Balanced gene losses, duplications and intensive rearrangements led to an unusual regularly sized genome in Arbutus unedo chloroplasts

Completely sequenced plastomes provide a valuable source of information about the duplication, loss, and transfer events of chloroplast genes and phylogenetic data for resolving relationships among major groups of plants. Moreover, they can also be useful for exploiting chloroplast genetic engineering technology. Ericales account for approximately six per cent of eudicot diversity with 11,545 species from which only three complete plastome sequences are currently available. With the aim of increasing the number of ericalean complete plastome sequences, and to open new perspectives in understanding Mediterranean plant adaptations, a genomic study on the basis of the complete chloroplast genome sequencing of Arbutus unedo and an updated phylogenomic analysis of Asteridae was implemented. The chloroplast genome of A. unedo shows extensive rearrangements but a medium size (150,897 nt) in comparison to most of angiosperms. A number of remarkable distinct features characterize the plastome of A. unedo: five-fold dismissing of the SSC region in relation to most angiosperms; complete loss or pseudogenization of a number of essential genes; duplication of the ndhH-D operon and its location within the two IRs; presence of large tandem repeats located near highly re-arranged regions and pseudogenes. All these features outline the primary evolutionary split between Ericaceae and other ericalean families. The newly sequenced plastome of A. unedo with the available asterid sequences allowed the resolution of some uncertainties in previous phylogenies of Asteridae

Search for Rare and Forbidden Charm Meson Decays D0--> V l+ l- and h h l l

We report the results of a search for flavor-changing neutral current, lepton-flavor, and lepton-number violating decays of the 3 and 4-body decay modes of D0 (and its antiparticle) containing muons and electrons. Using data from Fermilab charm hadroproduction experiment E791, we examine modes with two leptons and either a Rho(0), Kstar, or Phi vector meson or a non-resonant Pi Pi, K Pi, or K K pair of pseudoscalar mesons. No evidence for any of these decays is found. Therefore, we present branching-fraction upper limits at 90% confidence level for the 27 decay modes examined (18 new).Comment: 5 pages, 1 Figure, Submitted to PR

Increased Inter-Colony Fusion Rates Are Associated with Reduced COI Haplotype Diversity in an Invasive Colonial Ascidian Didemnum vexillum

Considerable progress in our understanding of the population genetic changes associated with biological invasions has been made over the past decade. Using selectively neutral loci, it has been established that reductions in genetic diversity, reflecting founder effects, have occurred during the establishment of some invasive populations. However, some colonial organisms may actually gain an ecological advantage from reduced genetic diversity because of the associated reduction in inter-colony conflict. Here we report population genetic analyses, along with colony fusion experiments, for a highly invasive colonial ascidian, Didemnum vexillum. Analyses based on mitochondrial cytochrome oxidase I (COI) partial coding sequences revealed two distinct D. vexillum clades. One COI clade appears to be restricted to the probable native region (i.e., north-west Pacific Ocean), while the other clade is present in widely dispersed temperate coastal waters around the world. This clade structure was supported by 18S ribosomal DNA (rDNA) sequence data, which revealed a one base-pair difference between the two clades. Recently established populations of D. vexillum in New Zealand displayed greatly reduced COI genetic diversity when compared with D. vexillum in Japan. In association with this reduction in genetic diversity was a significantly higher inter-colony fusion rate between randomly paired New Zealand D. vexillum colonies (80%, standard deviation ±18%) when compared with colonies found in Japan (27%, standard deviation ±15%). The results of this study add to growing evidence that for colonial organisms reductions in population level genetic diversity may alter colony interaction dynamics and enhance the invasive potential of newly colonizing species

The Whereabouts of an Ancient Wanderer: Global Phylogeography of the Solitary Ascidian Styela plicata

Genetic tools have greatly aided in tracing the sources and colonization history of introduced species. However, recurrent introductions and repeated shuffling of populations may have blurred some of the genetic signals left by ancient introductions. Styela plicata is a solitary ascidian distributed worldwide. Although its origin remains unclear, this species is believed to have spread worldwide by travelling on ship's hulls. The goals of this study were to infer the genetic structure and global phylogeography of S. plicata and to look for present-day and historical genetic patterns. Two genetic markers were used: a fragment of the mitochondrial gene Cytochrome Oxidase subunit I (COI) and a fragment of the nuclear gene Adenine Nucleotide Transporter/ADP-ATP Translocase (ANT). A total of 368 individuals for COI and 315 for ANT were sequenced from 17 locations worldwide. The levels of gene diversity were moderate for COI to high for ANT. The Mediterranean populations showed the least diversity and allelic richness for both markers, while the Indian, Atlantic and Pacific Oceans had the highest gene and nucleotide diversities. Network and phylogenetic analyses with COI and ANT revealed two groups of alleles separated by 15 and 4 mutational steps, respectively. The existence of different lineages suggested an ancient population split. However, the geographic distributions of these groups did not show any consistent pattern, indicating different phylogeographic histories for each gene. Genetic divergence was significant for many population-pairs irrespective of the geographic distance among them. Stochastic introduction events are reflected in the uneven distribution of COI and ANT allele frequencies and groups among many populations. Our results confirmed that S. plicata has been present in all studied oceans for a long time, and that recurrent colonization events and occasional shuffling among populations have determined the actual genetic structure of this species

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

The Seventeenth Data Release of the Sloan Digital Sky Surveys: Complete Release of MaNGA, MaStar and APOGEE-2 Data

