421 research outputs found
New methods in ambulatory blood pressure monitoring: Interactive monitoring and detection of posture and movement patterns
The Genomic Signature of Crop-Wild Introgression in Maize
The evolutionary significance of hybridization and subsequent introgression
has long been appreciated, but evaluation of the genome-wide effects of these
phenomena has only recently become possible. Crop-wild study systems represent
ideal opportunities to examine evolution through hybridization. For example,
maize and the conspecific wild teosinte Zea mays ssp. mexicana, (hereafter,
mexicana) are known to hybridize in the fields of highland Mexico. Despite
widespread evidence of gene flow, maize and mexicana maintain distinct
morphologies and have done so in sympatry for thousands of years. Neither the
genomic extent nor the evolutionary importance of introgression between these
taxa is understood. In this study we assessed patterns of genome-wide
introgression based on 39,029 single nucleotide polymorphisms genotyped in 189
individuals from nine sympatric maize-mexicana populations and reference
allopatric populations. While portions of the maize and mexicana genomes were
particularly resistant to introgression (notably near known
cross-incompatibility and domestication loci), we detected widespread evidence
for introgression in both directions of gene flow. Through further
characterization of these regions and preliminary growth chamber experiments,
we found evidence suggestive of the incorporation of adaptive mexicana alleles
into maize during its expansion to the highlands of central Mexico. In
contrast, very little evidence was found for adaptive introgression from maize
to mexicana. The methods we have applied here can be replicated widely, and
such analyses have the potential to greatly informing our understanding of
evolution through introgressive hybridization. Crop species, due to their
exceptional genomic resources and frequent histories of spread into sympatry
with relatives, should be particularly influential in these studies
Supernova Simulations and Strategies For the Dark Energy Survey
We present an analysis of supernova light curves simulated for the upcoming
Dark Energy Survey (DES) supernova search. The simulations employ a code suite
that generates and fits realistic light curves in order to obtain distance
modulus/redshift pairs that are passed to a cosmology fitter. We investigated
several different survey strategies including field selection, supernova
selection biases, and photometric redshift measurements. Using the results of
this study, we chose a 30 square degree search area in the griz filter set. We
forecast 1) that this survey will provide a homogeneous sample of up to 4000
Type Ia supernovae in the redshift range 0.05<z<1.2, and 2) that the increased
red efficiency of the DES camera will significantly improve high-redshift color
measurements. The redshift of each supernova with an identified host galaxy
will be obtained from spectroscopic observations of the host. A supernova
spectrum will be obtained for a subset of the sample, which will be utilized
for control studies. In addition, we have investigated the use of combined
photometric redshifts taking into account data from both the host and
supernova. We have investigated and estimated the likely contamination from
core-collapse supernovae based on photometric identification, and have found
that a Type Ia supernova sample purity of up to 98% is obtainable given
specific assumptions. Furthermore, we present systematic uncertainties due to
sample purity, photometric calibration, dust extinction priors, filter-centroid
shifts, and inter-calibration. We conclude by estimating the uncertainty on the
cosmological parameters that will be measured from the DES supernova data.Comment: 46 pages, 30 figures, resubmitted to ApJ as Revision 2 (final author
revision), which has subtle editorial differences compared to the published
paper (ApJ, 753, 152). Note that this posting includes PDF only due to a bug
in either the latex macros or the arXiv submission system. The source files
are available in the DES document database:
http://des-docdb.fnal.gov/cgi-bin/ShowDocument?docid=624
Gapless Assembly of Maize Chromosomes Using Long-Read Technologies
Creating gapless telomere-to-telomere assemblies of complex genomes is one of the ultimate challenges in genomics. We use two independent assemblies and an optical map-based merging pipeline to produce a maize genome (B73-Ab10) composed of 63 contigs and a contig N50 of 162 Mb. This genome includes gapless assemblies of chromosome 3 (236 Mb) and chromosome 9 (162 Mb), and 53 Mb of the Ab10 meiotic drive haplotype. The data also reveal the internal structure of seven centromeres and five heterochromatic knobs, showing that the major tandem repeat arrays (CentC, knob180, and TR-1) are discontinuous and frequently interspersed with retroelements
The variational Poisson cohomology
It is well known that the validity of the so called Lenard-Magri scheme of
integrability of a bi-Hamiltonian PDE can be established if one has some
precise information on the corresponding 1st variational Poisson cohomology for
one of the two Hamiltonian operators. In the first part of the paper we explain
how to introduce various cohomology complexes, including Lie superalgebra and
Poisson cohomology complexes, and basic and reduced Lie conformal algebra and
Poisson vertex algebra cohomology complexes, by making use of the corresponding
universal Lie superalebra or Lie conformal superalgebra. The most relevant are
certain subcomplexes of the basic and reduced Poisson vertex algebra cohomology
complexes, which we identify (non-canonically) with the generalized de Rham
complex and the generalized variational complex. In the second part of the
paper we compute the cohomology of the generalized de Rham complex, and, via a
detailed study of the long exact sequence, we compute the cohomology of the
generalized variational complex for any quasiconstant coefficient Hamiltonian
operator with invertible leading coefficient. For the latter we use some
differential linear algebra developed in the Appendix.Comment: 130 pages, revised version with minor changes following the referee's
suggestion
Characterization of introgression from the teosinte Zea mays ssp. mexicana to Mexican highland maize
