2,642 research outputs found
IView: introgression library visualization and query tool
<p>Abstract</p> <p>Background</p> <p>An introgression library is a family of near-isogenic lines in a common genetic background, each of which carries one or more genomic regions contributed by a donor genome. Near-isogenic lines are powerful genetic resources for the analysis of phenotypic variation and are important for map-base cloning genes underlying mutations and traits. With many thousands of distinct genotypes, querying introgression libraries for lines of interest is an issue. </p> <p>Results</p> <p>We have created IView, a tool to graphically display and query near-isogenic line libraries for specific introgressions. This tool incorporates a web interface for displaying the location and extent of introgressions. Each genetic marker is associated with a position on a reference map. Users can search for introgressions using marker names, or chromosome number and map positions. This search results in a display of lines carrying an introgression at the specified position. Upon selecting one of the lines, color-coded introgressions on all chromosomes of the line are displayed graphically.</p> <p>The source code for IView can be downloaded from <url>http://xrl.us/iview</url>. </p> <p>Conclusions</p> <p>IView will be useful for those wanting to make introgression data from their stock of germplasm searchable. </p
Accidental carbon monoxide poisoning presenting without a history of exposure: A case report
This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens
Type Ia Supernova Explosion Models
Because calibrated light curves of Type Ia supernovae have become a major
tool to determine the local expansion rate of the Universe and also its
geometrical structure, considerable attention has been given to models of these
events over the past couple of years. There are good reasons to believe that
perhaps most Type Ia supernovae are the explosions of white dwarfs that have
approached the Chandrasekhar mass, M_ch ~ 1.39 M_sun, and are disrupted by
thermonuclear fusion of carbon and oxygen. However, the mechanism whereby such
accreting carbon-oxygen white dwarfs explode continues to be uncertain. Recent
progress in modeling Type Ia supernovae as well as several of the still open
questions are addressed in this review. Although the main emphasis will be on
studies of the explosion mechanism itself and on the related physical
processes, including the physics of turbulent nuclear combustion in degenerate
stars, we also discuss observational constraints.Comment: 38 pages, 4 figures, Annual Review of Astronomy and Astrophysics, in
pres
Local Optical Probe of Motion and Stress in a multilayer graphene NEMS
Nanoelectromechanical systems (NEMSs) are emerging nanoscale elements at the
crossroads between mechanics, optics and electronics, with significant
potential for actuation and sensing applications. The reduction of dimensions
compared to their micronic counterparts brings new effects including
sensitivity to very low mass, resonant frequencies in the radiofrequency range,
mechanical non-linearities and observation of quantum mechanical effects. An
important issue of NEMS is the understanding of fundamental physical properties
conditioning dissipation mechanisms, known to limit mechanical quality factors
and to induce aging due to material degradation. There is a need for detection
methods tailored for these systems which allow probing motion and stress at the
nanometer scale. Here, we show a non-invasive local optical probe for the
quantitative measurement of motion and stress within a multilayer graphene NEMS
provided by a combination of Fizeau interferences, Raman spectroscopy and
electrostatically actuated mirror. Interferometry provides a calibrated
measurement of the motion, resulting from an actuation ranging from a
quasi-static load up to the mechanical resonance while Raman spectroscopy
allows a purely spectral detection of mechanical resonance at the nanoscale.
Such spectroscopic detection reveals the coupling between a strained
nano-resonator and the energy of an inelastically scattered photon, and thus
offers a new approach for optomechanics
The Non-Compact Weyl Equation
A non-compact version of the Weyl equation is proposed, based on the infinite
dimensional spin zero representation of the sl_2 algebra. Solutions of the
aforementioned equation are obtained in terms of the Kummer functions. In this
context, we discuss the ADHMN approach in order to construct the corresponding
non-compact BPS monopoles.Comment: 10 pages Latex. Extra comments and an Appendix added. To appear in
JHE
Calmodulin-like proteins localized to the conoid regulate motility and cell invasion by Toxoplasma gondii
Toxoplasma gondii contains an expanded number of calmodulin (CaM)-like proteins whose functions are poorly understood. Using a combination of CRISPR/Cas9-mediated gene editing and a plant-like auxin-induced degron (AID) system, we examined the roles of three apically localized CaMs. CaM1 and CaM2 were individually dispensable, but loss of both resulted in a synthetic lethal phenotype. CaM3 was refractory to deletion, suggesting it is essential. Consistent with this prediction auxin-induced degradation of CaM3 blocked growth. Phenotypic analysis revealed that all three CaMs contribute to parasite motility, invasion, and egress from host cells, and that they act downstream of microneme and rhoptry secretion. Super-resolution microscopy localized all three CaMs to the conoid where they overlap with myosin H (MyoH), a motor protein that is required for invasion. Biotinylation using BirA fusions with the CaMs labeled a number of apical proteins including MyoH and its light chain MLC7, suggesting they may interact. Consistent with this hypothesis, disruption of MyoH led to degradation of CaM3, or redistribution of CaM1 and CaM2. Collectively, our findings suggest these CaMs may interact with MyoH to control motility and cell invasion
Bioinformatics : indispensable, yet hidden in plain sight?
