[Show abstract][Hide abstract] ABSTRACT: Previously we developed genomic resources for orchids, including transcriptomic analyses using next-generation sequencing techniques and construction of a web-based orchid genomic database. Here, we report a modified molecular model of flower development in the Orchidaceae based on functional analysis of gene expression profiles in Phalaenopsis aphrodite (a moth orchid) that revealed novel roles for the transcription factors involved in floral organ pattern formation. Phalaenopsis orchid floral organ-specific genes were identified by microarray analysis. Several critical transcription factors including AP3, PI, AP1 and AGL6, displayed distinct spatial distribution patterns. Phylogenetic analysis of orchid MADS box genes was conducted to infer the evolutionary relationship among floral organ-specific genes. The results suggest that gene duplication MADS box genes in orchid may have resulted in their gaining novel functions during evolution. Based on these analyses, a modified model of orchid flowering was proposed. Comparison of the expression profiles of flowers of a peloric mutant and wild-type Phalaenopsis orchid further identified genes associated with lip morphology and peloric effects. Large scale investigation of gene expression profiles revealed that homeotic genes from the ABCDE model of flower development classes A and B in the Phalaenopsis orchid have novel functions due to evolutionary diversification, and display differential expression patterns.
PLoS ONE 11/2013; 8(11):e80462. DOI:10.1371/journal.pone.0080462 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Orchids display unique phenotypes, functional characteristics and ecological adaptations that are not found in model plants. In this study, we aimed to characterize the microRNA (miRNA) transcriptome and identify species- and tissue-specific miRNAs in Phalaenopsis aphrodite. After data filtering and cleanup, a total of 59,387,374 reads, representing 1,649,996 unique reads, were obtained from four P. aphrodite small RNA libraries. A systematic bioinformatics analysis pipeline was developed that can be used for miRNA and precursor mining, and target gene prediction in non-model plants. A total of 3,251 unique reads for 181 known plant miRNAs (belonging to 88 miRNA families), 23 new miRNAs and 91 precursors were identified. All the miRNA star sequences (miRNA*), the complementary strands of miRNA that from miRNA/miRNA* duplexes, of the predicted new miRNAs were detected in our small RNA libraries, providing additional evidence for their existence as new miRNAs in P. aphrodite. Furthermore, 240 potential miRNA-targets that appear to be involved in many different biological activities and molecular functions, especially transcription factors, were identified, suggesting that miRNAs can impact multiple processes in P. aphrodite. We also verified the cleavage sites for six targets using RNA ligase-mediated rapid amplification of 5′ ends assay. The results provide valuable information about the composition, expression and function of miRNA in P. aphrodite, and will aid functional genomics studies of orchids.
Electronic supplementary material
The online version of this article (doi:10.1007/s11103-013-0150-0) contains supplementary material, which is available to authorized users.
[Show abstract][Hide abstract] ABSTRACT: Leptin, a 167 amino acid peptide, is synthesized predominantly in the adipose tissues and plays a key role in the regulation of food intake and body weight. Recent studies indicate that leptin receptor is expressed with high levels in many brain regions that may regulate synaptic plasticity. Here we show that deprivation of rapid eye movement (REMD) sleep resulted in impairment of both cue and contextual fear memory. In parallel, surface expression of GluR1 was reduced in the amygdala. Intraperitoneal injection of leptin to the REMD mice rescued memory impairment and reversed surface GluR1 reduction. Using whole-cell recording to evaluate the synaptic function of the thalamus-lateral amygdala (LA) pathway, we found a decrease in frequency and amplitude of miniature excitatory postsynaptic currents (mEPSCs) concomitant with reduced AMPA/NMDA ratios in the REMD mice. By contrast, paired-pulse facilitation (PPF) was increased. The effects of REMD on mEPSCs and AMPA/NMDA ratio could be reversed by leptin treatment, whereas on PPR it could not. Phosphatase and tensin homolog (PTEN), a dual protein/lipid phosphatase, down-regulates the effect of the PI-3 kinase pathway. Fear conditioning increased whereas REMD led to a decrease in the phosphorylated states of PTEN, Akt, and glycogen synthase kinase-3β (GSK3β), and the effects of REMD were reversed by leptin. These results suggest that both pre- and postsynaptic functions of the thalamus-LA pathway were altered by fear conditioning and REMD in opposite directions. Leptin treatment reversed REMD-induced memory deficits primarily by a postsynaptic action by restoring surface expression of GluR1 without affecting PPR.