Background The spread of maize cultivation to the highlands of central Mexico was accompanied by substantial introgression from the endemic wild teosinte Zea mays ssp. mexicana, prompting the hypothesis that the transfer of beneficial variation facilitated local adaptation. Methods We used whole-genome sequence data to map regions of Zea mays ssp. mexicana introgression in three Mexican highland maize individuals. We generated a genetic linkage map and performed Quantitative Trait Locus mapping in an F2 population derived from a cross between lowland and highland maize individuals. Results Introgression regions ranged in size from several hundred base pairs to Megabase-scale events. Gene density within introgression regions was comparable to the genome as a whole, and over 1,000 annotated genes were located within introgression events. Quantitative Trait Locus mapping identified a small number of loci linked to traits characteristic of Mexican highland maize. Discussion Although there was no strong evidence to associate quantitative trait loci with regions of introgression, we nonetheless identified many Mexican highland alleles of introgressed origin that carry potentially functional sequence variants. The impact of introgression on stress tolerance and yield in the highland environment remains to be fully characterized
Essential versus accessory aspects of cell death: recommendations of the NCCD 2015
Cells exposed to extreme physicochemical or mechanical stimuli die in an uncontrollable manner, as a result of their immediate structural breakdown. Such an unavoidable variant of cellular demise is generally referred to as âaccidental cell deathâ (ACD). In most settings, however, cell death is initiated by a genetically encoded apparatus, correlating with the fact that its course can be altered by pharmacologic or genetic interventions. âRegulated cell deathâ (RCD) can occur as part of physiologic programs or can be activated once adaptive responses to perturbations of the extracellular or intracellular microenvironment fail. The biochemical phenomena that accompany RCD may be harnessed to classify it into a few subtypes, which often (but not always) exhibit stereotyped morphologic features. Nonetheless, efficiently inhibiting the processes that are commonly thought to cause RCD, such as the activation of executioner caspases in the course of apoptosis, does not exert true cytoprotective effects in the mammalian system, but simply alters the kinetics of cellular demise as it shifts its morphologic and biochemical correlates. Conversely, bona fide cytoprotection can be achieved by inhibiting the transduction of lethal signals in the early phases of the process, when adaptive responses are still operational. Thus, the mechanisms that truly execute RCD may be less understood, less inhibitable and perhaps more homogeneous than previously thought. Here, the Nomenclature Committee on Cell Death formulates a set of recommendations to help scientists and researchers to discriminate between essential and accessory aspects of cell death
Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline
BACKGROUND: Sequencing technology and assembly algorithms have matured to the point that high-quality de novo assembly is possible for large, repetitive genomes. Current assemblies traverse transposable elements (TEs) and provide an opportunity for comprehensive annotation of TEs. Numerous methods exist for annotation of each class of TEs, but their relative performances have not been systematically compared. Moreover, a comprehensive pipeline is needed to produce a non-redundant library of TEs for species lacking this resource to generate whole-genome TE annotations. RESULTS: We benchmark existing programs based on a carefully curated library of rice TEs. We evaluate the performance of methods annotating long terminal repeat (LTR) retrotransposons, terminal inverted repeat (TIR) transposons, short TIR transposons known as miniature inverted transposable elements (MITEs), and Helitrons. Performance metrics include sensitivity, specificity, accuracy, precision, FDR, and F1. Using the most robust programs, we create a comprehensive pipeline called Extensive de-novo TE Annotator (EDTA) that produces a filtered non-redundant TE library for annotation of structurally intact and fragmented elements. EDTA also deconvolutes nested TE insertions frequently found in highly repetitive genomic regions. Using other model species with curated TE libraries (maize and Drosophila), EDTA is shown to be robust across both plant and animal species. CONCLUSIONS: The benchmarking results and pipeline developed here will greatly facilitate TE annotation in eukaryotic genomes. These annotations will promote a much more in-depth understanding of the diversity and evolution of TEs at both intra- and inter-species levels. EDTA is open-source and freely available: https://github.com/oushujun/EDTA
A case of behavioural diversification in male floral function â the evolution of thigmonastic pollen presentation
The authors gratefully acknowledge funding provided by an Else-Neumann-Stipendium (http://www.fu-berlin.de/sites/promovieren/drs/nachwuchs/nachwuchs/nafoeg.html), Deutscher Akademischer Austausch Dienst (DAAD) and botconsult GmbH at different stages of data acquisition. We thank Tobias Grass, Joana Bergmann and Franziska Weber (Freie UniversitÀt Berlin) for help with data collection in the field and in the greenhouse. Nicole Schmandt, Federico Luebert, Juliana Chacón and Dietmar Quant (UniversitÀt Bonn) provided help in the molecular laboratory and the edition of the molecular dataset. We furthermore thank Markus Ackermann (Koblenz) for providing photographs, Philipp Klein (Berlin) for editing the video and Katy Jones (Berlin) for helpful comments on an earlier version of the manuscript. Rafael Acuña has been supported by the ALECOSTA scholarship program. Coverage of the article processing charge by the German Research Foundation via the Open Access Publication Fund of the Freie UniversitÀt Berlin is gratefully acknowledged.Peer reviewedPublisher PD
Conceptualising spirituality for medical research and health service provision
The need to take account of spirituality in research and health services provision is assuming ever greater importance. However the field has long been hampered by a lack of conceptual clarity about the nature of spirituality itself. We do not agree with the sceptical claim that it is impossible to conceptualise spirituality within a scientific paradigm. Our aims are to 1) provide a brief over-view of critical thinking that might form the basis for a useful definition of spirituality for research and clinical work and 2) demystify the language of spirituality for clinical practice and research
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