579 research outputs found
Harvesting the promising fruits of genomics: Applying genome sequencing technologies to crop breeding
Next generation sequencing (NGS) technologies are being used to generate whole genome sequences for a wide range of crop species. When combined with precise phenotyping methods, these technologies provide a powerful and rapid tool for identifying the genetic basis of agriculturally important traits and for predicting the breeding value of individuals in a plant breeding population. Here we summarize current trends and future prospects for utilizing NGS-based technologies to develop crops with improved trait performance and increase the efficiency of modern plant breeding. It is our hope that the application of NGS technologies to plant breeding will help us to meet the challenge of feeding a growing world population
Robust Vehicle Detection and Distance Estimation Under Challenging Lighting Conditions
Avoiding high computational costs and calibration issues involved in stereo-vision-based algorithms, this paper proposes real-time monocular-vision-based techniques for simultaneous vehicle detection and inter-vehicle distance estimation, in which the performance and robustness of the system remain competitive, even for highly challenging benchmark datasets. This paper develops a collision warning system by detecting vehicles ahead and, by identifying safety distances to assist a distracted driver, prior to occurrence of an imminent crash. We introduce adaptive global Haar-like features for vehicle detection, tail-light segmentation, virtual symmetry detection, intervehicle distance estimation, as well as an efficient single-sensor multifeature fusion technique to enhance the accuracy and robustness of our algorithm. The proposed algorithm is able to detect vehicles ahead at both day or night and also for short- and long-range distances. Experimental results under various weather and lighting conditions (including sunny, rainy, foggy, or snowy) show that the proposed algorithm outperforms state-of-the-art algorithms
Preserving Secrecy Under Refinement
We propose a general framework of secrecy and preservation of secrecy for labeled transition systems. Our definition of secrecy is parameterized by the distinguishing power of the observer, the properties to be kept secret, and the executions of interest, and captures a multitude of definitions in the literature. We define a notion of secrecy preserving refinement between systems by strengthening the classical trace-based refinement so that the implementation leaks a secret only when the specification also leaks it. We show that secrecy is in general not definable in µ-calculus, and thus not expressible in specification logics supported by standard model-checkers. However, we develop a simulation-based proof technique for establishing secrecy preserving refinement. This result shows how existing refinement checkers can be used to show correctness of an implementation with respect to a specification
Sharper and Simpler Nonlinear Interpolants for Program Verification
Interpolation of jointly infeasible predicates plays important roles in
various program verification techniques such as invariant synthesis and CEGAR.
Intrigued by the recent result by Dai et al.\ that combines real algebraic
geometry and SDP optimization in synthesis of polynomial interpolants, the
current paper contributes its enhancement that yields sharper and simpler
interpolants. The enhancement is made possible by: theoretical observations in
real algebraic geometry; and our continued fraction-based algorithm that rounds
off (potentially erroneous) numerical solutions of SDP solvers. Experiment
results support our tool's effectiveness; we also demonstrate the benefit of
sharp and simple interpolants in program verification examples
Development of genomic simple sequence repeat markers for yam
Yam (
Dioscorea
spp.) is a major staple crop
widely cultivated for its starchy tubers. To date,
very few marker resources are publicly avail
-
able as tools for genetic and genomic studies of
this economically important crop. In this study,
90 simple sequence repeat (SSR) markers were
developed from an enriched genomic library of
yellow Guinea yam (
D. cayenensis
Lam.). Cross-
amplification revealed that 85 (94.4%) and 51
(56.7%) of these SSRs could be successfully
transferred to the two major cultivated species
of
D. rotundata
Poir. and
D. alata
L., respec
-
tively. Polymorphisms in 30 markers selected
on the basis of reliability and reproducibility of
DNA bands were evaluated using a panel of 12
D. cayenensis
, 48
D. rotundata
, and 48
D. alata
accessions. Accordingly, number of alleles
per locus ranged from 2 to 8 in
D. cayenensis
(mean = 3.9), 3 to 30 in
D. rotundata
(mean =
13.9), and 2 to 22 in
D. alata
(mean = 12.1). The
average observed and expected heterozygosi
-
ties were 0.156 and 0.634 (
D. cayenensis
), 0.326
and 0.853 (
D. rotundata
), and 0.247 and 0.836
(
D. alata
), respectively. Clustering based on six
SSRs that were polymorphic in at least four of
the five cultivated
Dioscorea
species studied,
including
D. cayenensis
,
D. rotundata
,
D. alata
,
D. dumetorum
(Kunth) Pax., and
D. bulbifera
L.,
detected groups consistent with the phyloge
-
netic relationships of the species except for
D.
