534 research outputs found
A Chromosome-Scale Assembly of the Garden Orach (Atriplex hortensis L.) Genome Using Oxford Nanopore Sequencing
Atriplex hortensis (2n = 2x = 18, 1C genome size 1.1 gigabases), also known
as garden orach and mountain-spinach, is a highly nutritious, broadleaf annual of
the Amaranthaceae-Chenopodiaceae alliance (Chenopodiaceae sensu stricto, subfam.
Chenopodioideae) that has spread in cultivation from its native primary domestication
area in Eurasia to other temperate and subtropical regions worldwide. Atriplex L. is a
highly complex but, as understood now, a monophyletic group of mainly halophytic
and/or xerophytic plants, of which A. hortensis has been a vegetable of minor
importance in some areas of Eurasia (from Central Asia to the Mediterranean) at least
since antiquity. Nonetheless, it is a crop with tremendous nutritional potential due
primarily to its exceptional leaf and seed protein quantities (approaching 30%) and
quality (high levels of lysine). Although there is some literature describing the taxonomy
and production of A. hortensis, there is a general lack of genetic and genomic data
that would otherwise help elucidate the genetic variation, phylogenetic positioning, and
future potential of the species. Here, we report the assembly of the first high-quality,
chromosome-scale reference genome for A. hortensis cv. “Golden.” Long-read data
from Oxford Nanopore’s MinION DNA sequencer was assembled with the program
Canu and polished with Illumina short reads. Contigs were scaffolded to chromosome
scale using chromatin-proximity maps (Hi-C) yielding a final assembly containing 1,325
scaffolds with a N50 of 98.9 Mb – with 94.7% of the assembly represented in the nine
largest, chromosome-scale scaffolds. Sixty-six percent of the genome was classified
as highly repetitive DNA, with the most common repetitive elements being Gypsy-
(32%) and Copia-like (11%) long-terminal repeats. The annotation was completed using
MAKER which identified 37,083 gene models and 2,555 tRNA genes. Completeness of the genome, assessed using the Benchmarking Universal Single Copy Orthologs
(BUSCO) metric, identified 97.5% of the conserved orthologs as complete, with only
2.2% being duplicated, reflecting the diploid nature of A. hortensis. A resequencing
panel of 21 wild, unimproved and cultivated A. hortensis accessions revealed three
distinct populations with little variation within subpopulations. These resources provide
vital information to better understand A. hortensis and facilitate future study
The Dark Energy Survey Data Management System
The Dark Energy Survey collaboration will study cosmic acceleration with a
5000 deg2 griZY survey in the southern sky over 525 nights from 2011-2016. The
DES data management (DESDM) system will be used to process and archive these
data and the resulting science ready data products. The DESDM system consists
of an integrated archive, a processing framework, an ensemble of astronomy
codes and a data access framework. We are developing the DESDM system for
operation in the high performance computing (HPC) environments at NCSA and
Fermilab. Operating the DESDM system in an HPC environment offers both speed
and flexibility. We will employ it for our regular nightly processing needs,
and for more compute-intensive tasks such as large scale image coaddition
campaigns, extraction of weak lensing shear from the full survey dataset, and
massive seasonal reprocessing of the DES data. Data products will be available
to the Collaboration and later to the public through a virtual-observatory
compatible web portal. Our approach leverages investments in publicly available
HPC systems, greatly reducing hardware and maintenance costs to the project,
which must deploy and maintain only the storage, database platforms and
orchestration and web portal nodes that are specific to DESDM. In Fall 2007, we
tested the current DESDM system on both simulated and real survey data. We used
Teragrid to process 10 simulated DES nights (3TB of raw data), ingesting and
calibrating approximately 250 million objects into the DES Archive database. We
also used DESDM to process and calibrate over 50 nights of survey data acquired
with the Mosaic2 camera. Comparison to truth tables in the case of the
simulated data and internal crosschecks in the case of the real data indicate
that astrometric and photometric data quality is excellent.Comment: To be published in the proceedings of the SPIE conference on
Astronomical Instrumentation (held in Marseille in June 2008). This preprint
is made available with the permission of SPIE. Further information together
with preprint containing full quality images is available at
http://desweb.cosmology.uiuc.edu/wik
Modulation of RNA splicing enhances response to BCL2 inhibition in leukemia.
