111 research outputs found
Microsatellite primers for two threatened orchids in Florida: Encyclia tampensis and Cyrtopodium punctatum (Orchidaceae)1
Premise of the study: The Million Orchid Project at Fairchild Tropical Botanic Garden is an initiative to propagate native orchids for reintroduction into Miami?s urban landscapes. The aim of this study was to develop microsatellites for Encyclia tampensis and Cyrtopodium punctatum (Orchidaceae). Methods and Results: Ten microsatellites were developed for each species. For E. tampensis sampled from the natural population, allele numbers ranged from one to four, with an average observed heterozygosity (Ho) of 0.314 and average expected heterozygosity (He) of 0.281. For the individuals from cultivation, allele numbers ranged from one to six, with an average Ho of 0.35 and an average He of 0.224. For C. punctatum, allele numbers ranged from one to three, with an average Ho of 0.257 and an average He of 0.272. Conclusions: These microsatellites will be used to assess the genetic diversity of natural and cultivated populations with the intention of guiding genetic breeding under the Million Orchid Project
Information Rx: Prescribing Good Consumerism and Responsible Citizenship
Recent medical informatics and sociological literature has painted the image of a new type of patientâone that is reflexive and informed, with highly specified information needs and perceptions, as well as highly developed skills and tactics for acquiring information. Patients have been re-named âreflexive consumers.â At the same time, literature about the questionable reliability of web-based information has suggested the need to create both user tools that have pre-selected information and special guidelines for individuals to use to check the individual characteristics of the information they encounter. In this article, we examine suggestions that individuals must be assisted in developing skills for âreflexive consumerismâ and what these particular skills should be. Using two types of data (discursive data from websites and promotional items, and supplementary data from interviews and ethnographic observations carried out with those working to sustain these initiatives), we examine how users are directly addressed and discussed. We argue that these initiatives prescribe skills and practices that extend beyond finding and assessing information on the internet and demonstrate that they include ideals of consumerism and citizenship
Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas
This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing
molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin
Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context
Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts
Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas
Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN
Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images
Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images
of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL
maps are derived through computational staining using a convolutional neural network trained to
classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and
correlation with overall survival. TIL map structural patterns were grouped using standard
histopathological parameters. These patterns are enriched in particular T cell subpopulations
derived from molecular measures. TIL densities and spatial structure were differentially enriched
among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial
infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic
patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for
the TCGA image archives with insights into the tumor-immune microenvironment
The Physical Conditions of Emission-Line Galaxies at Cosmic Dawn from JWST/NIRSpec Spectroscopy in the SMACS 0723 Early Release Observations
We present rest-frame optical emission-line flux ratio measurements for five
galaxies observed by the JWST Near-Infared Spectrograph (NIRSpec) in the
SMACS 0723 Early Release Observations. We add several quality-control and
post-processing steps to the NIRSpec pipeline reduction products in order to
ensure reliable relative flux calibration of emission lines that are closely
separated in wavelength, despite the uncertain \textit{absolute}
spectrophotometry of the current version of the reductions. Compared to
galaxies in the literature, the galaxies have similar
[OIII]5008/H ratios, similar [OIII]4364/H
ratios, and higher (0.5 dex) [NeIII]3870/[OII]3728
ratios. We compare the observations to MAPPINGS V photoionization models and
find that the measured [NeIII]3870/[OII]3728,
[OIII]4364/H, and [OIII]5008/H emission-line
ratios are consistent with an interstellar medium that has very high ionization
(, units of cm~s), low metallicity (), and very high pressure (, units of
cm). The combination of [OIII]4364/H and
[OIII](4960+5008)/H line ratios indicate very high electron
temperatures of , further implying metallicities of
with the application of low-redshift calibrations for
``-based'' metallicities. These observations represent a tantalizing new
view of the physical conditions of the interstellar medium in galaxies at
cosmic dawn.Comment: Accepted for publication in AAS Journals. 14 pages, 6 figures, 3
table
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Semiochemical-based alternatives to synthetic toxicant insecticides for pollen beetle management
There is an urgent need to develop sustainable pest management systems to protect arable crops in order to replace the current over-reliance on synthetic insecticides. Semiochemicals are insect- or plant-derived chemicals that are used by organisms as information signals. Integrated pest management tools are currently in development that utilise semiochemicals to manipulate the behaviour of pest insects and their natural enemies to provide effective control of pests within the crop. These innovative tools usually require fewer inputs and can involve multiple elements therefore reducing the likelihood of resistance developing compared with use of synthetic toxicants. We review here the life cycle of the pollen beetle Brassicogethes aeneus (previously known as Meligethes aeneus) which is a pest insect of oilseed rape (Brassica napus) and describe the current knowledge of any behaviour mediated by semiochemicals in this species. We discuss the behavioural processes where semiochemical-based control approaches may be appropriate and consider how these approaches could be integrated into an integrated pest management strategy for this important arable crop
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Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas.
DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic response. We systematically analyzed somatic alterations to provide a comprehensive view of DDR deficiency across 33 cancer types. Mutations with accompanying loss of heterozygosity were observed in over 1/3 of DDR genes, including TP53 and BRCA1/2. Other prevalent alterations included epigenetic silencing of the direct repair genes EXO5, MGMT, and ALKBH3 in âŒ20% of samples. Homologous recombination deficiency (HRD) was present at varying frequency in many cancer types, most notably ovarian cancer. However, in contrast to ovarian cancer, HRD was associated with worse outcomes in several other cancers. Protein structure-based analyses allowed us to predict functional consequences of rare, recurrent DDR mutations. A new machine-learning-based classifier developed from gene expression data allowed us to identify alterations that phenocopy deleterious TP53 mutations. These frequent DDR gene alterations in many human cancers have functional consequences that may determine cancer progression and guide therapy
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