three sources of congruency: melody (whether the single voice was the same as the soprano voice of the harmonic sequence), chord progression (whether the single voice could be harmonized to give rise to the chord progression of the harmonic sequence), and key structure (whether or not the single voice implied modulation). When key changes occurred, sensitivity to sources of congruency was reduced. In Experiment 2, another interpretation of the results was examined: that consistency ratings were based on congruency in well-formedness. Listeners provided well-formedness ratings of the single voices and harmonic sequences. A multiple regression analysis suggested that consistency ratings were based not merely on well-formedness but on congruency in melody, chord progression, and key structure. In Experiment 3, listeners rated the extent of modulation in harmonic sequences and in each voice of the sequences. Discrimination between modulation conditions was greater for single voices than for harmonic sequences, suggesting that abstraction of key from melody may occur without reference to implied harmony. A partially hierarchical system for processing melody, harmony, and key is proposed.
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Affiliation(s)
- W F Thompson
- Department of Psychology, Atkinson College, York University, North York, ON, Canada
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43
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Frances S, White MJ, Edgerton MD, Jones AM, Elliott RC, Thompson WF. Initial characterization of a pea mutant with light-independent photomorphogenesis. Plant Cell 1992; 4:1519-1530. [PMID: 1467651 PMCID: PMC160238 DOI: 10.1105/tpc.4.12.1519] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We have identified a mutant of pea cultivar Alaska that has many of the characteristics normally associated with light-grown seedlings even when grown in complete darkness. We have designated this mutant lip1, for light independent photomorphogenesis. Etiolated wild-type pea seedlings are white to slightly yellow in color and have a distinct morphology characterized by elongated epicotyls and buds containing unexpanded leaves with small, undifferentiated cells. In contrast, mutant seedlings grown under the same conditions are yellow in color and have short epicotyls and expanded leaves showing clear cellular differentiation. Transmission electron microscopy revealed partially developed, agranal plastids in the dark-grown mutant, unlike wild-type seedlings that contain etioplasts with prolamellar bodies. The mutant also exhibits a much shorter lag period for chlorophyll accumulation when etiolated seedlings are transferred from darkness to white light. The dark-grown mutant has 10-fold less spectrally detectable phytochrome, which can be attributed to a 10-fold reduction in the level of the PHYA polypeptide. Cab, Fed1, and RbcS transcripts are present in dark-grown mutant seedlings at levels comparable to those produced in light-grown material. The levels of these transcripts show a normal decrease when green plants grown for 15 days in a light/dark cycle are transferred to continuous darkness. However, transcript levels remain high during dark treatment of seedlings grown for 9 days in continuous light, indicating that the dark adaptation response in this mutant is developmentally plastic. The lip1 mutant has several features in common with the deetiolated Arabidopsis mutants det1, det2, and cop1. However, there are also several important differences, including varying effects on phytochrome levels, organ-specific gene expression, plastid development, and response to dark adaptation.
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Affiliation(s)
- S Frances
- Department of Genetics, North Carolina State University, Raleigh 27695
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44
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Fitzmaurice WP, Lehman LJ, Nguyen LV, Thompson WF, Wernsman EA, Conkling MA. Development and characterization of a generalized gene tagging system for higher plants using an engineered maize transposon Ac. Plant Mol Biol 1992; 20:177-98. [PMID: 1327269 DOI: 10.1007/bf00014487] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
This report describes a series of transposon tagging vectors for dicotyledonous plants based on the maize transposable element Ac. This binary system includes the transposase (Ts) and the tagging element (Ds) on separate T-DNA vectors. Ts elements include versions in which transcription is driven either by the endogenous Ac promoter or by the cauliflower mosaic virus (CaMV) 35S promoter. Ds tagging element includes a gene conferring methotrexate (Mtx) resistance for selection and a supF gene to facilitate cloning of tagged sequences. The Ds element is flanked by a CaMV 35S promoter and the beta-glucuronidase (GUS) coding sequence so that GUS expression occurs upon excision of the element. We have transformed these Ts and Ds elements into tobacco and demonstrated that the Ts is functional with either promoter, and that the artificial Ds elements are capable of transposition. The amount of excision was found to depend upon both the individual Ts and Ds primary transformants used. Somatic excision of Ds was seen in up to 100% of progeny seedlings containing Ts and Ds. Germinal excision was detected in up to 48% of the progeny of plants containing both elements. Hence, this system can generate a sufficient number of events to be useful in gene tagging.
