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Since the publication of draft sequences for the human and mouse genomes, several groups have run large-scale comparisons of the sequences to detect regions of conserved sequence. An initial survey of these was published along with the draft mouse genome , with additional comparisons appearing since then . Briefly, pro... | 15369604_p0 | 15369604 | Background | 4.404693 | biomedical | Study | [
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Here, we apply the Eponine Windowed Sequence (EWS) sequence analysis method method which uses a Relevance Vector Machine (RVM) to extract a minimal set of short motifs which are able to discriminate between two sets of sequences: in this case, a positive set of conserved non-coding sequences and a negative set of rando... | 15369604_p1 | 15369604 | Background | 4.207819 | biomedical | Study | [
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We considered a set of alignments made by the blastz program between release NCBI33 of the human genome and release NCBIM30 of the mouse genome. Since unprocessed blastz aligns around 40% of human sequence to the mouse genome, we chose to focus on the 'tight' alignments. These are a subset of alignments which are resco... | 15369604_p2 | 15369604 | Results | 4.083272 | biomedical | Study | [
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In total, the tight blastz set contained 787173 blocks of sequence with high-scoring alignments between the two genomes. We considered only those blocks assigned to human chromosome 6, a 170 Mb chromosome which has recently undergone manual annotation of gene structures and other features . This chromosome included 441... | 15369604_p3 | 15369604 | Results | 4.109158 | biomedical | Study | [
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Since we were interested in non-coding features of the genome, we ignored all regions where an alignment overlaps an annotated gene structure. This removed 20.8% of aligned bases. It is possible that some genes, and especially pseudogenes, have been missed by the annotation process, so we also removed portions covered ... | 15369604_p4 | 15369604 | Results | 4.135834 | biomedical | Study | [
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A negative training set of equal size was prepared by picking 200-base windows at random from the non-coding, non-repetitive portions of chromosome 6, using the same criteria to define repeats and coding sequence. While it is probable that this set also included some functional sequences, we would expect them to be rep... | 15369604_p5 | 15369604 | Results | 3.802903 | biomedical | Study | [
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These two sets of sequence were presented to the Eponine Windowed Sequence machine learning system, as described in the methods section. Randomly chosen 5-base words were used as seed motifs, and three independent training runs were performed, each for 2000 cycles. The set of motifs used in model 1 is shown in table 1 ... | 15369604_p6 | 15369604 | Results | 3.006421 | biomedical | Study | [
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While the exact set of motifs used in the model varied somewhat from run to run, testing pairs of models on non-overlapping windows from a 1 Mb region of human chromosome 22 and plotting the scores showed that the model outputs were highly correlated . We calculated the Pearson correlation coefficient for all pairs, an... | 15369604_p7 | 15369604 | Results | 3.993884 | biomedical | Study | [
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We scanned genomic sequences using these models at a range of thresholds, and examined the results on the Ensembl genome browser using a Distributed Annotation System server. Visual inspection showed that many of the highest-scoring regions were localised near the start of genes. This prompted us to look at the distrib... | 15369604_p8 | 15369604 | Results | 4.193588 | biomedical | Study | [
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Evaluation of promoter-prediction methods on a large scale is a difficult exercise, since there are no large pieces of genomic sequence for which we can be certain we know the complete set of transcribed regions, and even in the case of well-known genes we often do not know the precise location at which transcription b... | 15369604_p9 | 15369604 | Results | 4.15755 | biomedical | Study | [
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We picked model 1 for further study. Using a score threshold of 0.91, this gives an accuracy of 0.68 and a coverage of 0.31. We compared the set of genes correctly detected by this model to two other methods: firstly, the EponineTSS predictor described in , and secondly, the published results from the PromoterInspector... | 15369604_p10 | 15369604 | Results | 4.101628 | biomedical | Study | [
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We investigated the robustness of the signal learned by this process by retraining models with a variety of seed word sizes, from 2 to 6 bases. During training, motifs can be trimmed to lengths shorter than that of the seed words (down to a minimum of 2 bases) but can never grow longer than the seed word size. When eva... | 15369604_p11 | 15369604 | Results | 4.075315 | biomedical | Study | [
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This suggests that a large fraction (but not all) of the information learned by these models can be encoded in dinucleotide frequencies. It is well known that many transcription start sites are close to regions of relatively high CpG dinucleotide composition (CpG islands) . To investigate the contribution that CpG dinu... | 15369604_p12 | 15369604 | Results | 4.104287 | biomedical | Study | [
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We have shown here that, when presented with a set of non-coding sequences which are strongly conserved between human and mouse, a simple motif-oriented machine learning system consistently builds models which are able to detect a substantial fraction of human promoter regions with good accuracy. This strongly suggests... | 15369604_p13 | 15369604 | Conclusions | 4.131089 | biomedical | Study | [
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It is interesting that the promoter model learned by this technique detected substantially the same set of promoters as found by the EponineTSS and PromoterInspector methods. It has previously been remarked that these two methods detect similar sets , but this could perhaps be explained by the fact that both methods we... | 15369604_p14 | 15369604 | Conclusions | 4.135934 | biomedical | Study | [
