The NAD(P)H dehydrogenase complex is encoded by 11 ndh genes in plant chloroplast (cp) genomes. However, ndh genes are truncated or deleted in some autotrophic Epidendroideae orchid cp genomes. To determine the evolutionary timing of the gene deletions and the genomic locations of the various ndh genes in orchids, the cp genomes of Vanilla planifolia, Paphiopedilum armeniacum, Paphiopedilum niveum, Cypripedium formosanum, Habenaria longidenticulata, Goodyera fumata and Masdevallia picturata were sequenced; these genomes represent Vanilloideae, Cypripedioideae, Orchidoideae and Epidendroideae subfamilies. Four orchid cp genome sequences were found to contain a complete set of ndh genes. In other genomes, ndh deletions did not correlate to known taxonomic or evolutionary relationships and deletions occurred independently after the orchid family split into different subfamilies. In orchids lacking cp encoded ndh genes, non cp localized ndh sequences were identified. In Erycina pusilla, at least 10 truncated ndh gene fragments were found transferred to the mitochondrial (mt) genome. The phenomenon of orchid ndh transfer to the mt genome existed in ndh-deleted orchids and also in ndh containing species.
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.
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.
The main purpose of the National Asthma Education Program was to provide asthma education to school nurses in Taiwan. It was also designed to enhance the knowledge and competence of school nurses in managing the asthmatic problems that children experience while in school. In addition to providing instruction about current asthma management skills, tools, and other relevant information, the program demonstrated the use of the peak flow meter for asthmatic children. A single, 4-hr session conducted in each county and city in Taiwan, the National Asthma Education Program began on August 1, 1999, and ended December 31, 2000. A total of 829 school nurses joined the program, with an overall attendance rate of 74%. Significant effects of this program on nurses' asthma care knowledge and competence and case management efficacy were noted. The participating school nurses' demographics, however, were found to be irrelevant to these effects. Expecting the training activities to help relieve the anxieties of managing asthmatic cases in the school environment, participants reported that the training was of much benefit to them. Development of a teaching program to elevate school nurses' capabilities in asthmatic student care in the school environment and the implications of such a program within Taiwanese schools were also discussed.
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 in terms of both 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 >380,000 non-redundant orchid transcript sequences, of which >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 (miRNAs), extending the information archived for this species to miRNA annotation, precursors and putative target genes. The P. aphrodite transcriptome information was further used to design probes for an oligonucleotide microarray, and expression profiling analysis was carried out. The 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.
The radial average-power distribution and normalized average power of orbital-angular-momentum (OAM) modes in a vortex Gaussian beam after passing through weak-to-strong atmospheric turbulence are theoretically formulated. Based on numerical calculations, the role of the intrinsic mode index, initial beam radius and turbulence strength in OAM-mode variations of a propagated vortex Gaussian beam is explored, and the validity of the pure-phase-perturbation approximation employed in existing theoretical studies is examined. Comparison between turbulence-induced OAM-mode scrambling of vortex Gaussian beams and that of either Laguerre-Gaussian (LG) beams or pure vortex beams has been made. Analysis shows that the normalized average power of OAM modes changes with increasing receiver-aperture size until it approaches a nearly stable value. For a receiver-aperture size of practical interest, OAM-mode scrambling is severer with a larger mode index or smaller initial beam radius besides stronger turbulence. Under moderate-to-strong turbulence condition, for two symmetrically-neighboring extrinsic OAM modes, the normalized average power of the one with an index closer to zero may be greater than that of the other one. The validity of the pure-phase-perturbation approximation is determined by the intrinsic mode index, initial beam radius and turbulence strength. It makes sense to jointly control the amplitude and phase of a fundamental Gaussian beam for producing an OAM-carrying beam.
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