Closure of the Entire Fistula With Highly Effective Chemocauterization Using the Distal Hood Endoscope: A Novel Procedure for the Treatment of Pyriform Sinus Fistula.

BACKGROUND: Pyriform sinus fistula (PSF) causes a recurrent abscess in the neck. Endoscopic chemocauterization with trichloroacetic acid (TCA) for PSF is a simple, reproducible, and reliable procedure for treating PSF; however, there is concern about complications caused by TCA overflowing into the larynx. To prevent these complications, we devised a highly effective chemocauterization using a distal hooded endoscope (HuDHE). Our aim is to determine the efficacy and safety of HuDHE in children with PSF. METHODS: The main features of HuDHE are as follows (1) an endoscope with a translucent silicon hood at the tip was made; (2) TCA was endoscopically injected into the PSF; and (3) the color change of the mucosa into PSF was endoscopically evaluated. Data on children receiving HuDHE for PSF in the past seven years were collected from medical records. RESULTS: Data were obtained for eight children receiving HuDHE. The success rate of treatment for PSF after the first TCA chemocauterization was 87.5% (7/8) and the cumulative success rate after the second treatment was 100% (8/8). None of the children had recurrent PSF or serious complications such as vocal cord paralysis after HuDHE. CONCLUSION: HuDHE appears to be a less invasive, safe, and effective treatment for PSF.

Congenital anomalies causing hemato/hydrocolpos: imaging findings, treatments, and outcomes.

Hemato/hydrocolpos due to congenital urogenital anomalies are rare conditions discovered in neonatal, infant, and adolescent girls. Diagnosis is often missed or delayed owing to its rare incidence and nonspecific symptoms. If early correct diagnosis and treatment cannot be performed, late complications such as tubal adhesion, pelvic endometriosis, and infertility may develop. Congenital urogenital anomalies causing hemato/hydrocolpos are mainly of four types: imperforate hymen, distal vaginal agenesis, transverse vaginal septum, and obstructed hemivagina and ipsilateral renal anomaly, and clinicians should have adequate knowledge about these anomalies. This article aimed to review the diagnosis and treatment of these urogenital anomalies by describing embryology, clinical presentation, imaging findings, surgical management, and postoperative outcomes.

Laser Microdissection-Mediated Isolation and In Vitro Transcriptional Amplification of Plant RNA.

Laser microdissection of cells allows for isolation of specific cells of interest for downstream analyses including transcriptional profiling. Plant cells present unique challenges for laser microdissection due to their cellulosic cell walls and large vacuoles. Here we present protocols for plant tissue preparation, laser microdissection of select plant cells, and linear amplification of RNA from dissected cells. Linear amplification of RNA from dissected cells allows sufficient RNA for subsequent quantitative analysis by RT-PCR, microarray, or RNA sequencing.

DNA extraction from freeze-dried plant tissue with CTAB in a 96-well format.

This protocol is a modified version of DNA isolation using cetyltrimethylammonium bromide (CTAB) and 96-well plates. It is high-throughput, which facilitates the analysis of large mapping populations. The DNA yield is adequate for at least 100-500 polymerase chain reaction (PCR) procedures.

Loss of RNA-dependent RNA polymerase 2 (RDR2) function causes widespread and unexpected changes in the expression of transposons, genes, and 24-nt small RNAs.

Transposable elements (TEs) comprise a substantial portion of many eukaryotic genomes and are typically transcriptionally silenced. RNA-dependent RNA polymerase 2 (RDR2) is a component of the RNA-directed DNA methylation (RdDM) silencing pathway. In maize, loss of mediator of paramutation1 (mop1) encoded RDR2 function results in reactivation of transcriptionally silenced Mu transposons and a substantial reduction in the accumulation of 24 nt short-interfering RNAs (siRNAs) that recruit RNA silencing components. An RNA-seq experiment conducted on shoot apical meristems (SAMs) revealed that, as expected based on a model in which RDR2 generates 24 nt siRNAs that suppress expression, most differentially expressed DNA TEs (78%) were up-regulated in the mop1 mutant. In contrast, most differentially expressed retrotransposons (68%) were down-regulated. This striking difference suggests that distinct silencing mechanisms are applied to different silencing templates. In addition, >6,000 genes (24% of analyzed genes), including nearly 80% (286/361) of genes in chromatin modification pathways, were differentially expressed. Overall, two-thirds of differentially regulated genes were down-regulated in the mop1 mutant. This finding suggests that RDR2 plays a significant role in regulating the expression of not only transposons, but also of genes. A re-analysis of existing small RNA data identified both RDR2-sensitive and RDR2-resistant species of 24 nt siRNAs that we hypothesize may at least partially explain the complex changes in the expression of genes and transposons observed in the mop1 mutant.

