Sites of rDNA transcription are widely dispersed through the nucleolus in Pisum sativum and can comprise single genes

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.

The dark-adaptation response of the de-etiolated pea mutant lip1 is modulated by external signals and endogenous programs

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.

Characterization of Post-Transcriptionally Suppressed Transgene Expression That Confers Resistance to Tobacco Etch Virus Infection in Tobacco

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.

Music performance and the perception of key

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.

Music performance and the perception of key

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.

High-level transgene expression in plant cells: effects of a strong scaffold attachment region from tobacco

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.

High-level transgene expression in plant cells: effects of a strong scaffold attachment region from tobacco

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.

Light-regulated expression of the Arabidopsis thaliana ferredoxin gene requires sequences upstream and downstream of the transcription initiation site

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.

Individual Members of the Cab Gene Family Differ Widely in Fluence Response

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.

Sensitivity to combinations of musical parameters: pitch with duration, and pitch pattern with durational pattern

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.

Light modulation of ferredoxin mRNA abundance requires an open reading frame

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.

Birthdates of neurons in the retinal ganglion cell layer of the ferret

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.

Sequence of Lhcb3*1, a gene encoding a Photosystem II chlorophyll a/b-binding protein in Pisum

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.

Scaffold attachment regions increase reporter gene expression in stably transformed plant cells

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.

Modeling perceived relationships between melody, harmony, and key

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.

Initial characterization of a pea mutant with light-independent photomorphogenesis

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.

Development and characterization of a generalized gene tagging system for higher plants using an engineered maize transposon Ac

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.

Expression of the chlorophyll-a/b-protein multigene family in pea (Pisum sativum L.) : Evidence for distinct developmental responses

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.

Light regulatory sequences are located within the 5' portion of the Fed-1 message sequence

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.

Both internal and external regulatory elements control expression of the pea Fed-1 gene in transgenic tobacco seedlings

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.

The pea ferredoxin I gene exhibits different light responses in pea and tobacco

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.

Asymmetry of perceived key movement in chorale sequences: converging evidence from a probe-tone analysis

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.

A perceptual investigation of polytonality

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.