Complete Plastome Sequences of Equisetum arvense and Isoetes flaccida: Implications for Phylogeny and Plastid Genome Evolution of Early Land Plant Lineages

Background Despite considerable progress in our understanding of land plant phylogeny, several nodes in the green tree of life remain poorly resolved. Furthermore, the bulk of currently available data come from only a subset of major land plant clades. Here we examine early land plant evolution using complete plastome sequences including two previously unexamined and phylogenetically critical lineages. To better understand the evolution of land plants and their plastomes, we examined aligned nucleotide sequences, indels, gene and nucleotide composition, inversions, and gene order at the boundaries of the inverted repeats. Results We present the plastome sequences of Equisetum arvense, a horsetail, and of Isoetes flaccida, a heterosporous lycophyte. Phylogenetic analysis of aligned nucleotides from 49 plastome genes from 43 taxa supported monophyly for the following clades: embryophytes (land plants), lycophytes, monilophytes (leptosporangiate ferns + Angiopteris evecta + Psilotum nudum + Equisetum arvense), and seed plants. Resolution among the four monilophyte lineages remained moderate, although nucleotide analyses suggested that P. nudum and E. arvense form a clade sister to A. evecta + leptosporangiate ferns. Results from phylogenetic analyses of nucleotides were consistent with the distribution of plastome gene rearrangements and with analysis of sequence gaps resulting from insertions and deletions (indels). We found one new indel and an inversion of a block of genes that unites the monilophytes. Conclusions Monophyly of monilophytes has been disputed on the basis of morphological and fossil evidence. In the context of a broad sampling of land plant data we find several new pieces of evidence for monilophyte monophyly. Results from this study demonstrate resolution among the four monilophytes lineages, albeit with moderate support; we posit a clade consisting of Equisetaceae and Psilotaceae that is sister to the true ferns, including Marattiaceae

Chloroplast Genome Sequence of the Moss Torula ruralis: Gene Content, Polymorphism, and Structural Arrangement Relative to Other Green Plant Chloroplast Genomes

Background Tortula ruralis, a widely distributed species in the moss family Pottiaceae, is increasingly used as a model organism for the study of desiccation tolerance and mechanisms of cellular repair. In this paper, we present the chloroplast genome sequence of T. ruralis, only the second published chloroplast genome for a moss, and the first for a vegetatively desiccation-tolerant plant. Results The Tortula chloroplast genome is ~123,500 bp, and differs in a number of ways from that of Physcomitrella patens, the first published moss chloroplast genome. For example, Tortula lacks the ~71 kb inversion found in the large single copy region of the Physcomitrella genome and other members of the Funariales. Also, the Tortula chloroplast genome lacks petN, a gene found in all known land plant plastid genomes. In addition, an unusual case of nucleotide polymorphism was discovered. Conclusions Although the chloroplast genome of Tortula ruralis differs from that of the only other sequenced moss, Physcomitrella patens, we have yet to determine the biological significance of the differences. The polymorphisms we have uncovered in the sequencing of the genome offer a rare possibility (for mosses) of the generation of DNA markers for fine-level phylogenetic studies, or to investigate individual variation within population

Heart transplantation and biomarkers: a review about their usefulness in clinical practice

Advanced heart failure (AdvHF) can only be treated definitively by heart transplantation (HTx), yet problems such right ventricle dysfunction (RVD), rejection, cardiac allograft vasculopathy (CAV), and primary graft dysfunction (PGD) are linked to a poor prognosis. As a result, numerous biomarkers have been investigated in an effort to identify and prevent certain diseases sooner. We looked at both established biomarkers, such as NT-proBNP, hs-troponins, and pro-inflammatory cytokines, and newer ones, such as extracellular vesicles (EVs), donor specific antibodies (DSA), gene expression profile (GEP), donor-derived cell free DNA (dd-cfDNA), microRNA (miRNA), and soluble suppression of tumorigenicity 2 (sST2). These biomarkers are typically linked to complications from HTX. We also highlight the relationships between each biomarker and one or more problems, as well as their applicability in routine clinical practice