Laser microdissection-mediated isolation and in vitro transcriptional amplification of plant RNA.

Protocols for laser microdissection and linear amplification of RNA from fixed, sectioned plant tissues are described. When combined with quantitative RT-PCR, microarray analysis, or RNA-sequencing, these procedures enable quantitative analyses of transcript accumulation from microscopic quantities of specific plant organs, tissues, or single cells.

Microdissection of shoot meristem functional domains.

The shoot apical meristem (SAM) maintains a pool of indeterminate cells within the SAM proper, while lateral organs are initiated from the SAM periphery. Laser microdissection-microarray technology was used to compare transcriptional profiles within these SAM domains to identify novel maize genes that function during leaf development. Nine hundred and sixty-two differentially expressed maize genes were detected; control genes known to be upregulated in the initiating leaf (P0/P1) or in the SAM proper verified the precision of the microdissections. Genes involved in cell division/growth, cell wall biosynthesis, chromatin remodeling, RNA binding, and translation are especially upregulated in initiating leaves, whereas genes functioning during protein fate and DNA repair are more abundant in the SAM proper. In situ hybridization analyses confirmed the expression patterns of six previously uncharacterized maize genes upregulated in the P0/P1. P0/P1-upregulated genes that were also shown to be downregulated in leaf-arrested shoots treated with an auxin transport inhibitor are especially implicated to function during early events in maize leaf initiation. Reverse genetic analyses of asceapen1 (asc1), a maize D4-cyclin gene upregulated in the P0/P1, revealed novel leaf phenotypes, less genetic redundancy, and expanded D4-CYCLIN function during maize shoot development as compared to Arabidopsis. These analyses generated a unique SAM domain-specific database that provides new insight into SAM function and a useful platform for reverse genetic analyses of shoot development in maize.

Regulation of small RNA accumulation in the maize shoot apex.

MicroRNAs (miRNAs) and trans-acting siRNAs (ta-siRNAs) are essential to the establishment of adaxial-abaxial (dorsoventral) leaf polarity. Tas3-derived ta-siRNAs define the adaxial side of the leaf by restricting the expression domain of miRNA miR166, which in turn demarcates the abaxial side of leaves by restricting the expression of adaxial determinants. To investigate the regulatory mechanisms that allow for the precise spatiotemporal accumulation of these polarizing small RNAs, we used laser-microdissection coupled to RT-PCR to determine the expression profiles of their precursor transcripts within the maize shoot apex. Our data reveal that the pattern of mature miR166 accumulation results, in part, from intricate transcriptional regulation of its precursor loci and that only a subset of mir166 family members contribute to the establishment of leaf polarity. We show that miR390, an upstream determinant in leaf polarity whose activity triggers tas3 ta-siRNA biogenesis, accumulates adaxially in leaves. The polar expression of miR390 is established and maintained independent of the ta-siRNA pathway. The comparison of small RNA localization data with the expression profiles of precursor transcripts suggests that miR166 and miR390 accumulation is also regulated at the level of biogenesis and/or stability. Furthermore, mir390 precursors accumulate exclusively within the epidermal layer of the incipient leaf, whereas mature miR390 accumulates in sub-epidermal layers as well. Regulation of miR390 biogenesis, stability, or even discrete trafficking of miR390 from the epidermis to underlying cell layers provide possible mechanisms that define the extent of miR390 accumulation within the incipient leaf, which patterns this small field of cells into adaxial and abaxial domains via the production of tas3-derived ta-siRNAs.

Tissue specificity and evolution of meristematic WOX3 function.

The WUSCHEL-related homeobox (WOX) gene PRESSED FLOWER1 (PRS1) performs a conserved function during lateral organ development in Arabidopsis (Arabidopsis thaliana). Expressed in the periphery of the shoot meristem, PRS1 recruits founder cells that form lateral domains of vegetative and floral organs. Null mutations in PRS1 cause the deletion of lateral stipules from leaves and of lateral sepals and stamens from flowers. Although PRS1 expression is described in the L1 layer, PRS1 recruits founder cells from all meristem layers. The mechanism of non-cell autonomous PRS1 function and the evolution of disparate WOX gene functions are investigated herein. Meristem layer-specific promoters reveal that both L1 and L1-L2 expression of PRS1 fail to fully rescue PRS1 function, and PRS1 protein does not traffic laterally or transversely between shoot meristem layers. PRS1 protein accumulates within all meristematic cell layers (L1-L2-L3) when expressed from the native promoter, presumably due to low-level transcription in the L2 and L3 layers. When driven from the PRS1 promoter, full rescue of vegetative and floral prs1 mutant phenotypes is provided by WUSCHEL1 (WUS1), which is normally expressed in the stem cell organizing center of shoot meristems. The data reveal that WUS1 and PRS1 can engage in equivalent protein-protein interactions and direct transcription of conserved target genes, suggesting that their subfunctionalization has evolved primarily via diverse promoter specificity. Unexpectedly, these results also suggest that meristematic stem cells and lateral organ founder cells are intrinsically similar and formed via equivalent processes such that their ultimate fate is dependent upon stage-specific and domain-specific positional signaling.

Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.).

All above-ground plant organs are derived from shoot apical meristems (SAMs). Global analyses of gene expression were conducted on maize (Zea mays L.) SAMs to identify genes preferentially expressed in the SAM. The SAMs were collected from 14-day-old B73 seedlings via laser capture microdissection (LCM). The RNA samples extracted from LCM-collected SAMs and from seedlings were hybridized to microarrays spotted with 37 660 maize cDNAs. Approximately 30% (10 816) of these cDNAs were prepared as part of this study from manually dissected B73 maize apices. Over 5000 expressed sequence tags (ESTs) (about 13% of the total) were differentially expressed (P < 0.0001) between SAMs and seedlings. Of these, 2783 and 2248 ESTs were up- and down-regulated in the SAM, respectively. The expression in the SAM of several of the differentially expressed ESTs was validated via quantitative RT-PCR and/or in situ hybridization. The up-regulated ESTs included many regulatory genes including transcription factors, chromatin remodeling factors and components of the gene-silencing machinery, as well as about 900 genes with unknown functions. Surprisingly, transcripts that hybridized to 62 retrotransposon-related cDNAs were also substantially up-regulated in the SAM. Complementary DNAs derived from the LCM-collected SAMs were sequenced to identify additional genes that are expressed in the SAM. This generated around 550 000 ESTs (454-SAM ESTs) from two genotypes. Consistent with the microarray results, approximately 14% of the 454-SAM ESTs from B73 were retrotransposon-related. Possible roles of genes that are preferentially expressed in the SAM are discussed.

Cell type-specific gene expression profiling in plants by using a combination of laser microdissection and high-throughput technologies.

Laser microdissection (LM) allows for the isolation of specific cells of interest from heterogeneous tissues under direct microscopic visualization with the assistance of a laser beam. By permitting global analyses of gene expression and metabolites in the selected cells, it is a powerful tool for understanding the biological processes in individual cell types during development or in response to various stimuli. Recently, LM technology has been successfully applied to the separation of individual plant cell types. Here, we provide an overview of applications of LM combined with high-throughput technologies including transcript analyses [microarrays, serial analysis of gene expression (SAGE) and 454-sequencing], proteomic analyses and metabolomic profiling, for cell type-specific gene expression analyses in plants.

Maize tissue preparation and extraction of RNA from target cells for genotyping.

INTRODUCTIONThe use of RNA for genotyping analysis can be advantageous because transcriptomes are significantly smaller than genomes and typically contain far fewer repetitive sequences. Laser capture microdissection (LCM) has been used successfully to isolate sequences (especially rare transcripts) that accumulate in specific tissues. Where the quantity of isolated material is limiting, amplification can be used to increase the amount of product. Upon conversion to cDNA, the product serves as template for 454 sequencing to produce expressed sequence tags for subsequent SNP analysis and detection.This protocol describes the preparation of acetone-fixed and paraffin-embedded maize seedling tissue sections. Once the sections are prepared, the PALM MicroBeam System, with its Laser Microdissection and Pressure Catapulting (LMPC) technology, is used to cut out cells of interest and "catapult" isolated tissues into collection caps. This tissue can then be used for RNA extraction.

T7-based RNA amplification for genotyping from maize shoot apical meristem.

INTRODUCTIONThe use of RNA for genotyping analysis can be advantageous because transcriptomes are significantly smaller than genomes and typically contain far fewer repetitive sequences. Laser capture microdissection (LCM) has been used successfully to isolate sequences (especially rare transcripts) that accumulate in specific tissues. The amount of RNA collected in a standard microdissection is often insufficient for global gene expression analysis but can be increased via linear amplification. Upon conversion to cDNA, the product serves as template for 454 sequencing to produce expressed sequence tags for subsequent SNP analysis and detection. This protocol describes how to amplify RNA extracted from laser-dissected and captured tissues and cells.

Diagnostic and prognostic impact of beta-catenin alterations in pediatric liver tumors.

