Complete response of skull base inverted papilloma to chemotherapy: Case report.

BackgroundInverted papilloma (IP) is the most common benign sinonasal neoplasm. Endoscopic techniques, improved understanding of pathophysiology, and novel surgical approaches have allowed rhinologists to treat IPs more effectively, with surgery being the mainstay of therapy. Frontal sinus IP poses a challenge for surgical therapy due to complex anatomy and potentially difficult surgical access.ObjectivesWe reported a unique case of a massive frontal sinus IP that presented with intracranial and orbital extension, with near resolution after chemotherapy.MethodsA retrospective case review of a patient with a frontal sinus IP treated at a tertiary academic medical center.ResultsA 75-year-old male patient presented with nasal obstruction, purulent nasal discharge, and a growing left supraorbital mass. Endoscopy demonstrated a mass that filled both frontal and ethmoid sinuses, with orbital invasion. There also was substantial erosion of the posterior table, which measured 1.73 × 1.40 cm. A biopsy specimen demonstrated IP with carcinoma in situ. The patient was deemed unresectable on initial evaluation and, subsequently, underwent chemotherapy (carboplatin and paclitaxel). The tumor had a dramatic response to chemotherapy, and the patient elected for definitive surgery to remove any residual disease. During surgery, only a small focus of IP was found along the superior wall of the frontal sinus. No tumor was found elsewhere, including at the site of skull base erosion. The final pathology was IP without carcinoma in situ or dysplasia.ConclusionThis was the first reported case of chemotherapeutic "debulking" of IP, which facilitated surgical resection, despite substantial intracranial and orbital involvement. Although nearly all IPs can be treated surgically, rare cases, such as unresectable tumors, may benefit from systemic chemotherapy

An Improved Method of RNA Isolation from Loblolly Pine (P. taeda L.) and Other Conifer Species

Tissues isolated from conifer species, particularly those belonging to the Pinaceae family, such as loblolly pine (Pinus taeda L.), contain high concentrations of phenolic compounds and polysaccharides that interfere with RNA purification. Isolation of high-quality RNA from these species requires rigorous tissue collection procedures in the field and the employment of an RNA isolation protocol comprised of multiple organic extraction steps in order to isolate RNA of sufficient quality for microarray and other genomic analyses. The isolation of high-quality RNA from field-collected loblolly pine samples can be challenging, but several modifications to standard tissue and RNA isolation procedures greatly improve results. The extent of general RNA degradation increases if samples are not properly collected and transported from the field, especially during large-scale harvests. Total RNA yields can be increased significantly by pulverizing samples in a liquid nitrogen freezer mill prior to RNA isolation, especially when samples come from woody tissues. This is primarily due to the presence of oxidizing agents, such as phenolic compounds, and polysaccharides that are both present at high levels in extracts from the woody tissues of most conifer species. If not removed, these contaminants can carry over leading to problems, such as RNA degradation, that result in low yields and a poor quality RNA sample. Carryover of phenolic compounds, as well as polysaccharides, can also reduce or even completely eliminate the activity of reverse transcriptase or other polymerases commonly used for cDNA synthesis. In particular, RNA destined to be used as template for double-stranded cDNA synthesis in the generation of cDNA libraries, single-stranded cDNA synthesis for PCR or qPCR's, or for the synthesis of microarray target materials must be of the highest quality if researchers expect to obtain optimal results. RNA isolation techniques commonly employed for many other plant species are often insufficient in their ability to remove these contaminants from conifer samples and thus do not yield total RNA samples suitable for downstream manipulations. In this video we demonstrate methods for field collection of conifer tissues, beginning with the felling of a forty year-old tree, to the harvesting of phloem, secondary xylem, and reaction wood xylem. We also demonstrate an RNA isolation protocol that has consistently yielded high-quality RNA for subsequent enzymatic manipulations

WebTraceMiner: a web service for processing and mining EST sequence trace files

Expressed sequence tags (ESTs) remain a dominant approach for characterizing the protein-encoding portions of various genomes. Due to inherent deficiencies, they also present serious challenges for data quality control. Before GenBank submission, EST sequences are typically screened and trimmed of vector and adapter/linker sequences, as well as polyA/T tails. Removal of these sequences presents an obstacle for data validation of error-prone ESTs and impedes data mining of certain functional motifs, whose detection relies on accurate annotation of positional information for polyA tails added posttranscriptionally. As raw DNA sequence information is made increasingly available from public repositories, such as NCBI Trace Archive, new tools will be necessary to reanalyze and mine this data for new information. WebTraceMiner (www.conifergdb.org/software/wtm) was designed as a public sequence processing service for raw EST traces, with a focus on detection and mining of sequence features that help characterize 3′ and 5′ termini of cDNA inserts, including vector fragments, adapter/linker sequences, insert-flanking restriction endonuclease recognition sites and polyA or polyT tails. WebTraceMiner complements other public EST resources and should prove to be a unique tool to facilitate data validation and mining of error-prone ESTs (e.g. discovery of new functional motifs)