Cerium Oxide Nanoparticles Protect Cardiac Progenitor Cells from Oxidative Stress

Cardiac progenitor cells (CPCs) are a promising autologous source of cells for cardiac regenerative medicine. However, CPC culture in vitro requires the presence of microenvironmental conditions (a complex array of bioactive substance concentration, mechanostructural factors, and physicochemical factors) closely mimicking the natural cell surrounding in vivo, including the capability to uphold reactive oxygen species (ROS) within physiological levels in vitro. Cerium oxide nanoparticles (nanoceria) are redox-active and could represent a potent tool to control the oxidative stress in isolated CPCs. Here, we report that 24 h exposure to 5, 10, and 50 !g/mL of nanoceria did not a!ect cell growth and function in cardiac progenitor cells, while being able to protect CPCs from H2O2-induced cytotoxicity for at least 7 days, indicating that nanoceria in an e!ective antioxidant. Therefore, these "ndings con"rm the great potential of nanoceria for controlling ROS-induced cell damage

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

Characterizing the multifaceted contribution of genetic and epigenetic factors to disease phenotypes is a major challenge in human genetics and medicine. We carried out high-resolution genetic, epigenetic, and transcriptomic profiling in three major human immune cell types (CD14$^{+}$ monocytes, CD16$^{+}$ neutrophils, and naive CD4$^{+}$ T cells) from up to 197 individuals. We assess, quantitatively, the relative contribution of $\textit{cis}$-genetic and epigenetic factors to transcription and evaluate their impact as potential sources of confounding in epigenome-wide association studies. Further, we characterize highly coordinated genetic effects on gene expression, methylation, and histone variation through quantitative trait locus (QTL) mapping and allele-specific (AS) analyses. Finally, we demonstrate colocalization of molecular trait QTLs at 345 unique immune disease loci. This expansive, high-resolution atlas of multi-omics changes yields insights into cell-type-specific correlation between diverse genomic inputs, more generalizable correlations between these inputs, and defines molecular events that may underpin complex disease risk.This work was predominantly funded by the EU FP7 High Impact Project BLUEPRINT (HEALTH-F5-2011-282510) and the Canadian Institutes of Health Research (CIHR EP1-120608). The research leading to these results has received funding from the European Union's Seventh Framework Programme (FP7/2007-2013) under grant agreement no 282510 (BLUEPRINT), the European Molecular Biology Laboratory, the Max Planck society, the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013-2017’, SEV-2012-0208 and Spanish National Bioinformatics Institute (INB-ISCIII) PT13/0001/0021 co-funded by FEDER "“Una Manera de hacer Europa”. D.G. is supported by a “la Caixa”-Severo Ochoa pre-doctoral fellowship, M.F. was supported by the BHF Cambridge Centre of Excellence [RE/13/6/30180], K.D. is funded as a HSST trainee by NHS Health Education England, S.E. is supported by a fellowship from La Caixa, V.P. is supported by a FEBS long-term fellowship and N.S.'s research is supported by the Wellcome Trust (Grant Codes WT098051 and WT091310), the EU FP7 (EPIGENESYS Grant Code 257082 and BLUEPRINT Grant Code HEALTH-F5-2011-282510) and the NIHR BRC. The Blood and Transplant Unit (BTRU) in Donor Health and Genomics is part of and funded by the National Institute for Health Research (NIHR) and is a partnership between the University of Cambridge and NHS Blood and Transplant (NHSBT) in collaboration with the University of Oxford and the Wellcome Trust Sanger Institute. The T-cell data was produced by the McGill Epigenomics Mapping Centre (EMC McGill). It is funded under the Canadian Epigenetics, Environment, and Health Research Consortium (CEEHRC) by the Canadian Institutes of Health Research and by Genome Quebec (CIHR EP1-120608), with additional support from Genome Canada and FRSQ. T.P. holds a Canada Research Chair

Cardiovascular outcomes in renal transplant recipients: Feasibility and clinical role of 2D speckle tracking to assess myocardial function