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One distinct group of promoters, which previous results show may correspond to this easily detected family, is the set of promoters associated with CpG islands . However, while a number of the motifs listed in table 1 are G/C rich and/or contain the CpG dinucleotide, by no means all of the motifs match this description... | 15369604_p15 | 15369604 | Conclusions | 4.253947 | biomedical | Study | [
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Human genome sequence release NCBI33 and mouse genome release NCBIM30 were extracted from Ensembl databases , which also contained gene predictions from Genscan and repeat data from RepeatMasker and trf . Curated annotation of gene structures on human chromosome 6 was obtained from the Vega database . Vega and Ensembl ... | 15369604_p16 | 15369604 | Genomic sequence and annotation | 4.105514 | biomedical | Study | [
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Human-mouse genome alignments were generated by the blastz alignment program. These were subsequently re-scored and filtered to give a 'tight' set of high-confidence alignments, as described in . We downloaded the tight alignment set from the UCSC genome website . | 15369604_p17 | 15369604 | Genome alignments | 3.715925 | biomedical | Study | [
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A 16.3 Mb pseudochromosome sequence was produced based on version 2.3 of the curated annotation for human chromosome 22. This includes all the experimentally-validated gene structures and their upstream regions, while omitting regions containing genes that are predicted but not fully verified. In the case of a pair of ... | 15369604_p18 | 15369604 | Pseudochromosome for testing promoter-finding methods | 4.167931 | biomedical | Study | [
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The Eponine Windowed Sequence (EWS) model is designed by analogy to the Eponine Anchored Sequence model first described in , but rather than targeting individual points in the sequence, it is designed to classify small regions or windows of a sequence, based purely on their own sequence content. | 15369604_p19 | 15369604 | Eponine Windowed Sequence learning | 3.175628 | biomedical | Other | [
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The EWS model uses the Relevance Vector Machine algorithm to drive the training process. Relevance Vector Machines solve classification and regression problems by building Generalised Linear Models (GLMs) as weighted sums of a "working set" of basis functions. During the training process, those basis functions which ar... | 15369604_p20 | 15369604 | Eponine Windowed Sequence learning | 3.0407 | biomedical | Other | [
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The "sensors" of the EWS model are DNA position-weight matrices , which make convenient models of short sequence motifs. When using weight matrices to analyse sequence windows, we sum the weight matrix probability scores for all possible positions within the sequence. Normalising for the length of the sequence being in... | 15369604_p21 | 15369604 | Eponine Windowed Sequence learning | 3.87899 | biomedical | Other | [
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where W ( s ) is the probability that sequence s was emitted by weight matrix W , | S | is the sequence length, | W | is the weight matrix length, and denotes a subsequence from i to j . | 15369604_p22 | 15369604 | Eponine Windowed Sequence learning | 3.226629 | biomedical | Other | [
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An initial set of basis functions is proposed by taking all possible DNA motifs of a specified length (typically 5) and generating weight matrices which preferentially recognise these motifs. As the relevance vector machine trainer removes non-informative basis functions from the working set, they are replaced by apply... | 15369604_p23 | 15369604 | Eponine Windowed Sequence learning | 3.890726 | biomedical | Study | [
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• Generate a new weight matrix in which each column is a sample from a Dirichlet distribution with its mode equal to the weights in the corresponding column of the parent weight matrix. | 15369604_p24 | 15369604 | Eponine Windowed Sequence learning | 2.41156 | biomedical | Other | [
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• Generate a new weight matrix one column shorter than the parent by removing either the first of the last column. | 15369604_p25 | 15369604 | Eponine Windowed Sequence learning | 1.393535 | other | Other | [
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By using these sampling rules, the trainer is able to explore motif space. The process of generating candidate motifs using these rules then selecting the most informative using the RVM can be seen as a form of genetic algorithm. | 15369604_p26 | 15369604 | Eponine Windowed Sequence learning | 2.300513 | biomedical | Other | [
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TD and TH conceived and designed this study, and analysed results. TD implemented the Eponine machine learning system and drafted the manuscript. All authors read and approved the final manuscript. | 15369604_p27 | 15369604 | Authors' contributions | 0.954128 | other | Other | [
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Development of eukaryotic cells towards particular cell fates is regulated by complex and dynamic changes in gene expression. These changes, when monitored on a genome-wide scale, provide a detailed framework for the analysis and modeling of cellular development. To monitor patterns of gene expression it is important t... | 15535861_p0 | 15535861 | Background | 4.029372 | biomedical | Study | [
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Transcriptomic studies of single cell types in plants have focused on diploid sporophytic cell types, including undifferentiated cell suspensions , leaf epidermal and mesophyll cells , stomatal guard cells and cultured mesophyll cells . These studies have provided valuable information about gene expression in single ce... | 15535861_p1 | 15535861 | Background | 4.364785 | biomedical | Study | [
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In contrast to such enabling technologies and procedures developed for sporophytic cell types there have been no studies that provide a genome-wide perspective of cell fate determination and differentiation during haploid gametophyte development. The haploid male gametophyte generation of flowering plants has a simple ... | 15535861_p2 | 15535861 | Background | 4.207327 | biomedical | Review | [
