Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

Recent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth–death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies.Universidad de Costa Rica/[814-B8-257]/UCR/Costa RicaUniversidad de Costa Rica/[814-B6-140]/UCR/Costa RicaIDEA WILD/[]//Estados UnidosSociedad Colombiana de Orquideología/[]/SCO/ColombiaFundação de Amparo à Pesquisa do Estado de São Paulo/[11/08308-9]/FAPESP/BrasilFundação de Amparo à Pesquisa do Estado de São Paulo/[13/19124-1]/FAPESP/BrasilSwiss Orchid Foundation/[]//SuizaRoyal Botanic Gardens, Kew/[]//InglaterraSwedish Research Council/[2019-05191]//SueciaSwedish Foundation for Strategic Research/[FFL15-0196]/SSF/SueciaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Jardín Botánico Lankester (JBL

Detailed Anatomical and Electrophysiological Models of Human Atria and Torso for the Simulation of Atrial Activation

Atrial arrhythmias, and specifically atrial fibrillation (AF), induce rapid and irregular activation patterns that appear on the torso surface as abnormal P-waves in electrocardiograms and body surface potential maps (BSPM). In recent years both P-waves and the BSPM have been used to identify the mechanisms underlying AF, such as localizing ectopic foci or high-frequency rotors. However, the relationship between the activation of the different areas of the atria and the characteristics of the BSPM and P-wave signals are still far from being completely understood. In this work we developed a multi-scale framework, which combines a highly-detailed 3D atrial model and a torso model to study the relationship between atrial activation and surface signals in sinus rhythm. Using this multi scale model, it was revealed that the best places for recording P-waves are the frontal upper right and the frontal and rear left quadrants of the torso. Our results also suggest that only nine regions (of the twenty-one structures in which the atrial surface was divided) make a significant contribution to the BSPM and determine the main P-wave characteristics.This work was partially supported by the "VI Plan Nacional de Investigacion Cientifica, Desarrollo e Innovacion Tecnologica" from the Ministerio de Economia y Competitividad of Spain and the European Commission (European Regional Development Funds - ERDF - FEDER), Award Number: TIN2012-37546-C03-01 (Recipient: Ana Ferrer); the "Programa Estatal de Investigacion, Desarrollo e Innovacion Orientado a los Retos de la Sociedad" from the Ministerio de Economia y Competitividad and the European Commission (European Regional Development Funds - ERDF - FEDER), Award Number: TIN2014-59932-JIN (Recipient: Rafael Sebastion); and the "Programa Prometeo" from the Generalitat Valenciana, Award Number: 2012/030 (Recipient: Laura Martinez).Ferrer Albero, A.; Sebastián Aguilar, R.; Sánchez Quintana, D.; Rodriguez, JF.; Godoy, EJ.; Martinez, L.; Saiz Rodríguez, FJ. (2015). Detailed Anatomical and Electrophysiological Models of Human Atria and Torso for the Simulation of Atrial Activation. PLoS ONE. 10(11):1-29. https://doi.org/10.1371/journal.pone.0141573S129101

Hepatoprotective and Anti-Inflammatory Activities of the Cnidoscolus chayamansa (Mc Vaugh) Leaf Extract in Chronic Models

Previous report described that CHCl3:MeOH extract of C. chayamansa leaves and pure compounds (moretenol, moretenyl acetate, kaempferol-3,7-dimethyl ether, and 5-hydroxy-7-3′,4′-trimethoxyflavanone) showed important topical and systemic anti-inflammatory activity in acute model, as well as in vitro antimycobacterial and antiprotozoal activities. In this paper, we describe the in vivo hepatoprotective and anti-inflammatory effects of the CHCl3:MeOH extract in chronic model and the isolation of additional compounds (moretenone and lupeol acetate). The hepatoprotective activity was determined at 39 days using Balb/c mice with liver damage induced with an antitubercular drug (RIF/INH/PZA). The anti-inflammatory activity was evaluated in a chronic model induced with CFA and in two acute models (TPA and carrageenan). In addition, moretenone and lupeol acetate were isolated and identified by spectroscopic data. Lupeol acetate is a main compound present in fractions 14-42, and this fraction was the majority fraction from the extract; from this moretenone was obtained. In animals with liver damage, the extract at 200 and 400 mg/kg induced better body weight gain with respect to positive control (Silymarin); in addition, the mice that received the extract at 200 mg/kg and Silymarin exhibited slight steatosis; however, the animals’ livers at 400 mg/kg did not show steatosis. The extract and fractions 14-42 showed a good anti-inflammatory activity by TPA model (DE50 = 1.58 and 1.48 mg/ear) and by carrageenan model (DE50 = 351.53 and 50.11 mg/kg). In the chronic inflammatory test, the extract at three doses revealed a similar effect to that of phenylbutazone, although the body weight gain was better in animals that received the extract at 900 mg/kg. Conclusion. The CHCl3:MeOH extract showed significant anti-inflammatory and good hepatoprotective effect on chronic models. The fraction containing moretenone and lupeol acetate as main compounds was more active than extract in both acute models of inflammation