BACKGROUND: Bioinformatics has multitudinous identities, organisational alignments and disciplinary links. This variety allows bioinformaticians and bioinformatic work to contribute to much (if not most) of life science research in profound ways. The multitude of bioinformatic work also translates into a multitude of credit-distribution arrangements, apparently dismissing that work. RESULTS: We report on the epistemic and social arrangements that characterise the relationship between bioinformatics and life science. We describe, in sociological terms, the character, power and future of bioinformatic work. The character of bioinformatic work is such that its cultural, institutional and technical structures allow for it to be black-boxed easily. The result is that bioinformatic expertise and contributions travel easily and quickly, yet remain largely uncredited. The power of bioinformatic work is shaped by its dependency on life science work, which combined with the black-boxed character of bioinformatic expertise further contributes to situating bioinformatics on the periphery of the life sciences. Finally, the imagined futures of bioinformatic work suggest that bioinformatics will become ever more indispensable without necessarily becoming more visible, forcing bioinformaticians into difficult professional and career choices. CONCLUSIONS: Bioinformatic expertise and labour is epistemically central but often institutionally peripheral. In part, this is a result of the ways in which the character, power distribution and potential futures of bioinformatics are constituted. However, alternative paths can be imagined
Nitrogen transfer from forage legumes to nine neighbouring plants in a multi-species grassland
Legumes play a crucial role in nitrogen supply to grass-legume mixtures for ruminant fodder. To quantify N transfer from legumes to neighbouring plants in multi-species grasslands we established a grass-legume-herb mixture on a loamy-sandy site in Denmark. White clover (Trifolium repens L.), red clover (Trifolium pratense L.) and lucerne (Medicago sativa L.) were leaf-labelled with 15N enriched urea during one growing season. N transfer to grasses
(Lolium perenne L. and xfestulolium), white clover, red clover, lucerne, birdsfoot trefoil (Lotus corniculatus
L.), chicory (Cichorium intybus L.), plantain (Plantago
lanceolata L.), salad burnet (Sanguisorba minor L.)and caraway (Carum carvi L.) was assessed. Neighbouring plants contained greater amounts of N derived from white clover (4.8 gm-2) compared with red clover (2.2 gm-2) and lucerne (1.1 gm-2). Grasses having fibrous roots received greater amounts of N from legumes than dicotyledonous plants which generally have taproots. Slurry application mainly increased N transfer from legumes to grasses. During the growing season the three legumes transferred approximately 40 kg N ha-1 to neighbouring plants. Below-ground N transfer from legumes to neighbouring plants differed among nitrogen donors and nitrogen receivers and may depend on root characteristics and regrowth strategies of plant species in the multi-species grassland
Mechanical Strength of 17 134 Model Proteins and Cysteine Slipknots
A new theoretical survey of proteins' resistance to constant speed stretching
is performed for a set of 17 134 proteins as described by a structure-based
model. The proteins selected have no gaps in their structure determination and
consist of no more than 250 amino acids. Our previous studies have dealt with
7510 proteins of no more than 150 amino acids. The proteins are ranked
according to the strength of the resistance. Most of the predicted top-strength
proteins have not yet been studied experimentally. Architectures and folds
which are likely to yield large forces are identified. New types of potent
force clamps are discovered. They involve disulphide bridges and, in
particular, cysteine slipknots. An effective energy parameter of the model is
estimated by comparing the theoretical data on characteristic forces to the
corresponding experimental values combined with an extrapolation of the
theoretical data to the experimental pulling speeds. These studies provide
guidance for future experiments on single molecule manipulation and should lead
to selection of proteins for applications. A new class of proteins, involving
cystein slipknots, is identified as one that is expected to lead to the
strongest force clamps known. This class is characterized through molecular
dynamics simulations.Comment: 40 pages, 13 PostScript figure
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