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Recent progress in understanding of molecular and cellular aspects of pollen development has emerged from genetic studies that have identified mutants in Arabidopsis that affect all phases of pollen development . In parallel, cDNA libraries and databanks have been obtained for sperm cells in maize, lily, tobacco and Pl... | 15535861_p3 | 15535861 | Background | 4.197473 | biomedical | Study | [
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Some initial progress has been made towards the definition of the male gametophytic transcriptome of Arabidopsis using serial analysis of gene expression (SAGE) and Affymetrix AG microarrays that harbor probes for approximately 8,000 different genes . These studies have provided valuable insight into the complexity of ... | 15535861_p4 | 15535861 | Background | 4.144932 | biomedical | Review | [
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Here we describe spore isolation procedures for Arabidopsis and the use of Affymetrix ATH1 Genome Arrays to analyze transcript expression profiles throughout four successive stages of male gametophyte development in Arabidopsis . Isolated spore populations were large enough to enable RNA extraction for direct microarra... | 15535861_p5 | 15535861 | Background | 4.233756 | biomedical | Study | [
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Transcriptome profiling throughout microgametogenesis in Arabidopsis required the introduction of a procedure for the isolation of homogeneous populations of viable spores at precisely defined stages of development. The method was based on centrifugation of isolated mixed spores in a Percoll step-gradient . Large homog... | 15535861_p6 | 15535861 | Isolation and characterization of developing spores | 4.129242 | biomedical | Study | [
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Microscopic examination of isolated spore populations revealed no contaminating sporophytic cells and little or no other cellular debris . Vital staining revealed more than 90% viable spores at each stage (data not shown). The purity of spore populations was evaluated by DAPI staining . The UNM population was the most ... | 15535861_p7 | 15535861 | Isolation and characterization of developing spores | 4.187575 | biomedical | Study | [
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Arabidopsis ATH1 Genome Arrays were used to explore the dynamics of gene expression throughout male gametophyte development in comparison with sporophytic tissues. Microarrays were hybridized with cRNA probes made from total RNA purified from isolated spores. Hybridization data from two biological replicates derived fr... | 15535861_p8 | 15535861 | Developmental changes in the male gametophytic transcriptome | 4.1635 | biomedical | Study | [
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We have previously confirmed and validated the expression pattern of 15 putative pollen-specific genes identified using Affymetrix AG arrays by reverse transcription-PCR analysis . Similarly we validated the current ATH1 datasets by RT-PCR analysis in two separate experiments that included analysis of 41 genes encoding... | 15535861_p9 | 15535861 | Developmental changes in the male gametophytic transcriptome | 4.093526 | biomedical | Study | [
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The ATH1 Genome Array harbors oligonucleotide probes representing 22,591 genes based on the Arabidopsis Genome Initiative annotation. This represents 80.7% of the most recent estimate of 28,000 protein-coding genes in Arabidopsis . Of these, 13,977 genes gave a consistently positive expression signal in at least one st... | 15535861_p10 | 15535861 | Developmental changes in the male gametophytic transcriptome | 4.215282 | biomedical | Study | [
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} |
To identify genes expressed preferentially or specifically in developing male gametophytes, hybridization data was compared with sporophytic ATH1 datasets (COT, LEF, PET, STM, ROT and RHR; see Additional data file 1). Transcripts with a consistent positive expression signal in at least one stage of male gametophyte dev... | 15535861_p11 | 15535861 | Developmental changes in the male gametophytic transcriptome | 4.125002 | biomedical | Study | [
0.9992294311523438,
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0.9995176792144775,
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] | en | 0.999997 | {
"en": 0.9999968399661715
} |
Analysis of the distribution of transcripts among three abundance classes: high (up to 10-fold less than the maximum signal), medium (10- to 100- fold less) and low (more than 100-fold less) , revealed a decrease in the proportion of transcripts forming the high-abundance class during development from 20% to 12%. On th... | 15535861_p12 | 15535861 | Developmental changes in the male gametophytic transcriptome | 4.331929 | biomedical | Study | [
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] | en | 0.999997 | {
"en": 0.9999974027414614
} |
Scatter-plot analysis was used to examine in more detail the complexity of the mRNA decline after PMII. The expression levels of individual genes were normalized using a scale of 0 to 100. Genes coexpressed in pairs of datasets were plotted using a logarithmic scale and a correlation coefficient ( R value) calculated .... | 15535861_p13 | 15535861 | Developmental changes in the male gametophytic transcriptome | 4.268426 | biomedical | Study | [
0.9993243217468262,
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] | [
0.999250590801239,
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] | en | 0.999996 | {
"en": 0.9999964949602226
} |
The relationship between cell proliferation activities and transcriptome profiles was examined by comparison of early UNM and late MPG stages with a publicly available suspension cell culture dataset. These comparisons demonstrated that the microspore transcriptome was significantly more similar to that of cell suspens... | 15535861_p14 | 15535861 | Developmental changes in the male gametophytic transcriptome | 4.124085 | biomedical | Study | [
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] | en | 0.999997 | {
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} |
To identify gametophytic genes that may form co-regulated clusters, all 13,977 male gametophyte-expressed genes were hierarchically clustered using EPCLUST clustering and analysis software. Application of a threshold value of 0.05 resulted in the definition of 39 gene clusters covering all phases of male gametophyte de... | 15535861_p15 | 15535861 | Co-regulated clusters of gametophytic genes | 4.15751 | biomedical | Study | [
