Genotypic analysis of receptor-like protein kinases with leucine-rich repeat motifs

Abstract only availableReceptor-like protein kinases (RLKs) are transmembrane proteins that transmit extracellular signals across a membrane with the use of an intracellular kinase domain. RLKs play important roles in plant growth and development, plant-microbe interactions, and defense responses. In Arabidopsis thaliana, a commonly used genetic model system for plants, 417 genes encode RLKs. Though plant RLKs have a monophyletic origin and belong to a clade that also contains the animal Pelle cytoplasmic kinases, they can be divided into distinct families based on their extracellular motifs. The most common extracellular motif in plant RLKs are the leucine-rich repeat that are thought to be involved in protein-protein interactions. Over half of RLKS found in Arabidopsis thaliana have leucine-rich repeat extracellular motifs. As a genetic model, the genome of Arabidopsis has been fully sequenced; however, the functions of many genes are still unknown. To uncover their function, experiments are being done using the principles of reverse genetics. By inserting T-DNA segments into the genome, the function of a gene can be disrupted. The T-DNA insertion into a gene would prevent a functional protein from being produced. Without the production of this protein, a specific mutant phenotype is likely to result. However, duplication of genes with similar sequences and therefore, possibly similar functions, may hinder the production of a mutant phenotype. As such, all the genes must also be rendered functionless. Our experiment consisted of creating functional knock-outs for genes found in families XIe, XIh, XIg, and XId. Single and double mutants were then genotyped to see if any heterozygous or homozygous progeny had been produced and had survived. Sequencing of the flanking regions of the t-DNA insert was also completed. Twelve of thirteen genes yielded single mutant homozygotes. Of the six double mutant crosses genotyped, all yielded heterozygotes. Crosses were then made between homozygotes of one line of a particular gene with those from another line of a different, but related gene. Results for function and phenotype are pending.NSF-REU Biology & Biochemistr

Photometric Observations of Three High Mass X-Ray Binaries and a Search for Variations Induced by Orbital Motion

We searched for long period variation in V-band, Ic-band and RXTE X-ray light curves of the High Mass X-ray Binaries (HMXBs) LS 1698 / RX J1037.5-5647, HD 110432 / 1H 1249-637 and HD 161103 / RX J1744.7-2713 in an attempt to discover orbitally induced variation. Data were obtained primarily from the ASAS database and were supplemented by shorter term observations made with the 24- and 40-inch ANU telescopes and one of the robotic PROMPT telescopes. Fourier periodograms suggested the existence of long period variation in the V-band light curves of all three HMXBs, however folding the data at those periods did not reveal convincing periodic variation. At this point we cannot rule out the existence of long term V-band variation for these three sources and hints of longer term variation may be seen in the higher precision PROMPT data. Long term V-band observations, on the order of several years, taken at a frequency of at least once per week and with a precision of 0.01 mag, therefore still have a chance of revealing long term variation in these three HMXBs.Comment: Accepted, RAA, May, 201

Antología I. Taller Literario Mariano Lebrón Saviñón

Nan Chevalier (biografía): Reynaldo Paulino (Nan) Chevalier nació en Puerto Plata, República Dominicana, en 1965. Se licenció en letras y en psicología en la Universidad Autónoma de Santo Domingo (UASD), donde cursó un posgrado en lengua y literatura y una maestría en literatura hispanoamericana. Fue director de la Escuela de Letras de la UASD; en la actualidad es director del Departamento de Español de UNAPEC. Ha publicado Las formas que retornan (poemas), Editora Búho, 1998; Ave de mal agüero (poemas), Letra Gráfica, 2003; La segunda señal (cuentos), Letra Gráfica, 2003; Ciudad de mis ruinas (novela), Letra Gráfica, 2007; Antihéroes onettianos: habitantes de proyectos fallidos (Colección Premios FUNGLODE 2011-Ensayo), Serigraf, 2012; El muñeco de trapos (Colección Premios FUNGLODE 2011-Cuento), Serigraf, 2012; El hombre que parecía esconderse (novela), Alfaguara, 2014; El domador de fieras y otros nanorrelatos (minificción), Editora Nacional, 2015; La recámara aislante del tiempo (cuentos), Búho, 2014, y Viaje sin retorno desde un puerto fantasma (novela), Búho, 2015. Sus textos han sido incluidos en revistas y antologías, como Juego de imágenes: la nueva poesía dominicana, de Frank Martínez y Néstor Rodríguez (editores); La espiral sonora (Antología del poema en prosa en Santo Domingo 1890-2000), Basilio Belliard (compilador); Poemas de último minuto, Mónica Volonteri (compiladora); Al filo del agua: XX años de poesía dominicana, Miguel Antonio Jiménez (compilador); Vendimia Primera, Luis R. Santos (compilador), Colección de cuentos del Banco Central de la República Dominicana; Puente de palabras: Compilación de cuentos costarricenses y dominicanos, Avelino Stanley (compilador); Alforja, Revista de Poesía, Hernán Lara Zavala (editor), México; Coloquios, José Manuel Fernández Pequeño (editor); Vetas, Clodomiro Moquete (editor); Voci da Quisqueya, María Antonieta Ferro (compiladora), Italia; El cuerno de oro (cuentos sobre infidelidades), Eulogio Javier (compilador), Guatemala, 2008; La ciudad en nosotros, Soledad Álvarez (compiladora); País Cultural, Basilio Belliard (editor), 2009; Algarero cultural, número 18, Javier Payeros/Valentín Amaro (editores), Guatemala; Ruptura del límite, Avelino Stanley (compilador), Bogotá; Sieteculebras. Revista andina de cultura, Perú; El viaje, Luis Reinaldo Pérez (editor); y Los nuevos caníbales, Puerto Rico, 2015. Ha recibido, entre otros, el Premio FUNGLODE de Cuento (2011); y el Premio Único del III Concurso Nacional de Minificción, Ministerio de Cultura de la República Dominicana (2013).La vida interna de un taller literario está llena de aventuras espirituales e intelectuales. Sus integrantes se embarcan en la lectura de importantes textos literarios pertenecientes tanto a la tradición nacional y la propia lengua como a tradiciones de otros países y de otros idiomas. Esas lecturas, que son compartidas, van enriqueciendo la vida gracias a las originales historias, al dominio lingüístico y a la complejidad de las visiones puestas en juego en cada obra. Es así como todos los integrantes van madurando sus particulares concepciones del mundo y van aprendiendo a educar su íntima búsqueda de la belleza. Búsqueda que va fortaleciéndose a medida que cada tallerista va encontrándose a sí mismo a través de esos juegos de espejos que son los libros. Suele suceder, entonces, que la propia voz comience a tomar forma y que demande expresarse por unos cauces que les sean originarios. Es cuando surgen las obras, las florescencias, las creaciones que ayudan a forjar para uno mismo un lugar habitable en el mundo. Esta antología es precisamente la primera muestra pública de las voces emergentes de los miembros del Taller Literario Mariano Lebrón Saviñón, uno de los órganos culturales de la Universidad APEC. La componen textos llenos de vida y pasión, de una mirada maravillada a esta existencia convulsa, que puede a veces ser turbulenta, pero que siempre es hermosa. Son textos para olvidarse de sí y perderse en la inquietante lumbre que ofrecen