En busca de los colores ocultos del arrecife

En el mundo natural, la oscuridad, más que con la inactividad, ha sido frecuentemente asociada con el descubrimiento de nuevos mundos y facetas. Es por esto que la frase popular "se puede encontrar luz en medio de las tinieblas" no suena a invención, si esa luz se interpreta como el conocimiento que proviene de explorar "con las luces apagadas". El mundo marino ha sido un gran ejemplo de esto, pues la búsqueda de respuestas sumergidas más allá de nuestra zona de comodidad -mucho más allá de donde la luz llega- ha conducido a nuevos hallazgos biológicos, como los ecosistemas arrecifales de profundidad y las fuentes hidrotermales submarina

Neutron instruments simulations using machine learning techniques with KDSource

The design of neutron instruments usually is related to the simulations of neutron beams. These simulations are normally decoupled from the neutron source since the nuclear reactions that govern the generation of neutrons in the source are independent of the specific interactions that take place in the neutron beam path. Also, neutron beams are usually transported far away from the source to reduce the background signal in the measurements and the radiation dose of the personnel. When evaluating the neutron beam under different operating conditions, it is useful to have a source that can be re-sampled. KDSource [1,2] is an open-source code that uses the adaptive multivariate Kernel Density Estimation (KDE) method to estimate the source distribution at a given point in the beam trajectory, which seeks to overcome limitations of other variance-reduction techniques. The approach presents a novel methodology to optimize source modelling, which may be especially suited for neutron beam and radiation shielding simulations. The core idea of the methodology is to use some machine learning libraries and algorithms to optimize the bandwidth selection for each source variable. With this strategy, smooth estimates of the variable distributions may be obtained from particle lists at a given point in a simulation that maintains correlations among all the variables. The code implements the proposed methodology in Python, and it consists of a module for KDE model optimization, and another for sampling (i.e. generating new particles using the previously optimized model). This work aims to present the KDSource code with some usage examples to design the neutron imaging instruments for the HBS project. [1] N.S. Schmidt, O.I. Abbate, Z.M. Prieto, J.I. Robledo, J.I. Márquez Damián, A.A. Márquez, J. Dawidowski, 2022. KDSource, a tool for the generation of Monte Carlo particle sources using kernel density estimation. Ann. Nucl. Energy 177. URL: https://doi.org/10.1016/j.anucene.2022.109309 [2] O.I. Abbate, N.S. Schmidt, Z.M. Prieto, J.I. Robledo, J.I. Márquez Damián, A.A. Márquez, J. Dawidowski, 2021. KDSource, a tool for the generation of Monte Carlo particle sources using kernel density estimation. GitHub repository. URL: https://github.com/KDSource/KDSourc

Early Transcriptomic Response to LDL and oxLDL in Human Vascular Smooth Muscle Cells.

Although nowadays it is well known that the human transcriptome can importantly vary according to external or environmental condition, the reflection of this concept when studying oxidative stress and its direct relationship with gene expression profiling during the process of atherogenesis has not been thoroughly achieved.The ability to analyze genome-wide gene expression through transcriptomics has shown that the genome responds dynamically to diverse stimuli. Here, we describe the transcriptome of human vascular smooth muscle cells (hVSMC) stimulated by native and oxidized low-density lipoprotein (nLDL and oxLDL respectively), with the aim of assessing the early molecular changes that induce a response in this cell type resulting in a transcriptomic transformation. This expression has been demonstrated in atherosclerotic plaques in vivo and in vitro, particularly in the light of the oxidative modification hypothesis of atherosclerosis.Total RNA was isolated with TRIzol reagent (Life Technologies) and quality estimated using an Agilent 2100 bioanalyzer. The transcriptome of hVSMC under different experimental conditions (1,5 and 24 hours for nLDL and oxLDL) was obtained using the GeneChip Human Gene 1.0 ST (Affymetrix) designed to measure gene expression of 28,869 well-annotated genes. A fixed fold-change cut-off corresponding to ± 2 was used to identify genes exhibiting the most significant variation and statistical significance (P< 0.05), and 8 genes validated by qPCR using Taqman probes.10 molecular processes were significantly affected in hVSMC: Apoptosis and cell cycle, extracellular matrix remodeling, DNA repair, cholesterol efflux, cGMP biosynthesis, endocytic mechanisms, calcium homeostasis, redox balance, membrane trafficking and finally, the immune response to inflammation. The evidence we present supporting the hypothesis for the involvement of oxidative modification of several processes and metabolic pathways in atherosclerosis is strengthen by the fact that gene expression patterns obtained when hVSMC are incubated for a long period of time in the presence of nLDL, correspond very much the same as when cells are incubated for a short period of time in the presence of chemically modified oxLDL. Our results indicate that under physiological conditions and directly related to specific environmental conditions, LDL particles most probably suffer chemical modifications that initially serve as an alert signal to overcome a harmful stimulus that with time might get transformed to a pathological pattern and therefore consolidate a pathological condition