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Affiliation(s)
- W P Fitzmaurice
- Department of Botany, North Carolina State University, Raleigh 27695
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45
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White MJ, Fristensky BW, Falconet D, Childs LC, Watson JC, Alexander L, Roe BA, Thompson WF. Expression of the chlorophyll-a/b-protein multigene family in pea (Pisum sativum L.) : Evidence for distinct developmental responses. Planta 1992; 188:190-198. [PMID: 24178255 DOI: 10.1007/bf00216813] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/20/1992] [Indexed: 06/02/2023]
Abstract
To measure transcript levels for individual members of the Cab (chlorophyll a/b protein) multigene family in pea under a range of developmental situations, we developed a system using cDNA synthesis, the polymerase chain reaction (PCR), and chemiluminescence detection. In order to design gene-specific PCR primers for all genes, a partial genomic clone for a fifth, Type I LHCII (light-harvesting complex of photosystem II) gene, Cab-9 The Cab-9 sequence appears in the Genbank/EMBL databases under the accession number M86906 , was isolated and sequenced. All seven known Cab genes in pea are expressed in light-grown buds and leaves, including several genes previously known only from genomic clones. There appear to be at least two groups of Cab genes in pea which differ in their response to light and development. The first group (consisting of Cab-8, AB96, Cab-215 and Cab-315) includes Type I, Type II and Type III genes, shows a relatively strong response to red light, and has bud transcript levels similar to or slightly higher than leaves. The second group, consisting of the Type I genes Cab-9, AB80 and AB66, shows little or no transcript accumulation 24 h after a red light pulse, and has higher transcript levels in leaves than in buds. Transcript levels for genes in this second group appear to be lower than those of the first group in all developmental situations examined. These data indicate that there has been an evolutionary divergence of the responses to light and development among the Type I LHCII genes.
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Affiliation(s)
- M J White
- Department of Botany, North Carolina State University, 27695, Raleigh, NC, USA
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46
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Abstract
We have previously shown that element(s) mediating a light-induced increase in the abundance of Fed-1 mRNA in the leaves of transgenic tobacco plants are located within the transcribed portion of the gene. As part of an effort to define the mechanism of this effect, we report here that cis-acting elements capable of mediating a 5-fold light-induced increase in the abundance of this mRNA are located within a region comprising the 5' leader and first third of the Fed-1 coding sequence. No activity was detected in the 3' untranslated region of the gene. In a gain-of-function assay, the 5' region was found to be capable of conferring light responsiveness on three different reporter sequences, although experiments with the gusA reporter were complicated by an apparent negative light effect on the stability of this mRNA. Deletion experiments show that at least one essential light regulatory element is located in the 5' untranslated region of Fed-1 between nucleotides +19 and +57. Additional Fed-1 sequences, including a portion of the protein coding region, are required to confer positive responsiveness on the gusA reporter. These additional sequences may include specific light regulatory elements or simply provide an environment in which the leader element can function normally.
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Affiliation(s)
- L F Dickey
- Department of Botany, North Carolina State University, Raleigh 27695-7612
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47
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Gallo-Meagher M, Sowinski DA, Elliott RC, Thompson WF. Both internal and external regulatory elements control expression of the pea Fed-1 gene in transgenic tobacco seedlings. Plant Cell 1992; 4:389-95. [PMID: 1498599 PMCID: PMC160139 DOI: 10.1105/tpc.4.4.389] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In previous studies using leaves of light-grown transgenic tobacco plants, we have shown that sequences located within the transcribed region of the pea Fed-1 gene (encoding ferredoxin I) are major cis-acting determinants of light-regulated mRNA accumulation. However, we show here that these internal sequences are less important for the Fed-1 light response in etiolated tobacco seedlings than they are in green leaves and that upstream elements confer organ specificity and contribute significantly to Fed-1 light responses in etiolated material. Light effects mediated by upstream response elements are thus most pronounced during the initial induction of gene activity, whereas internal elements play a more prominent role in modulating Fed-1 expression once the gene is already active.