Therapy resistance is a major challenge in the treatment of cancer. Here, we performed CRISPR-Cas9 screens across a broad range of therapies used in acute myeloid leukemia to identify genomic determinants of drug response. Our screens uncover a selective dependency on RNA splicing factors whose loss preferentially enhances response to the BCL2 inhibitor venetoclax. Loss of the splicing factor RBM10 augments response to venetoclax in leukemia yet is completely dispensable for normal hematopoiesis. Combined RBM10 and BCL2 inhibition leads to mis-splicing and inactivation of the inhibitor of apoptosis XIAP and downregulation of BCL2A1, an anti-apoptotic protein implicated in venetoclax resistance. Inhibition of splicing kinase families CLKs (CDC-like kinases) and DYRKs (dual-specificity tyrosine-regulated kinases) leads to aberrant splicing of key splicing and apoptotic factors that synergize with venetoclax, and overcomes resistance to BCL2 inhibition. Our findings underscore the importance of splicing in modulating response to therapies and provide a strategy to improve venetoclax-based treatments
PIKfyve regulates CaV1.2 degradation and prevents excitotoxic cell death
Neuronal Ca levels are regulated by glutamate receptor activation, which recruits PIKfyve to voltage-gated Ca channels, prompting their degradation
Assistive technologies to address capabilities of people with dementia: from research to practice
Assistive technologies (AT) became pervasive and virtually present in all our life domains. They can be either an enabler or an obstacle leading to social exclusion. The Fondation Médéric Alzheimer gathered international experts of dementia care, with backgrounds in biomedical, human and social sciences, to analyse how AT can address the capabilities of people with dementia, on the basis of their needs. Discussion covered the unmet needs of people with dementia, the domains of daily life activities where AT can provide help to people with dementia, the enabling and empowering impact of technology to improve their safety and wellbeing, barriers and limits of use, technology assessment, ethical and legal issues. The capability approach (possible freedom) appears particularly relevant in person-centered dementia care and technology development. The focus is not on the solution, rather on what the person can do with it: seeing dementia as disability, with technology as an enabler to promote capabilities of the person, provides a useful framework for both research and practice. This article summarizes how these concepts took momentum in professional practice and public policies in the past fifteen years (2000-2015), discusses current issues in the design, development and economic model of AT for people with dementia, and covers how these technologies are being used and assessed
Priorities for synthesis research in ecology and environmental science
ACKNOWLEDGMENTS We thank the National Science Foundation grant #1940692 for financial support for this workshop, and the National Center for Ecological Analysis and Synthesis (NCEAS) and its staff for logistical support.Peer reviewedPublisher PD
Priorities for synthesis research in ecology and environmental science
ACKNOWLEDGMENTS We thank the National Science Foundation grant #1940692 for financial support for this workshop, and the National Center for Ecological Analysis and Synthesis (NCEAS) and its staff for logistical support.Peer reviewedPublisher PD
Rhamnolipids: diversity of structures, microbial origins and roles
Rhamnolipids are glycolipidic biosurfactants produced by various bacterial species. They were initially found as exoproducts of the opportunistic pathogen Pseudomonas aeruginosa and described as a mixture of four congeners: α-L-rhamnopyranosyl-α-L-rhamnopyranosyl-β-hydroxydecanoyl-β-hydroxydecanoate (Rha-Rha-C10-C10), α-L-rhamnopyranosyl-α-L-rhamnopyranosyl-β-hydroxydecanoate (Rha-Rha-C10), as well as their mono-rhamnolipid congeners Rha-C10-C10 and Rha-C10. The development of more sensitive analytical techniques has lead to the further discovery of a wide diversity of rhamnolipid congeners and homologues (about 60) that are produced at different concentrations by various Pseudomonas species and by bacteria belonging to other families, classes, or even phyla. For example, various Burkholderia species have been shown to produce rhamnolipids that have longer alkyl chains than those produced by P. aeruginosa. In P. aeruginosa, three genes, carried on two distinct operons, code for the enzymes responsible for the final steps of rhamnolipid synthesis: one operon carries the rhlAB genes and the other rhlC. Genes highly similar to rhlA, rhlB, and rhlC have also been found in various Burkholderia species but grouped within one putative operon, and they have been shown to be required for rhamnolipid production as well. The exact physiological function of these secondary metabolites is still unclear. Most identified activities are derived from the surface activity, wetting ability, detergency, and other amphipathic-related properties of these molecules. Indeed, rhamnolipids promote the uptake and biodegradation of poorly soluble substrates, act as immune modulators and virulence factors, have antimicrobial activities, and are involved in surface motility and in bacterial biofilm development
Genetic improvement of tomato by targeted control of fruit softening
Controlling the rate of softening to extend shelf life was a key target for researchers engineering genetically modified (GM) tomatoes in the 1990s, but only modest improvements were achieved. Hybrids grown nowadays contain 'non-ripening mutations' that slow ripening and improve shelf life, but adversely affect flavor and color. We report substantial, targeted control of tomato softening, without affecting other aspects of ripening, by silencing a gene encoding a pectate lyase
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