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} |
The majority of male gametophyte-expressed genes (52%) were grouped into four clusters (25, 27, 29 and 35) comprising early expressed genes repressed after PMII. Several large gene clusters collectively containing 1,899 genes (13.6%) were associated with pollen maturation. These were activated or upregulated between BC... | 15535861_p16 | 15535861 | Co-regulated clusters of gametophytic genes | 4.220909 | biomedical | Study | [
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We focused our further analysis on three key categories of genes with likely regulatory significance in male gametophyte development; core cell-cycle genes, transcription factors and core translation factors . Core cell-cycle genes were defined according to TAIR . Genes comprising Arabidopsis transcription factor famil... | 15535861_p17 | 15535861 | Expression of regulatory genes throughout male gametophyte development | 4.048983 | biomedical | Study | [
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] | [
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] | en | 0.999998 | {
"en": 0.9999978147729539
} |
Among 61 core cell-cycle genes, 55 genes were present on the ATH1 GeneChip and 45 (82%) of these were expressed in the male gametophyte (see Additional data file 1). Representative(s) of all families and subfamilies were expressed. The majority of gametophytic core cell-cycle genes showed similar expression profiles , ... | 15535861_p18 | 15535861 | Core cell-cycle genes | 4.129916 | biomedical | Study | [
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] | [
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] | en | 0.999996 | {
"en": 0.9999962978949064
} |
We identified 1,594 genes encoding putative transcription factors that were divided into 34 gene families (see Additional data file 1). Their representation on the ATH1 GeneChip was 1,350 (85%). Of these, 608 (45%) were expressed in the male gametophyte, including 54 (15.7%) that were male gametophyte-specific. There w... | 15535861_p19 | 15535861 | Putative transcription factors | 4.212017 | biomedical | Study | [
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] | en | 0.999996 | {
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} |
The dominant expression pattern of transcription factor genes reflected the general repression of mRNA diversity between BCP and TCP stages . Besides a limited number of constitutively expressed genes, two major transcription factor gene groups could be distinguished. One contained a major group of early-expressed gene... | 15535861_p20 | 15535861 | Putative transcription factors | 4.140104 | biomedical | Study | [
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] | en | 0.999995 | {
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Among 100 annotated core translation factor genes, 82 were present on the ATH1 GeneChip and 75 (91%) of these were expressed in the male gametophyte (see Additional data file 1). The vast majority of translation factor genes belonged to the early group and these were strongly expressed . Reflecting the constitutive req... | 15535861_p21 | 15535861 | Core translation factors | 4.187117 | biomedical | Study | [
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The rapid decline of mRNAs encoding translation initiation factors after bicellular stage and the parallel de novo synthesis of a new set of late pollen transcription factors, suggested storage of translation factors and ongoing transcription after pollen germination. Therefore we investigated the dependence of Arabido... | 15535861_p22 | 15535861 | Integrating transcriptomic and experimental data | 4.413005 | biomedical | Study | [
0.9993746876716614,
0.0003894397523254156,
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] | [
0.9988640546798706,
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0.00011028235894627869
] | en | 0.999996 | {
"en": 0.9999956638576294
} |
To identify patterns of gene expression involved in Arabidopsis male gametophyte development, we compared the transcriptomes of isolated spores at four discrete developmental stages using ATH1 microarrays. ATH1 microarrays harbor probe sets for 22,591 annotated genes . Of these, 61.9% (13,977 genes) gave positive hybri... | 15535861_p23 | 15535861 | Discussion | 4.17686 | biomedical | Study | [
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0.9994082450866699,
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0.00005129320561536588
] | en | 0.999997 | {
"en": 0.9999969930400753
} |
As the proportion of known genes embedded on the ATH1 array is 80.7%, we estimate the total number of genes expressed throughout Arabidopsis male gametophyte development to be more than 17,000. Similarly, the total number of genes expressed at individual developmental stages is estimated to be 14,300 at UNM stage, 14,8... | 15535861_p24 | 15535861 | Discussion | 4.177797 | biomedical | Study | [
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0.0004679824924096465,
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] | en | 0.999996 | {
"en": 0.9999956486775466
} |
Two recent studies of the Arabidopsis mature pollen transcriptome using Affymetrix 8K AG arrays led to the identification of 992 and 1,584 pollen-expressed mRNAs, respectively . Results obtained with ATH1 and AG arrays are considered comparable and largely independent of the different probe sets used . However, there w... | 15535861_p25 | 15535861 | Discussion | 4.471972 | biomedical | Study | [
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} |
Developmental analysis of transcriptome data revealed two striking features, a sharp reduction in transcript diversity after BCP stage and a major shift in mRNA populations between BCP and TCP stages. The decline in mRNA diversity after BCP stage is associated with terminal differentiation as well as the documented phe... | 15535861_p26 | 15535861 | Discussion | 4.268936 | biomedical | Study | [
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0.9993077516555786,
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] | en | 0.999996 | {
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} |
It is interesting that the expression profiles of UNM stage and BCP stages are similar despite the presence of two different cell types in pollen grains at BCP stage - the larger vegetative cell and the smaller generative cell. Given the limited volume of cytoplasm associated with the generative cell, developmental cha... | 15535861_p27 | 15535861 | Discussion | 4.252969 | biomedical | Study | [