dumetorum
. These new SSR markers are invalu
-
able resources for applications such as genetic
diversity analysis and marker-assisted breedingYam (
Dioscorea
spp.) is a major staple crop
widely cultivated for its starchy tubers. To date,
very few marker resources are publicly avail
-
able as tools for genetic and genomic studies of
this economically important crop. In this study,
90 simple sequence repeat (SSR) markers were
developed from an enriched genomic library of
yellow Guinea yam (
D. cayenensis
Lam.). Cross-
amplification revealed that 85 (94.4%) and 51
(56.7%) of these SSRs could be successfully
transferred to the two major cultivated species
of
D. rotundata
Poir. and
D. alata
L., respec
-
tively. Polymorphisms in 30 markers selected
on the basis of reliability and reproducibility of
DNA bands were evaluated using a panel of 12
D. cayenensis
, 48
D. rotundata
, and 48
D. alata
accessions. Accordingly, number of alleles
per locus ranged from 2 to 8 in
D. cayenensis
(mean = 3.9), 3 to 30 in
D. rotundata
(mean =
13.9), and 2 to 22 in
D. alata
(mean = 12.1). The
average observed and expected heterozygosi
-
ties were 0.156 and 0.634 (
D. cayenensis
), 0.326
and 0.853 (
D. rotundata
), and 0.247 and 0.836
(
D. alata
), respectively. Clustering based on six
SSRs that were polymorphic in at least four of
the five cultivated
Dioscorea
species studied,
including
D. cayenensis
,
D. rotundata
,
D. alata
,
D. dumetorum
(Kunth) Pax., and
D. bulbifera
L.,
detected groups consistent with the phyloge
-
netic relationships of the species except for
D.
dumetorum
. These new SSR markers are invalu
-
able resources for applications such as genetic
diversity analysis and marker-assisted breedin
Analysis of the need for biotechnology research on cassava, yam, and plantain
Cassava, yam, and plantain are staple food crops essential to food security in the humid and Sub-humid tropics of Africa. However, these crops have long growth cycles, high perishability and slow multiplication rates of propagation materials, and they are subject to a number of biological stresses. These stresses include diseases, insects, mites, nematodes, and weeds. There are gaps in our knowledge, especially in the area of genetics, which influence the pace of breeding. Intensification of research is needed in cytogenetics, molecular genetics, in vitro culture, cry op reservation, and disease diagnosis
Resonant Inelastic X-ray Scattering Studies of Elementary Excitations
In the past decade, Resonant Inelastic X-ray Scattering (RIXS) has made
remarkable progress as a spectroscopic technique. This is a direct result of
the availability of high-brilliance synchrotron X-ray radiation sources and of
advanced photon detection instrumentation. The technique's unique capability to
probe elementary excitations in complex materials by measuring their energy-,
momentum-, and polarization-dependence has brought RIXS to the forefront of
experimental photon science. We review both the experimental and theoretical
RIXS investigations of the past decade, focusing on those determining the
low-energy charge, spin, orbital and lattice excitations of solids. We present
the fundamentals of RIXS as an experimental method and then review the
theoretical state of affairs, its recent developments and discuss the different
(approximate) methods to compute the dynamical RIXS response. The last decade's
body of experimental RIXS data and its interpretation is surveyed, with an
emphasis on RIXS studies of correlated electron systems, especially transition
metal compounds. Finally, we discuss the promise that RIXS holds for the near
future, particularly in view of the advent of x-ray laser photon sources.Comment: Review, 67 pages, 44 figure
Ferredoxin containing bacteriocins suggest a novel mechanism of iron uptake in <i>Pectobacterium spp</i>
In order to kill competing strains of the same or closely related bacterial species, many bacteria produce potent narrow-spectrum protein antibiotics known as bacteriocins. Two sequenced strains of the phytopathogenic bacterium <i>Pectobacterium carotovorum</i> carry genes encoding putative bacteriocins which have seemingly evolved through a recombination event to encode proteins containing an N-terminal domain with extensive similarity to a [2Fe-2S] plant ferredoxin and a C-terminal colicin M-like catalytic domain. In this work, we show that these genes encode active bacteriocins, pectocin M1 and M2, which target strains of <i>Pectobacterium carotovorum</i> and <i>Pectobacterium atrosepticum</i> with increased potency under iron limiting conditions. The activity of pectocin M1 and M2 can be inhibited by the addition of spinach ferredoxin, indicating that the ferredoxin domain of these proteins acts as a receptor binding domain. This effect is not observed with the mammalian ferredoxin protein adrenodoxin, indicating that <i>Pectobacterium spp.</i> carries a specific receptor for plant ferredoxins and that these plant pathogens may acquire iron from the host through the uptake of ferredoxin. In further support of this hypothesis we show that the growth of strains of <i>Pectobacterium carotovorum</i> and <i>atrosepticum</i> that are not sensitive to the cytotoxic effects of pectocin M1 is enhanced in the presence of pectocin M1 and M2 under iron limiting conditions. A similar growth enhancement under iron limiting conditions is observed with spinach ferrodoxin, but not with adrenodoxin. Our data indicate that pectocin M1 and M2 have evolved to parasitise an existing iron uptake pathway by using a ferredoxin-containing receptor binding domain as a Trojan horse to gain entry into susceptible cells
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