Multi-Species Transcriptome Assemblies of Cultivated and Wild Lentils (Lens sp.) Provide a First Glimpse at the Lentil Pangenome

[EN] Lentils (Lens sp.) are one of the main sources of protein for humans in many regions, in part because their rusticity allows them to withstand semi-dry climates and tolerate a wide spectrum of pests. Both are also highly sought-after attributes to face climate change. Wild accessions, rather than cultivated varieties, are typically the holders of most influential alleles for rusticity traits. However, most genomic and transcriptomic research conducted in lentils has been carried out on commercial accessions (L. culinaris), while wild relatives have been largely neglected. Herein, we assembled, annotated, and evaluated the transcriptomes of eight lentil accessions, including the cultivated Lens culinaris and the wild relatives: L. orientalis, L. tomentosus, L. ervoides, L. lamottei, L. nigricans, and two L. odemensis. The assemblies allowed, for the first time, a comparison among different lentil taxa at the coding sequence level, providing further insights into the evolutionary relationships between cultivated and wild germplasm and suggesting a grouping of the seven accessions into at least three conceivable gene pools. Moreover, orthologous clustering allowed a first estimation of the lentil pan-transcriptome. It is composed of 15,910 core genes, encoded in all accessions, and 24,226 accessory genes. The different pan-transcriptome clusters were also screened for Pfam-domain enrichment. The present study has a high novelty, as it is the first pan-transcriptome analysis using six wild species in addition to cultivated species. Because of the amount of transcript sequences provided, our findings will greatly boost lentil research and assist breeding efforts.S

Think tank UNACHI-CIRN: investigación científica al servicio de la empresa y la sociedad.

Este documento presenta las actividades y productos logrados mediante la ejecución de pasantía de la Dra. Dianela Costamagna del INTA (Instituto Nacional de Tecnología Agropecuaria) de Argentina y el MSc. Eduard Villarreal del CIRN (Centro de Investigación en Recursos Naturales) de la UNACHI en Panamá. Al poner en contacto investigadores de Centros de Investigación de 2 o más países se logra potenciar las capacidades investigativas de estos centros y de sus investigadores, ya que se da un intercambio de conocimientos, experiencias y visión de nuevas estrategias para atacar y solucionar un problema o situación común que afronten los países. Mediante el presente informe, se puede evidenciar cómo el conocimiento del impacto de las micotoxinas en la cadena láctea puede evitar problemas de inocuidad en el producto lácteo, problemas de salud en la población, al igual que en la producción de los hatos ganaderos, y cómo se puede, con la ayuda de las ciencias, mejorar la productividad en uno de los rubros insignia de la región, todo ésto de la mano del INTA de Argentina, país con una tradición ganadera de gran importancia a nivel mundial, que pone a disposición sus investigaciones para un intercambio científico de altura y de gran impacto para la competitividad productiva de la región y del país

Tratado de justicia restaurativa. Un enfoque integrador

Esta obra nos presenta a la Justicia Restaurativa desde la configuración del derecho penal y los procesos de la misma en el orden penitenciario, en las comunidades escolares, en la igualdad de género. Realzando así mismo la habiliades del facilitador que habrá de llevarla a cabo, como parte integral de un nuevo paradigma en la formación de recursos humnos que atiendan la inminente necesidad de este tipo de ejercicio y en las redes primarias de apoyo, como elemento restaurativo para las mujeres víctimas de violencia doméstica, dónde ha crecido la respuesta de la sociedad para abatir este sector de la violenci

Enhancing the First-Pass Effect in Acute Stroke: The Impact of Stent Retriever Characteristics

Introduction: Although stentrievers (SRs) have been a mainstay of mechanical thrombectomy (MT), and current guidelines recommend the use of SRs in the treatment of large vessel occlusion stroke (LVO), there is a paucity of studies in the literature comparing SRs directly against each other in terms of mechanical and functional properties. Timely access to endovascular therapy and the ability to restore intracranial flow in a safe, efficient, and efficacious manner have been critical to the success of MT. This study aimed to investigate the impact of contemporary SR characteristics, including model, brand, size, and length, on the first-pass effect (FPE) in patients with acute ischemic stroke. Methods: Consecutive patients with M1 occlusion treated with a single SR+BGC were recruited from the ROSSETTI registry. The primary outcome was the FPE that was defined as modified (mFPE) or true (tFPE) for the achievement of modified thrombolysis in cerebral infarction (mTICI) grades 2b-3 or 3 after a single device pass, respectively. We compared patients who achieved mFPE with those who achieved tFPE according to SR characteristics. Results: We included 610 patients (52.3% female and 47.7% male, mean age 75.1 +/- 13.62 years). mFPE was achieved in 357 patients (58.5%), whereas tFPE was achieved in 264 (43.3%). There was no significant association between SR characteristics and mFPE or tFPE. Specifically, the SR size did not show a statistically significant relationship with improvement in FPE. Similarly, the length of the SR did not yield significant differences in the mFPE and tFPE, even when the data were grouped. Conclusions: Our data indicate that contemporary SR-mediated thrombectomy characteristics, including model, brand, size, and length, do not significantly affect the FPE

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

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