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0.999347984790802,
0.0002458867966197431,
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] | en | 0.999997 | {
"en": 0.9999969175223604
} |
In contrast, generative cell fate appears to be dependent on asymmetric division at pollen mitosis I . Sperm-cell cDNAs and databanks recently established in maize, lily, tobacco and Plumbago zelanica provide valuable gametic gene-expression data in other species. Although our data do not provide direct information abo... | 15535861_p28 | 15535861 | Discussion | 4.106032 | biomedical | Study | [
0.9992923736572266,
0.00015832186909392476,
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] | en | 0.999995 | {
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} |
Hierarchical cluster analysis provided detailed evidence for the dramatic switch between early and late developmental programs. We identified 39 gene clusters that could correspond to co-regulated genes. These included early clusters, several clusters of late genes, those with constitutive expression profiles and clust... | 15535861_p29 | 15535861 | Discussion | 4.261786 | biomedical | Study | [
0.9993436932563782,
0.0003269164590165019,
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0.9991599321365356,
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} |
Our analysis revealed completely different expression profiles of transcription factors when compared to core translation factors. The majority of core translation factors belonged to the early-group genes with few that were male gametophyte-specific. This may be expected, given that many genes are involved in general ... | 15535861_p30 | 15535861 | Discussion | 4.216772 | biomedical | Study | [
0.9992127418518066,
0.00031817902345210314,
0.0004690955101978034
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] | en | 0.999996 | {
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Conversely, transcription factors showed more diverse spectra of expression profiles including early, constitutive and late. There was a considerable variation in the expression profiles of individual transcription factor families. The most over-represented was the C3H family, members of which are known to have roles i... | 15535861_p31 | 15535861 | Discussion | 4.194817 | biomedical | Study | [
0.9989812970161438,
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0.999405026435852,
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The majority of core translation factors belonged to the early gene clusters. In contrast, a significant number of transcription-factor genes were strongly expressed during pollen maturation. These data alone did not obviously support the fact that pollen germination and early tube growth in many species are largely in... | 15535861_p32 | 15535861 | Discussion | 4.396548 | biomedical | Study | [
0.9992606043815613,
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0.9991426467895508,
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The key impact of this work is that it provides a genome-wide view of the complexity of gene expression during single cell development in plants. Analysis of the male gametophytic transcriptome provides comprehensive and unequivocal evidence for the unique state of differentiation that distinguishes the developing male... | 15535861_p33 | 15535861 | Conclusions | 4.252004 | biomedical | Study | [
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Arabidopsis thaliana ecotype Landsberg erecta plants were grown in controlled-environment cabinets at 21°C under illumination of 150 μmol/m 2 /sec with a 16-h photoperiod. Isolated spores from three stages of immature male gametophyte were obtained by modification of the protocol of Kyo and Harada . After removal of op... | 15535861_p34 | 15535861 | Plant material and spore isolation | 4.256904 | biomedical | Study | [
0.9992973804473877,
0.000360027770511806,
0.0003426040057092905
] | [
0.9989476799964905,
0.0004938172060064971,
0.00048126891488209367,
0.00007729611388640478
] | en | 0.999998 | {
"en": 0.9999979104180741
} |
Total RNA was extracted from 50 mg of isolated spores at each developmental stage using the RNeasy Plant Kit (Qiagen) according to the manufacturer's instructions. The yield and RNA purity was determined spectrophotometrically and using an Agilent 2100 Bioanalyzer at the NASC. | 15535861_p35 | 15535861 | RNA extraction, probe preparation and DNA chip hybridization | 3.909609 | biomedical | Study | [
0.9995385408401489,
0.00016521177894901484,
0.00029624838498421013
] | [
0.9927782416343689,
0.006439493969082832,
0.0006372276111505926,
0.0001451235730201006
] | en | 0.999996 | {
"en": 0.9999957175554638
} |
Biotinylated target RNA was prepared from 20 μg of total RNA as described in the Affymetrix GeneChip expression analysis technical manual. Double-stranded cDNA was synthesized using SuperScript Choice System (Life Technologies) with oligo(dT) 24 primer fused to T7 RNA polymerase promoter. Biotin-labeled target cRNA was... | 15535861_p36 | 15535861 | RNA extraction, probe preparation and DNA chip hybridization | 4.132455 | biomedical | Study | [
0.9994151592254639,
0.00033197092125192285,
0.00025291653582826257
] | [
0.9640445709228516,
0.034253813326358795,
0.0012731256429105997,
0.00042844784911721945
] | en | 0.999997 | {
"en": 0.9999967880664415
} |
Arabidopsis ATH1 Genome Arrays were hybridized with 15 μg labeled target cRNA for 16 h at 45°C. Microarrays were stained with streptavidin-phycoerythrin solution and scanned with an Agilent 2500A GeneArray Scanner. | 15535861_p37 | 15535861 | RNA extraction, probe preparation and DNA chip hybridization | 3.874706 | biomedical | Study | [
0.9990206956863403,
0.00020593759836629033,
0.00077343505108729
] | [
0.9382506012916565,
0.06044868007302284,
0.001004548859782517,
0.0002961903519462794
] | en | 0.999998 | {
"en": 0.9999978679977486
} |
Sporophytic data from public baseline GeneChip experiments used for comparison with the pollen transcriptome were downloaded from the NASC website . The list of dataset codes was as follows: COT (three replicates), Cornah_A4-cornah-wsx_SLD_REP1-3; LEF (three replicates), A4-LLOYD-CON_REP1-3; PET (three replicates), Mil... | 15535861_p38 | 15535861 | Data analysis | 3.498385 | biomedical | Study | [
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0.9715606570243835,
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0.0007512920419685543,
0.00017570506315678358
] | en | 0.999999 | {
"en": 0.9999988209917543
} |