Left ventricular (LV) function is normally improved after renal transplant; however, cardiovascular mortality remains elevated. Moderate physical activity has a positive impact on myocardial function; however, few data are available about the role of 2D echocardiography (2DE) and 2D speckle tracking echocardiography (2DSTE) on renal transplant recipients (RTR). From a large cohort of RTR submitted to a supervised exercise as the prescription program, 10 subjects who were regularly trained were studied for sixth months. They underwent periodically an echo evaluation (ESAOTE MyLab 50), cardiopulmonary test (CPT) and strength test for the lower and upper limbs. The LV function study was completed with the speckle tracking longitudinal strain (Lo Strain) measure calculated by dedicated software (XStrain\u2013Esaote) at the end of the protocol. All of the cardiovascular parameters were normal: the ejection fraction (EF) increased significantly (from 62.7 \ub1 4 to 67.2 \ub1 2.3 with p < 0.05), as well as the anaerobic threshold (15.3 \ub1 6.8 to 20.5 \ub1 10.1 with p < 0.05). Particularly, the global longitudinal strain (GLS) values were within the normal range (-19.2% \ub1 5.1), maintaining the physiological gradient from the basal (-13.2 \ub1 4.1; -16.5 \ub1 5.21) to the apex level (-21 \ub1 2.3; -25.7 \ub1 -7.0). 2D speckle tracking echocardiography (2DSTE) can be effectively used to confirm the presence of preserved physiological myocardial function in post-renal transplantation subjects submitted to a physical training

Left atrium: the last bulwark before overt heart failure

Heart failure (HF) with preserved ejection fraction (HFpEF) has emerged as an important public health issue in recent years. It represents the most common type of HF in ambulatory setting, and it has been recognized as a different entity from the reduced ejection fraction (EF) form. In HFpEF, continuous growing attention has been focused on the role of the left atrium (LA) in preserving good ventricular function and asymptomatic condition of the patient since the very first stages of diastolic dysfunction (DD). Non-invasive and complete echocardiographic evaluation of diastolic phase cannot exempt from accurately analyzed LA size, mostly LA volume, and its function, in particular LA myocardial deformation by speckle tracking echocardiography (STE). This review examines the expanding role of the LA in DD and HFpEF and the importance of its complete assessment in various settings, from diagnosis to correlation with major cardiovascular events. © 2016, Springer Science+Business Media New York

Ablation therapy for ventricular arrhythmias in patients with LVAD: Multiple faces of an electrophysiological challenge

Left ventricular assist device implantation is a recognized treatment option for patients with advanced heart failure refractory to medical therapy and can be used both as bridge to transplantation and as destination therapy. The risk of ventricular arrhythmias is common after left ventricular assist device implantation and is influenced by pre-, peri and post-operative determinants. The management of ventricular arrhythmias can be a challenge when they become refractory to medication or to device therapy and their impact on prognosis can be detrimental despite the mechanical support. In this setting, catheter ablation is being increasingly recognized as a feasible option for patients in which standard therapeutic strategies fail, but also with preventive purpose. Catheter ablation is being increasingly considered for the management of ventricular arrhythmias in patients with left ventricular assist device despite complex clinical and technical peculiarities due to the characteristics of the mechanical support. Much conflicting data exist regarding the predictors of success of the procedure and the rate of recurrence. In this review we discuss the latest evidences regarding catheter ablation of ventricular arrhythmias in this subset of patients, focusing on clinical characteristics, arrhythmia etiology, technical aspects and postprocedural features which must be considered by the electrophysiologist

Left atrial strain: A useful index in atrial fibrillation

Left atrial (LA) strain is a speckle tracking echocardiography (STE)-derived parameter applied to the analysis of chamber function that provides highly reproducible measures of LA deformation by a non-Doppler, angle-independent quantification. In recent years, data regarding accuracy and clinical application of LA strain are rapidly increasing. This review describes the main features of LA strain and examines the role of STE in the evaluation of various aspects of AF, as the risk of developing the arrhythmia in general population, the evaluation of LA fibrosis and LA impairment, the quantification of cardioembolic risk and of recurrence after cardioversion or ablation therapies