Absolute Calibration and Characterization of the Multiband Imaging Photometer for Spitzer. II. 70 micron Imaging

The absolute calibration and characterization of the Multiband Imaging Photometer for Spitzer (MIPS) 70 micron coarse- and fine-scale imaging modes are presented based on over 2.5 years of observations. Accurate photometry (especially for faint sources) requires two simple processing steps beyond the standard data reduction to remove long-term detector transients. Point spread function (PSF) fitting photometry is found to give more accurate flux densities than aperture photometry. Based on the PSF fitting photometry, the calibration factor shows no strong trend with flux density, background, spectral type, exposure time, or time since anneals. The coarse-scale calibration sample includes observations of stars with flux densities from 22 mJy to 17 Jy, on backgrounds from 4 to 26 MJy sr^-1, and with spectral types from B to M. The coarse-scale calibration is 702 +/- 35 MJy sr^-1 MIPS70^-1 (5% uncertainty) and is based on measurements of 66 stars. The instrumental units of the MIPS 70 micron coarse- and fine-scale imaging modes are called MIPS70 and MIPS70F, respectively. The photometric repeatability is calculated to be 4.5% from two stars measured during every MIPS campaign and includes variations on all time scales probed. The preliminary fine-scale calibration factor is 2894 +/- 294 MJy sr^-1 MIPS70F^-1 (10% uncertainty) based on 10 stars. The uncertainty in the coarse- and fine-scale calibration factors are dominated by the 4.5% photometric repeatability and the small sample size, respectively. The 5-sigma, 500 s sensitivity of the coarse-scale observations is 6-8 mJy. This work shows that the MIPS 70 micron array produces accurate, well calibrated photometry and validates the MIPS 70 micron operating strategy, especially the use of frequent stimulator flashes to track the changing responsivities of the Ge:Ga detectors.Comment: 19 pages, PASP, in pres

The Democratic Biopolitics of PrEP

PrEP (Pre-Exposure Prophylaxis) is a relatively new drug-based HIV prevention technique and an important means to lower the HIV risk of gay men who are especially vulnerable to HIV. From the perspective of biopolitics, PrEP inscribes itself in a larger trend of medicalization and the rise of pharmapower. This article reconstructs and evaluates contemporary literature on biopolitical theory as it applies to PrEP, by bringing it in a dialogue with a mapping of the political debate on PrEP. As PrEP changes sexual norms and subjectification, for example condom use and its meaning for gay subjectivity, it is highly contested. The article shows that the debate on PrEP can be best described with the concepts ‘sexual-somatic ethics’ and ‘democratic biopolitics’, which I develop based on the biopolitical approach of Nikolas Rose and Paul Rabinow. In contrast, interpretations of PrEP which are following governmentality studies or Italian Theory amount to either farfetched or trivial positions on PrEP, when seen in light of the political debate. Furthermore, the article is a contribution to the scholarship on gay subjectivity, highlighting how homophobia and homonormativity haunts gay sex even in liberal environments, and how PrEP can serve as an entry point for the destigmatization of gay sexuality and transformation of gay subjectivity. ‘Biopolitical democratization’ entails making explicit how medical technology and health care relates to sexual subjectification and ethics, to strengthen the voice of (potential) PrEP users in health politics, and to renegotiate the profit and power of Big Pharma

A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation

(0) Save to: more options A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation Author(s): Howe, GT (Howe, Glenn T.)[ 1 ] ; Yu, JB (Yu, Jianbin)[ 1 ] ; Knaus, B (Knaus, Brian)[ 2 ] ; Cronn, R (Cronn, Richard)[ 2 ] ; Kolpak, S (Kolpak, Scott)[ 1 ] ; Dolan, P (Dolan, Peter)[ 3 ] ; Lorenz, WW (Lorenz, W. Walter)[ 4 ] ; Dean, JFD (Dean, Jeffrey F. D.)[ 4 ] Source: BMC GENOMICS Volume: 14 Article Number: 137 DOI: 10.1186/1471-2164-14-137 Published: FEB 28 2013 Times Cited: 0 (from Web of Science) Cited References: 81 [ view related records ] Citation Map Abstract: Background: Douglas-fir (Pseudotsuga menziesii), one of the most economically and ecologically important tree species in the world, also has one of the largest tree breeding programs. Although the coastal and interior varieties of Douglas-fir (vars. menziesii and glauca) are native to North America, the coastal variety is also widely planted for timber production in Europe, New Zealand, Australia, and Chile. Our main goal was to develop a SNP resource large enough to facilitate genomic selection in Douglas-fir breeding programs. To accomplish this, we developed a 454-based reference transcriptome for coastal Douglas-fir, annotated and evaluated the quality of the reference, identified putative SNPs, and then validated a sample of those SNPs using the Illumina Infinium genotyping platform. Results: We assembled a reference transcriptome consisting of 25,002 isogroups (unique gene models) and 102,623 singletons from 2.76 million 454 and Sanger cDNA sequences from coastal Douglas-fir. We identified 278,979 unique SNPs by mapping the 454 and Sanger sequences to the reference, and by mapping four datasets of Illumina cDNA sequences from multiple seed sources, genotypes, and tissues. The Illumina datasets represented coastal Douglas-fir (64.00 and 13.41 million reads), interior Douglas-fir (80.45 million reads), and a Yakima population similar to interior Douglas-fir (8.99 million reads). We assayed 8067 SNPs on 260 trees using an Illumina Infinium SNP genotyping array. Of these SNPs, 5847 (72.5%) were called successfully and were polymorphic. Conclusions: Based on our validation efficiency, our SNP database may contain as many as similar to 200,000 true SNPs, and as many as similar to 69,000 SNPs that could be genotyped at similar to 20,000 gene loci using an Infinium II array-more SNPs than are needed to use genomic selection in tree breeding programs. Ultimately, these genomic resources will enhance Douglas-fir breeding and allow us to better understand landscape-scale patterns of genetic variation and potential responses to climate change.Keywords: Genome wide association, Pseudotsuga menziesii, Seed orchard, Complex traits, Pinus taeda. L., Population, Generation, Database, Selection, White spruc