All gametophytic and sporophytic datasets were normalized using freely available dChip 1.3 software . The reliability and reproducibility of analyses was ensured by the use of duplicates or triplicates in each experiment, the normalization of all 26 arrays to the median probe intensity level and the use of normalized C... | 15535861_p39 | 15535861 | Data analysis | 4.124419 | biomedical | Study | [
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0.000300131127005443,
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] | en | 0.999998 | {
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Microsoft Excel was used to manage and filter the microarray data. For annotation of genes present on the ATH1 Array, the Arabidopsis Genome Annotation Release 3.0 published by The Institute for Genomic Research was used. Genes were sorted into functional categories created according to data mined from the Munich Infor... | 15535861_p40 | 15535861 | Data analysis | 3.984634 | biomedical | Study | [
0.9994838237762451,
0.0001591538602951914,
0.0003569992259144783
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The following additional data is available with the online version of this article: Additional data file 1 is an Excel file containing the following items. The table Data contains the complete transcriptomic datasets used. Data were normalized using dChip 1.3 as described in Materials and methods. Expression signal val... | 15535861_p41 | 15535861 | Additional data files | 4.147919 | biomedical | Study | [
0.9993059635162354,
0.00016634739586152136,
0.0005277270684018731
] | [
0.9974976181983948,
0.0018095942214131355,
0.0006011960213072598,
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] | en | 0.999995 | {
"en": 0.9999948342017566
} |
The catecholamines (dopamine, norepinephrine and epinephrine) are a group of biogenic amines possessing a substituted 3, 4-dihydroxy phenyl ring that are widespread in the animal kingdom; but they have also been detected in plants . The role of catecholamines in plants is poorly documented, but it is clear that they ar... | 15701180_p0 | 15701180 | Background | 4.558156 | biomedical | Study | [
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0.000581240514293313,
0.00042242955532856286
] | [
0.9988269209861755,
0.0003471947566140443,
0.0006723951082676649,
0.00015345937572419643
] | en | 0.999997 | {
"en": 0.9999965968361577
} |
Solanum tuberosum plants transformed with pHD1-BinAR, a plasmid carrying a cDNA for the human dopamine receptor under the control of the CaMV 35S promoter , were pre-selected by means of PCR with the primers for neomycin phosphotransferase (kanamycin) gene and then selected by northern blot analysis with a HD1 specific... | 15701180_p1 | 15701180 | Transgenic plant selection | 4.287649 | biomedical | Study | [
0.9992697834968567,
0.000388946442399174,
0.00034124753437936306
] | [
0.999340832233429,
0.00022422830807045102,
0.0003497148281894624,
0.00008512800559401512
] | en | 0.999997 | {
"en": 0.9999969426319737
} |
Tubers of HD1 plants grown in a field were harvested after four months and analyzed. All examined transgenic lines produced more tubers per plant. The yield was not significantly changed since increase in tuber number was accompanied by decrease in tuber weight (Table 1 ). There were no obvious morphological difference... | 15701180_p2 | 15701180 | Phenotype analysis | 2.946006 | biomedical | Study | [
0.982093870639801,
0.0007206661975942552,
0.017185350880026817
] | [
0.9974330067634583,
0.002217670902609825,
0.0002475559012964368,
0.00010177867079619318
] | en | 0.999997 | {
"en": 0.999996862338652
} |
In order to develop an easy and reliable assay for the quantitative and qualitative determination of catecholamines in plants, the suitability of gas chromatography coupled to a quadruple mass spectrometer (GCMS) was recently investigated. A sensitive GCMS method based on the analysis of the trimethylsilylated catechol... | 15701180_p3 | 15701180 | Catecholamine level | 4.123064 | biomedical | Study | [
0.9995372295379639,
0.00018537291907705367,
0.00027743243845179677
] | [
0.999242901802063,
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] | en | 0.999995 | {
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} |
In contrast to the previous studies performed on plants over-expressing tyrosine decarboxylase , which controls an important step of catecholamine synthesis, the goal of our work was to stimulate an alternative signalling pathway by introducing human dopamine receptor. Surprisingly the expression of dopamine receptor r... | 15701180_p4 | 15701180 | Catecholamine level | 4.096666 | biomedical | Study | [
0.9994332194328308,
0.000240643770666793,
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] | [
0.9995614886283875,
0.00019203414558432996,
0.00020037293143104762,
0.000046024328185012564
] | en | 0.999998 | {
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} |
Following our recent finding that the action of dopamine and norepinephrine in potato is on starch mobilization, we decided to analyze transgenic tubers expressing dopamine receptor for soluble sugars and starch content. All transgenic plants showed decreased starch content, with levels that ranged from 20 to 60% perce... | 15701180_p5 | 15701180 | Determination of carbohydrate content in tubers of transgenic plants | 4.097103 | biomedical | Study | [
0.9993376135826111,
0.00021624859073199332,
0.0004461695207282901
] | [
0.999559223651886,
0.00015376883675344288,
0.00024357845541089773,
0.00004352045289124362
] | en | 0.999997 | {
"en": 0.9999965454806655
} |
Changes in carbohydrate are most likely responsible for the altered phenotype of transgenic HD1 tubers. Reduced tuber mass can be explained by decreased starch content whereas increased tuber number by the increase of soluble sugar concentration. | 15701180_p6 | 15701180 | Determination of carbohydrate content in tubers of transgenic plants | 3.249133 | biomedical | Study | [
0.9891639947891235,
0.0003974534338340163,
0.010438506491482258
] | [
0.9386999011039734,
0.05947018414735794,
0.001536178053356707,
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] | en | 0.999996 | {
"en": 0.9999957011161003
} |
Under normal growth conditions the major flux in potato tuber carbon metabolism is the conversion of sucrose through hexose phosphates to starch . | 15701180_p7 | 15701180 | Sucrose – starch metabolism | 3.084377 | biomedical | Other | [
0.9832648634910583,
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] | en | 0.999998 | {
"en": 0.9999984505260906