[Show abstract][Hide abstract] ABSTRACT: A specialized orchid database, named Orchidstra (URL: http://orchidstra.abrc.sinica.edu.tw) has been constructed to collect, annotate and share genomic information for orchid functional genomics studies. The Orchidaceae is a large family of Angiosperms that exhibits extraordinary biodiversity both in terms of the number of species and their distribution worldwide. Orchids exhibit many unique biological features; however, investigation of these traits is currently constrained due to the limited availability of genomic information. Transcriptome information for five orchid species and one commercial hybrid has been included in the Orchidstra database. Altogether, these comprise more than 380,000 non-redundant orchid transcript sequences, of which more than 110,000 are protein coding genes. Sequences from the transcriptome shotgun assembly (TSA) were obtained either from output reads from next generation sequencing technologies assembled into contigs, or from conventional cDNA library approaches. An annotation pipeline using Gene Ontology, KEGG and Pfam was built to assign gene descriptions and functional annotation to protein coding genes. Deep sequencing of small RNA was also performed for Phalaenopsis aphrodite to search for microRNAs, extending the information archived for this species to miRNA annotation, precursors and putative target genes. The Phalaenopsis aphrodite transcriptome information was further used to design probes for an oligonucleotide microarray and expression profiling analysis was carried out. Intensities of hybridized probes derived from microarray assays of various tissues were incorporated into the database as part of the functional evidence. In the future, the content of the Orchidstra database will be expanded with transcriptome data and genomic information from more orchid species.
[Show abstract][Hide abstract] ABSTRACT: Phalaenopsis aphrodite Rchb. f. is an epiphyte native to tropical broadleaf forest in Taiwan. Epiphytic roots attach to the surface of tree trunks instead of growing in soil. Unique structures and morphology of Phalaenopsis roots include velamen outside epidermis, passage cells in endodermis, absence of root hairs, and lack or absence of branch roots. Understanding the mechanism of nutrient uptake and metabolism in Phalaenopsis is important to determine how efficient nutrient usage is achieved under intermittent supply. Phalaenopsis Sogo Yukidian ‘V3’ was fertilized with various deficient concentrations of N, P, and K every 2 weeks. After 8 weeks of treatment in 30/25°C, plants were transferred to 25/20°C to induce spiking. No apparent phenotype differences were observed from treatments of N, P, or K deficiency after 8 weeks in the vegetative stage. However, the treatments affected spiking rates dramatically and deficiency symptoms started to show on the leaf after flowering. Microarray analysis revealed differential gene expression in roots. There were 11 up-regulated and 37 down-regulated genes commonly appearing in roots under N, P, or K deficiency stress. The transcript level of a phosphate transporter increased significantly under phosphate deficiency. One of the zinc finger transcription factors, GATA, increased under N, P, or K deficiency stress. Mineral contents between treatments were analyzed using inductively coupled plasma spectroscopy. Leaf iron concentration was lower under phosphate deficiency.
[Show abstract][Hide abstract] ABSTRACT: Being one of the largest families in the angiosperms, Orchidaceae display a great biodiversity resulting from adaptation to diverse habitats. Genomic information on orchids is rather limited, despite their unique and interesting biological features, thus impeding advanced molecular research. Here we report a strategy to integrate sequence outputs of the moth orchid, Phalaenopsis aphrodite, from two high-throughput sequencing platform technologies, Roche 454 and Illumina/Solexa, in order to maximize assembly efficiency. Tissues collected for cDNA library preparation included a wide range of vegetative and reproductive tissues. We also designed an effective workflow for annotation and functional analysis. After assembly and trimming processes, 233,823 unique sequences were obtained. Among them, 42,590 contigs averaging 875 bp in length were annotated to protein-coding genes, of which 7,263 coding genes were found to be nearly full length. The sequence accuracy of the assembled contigs was validated to be as high as 99.9%. Genes with tissue-specific expression were also categorized by profiling analysis with RNA-Seq. Gene products targeted to specific subcellular localizations were identified by their annotations. We concluded that, with proper assembly to combine outputs of next-generation sequencing platforms, transcriptome information can be enriched in gene discovery, functional annotation and expression profiling of a non-model organism.