Hepatoblastoma (HBL), a major childhood malignant neoplasm, represents the most frequent malignant liver tumor in childhood. Recent reports have shown the CTNNB1 coding beta-catenin protein to be frequently mutated or deleted at hot-spot regions involving exon 3 in HBL. We investigated the genetic alterations of the CTNNB1 coding beta-catenin protein and expression of several genes downstream of Wnt signals in 4 benign and 17 malignant pediatric liver tumors (PLTs) consisting of 15 HBL, 1 hepatocellular carcinoma, and 1 hepatic immature sarcoma. Of 17 malignant PLTs, 10 (56%) revealed pathogenic alterations of the CTNNB1 gene, including 4 with missense mutations at codons 28, 32, 34 or 44, and 6 with interstitial deletions that partially or totally affected exon 3. All 6 deletions were in-frame deletions without a frame shift. The high frequency without any correlation to histological type indicates that the CTNNB1 gene alteration is a crucial event in the tumorigenesis of malignant PLTs. The immunohistochemical studies in 17 malignant PLTs demonstrated the nuclear/cytoplasmic accumulation of beta-catenin to be positive in all tumor specimens except for one hepatic sarcoma. A histological examination revealed all HBL cases involving tumors without detectable CTNNB1 gene alterations to show high expression of beta-catenin, thus indicating the accumulation of beta-catenin to be a common event in malignant PLTs, including HBL and hepatocellular carcinoma. Among the Wnt signal genes downstream of beta-catenin, E-cadherin is expressed in all malignant PLTs, while cyclin D1 expression was significantly detected in malignant PLTs with an advanced stage of disease. An immunohistological examination of nuclear accumulation of beta-catenin may thus be useful for diagnosing malignant PLTs. On the other hand, the expression of cyclin D1, a gene downstream of beta-catenin, might play a role in tumor progression.

Anaconda, a new class of transposon belonging to the Mu superfamily, has diversified by acquiring host genes during rice evolution.

A new type of transposon, named Anaconda (Anac) has been found in rice (Oryza sativa). In this paper, we demonstrate that Anaconda elements have diversified by acquisition of host cellular genes, amplification of the elements, and substitution and deletion of short segments. We identified four Anaconda elements in studies of rice alternative oxidase (AOX) genes, and subsequently isolated an additional 23 elements based on the identity of their terminal inverted repeats (TIRs). The Anaconda elements have long TIRs (114-458 bp). They also have direct repeats of 9 or 10 bp in their flanking regions that are thought to have been generated upon transposition. These structural features reveal that the Anaconda elements belong to the Mu superfamily. The most prominent feature of the Anaconda elements is the high frequency with which they have acquired host cellular genes. Of the 27 elements found here, 19 appear to have sequences presumably derived from rice genes, for example, the genes for AOX1c (four elements), cytochrome P450 (five elements), L: -asparaginase (five elements), and PCF8 (two elements). Four elements, AnacA1-A4, have both the AOX1c and P450 genes. One element, AnacB14, involves a gene similar to mudrA of maize MuDR. Database analyses revealed that the loci of 26 of the 27 Anaconda elements in the subspecies japonica are the same as those in the subspecies indica. This suggests that these elements were incorporated before the divergence of these two subspecies.

The rice pyruvate decarboxylase 3 gene, which lacks introns, is transcribed in mature pollen.

The rice pyruvate decarboxylase 3 gene (PDC3), which has no introns, was previously postulated to be a pseudogene because no PDC3 mRNA had been detected, even under anaerobic conditions. However, in this study, it was found that rice PDC3 transcripts accumulated in panicles after heading. Within anthers obtained from the panicles, PDC3 was shown to be transcribed in mature pollen by in situ hybridization. These results suggest that the rice PDC3 is a functional gene. Its product may play a role in aerobic alcoholic fermentation in mature pollen.

AOX1c, a novel rice gene for alternative oxidase; comparison with rice AOX1a and AOX1b.

A novel gene for alternative oxidase (AOX) was isolated from rice (Oryza sativa L.) and characterized. The deduced amino acid sequence of the novel AOX gene contains features that are conserved among other AOXs. This AOX gene was designated AOX1c based on a phylogenetic analysis of the AOX genes. Northern hybridization analyses revealed that AOX1c and AOX1a/AOX1b transcripts accumulated differently in various rice organs and rice seedlings under low temperature conditions. AOX1c mRNA was mainly present in young leaves under constant light, mature leaves and panicles after heading, but it was not detected in young etiolated leaves and young roots of seedlings or young panicles. On the other hand, the mRNAs of the rice AOX1a and AOX1b genes were mainly present in young roots and mature leaves. Under low temperature conditions, the steady-state mRNA levels of the rice AOX1a and AOX1b genes clearly increased with time but the rice AOX1c gene was apparently not responsive to low temperature. The rice AOX gene family and differences in their regulation are discussed.