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Since HD1 plants were characterized by changed concentrations of both soluble sugars and starch we measured the activities of enzymes involved in this pathway. Sucrose transported from leaves is symplastically unloaded from the phloem and degraded by sucrose synthase (SuSy). ADP-glucose phosphorylase (AGPase) converts ... | 15701180_p8 | 15701180 | Sucrose – starch metabolism | 4.15633 | biomedical | Study | [
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0.0006528469384647906
] | [
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] | en | 0.999997 | {
"en": 0.9999965239061759
} |
Activities of AGPase and SuSy were significantly decreased in HD1 plants to 56% and 68% of the wild type level, respectively . In agreement with their roles in starch synthesis, and their proposed coordinated regulation, activities of both enzymes and starch content were all significantly correlated (cor >0.9). | 15701180_p9 | 15701180 | Sucrose – starch metabolism | 4.05737 | biomedical | Study | [
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] | [
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] | en | 0.999997 | {
"en": 0.9999967857621159
} |
Phosphoglucomutase (PGM) catalyzes the conversion of glucose-1-phosphate to glucose-6-phosphate. Tubers are characterized by the presence of cytosolic and plastidial isoforms of phosphoglucomutase. Repression of either of them results in plants with decreased starch levels pointing out the importance of the enzyme for ... | 15701180_p10 | 15701180 | Sucrose – starch metabolism | 4.192892 | biomedical | Study | [
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0.00025739011471159756,
0.0004608033050317317
] | [
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] | en | 0.999996 | {
"en": 0.9999959062081216
} |
To establish whether enhanced starch mobilization also contributed to the observed decreases in starch content we measured the activity of starch phosphorylase. In two out of the four examined transgenic lines the activity of starch phosphorylase was significantly increased, further contributing to decreased starch con... | 15701180_p11 | 15701180 | Sucrose – starch metabolism | 3.891469 | biomedical | Study | [
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0.000293849065201357,
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] | [
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] | en | 0.999997 | {
"en": 0.9999973134909386
} |
Moreover HD1 expression led to activation of sucrose phosphate synthase (SPS), responsible for sucrose production. Maximum SPS activity (measured wih saturating substrates, Vmax) only changed in two lines, whilst activity of the enzyme measured in the assay that contained limiting substrate concentration (Vmax/Km) and ... | 15701180_p12 | 15701180 | Sucrose – starch metabolism | 4.120253 | biomedical | Study | [
0.9993693232536316,
0.00021347728034015745,
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] | [
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0.00005681549373548478
] | en | 0.999998 | {
"en": 0.9999976558813314
} |
1/Km, correlated well with the sucrose content of transgenic tubers (cor -0.81) . | 15701180_p13 | 15701180 | Sucrose – starch metabolism | 3.275309 | biomedical | Study | [
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0.0005207686335779727,
0.005727387499064207
] | [
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0.005525962915271521,
0.0003743274137377739,
0.00014463586558122188
] | en | 0.999998 | {
"en": 0.9999979137129739
} |
The high concentrations of glucose and glc-6-P measured in the HD1 plants indicated changes in the glycolytic pathway. However, activities of glycolytic enzymes (hexokinase, phosphofructokinase and enolase) were not changed. The only exception was pyruvate kinase, which showed a significant decrease of activity in all ... | 15701180_p14 | 15701180 | Glycolysis/TCA cycle | 4.136599 | biomedical | Study | [
0.9993144273757935,
0.0002880146203096956,
0.00039753978489898145
] | [
0.9995667338371277,
0.00015869809431023896,
0.0002208345104008913,
0.00005379934736993164
] | en | 0.999997 | {
"en": 0.9999965930692547
} |
In contrast to the vast knowledge concerning the role and action of catecholamines in mammals, very little is known about the physiological significance of catecholamines in plants. Since most of the components of animal catecholamine signaling pathway have been also identified in plants (G-proteins, cAMP, PKA homologs... | 15701180_p15 | 15701180 | Discussion | 4.136292 | biomedical | Study | [
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0.0001691511133685708,
0.0003675886837299913
] | [
0.9961705803871155,
0.0005123745067976415,
0.003236171556636691,
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] | en | 0.999997 | {
"en": 0.9999970408373068
} |
The only component of mammalian catecholamine signaling pathway that to date has not been identified in plants is the catecholamine receptor. We transformed potato plants with a cDNA encoding human dopamine receptor (HD1) in order to analyze whether the presence of a receptor affects the endogenous catecholamine action... | 15701180_p16 | 15701180 | Discussion | 4.354183 | biomedical | Study | [
0.9993658661842346,
0.00037302137934602797,
0.00026114666252397
] | [
0.9992020726203918,
0.00024734920589253306,
0.00045824196422472596,
0.00009231259173247963
] | en | 0.999996 | {
"en": 0.9999961243017546
} |
Therefore we suggest that the exogenous receptor activates catecholamine action in potato plants. A difference in enzyme activities involved in starch biosynthesis was noted. The sucrose level was comparable in HD1 and TD plants and consistent with enhanced activity of SPS. Activity of starch phosphorylase was signific... | 15701180_p17 | 15701180 | Discussion | 4.109247 | biomedical | Study | [
0.9992179870605469,
0.00019103946397081017,
0.0005909492028877139
] | [
0.9995285272598267,
0.00024924983154051006,
0.00018088905198965222,
0.00004136958159506321
] | en | 0.999996 | {
"en": 0.9999962960479848
} |
The previously reported positive correlation between catecholamine level and soluble sugars content and negative correlation with starch level for tubers of potatoes over -expressing tyrosine decarboxylase and in tubers stored at 4°C , was also found in our study. Expression of a dopamine receptor resulted in increased... | 15701180_p18 | 15701180 | Expression of HD1 in potato ( Solanum tuberosum ) results in altered carbon metabolism | 4.093778 | biomedical | Study | [
0.9994567036628723,
0.0001940033835126087,
0.0003492863615974784
] | [
0.9994227886199951,
0.000229922792641446,
0.00029618493863381445,
0.00005116233660373837
] | en | 0.999999 | {
"en": 0.9999985998639311
} |