This paper documents the seventeenth data release (DR17) from the Sloan Digital Sky Surveys; the fifth and final release from the fourth phase (SDSS-IV). DR17 contains the complete release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, which reached its goal of surveying over 10,000 nearby galaxies. The complete release of the MaNGA Stellar Library (MaStar) accompanies this data, providing observations of almost 30,000 stars through the MaNGA instrument during bright time. DR17 also contains the complete release of the Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) survey which publicly releases infra-red spectra of over 650,000 stars. The main sample from the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), as well as the sub-survey Time Domain Spectroscopic Survey (TDSS) data were fully released in DR16. New single-fiber optical spectroscopy released in DR17 is from the SPectroscipic IDentification of ERosita Survey (SPIDERS) sub-survey and the eBOSS-RM program. Along with the primary data sets, DR17 includes 25 new or updated Value Added Catalogs (VACs). This paper concludes the release of SDSS-IV survey data. SDSS continues into its fifth phase with observations already underway for the Milky Way Mapper (MWM), Local Volume Mapper (LVM) and Black Hole Mapper (BHM) surveys

Multiancestry analysis of the HLA locus in Alzheimer’s and Parkinson’s diseases uncovers a shared adaptive immune response mediated by HLA-DRB1*04 subtypes

Across multiancestry groups, we analyzed Human Leukocyte Antigen (HLA) associations in over 176,000 individuals with Parkinson’s disease (PD) and Alzheimer’s disease (AD) versus controls. We demonstrate that the two diseases share the same protective association at the HLA locus. HLA-specific fine-mapping showed that hierarchical protective effects of HLA-DRB1*04 subtypes best accounted for the association, strongest with HLA-DRB1*04:04 and HLA-DRB1*04:07, and intermediary with HLA-DRB1*04:01 and HLA-DRB1*04:03. The same signal was associated with decreased neurofibrillary tangles in postmortem brains and was associated with reduced tau levels in cerebrospinal fluid and to a lower extent with increased Aβ42. Protective HLA-DRB1*04 subtypes strongly bound the aggregation-prone tau PHF6 sequence, however only when acetylated at a lysine (K311), a common posttranslational modification central to tau aggregation. An HLA-DRB1*04-mediated adaptive immune response decreases PD and AD risks, potentially by acting against tau, offering the possibility of therapeutic avenues

Actividad sexual en adolescencia temprana: problema de salud pública en una ciudad colombiana

Antecedentes: El inicio de Ia actividad sexual en adolescentes, está asociada a pobre planificación familiar (PF), mayor tasa de fecundidad y riesgo de adquisición de enfermedades de transmisión sexual (ETS). Objetivo: Evaluar el impacto sobre la fecundidad, planificación familiar y lesiones de cuello uterino en una población de adolescentes y jóvenes, que iniciaron actividad sexual en la adolescencia. Método: Estudio de cohorte retrospectiva. Incluyó 845 adolescentes y jóvenes que iniciaron actividad sexual en la adolescencia y que consultaron a una Institución Prestadora de Servicios de Salud en Tuluá, Colombia. El análisis incluyó estadísticas descriptivas, análisis de riesgo relativo (RR) y atribuible a la exposición (RAexp) expresado en porcentaje, como indicadores de asociación. Resultados: Hubo 203 adolescentes y 642 jóvenes. El promedio de edad de inicio de la actividad sexual fue 16 años (±1,6 años). El 49% no realizaba PF, 34,7% tenía ≥1 hijo y 6,9% alguna lesión en cuello uterino. Hubo asociación entre actividad sexual en la adolescencia temprana y tener un hijo, al compararlo con el inicio de la actividad sexual en la adolescencia media (RR: 1,6; IC 95%: 1,2-2,1. RAexp0/35,7%; IC 95%: 13,3-52,4%) y tardía (RR: 2; IC 95%: 1,5-2,6. RAexp0/49%; IC 95%: 31,7-62%). Conclusiones: Nuestros resultados confirman el inicio precoz de la actividad sexual en adolescentes, el bajo uso de anticonceptivos y el riesgo de lesiones cervicales. Programas educativos conducentes al retraso del inicio de la actividad sexual, el uso de métodos anticonceptivos efectivos y de barrera, permitirán reducir las cifras encontradas en este estudio

Prevalencia de lesiones de bajo y alto grado de cuello uterino en una ciudad colombiana

Objetivo: Determinar la prevalencia de las lesiones de bajo y alto grado de cuello uterino en una Institución Prestadora de Servicios de Salud de Tuluá, Colombia, entre los años 2008-2010. Métodos: Se realizó un estudio descriptivo retrospectivo en el que se incluyeron mujeres entre los 15 y 75 años, residentes en el Municipio de Tuluá. Se evaluo la normalidad de las variables cuantitativas, empleándose la mediana o el promedio con sus varianzas según su distribución, y frecuencias y proporciones para las variables categóricas. Resultados: Se incluyeron 3.539 mujeres. La mediana de la edad fue 38 años con rango intercuartil (RI: 29-46 años), la mediana del número de partos 1 (RI: 0-3). En relación a la seguridad social y uso de métodos anticonceptivos, la mayoría eran particulares y no utilizaban ningún método. El 87,5% de las citologías se reportaron como negativas, 8,2% lesión de bajo grado (LSIL), 2,6% células escamosas atípicas de significado indeterminado (ASC-US), 0,9% lesiones de alto grado (HSIL), 0,4% células escamosas atípicas de significado indeterminado de alto grado ASC-H, 0,4% células glandulares atípicas de significado incierto (ASGUS) y 0,2% carcinoma invasor. Conclusión: La prevalencia de las anormalidades citológicas fue baja en todos los grupos analizados, sin embargo, existe un mayor número de LSIL hacia la cuarta década de la vida y en aquellas que iniciaron su vida sexual después de los 40 años. De igual manera se encontró una relación inversa entre el número de partos, planificación familiar hormonal y aparición de lesiones pre neoplásicas