Activation of defence pathways in Scots pine bark after feeding by pine weevil (Hylobius abietis)

Background: During their lifetime, conifer trees are exposed to numerous herbivorous insects. To protect themselves against pests, trees have developed a broad repertoire of protective mechanisms. Many of the plant's defence reactions are activated upon an insect attack, and the underlying regulatory mechanisms are not entirely understood yet, in particular in conifer trees. Here, we present the results of our studies on the transcriptional response and the volatile compounds production of Scots pine (Pinus sylvestris) upon the large pine weevil (Hylobius abietis) feeding. Results: Transcriptional response of Scots pine to the weevil attack was investigated using a novel customised 36.4 K Pinus taeda microarray. The weevil feeding caused large-scale changes in the pine transcriptome. In total, 774 genes were significantly up-regulated more than 4-fold (p = 0.05), whereas 64 genes were significantly down-regulated more than 4-fold. Among the up-regulated genes, we could identify genes involved in signal perception, signalling pathways, transcriptional regulation, plant hormone homeostasis, secondary metabolism and defence responses. The weevil feeding on stem bark of pine significantly increased the total emission of volatile organic compounds from the undamaged stem bark area. The emission levels of monoterpenes and sesquiterpenes were also increased. Interestingly, we could not observe any correlation between the increased production of the terpenoid compounds and expression levels of the terpene synthase-encoding genes. Conclusions: The obtained data provide an important insight into the transcriptional response of conifer trees to insect herbivory and illustrate the massive changes in the host transcriptome upon insect attacks. Moreover, many of the induced pathways are common between conifers and angiosperms. The presented results are the first ones obtained by the use of a microarray platform with an extended coverage of pine transcriptome (36.4 K cDNA elements). The platform will further facilitate the identification of resistance markers with the direct relevance for conifer tree breeding.Peer reviewe

Conifer DBMagic: a database housing multiple de novo transcriptome assemblies for 12 diverse conifer species

Conifers comprise an ancient and widespread plant lineage of enormous commercial and ecological value. However, compared to model woody angiosperms, such as Populus and Eucalyptus, our understanding of conifers remains quite limited at a genomic level. Large genome sizes (10,000–40,000 Mbp) and large amounts of repetitive DNA have limited efforts to produce a conifer reference genome, and genomic resource development has focused primarily on characterization of expressed sequences. Here, we report the completion of a conifer transcriptome sequencing project undertaken in collaboration with the U.S. DOE Joint Genome Institute that resulted in production of almost 12 million sequence reads. Five loblolly pine (Pinus taeda) cDNA libraries representing multiple tissues, treatments, and genotypes produced over four million sequence reads that, along with available Sanger expressed sequence tags, were used to create contig assemblies using three different assembly algorithms: Newbler, MiraEST, and NGen. In addition, libraries from 11 other conifer species, as well as one member of the Gnetales (Gnetum gnemon), produced 0.4 to 1.2 million sequence reads each. Among the selected conifer species were representatives of each of the seven phylogenetic families in the Coniferales: Araucariaceae, Cephalotaxaceae, Cupressaceae, Pinaceae, Podocarpaceae, Sciadopityaceae, and Taxaceae. Transcriptome builds for each species were generated using each of the three assemblers. All contigs for every species generated using each assembler can be obtained from Conifer DBMagic, a public database for searching, viewing, and downloading contig sequences, the associated sequence reads, and their annotations.Keywords: Database, Gene models, Pinus, Comparative phylogenomics, Annotation, Transcriptome, Coniferale