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

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

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

A REVERSE SHOCK in GRB 160509A

We present the second multi-frequency radio detection of a reverse shock in a γ-ray burst. By combining our extensive radio observations of the Fermi-Large Area Telescope γ-ray burst 160509A at z = 1.17 up to 20 days after the burst with Swift X-ray observations and ground-based optical and near-infrared data, we show that the afterglow emission comprises distinct reverse shock and forward shock contributions: the reverse shock emission dominates in the radio band at ≲10 days, while the forward shock emission dominates in the X-ray, optical, and near-infrared bands. Through multi-wavelength modeling, we determine a circumburst density of , supporting our previous suggestion that a low-density circumburst environment is conducive to the production of long-lasting reverse shock radiation in the radio band. We infer the presence of a large excess X-ray absorption column, N H ≈ 1.5 ×1022 , and a high rest-frame optical extinction, A V ≈ 3.4 mag. We identify a jet break in the X-ray light curve at , and thus derive a jet opening angle of , yielding a beaming-corrected kinetic energy and radiated γ-ray energy of erg and erg (1-104 keV, rest frame), respectively. Consistency arguments connecting the forward shocks and reverse shocks suggest a deceleration time of s ≈ T 90, a Lorentz factor of , and a reverse-shock-to-forward-shock fractional magnetic energy density ratio of . Our study highlights the power of rapid-response radio observations in the study of the properties and dynamics of γ-ray burst ejecta. © 2016. The American Astronomical Society. All rights reserved

Cloning and variation of ground state intestinal stem cells

Stem cells of the gastrointestinal tract, pancreas, liver, and other columnar epithelia collectively resist cloning in their elemental states. Here we demonstrate the cloning and propagation of highly clonogenic, “ground state” stem cells of the human intestine and colon. We show that derived stem cell pedigrees sustain limited copy number and sequence variation despite extensive serial passaging and display exquisitely precise, cell-autonomous commitment to epithelial differentiation consistent with their origins along the intestinal tract. This developmentally patterned and epigenetically maintained commitment of stem cells likely enforces the functional specificity of the adult intestinal tract. Using clonally-derived colonic epithelia, we show that toxins A or B of the enteric pathogen C. difficile recapitulate the salient features of pseudomembranous colitis. The stability of the epigenetic commitment programs of these stem cells, coupled with their unlimited replicative expansion and maintained clonogenicity, suggests certain advantages for their use in disease modeling and regenerative medicine

Energetic eruptions leading to a peculiar hydrogen-rich explosion of a massive star

Every supernova so far observed has been considered to be the terminal explosion of a star. Moreover, all supernovae with absorption lines in their spectra show those lines decreasing in velocity over time, as the ejecta expand and thin, revealing slower-moving material that was previously hidden. In addition, every supernova that exhibits the absorption lines of hydrogen has one main light-curve peak, or a plateau in luminosity, lasting approximately 100 days before declining1. Here we report observations of iPTF14hls, an event that has spectra identical to a hydrogen-rich core-collapse supernova, but characteristics that differ extensively from those of known supernovae. The light curve has at least five peaks and remains bright for more than 600 days; the absorption lines show little to no decrease in velocity; and the radius of the line-forming region is more than an order of magnitude bigger than the radius of the photosphere derived from the continuum emission. These characteristics are consistent with a shell of several tens of solar masses ejected by the progenitor star at supernova-level energies a few hundred days before a terminal explosion. Another possible eruption was recorded at the same position in 1954. Multiple energetic pre-supernova eruptions are expected to occur in stars of 95 to 130 solar masses, which experience the pulsational pair instability2,3,4,5. That model, however, does not account for the continued presence of hydrogen, or the energetics observed here. Another mechanism for the violent ejection of mass in massive stars may be required