In mammalian systems epinephrine and norepinephrine regulate glycogen turnover by stimulating glycogen mobilization and inhibiting glycogen synthesis. This appears similar in potato, with decreased starch content in HD1 tubers being a consequence of both inhibition of starch synthesis and enhanced starch mobilization. ... | 15701180_p19 | 15701180 | Expression of HD1 in potato ( Solanum tuberosum ) results in altered carbon metabolism | 4.718836 | biomedical | Study | [
0.9990531802177429,
0.0005847412976436317,
0.00036207708762958646
] | [
0.9976575374603271,
0.0006296201609075069,
0.0014207307249307632,
0.0002920459082815796
] | en | 0.999997 | {
"en": 0.9999970379994723
} |
Since the level of 14-3-3 proteins was not changed in any of the transgenic lines (data not shown) it is thus suggested that enzyme phosphorylation targeted to the stress site is responsible for its activity enhancement in HD1 plants. | 15701180_p20 | 15701180 | Expression of HD1 in potato ( Solanum tuberosum ) results in altered carbon metabolism | 3.046356 | biomedical | Study | [
0.99591463804245,
0.00039142800960689783,
0.003693877486512065
] | [
0.9917601943016052,
0.007661499548703432,
0.00038709279033355415,
0.00019134202739223838
] | en | 0.999998 | {
"en": 0.999997677306778
} |
In mammals the action of epinephrine and norepinephrine is mediated by phosphorylation of enzymes involved in glycogen mobilization and synthesis. Very recent studies reported direct evidence that enzymes of starch metabolism (amylopectin synthesis) are regulated by protein phosphorylation and indicate a wider role for... | 15701180_p21 | 15701180 | Expression of HD1 in potato ( Solanum tuberosum ) results in altered carbon metabolism | 4.070583 | biomedical | Study | [
0.9994494318962097,
0.00013148618745617568,
0.0004189899191260338
] | [
0.9867450594902039,
0.004476399626582861,
0.008616817183792591,
0.00016172548930626363
] | en | 0.999995 | {
"en": 0.9999953794789794
} |
In mammalian systems, catecholamines serve as stress hormones increasing as a result of stress. In order to see whether or not a similar response occurs in plants, leaves of potato plants were wounded and catecholamines levels prior to and 5, 10 and 13 min after wounding were determined. Although the data varied, there... | 15701180_p22 | 15701180 | Catecholamines – the new stress hormones in plants? | 4.46999 | biomedical | Study | [
0.9993453621864319,
0.0003712550678756088,
0.00028345349710434675
] | [
0.9980677962303162,
0.0003286123101133853,
0.0014847195707261562,
0.00011880094825755805
] | en | 0.999998 | {
"en": 0.9999980692650419
} |
Introducing humane dopamine receptor into plant cells can be considered as controversial but the obtained data would argue for the value of our approach. | 15701180_p23 | 15701180 | Conclusions | 1.969746 | biomedical | Other | [
0.9753209948539734,
0.0010548575082793832,
0.02362413890659809
] | [
0.3600408434867859,
0.6330552101135254,
0.005269109271466732,
0.0016348488861694932
] | en | 0.999996 | {
"en": 0.9999961155449526
} |
Vast changes in the activities of key enzymes mediating carbon metabolism of potato tuber (in HD plants) led to a dramatic reduction of starch but increased sucrose content. The relation between catecholamine, primary carbon metabolism and stress seems possible. We speculate that similarly to situation in animal cells ... | 15701180_p24 | 15701180 | Conclusions | 4.158563 | biomedical | Study | [
0.9992349147796631,
0.0001824799837777391,
0.000582605367526412
] | [
0.9988897442817688,
0.0007487176335416734,
0.00029248945065774024,
0.00006910124648129568
] | en | 0.999998 | {
"en": 0.9999975099809085
} |
Similarly plants expressing HD2 showed no changes in carbohydrate metabolism (data not shown). The obvious next step would be further investigation of our plants with respect to their kinase activity as well as cAMP levels. In parallel we have made efforts to identify a plant dopamine receptor. | 15701180_p25 | 15701180 | Conclusions | 2.451626 | biomedical | Study | [
0.9911333918571472,
0.0005146369221620262,
0.008351976051926613
] | [
0.9602277278900146,
0.038580697029829025,
0.0008018825319595635,
0.00038971920730546117
] | en | 0.999995 | {
"en": 0.9999953578834833
} |
Potato plants ( Solanum tuberosum L. cv. Desiree) obtained from "Saatzucht Fritz Lange KG" (Bad Schwartau, Germany) were cultivated in a greenhouse in soil under 16 h light (22°C) and 8 h dark (15°C) regime. Plants were grown in individual pots and watered daily. For analysis, the leaves were harvested at noon from 30-... | 15701180_p26 | 15701180 | Plant material | 3.4222 | biomedical | Study | [
0.9921680092811584,
0.0003758993116207421,
0.007456135004758835
] | [
0.9904265999794006,
0.008960584178566933,
0.000482355710119009,
0.00013054355804342777
] | en | 0.999997 | {
"en": 0.9999969751363339
} |
The 1.3 kb SmaI, XbaI cDNA encoding HD1 from Homo sapiens ((kindly provided by Marc G.Caron (Duke University, Medical Center); [EMB: XX55760])), was ligated in the sense orientation into the same restriction site of the plant binary vector under the control of the 35S CaMV promoter and Nos terminator. The vector was in... | 15701180_p27 | 15701180 | Construction of a transgenic plant | 4.22032 | biomedical | Study | [
0.9993709921836853,
0.00031851971289142966,
0.0003104748611804098
] | [
0.9988012313842773,
0.0007934047025628388,
0.00032120285322889686,
0.00008408342546317726
] | en | 0.999995 | {
"en": 0.9999952052045702
} |
Total RNA was prepared from frozen plant material using the guanidinium hydrochloride method. Following electrophoresis (1.5% (w/v) agarose, 15% formaldehyde (w/v)), RNA was transferred to nylon membranes (Hybond N, Amersham, UK). Membranes were hybridised overnight at 42°C in 250 mmol sodium phosphate buffer (pH 7.2) ... | 15701180_p28 | 15701180 | Northern blot analysis | 4.103244 | biomedical | Study | [
0.9993300437927246,
0.0002511450438760221,
0.0004188290040474385
] | [
0.9975970387458801,
0.0019109962740913033,
0.0004139058873988688,
0.0000781402486609295
] | en | 0.999997 | {
"en": 0.9999973166567537
} |
Proteins were extracted from frozen plant material using extraction buffer E (100 mM Hepes-NaOH, pH 7.4, 10 mM MgCl 2 , 1 mM EDTA, 1 mM EGTA, 20%glycerol (v/v), 0.5 mM PMSF, 70 mM beta-mercaptoethanol) supplemented either with 0.1% or 1% TritonX- 100 (v/v). The assessment of the expression of HD1 gene by means of weste... | 15701180_p29 | 15701180 | Western blot analysis | 4.105913 | biomedical | Study | [
0.9992635846138,
0.00023853140010032803,
0.0004979193327017128
] | [
0.9993545413017273,
0.00036079439450986683,
0.0002421697718091309,
0.00004242960494593717
] | en | 0.999998 | {
"en": 0.9999983347251001
} |
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