[Show abstract][Hide abstract] ABSTRACT: Understanding the neurophysiology of fear extinction has important implications for the treatment of post-traumatic stress disorders. Here we report that fear conditioning resulted in an increase in AMPA/NMDA ratio as well as depression of paired-pulse facilitation (PPF) in neurons of the lateral nucleus of amygdala. These conditioning-induced changes in synaptic transmission were not affected by extinction training. D-cycloserine (DCS), a partial agonist at the glycine-binding site of the NMDA receptor, facilitated extinction and reversed the increase in AMPA/NMDA ratio without altering the depression of PPF when administered before extinction training. Extinction training, however, significantly increased the frequency and amplitude of miniature inhibitory post-synaptic currents and these effects were unaffected by the DCS treatment. Disruption of AMPA receptor endocytosis with a synthetic peptide containing a short C-terminal sequence of GluR2 (869YKEGYNVYG877, GluR23Y) specifically blocked DCS-induced reversal of AMPA/NMDA ratio and the facilitation of extinction. These results suggest that extinction training mainly increases inhibitory transmission leaving conditioning-induced excitatory association unaltered. DCS does not affect inhibitory transmission but reverses the conditioning-induced post-synaptic memory trace when administered before extinction training.
The International Journal of Neuropsychopharmacology 09/2009; 13(3):335-45. DOI:10.1017/S1461145709990678 · 4.01 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Understanding the mechanism of how fear memory can be extinguished could provide potential therapeutic strategies for the treatment of posttraumatic stress disorders. Here we show that infusion of CB1 receptor antagonist into the infralimbic (IL) subregion of the medial prefrontal cortex (mPFC) retarded cue-alone-induced reduction of fear-potentiated startle. Conversely, cannabinoid agonist WIN55212-2 (WIN) facilitated the extinction. Unexpectedly, administration of WIN without cue-alone trials reduced startle potentiation in a dose-dependent manner. The effect of cannabinoid agonists was mimicked by endocannabinoid uptake or fatty acid amide hydrolase inhibitors. Rats were trained with 10 conditioned stimulus (CS(+)) (yellow light)-shock pairings. Extinction training with CS(+) (yellow light)-alone but not CS(-) (blue light)-alone trials decreased fear-potentiated startle. Intra-IL infusion of WIN before CS(-)-alone trials decreased startle potentiation, suggesting that the cannabinoid agonist decreased conditioned fear irrespective of whether the rats underwent CS(+)- or CS(-)-alone trials. Cannabinoid agonists activated extracellular signal-regulated kinases (ERKs) in mPFC slices, and ERK inhibitor blocked the effect of cannabinoid agonists on fear-potentiated startle. These results suggest that CB1 receptors acting through the phosphorylation of ERK are involved not only in the extinction of conditioned fear but also in the adaptation to aversive situations in general.
[Show abstract][Hide abstract] ABSTRACT: We recently demonstrated that microRNA399 (miR399) controls inorganic phosphate (Pi) homeostasis by regulating the expression of UBC24 encoding a ubiquitin-conjugating E2 enzyme in Arabidopsis (Arabidopsis thaliana). Transgenic plants overexpressing miR399 accumulated excessive Pi in the shoots and displayed Pi toxic symptoms. In this study, we revealed that a previously identified Pi overaccumulator, pho2, is caused by a single nucleotide mutation resulting in early termination within the UBC24 gene. The level of full-length UBC24 mRNA was reduced and no UBC24 protein was detected in the pho2 mutant, whereas up-regulation of miR399 by Pi deficiency was not affected. Several characteristics of Pi toxicity in the pho2 mutant were similar to those in the miR399-overexpressing and UBC24 T-DNA knockout plants: both Pi uptake and translocation of Pi from roots to shoots increased and Pi remobilization within leaves was impaired. These phenotypes of the pho2 mutation could be rescued by introduction of a wild-type copy of UBC24. Kinetic analyses revealed that greater Pi uptake in the pho2 and miR399-overexpressing plants is due to increased Vmax. The transcript level of most PHT1 Pi transporter genes was not significantly altered, except PHT1;8 whose expression was enhanced in Pi-sufficient roots of pho2 and miR399-overexpressing compared with wild-type plants. In addition, changes in the expression of several organelle-specific Pi transporters were noticed, which may be associated with the redistribution of intracellular Pi under excess Pi. Furthermore, miR399 and UBC24 were colocalized in the vascular cylinder. This observation not only provides important insight into the interaction between miR399 and UBC24 mRNA, but also supports their systemic function in Pi translocation and remobilization.