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Affiliation(s)
- M Gallo-Meagher
- Department of Genetics, North Carolina State University, Raleigh 27695
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48
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Abstract
We monitored Fed-1 (encoding ferredoxin I) mRNA levels in etiolated transgenic tobacco seedlings containing the intact pea Fed-1 gene to determine if the characteristic light responses of this gene in pea seedlings are also observed in transgenic tobacco. Fed-1 transcript levels in transgenic tobacco seedlings closely paralleled those of the native gene in pea buds when etiolated seedlings were transferred to white light. However, the response to red light was much smaller in tobacco than in pea and was not efficiently reversed by far-red light. The red light response of endogenous tobacco ferredoxin transcripts is closely comparable to that of the Fed-1 transgene, with a similar lack of photoreversibility. Thus, the pea Fed-1 transgene responds normally to tobacco gene-regulatory factors, but these factors are less influenced by phytochrome in tobacco cotyledons than in pea buds.
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Affiliation(s)
- M Gallo-Meagher
- Department of Genetics, North Carolina State University, Raleigh 27695
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49
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Abstract
In a probe-tone experiment, two groups of listeners--one trained, the other untrained, in traditional music theory--rated the goodness of fit of each of the 12 notes of the chromatic scale to four-voice harmonic sequences. Sequences were 12 simplified excerpts from Bach chorales, 4 nonmodulating, and 8 modulating. Modulations occurred either one or two steps in either the clockwise or the counterclockwise direction on the cycle of fifths. A consistent pattern of probe-tone ratings was obtained for each sequence, with no significant differences between listener groups. Two methods of analysis (Fourier analysis and regression analysis) revealed a directional asymmetry in the perceived key movement conveyed by modulating sequences. For a given modulation distance, modulations in the counterclockwise direction effected a clearer shift in tonal organization toward the final key than did clockwise modulations. The nature of the directional asymmetry was consistent with results reported for identification and rating of key change in the sequences (Thompson & Cuddy, 1989a). Further, according to the multiple-regression analysis, probe-tone ratings did not merely reflect the distribution of tones in the sequence. Rather, ratings were sensitive to the temporal structure of the tonal organization in the sequence.
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Affiliation(s)
- L L Cuddy
- Department of Psychology, Queen's University, Kingston, Ontario, Canada
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50
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Abstract
Four experiments investigated the perception of tonal structure in polytonal music. The experiments used musical excerpts in which the upper stave of the music suggested a different key than the lower stave. In Experiment 1, listeners rated the goodness of fit of probe tones following an excerpt from Dubois's Circus. Results suggested that listeners were sensitive to two keys, and weighted them according to their perceived importance within the excerpt. Experiment 2 confirmed that music within each stave reliably conveyed key structure on its own. In Experiment 3, listeners rated probe tones following an excerpt from Milhaud's Sonata No. 1 for Piano, in which different keys were conveyed in widely separate pitch registers. Ratings were collected across three octaves. Listeners did not associate each key with a specific register. Rather, ratings for all three octave registers reflected only the key associated with the upper stave. Experiment 4 confirmed that the music within each stave reliably conveyed key structure on its own. It is suggested that when one key predominates in a polytonal context, other keys may not contribute to the overall perceived tonal structure. The influence of long-term knowledge and immediate context on the perception of tonal structure in polytonal music is discussed.
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Affiliation(s)
- W F Thompson
- Department of Psychology, Atkinson College, York University, Ontario, Canada
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