243 research outputs found
Single-cell genomic analysis in plants
Individual cells in an organism are variable, which strongly impacts cellular processes. Advances in sequencing technologies have enabled single-cell genomic analysis to become widespread, addressing shortcomings of analyses conducted on populations of bulk cells. While the field of single-cell plant genomics is in its infancy, there is great potential to gain insights into cell lineage and functional cell types to help understand complex cellular interactions in plants. In this review, we discuss current approaches for single-cell plant genomic analysis, with a focus on single-cell isolation, DNA amplification, next-generation sequencing, and bioinformatics analysis. We outline the technical challenges of analysing material from a single plant cell, and then examine applications of single-cell genomics and the integration of this approach with genome editing. Finally, we indicate future directions we expect in the rapidly developing field of plant single-cell genomic analysis
Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding
The gene content of plants varies between individuals of the same species due to gene presence/absence variation, and selection can alter the frequency of specific genes in a population. Selection during domestication and breeding will modify the genomic landscape, though the nature of these modifications is only understood for specific genes or on a more general level (e.g., by a loss of genetic diversity). Here we have assembled and analyzed a soybean (Glycine spp.) pangenome representing more than 1,000 soybean accessions derived from the USDA Soybean Germplasm Collection, including both wild and cultivated lineages, to assess genomewide changes in gene and allele frequency during domestication and breeding. We identified 3,765 genes that are absent from the Lee reference genome assembly and assessed the presence/absence of all genes across this population. In addition to a loss of genetic diversity, we found a significant reduction in the average number of protein-coding genes per individual during domestication and subsequent breeding, though with some genes and allelic variants increasing in frequency associated with selection for agronomic traits. This analysis provides a genomic perspective of domestication and breeding in this important oilseed crop
Ferromagnetism and Canted Spin Phase in AlAs/GaMnAs Single Quantum Wells: Monte Carlo Simulation
The magnetic order resulting from a confinement-adapted
Ruderman-Kittel-Kasuya-Yosida indirect exchange between magnetic moments in the
metallic phase of a AlAs/Ga(1-x)Mn(x)As quantum well is studied by Monte Carlo
simulation. This coupling mechanism involves magnetic moments and carriers
(holes), both coming from the same Mn(2+) ions. It leads to a paramagnetic, a
ferromagnetic, or a canted spin phase, depending on the carrier concentration,
and on the magnetic layer width. It is shown that high transition temperatures
may be obtained.Comment: 7 figure
Global agricultural intensification during climate change: A role for genomics
Summary: Agriculture is now facing the 'perfect storm' of climate change, increasing costs of fertilizer and rising food demands from a larger and wealthier human population. These factors point to a global food deficit unless the efficiency and resilience of crop production is increased. The intensification of agriculture has focused on improving production under optimized conditions, with significant agronomic inputs. Furthermore, the intensive cultivation of a limited number of crops has drastically narrowed the number of plant species humans rely on. A new agricultural paradigm is required, reducing dependence on high inputs and increasing crop diversity, yield stability and environmental resilience. Genomics offers unprecedented opportunities to increase crop yield, quality and stability of production through advanced breeding strategies, enhancing the resilience of major crops to climate variability, and increasing the productivity and range of minor crops to diversify the food supply. Here we review the state of the art of genomic-assisted breeding for the most important staples that feed the world, and how to use and adapt such genomic tools to accelerate development of both major and minor crops with desired traits that enhance adaptation to, or mitigate the effects of climate change. >
The Superconducting TESLA Cavities
The conceptional design of the proposed linear electron-positron collider
TESLA is based on 9-cell 1.3 GHz superconducting niobium cavities with an
accelerating gradient of Eacc >= 25 MV/m at a quality factor Q0 > 5E+9. The
design goal for the cavities of the TESLA Test Facility (TTF) linac was set to
the more moderate value of Eacc >= 15 MV/m. In a first series of 27
industrially produced TTF cavities the average gradient at Q0 = 5E+9 was
measured to be 20.1 +- 6.2 MV/m, excluding a few cavities suffering from
serious fabrication or material defects. In the second production of 24 TTF
cavities additional quality control measures were introduced, in particular an
eddy-current scan to eliminate niobium sheets with foreign material inclusions
and stringent prescriptions for carrying out the electron-beam welds. The
average gradient of these cavities at Q0 = 5E+9 amounts to 25.0 +- 3.2 MV/m
with the exception of one cavity suffering from a weld defect. Hence only a
moderate improvement in production and preparation techniques will be needed to
meet the ambitious TESLA goal with an adequate safety margin. In this paper we
present a detailed description of the design, fabrication and preparation of
the TESLA Test Facility cavities and their associated components and report on
cavity performance in test cryostats and with electron beam in the TTF linac.
The ongoing R&D towards higher gradients is briefly addressed.Comment: 45 pages (Latex), 39 figures (Encapsulated Postscript), 53 Author
Application of genomicsassisted breeding for generation of climate resilient crops: progress and prospects
CCAFS Climat
A measurement of the W boson mass using large rapidity electrons
We present a measurement of the W boson mass using data collected by the D0
experiment at the Fermilab Tevatron during 1994--1995. We identify W bosons by
their decays to e-nu final states where the electron is detected in a forward
calorimeter. We extract the W boson mass, Mw, by fitting the transverse mass
and transverse electron and neutrino momentum spectra from a sample of 11,089 W
-> e nu decay candidates. We use a sample of 1,687 dielectron events, mostly
due to Z -> ee decays, to constrain our model of the detector response. Using
the forward calorimeter data, we measure Mw = 80.691 +- 0.227 GeV. Combining
the forward calorimeter measurements with our previously published central
calorimeter results, we obtain Mw = 80.482 +- 0.091 GeV
Measurement of the p-pbar -> Wgamma + X cross section at sqrt(s) = 1.96 TeV and WWgamma anomalous coupling limits
The WWgamma triple gauge boson coupling parameters are studied using p-pbar
-> l nu gamma + X (l = e,mu) events at sqrt(s) = 1.96 TeV. The data were
collected with the DO detector from an integrated luminosity of 162 pb^{-1}
delivered by the Fermilab Tevatron Collider. The cross section times branching
fraction for p-pbar -> W(gamma) + X -> l nu gamma + X with E_T^{gamma} > 8 GeV
and Delta R_{l gamma} > 0.7 is 14.8 +/- 1.6 (stat) +/- 1.0 (syst) +/- 1.0 (lum)
pb. The one-dimensional 95% confidence level limits on anomalous couplings are
-0.88 < Delta kappa_{gamma} < 0.96 and -0.20 < lambda_{gamma} < 0.20.Comment: Submitted to Phys. Rev. D Rapid Communication
Measurement of the ttbar Production Cross Section in ppbar Collisions at sqrt{s} = 1.96 TeV using Kinematic Characteristics of Lepton + Jets Events
We present a measurement of the top quark pair ttbar production cross section
in ppbar collisions at a center-of-mass energy of 1.96 TeV using 230 pb**{-1}
of data collected by the DO detector at the Fermilab Tevatron Collider. We
select events with one charged lepton (electron or muon), large missing
transverse energy, and at least four jets, and extract the ttbar content of the
sample based on the kinematic characteristics of the events. For a top quark
mass of 175 GeV, we measure sigma(ttbar) = 6.7 {+1.4-1.3} (stat) {+1.6- 1.1}
(syst) +/-0.4 (lumi) pb, in good agreement with the standard model prediction.Comment: submitted to Phys.Rev.Let
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