[Show abstract][Hide abstract] ABSTRACT: In this study, we reveal a mechanism by which plants regulate inorganic phosphate (Pi) homeostasis to adapt to environmental changes in Pi availability. This mechanism involves the suppression of a ubiquitin-conjugating E2 enzyme by a specific microRNA, miR399. Upon Pi starvation, the miR399 is upregulated and its target gene, a ubiquitin-conjugating E2 enzyme, is downregulated in Arabidopsis thaliana. Accumulation of the E2 transcript is suppressed in transgenic Arabidopsis overexpressing miR399. Transgenic plants accumulated five to six times the normal Pi level in shoots and displayed Pi toxicity symptoms that were phenocopied by a loss-of-function E2 mutant. Pi toxicity was caused by increased Pi uptake and by translocation of Pi from roots to shoots and retention of Pi in the shoots. Moreover, unlike wild-type plants, in which Pi in old leaves was readily retranslocated to other developing young tissues, remobilization of Pi in miR399-overexpressing plants was impaired. These results provide evidence that miRNA controls Pi homeostasis by regulating the expression of a component of the proteolysis machinery in plants.
The Plant Cell 03/2006; 18(2):412-21. DOI:10.1105/tpc.105.038943 · 9.34 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Vernalization is required to induce flowering in cabbage (Brassica oleracea var Capitata L.). Since FLOWERING LOCUS C (FLC) was identified as a major repressor of flowering in the vernalization pathway in Arabidopsis (Arabidopsis thaliana), two homologs of AtFLC, BoFLC3-2 and BoFLC4-1, were isolated from cabbage to investigate the molecular mechanism of vernalization in cabbage flowering. In addition to the sequence homology, the genomic organization of cabbage FLC is similar to that of AtFLC, except that BoFLC has a relatively smaller intron 1 compared to that of AtFLC. A vernalization-mediated decrease in FLC transcript level was correlated with an increase in FT transcript level in the apex of cabbage. This observation is in agreement with the down-regulation of FT by FLC in Arabidopsis. Yet, unlike that in Arabidopsis, the accumulation of cabbage FLC transcript decreased after cold treatment of leafy plants but not imbibed seeds, which is consistent with the promotion of cabbage flowering by vernalizing adult plants rather than seeds. To further dissect the different regulation of FLC expression between seed-vernalization-responsive species (e.g. Arabidopsis) and plant-vernalization-responsive species (e.g. cabbage), the pBoFLC4-1BoFLC4-1GUS construct was introduced into Arabidopsis to examine its vernalization response. Down-regulation of the BoFLC4-1GUS construct by seed vernalization was unstable and incomplete; in addition, the expression of BoFLC4-1GUS was not suppressed by vernalization of transgenic rosette-stage Arabidopsis plants. We propose a hypothesis to illustrate the distinct mechanism by which vernalization regulates the expression of FLC in cabbage and Arabidopsis.
[Show abstract][Hide abstract] ABSTRACT: Although the underlying mechanism is not elucidated, it has been postulated repeatedly that deprivation of sleep, particularly rapid eye movement (REM) sleep, affects learning. Here we report that memory for newly acquired information is impaired after a specific period of REM sleep deprivation (REMD). Memory retrieval-induced phosphorylation of protein kinases in the rat amygdala is abrogated by REMD that is associated with an increase in the expression of a dual protein/lipid phosphatase PTEN. REMD given before training is without effect, suggesting the lack of effect on the acquisition of memory. Intra-amygdala administration of antisense but not sense or scrambled oligonucleotides for PTEN prevents REMD-induced decrease in protein phosphorylation and impairment of fear memory. Thus, REMD interferes with the process of memory retention via the activation of PTEN.
[Show abstract][Hide abstract] ABSTRACT: Due to its economic importance, small genome size, and co-linear gene organization with other cereal grasses, rice has been chosen as a model organism for genome sequencing. ASPGC is currently working on the high-throughput sequencing project of rice chromosome 5. Bioinformatics study is also carried out to understand the genome and its complexity. ASPGC also works on EST, SAGE and insertional mutants of rice. The crop improvement relies on genomic technology more and more recently. Through the structural and functional genomic study, this team hopes to add more information and tools for the rice research community.