191 research outputs found
Three--body Correlation Effects on the Spin Dynamics of Double--Exchange Ferromagnets
We present a variational calculation of the spin wave excitation spectrum of
double--exchange ferromagnets in different dimensions. Our theory recovers the
Random Phase approximation and 1/S expansion results as limiting cases and can
be used to study the intermediate exchange coupling and electron concentration
regime relevant to the manganites. In particular, we treat exactly the long
range three--body correlations between a Fermi sea electron--hole pair and a
magnon excitation and show that they strongly affect the spin dynamics in the
parameter range relevant to experiments in the manganites. The manifestations
of these correlations are many-fold. We demonstrate that they significantly
change the ferromagnetic phase boundary. In addition to a decrease in the
magnon stiffness, we obtain an instability of the ferromagnetic state against
spin wave excitations close to the Brillouin zone boundary.Within a range of
intermediate concentrations, we find a strong softening of the spin wave
dispersion as compared to the Heisenberg ferromagnet with the same stiffness,
which changes into hardening for other concentrations. We discuss the relevance
of these results to experiments in colossal magnetoresistance ferromagnets.Comment: 14 pages, 11 figures, published in Phys. Rev. B (1 figure added,
references added
Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling
Sparidae (Teleostei: Spariformes) are a family of fish constituted by approximately 150 species with high popularity and commercial value, such as porgies and seabreams. Although the phylogeny of this family has been investigated multiple times, its position among other teleost groups remains ambiguous. Most studies have used a single or few genes to decipher the phylogenetic relationships of sparids. Here, we conducted a thorough phylogenomic analysis using five recently available Sparidae gene-sets and 26 high-quality, genome-predicted teleost proteomes. Our analysis suggested that Tetraodontiformes (puffer fish, sunfish) are the closest relatives to sparids than all other groups used. By analytically comparing this result to our own previous contradicting finding, we show that this discordance is not due to different orthology assignment algorithms; on the contrary, we prove that it is caused by the increased taxon sampling of the present study, outlining the great importance of this aspect in phylogenomic analyses in general
Muscle and liver transcriptome characterization and genetic marker discovery in the farmed meagre, Argyrosomus regius
Meagre (Argyrosomus regius), a teleost fish of the family Sciaenidae, is part of a group of marine fish species considered new for Mediterranean aquaculture representing the larger fish cultured in the region. Meagre aquaculture started ~ 25 years ago in West Mediterranean, and the supply of juveniles has been dominated by few hatcheries. This fact has raised concerns on possible inbreeding, urging the need for genetic information on the species and for an assessment of the polymorphisms found in the genome. To that end we characterized the muscle and liver transcriptome of a pool of meagre individuals, from different families and phenotypic size, to obtain a backbone that can support future studies regarding physiology, immunology and genetics of the species. The assembled transcripts were assigned to a wide range of biological processes including growth, reproduction, metabolism, development, stress and behavior. Then, to infer its genetic diversity and provide a catalogue of markers for future use, we scanned the reconstructed transcripts for polymorphic genetic markers. Our search revealed a total of 42,933 high quality SNP and 20,581 STR markers. We found a relatively low rate of polymorphism in the transcriptome that may indicate that inbreeding has taken place. This study has led to a catalogue of genetic markers at the expressed part of the genome and has set the ground for understanding growth and other traits of interest in meagre.info:eu-repo/semantics/acceptedVersio
Cell Patterning via Laser Micro/nano Structured Silicon Surfaces
The surface topography of biomaterials can have an important impact on cellular adhesion, growth and proliferation. Apart from the overall roughness, the detailed morphological features, at all length scales, significantly affect the cell-biomaterial interactions in a plethora of applications including structural implants, tissue engineering scaffolds and biosensors. In this study, we present a simple, one-step direct laser patterning technique to fabricate nanoripples and dual-rough hierarchical micro/nano structures to control SW10 cell attachment and migration. It is shown that, depending on the laser processing conditions, distinct cell-philic or cell-repellant patterned areas can be attained with a desired motif. We envisage that our technique could enable spatial patterning of cells in a controllable manner, giving rise to advanced capabilities in cell biology research
Linkage mapping, comparative genome analysis, and QTL detection for growth in a non-model teleost, the meagre Argyrosomus regius, using ddRAD sequencing
Meagre (Argyrosomus regius), is a benthopelagic species rapidly emerging in aquaculture, due to its low food to biomass conversion rate, good fillet yield and ease of production. Tracing a species genomic background along with describing the genetic basis of important traits can greatly influence both conservation strategies and production perspectives. In this study, we employed ddRAD sequencing of 266 fish from six F1 meagre families, to construct a high-density genetic map comprising 4529 polymorphic SNP markers. The QTL mapping analysis provided a genomic appreciation for the weight trait identifying a statistically significant QTL on linkage group 15 (LG15). The comparative genomics analysis with six teleost species revealed an evolutionarily conserved karyotype structure. The synteny observed, verified the already well-known fusion events of the three-spine stickleback genome, reinforced the evidence of reduced evolutionary distance of Sciaenids with the Sparidae family, reflected the evolutionary proximity with Dicentrarchus labrax, traced several putative chromosomal rearrangements and a prominent putative fusion event in meagre’s LG17. This study presents novel elements concerning the genome evolutionary history of a non-model teleost species recently adopted in aquaculture, starts to unravel the genetic basis of the species growth-related traits, and provides a high-density genetic map as a tool that can help to further establish meagre as a valuable resource for research and production.info:eu-repo/semantics/publishedVersio
Mineralisation of surfactants using ultrasound and the Advanced Fenton Process
The destruction of the surfactants, sodium dodecylbenzene sulfonate (DBS) and dodecyl pyridinium chloride (DPC), using an advanced oxidation process is described. The use of zero valent iron (ZVI) and hydrogen peroxide at pH = 2.5 (the advanced Fenton process), with and without, the application of 20 kHz ultrasound leads to extensive mineralisation of both materials as determined by total organic carbon (TOC)measurements. For DBS, merely stirring with ZVI and H2O2 at 20°C leads to a 51% decrease in TOC, but using 20 kHz ultrasound at 40°C, maintaining the pH at 2.5 throughout and adding extra amounts of ZVI and H2O2 during the degradation, then the extent of mineralisation of DBS is substantially increased to 93%. A similar result is seen for DPC where virtually no degradation occurs at 20°C, but if extra amounts of both ZVI and hydrogen peroxide are introduced during the reaction at 40°C and the pH is maintained at 2.5, then an 87% mineralisation of DPC is obtained. The slow latent remediation of both surfactants and the mechanism of degradation are also discussed
Evaluation of the chemical and physical changes induced by KrF laser irradiation of tempera paints
A systematic study of the chemical and physical changes induced by exposure to UV (248 nm) excimer laser light of unvarnished tempera paint samples has been undertaken as a part of the research activities included in the European project "Advanced workstation for controlled laser cleaning of artworks". The direct exposure of the paint to the UV laser configures the worst case scenario of laser cleaning, as a thin protective layer of varnish is normally left to minimize the dose of UV radiation that reaches the paint surface. However, in the practice of laser cleaning, there is a need to characterize and quantify the possible effects of direct UV laser irradiation of unvarnished paints. To this purpose, a broad range of techniques have been used including profilometry, colorimetry, optical and vibrational spectroscopic techniques, such as laser-induced fluorescence (LIF), laser-induced breakdown spectroscopy (LIBS), Fourier transform Raman (FTR) and infrared (FTIR), and analytical mass spectrometric techniques, like direct-temperature-resolved mass spectrometry (DTMS) and laser desorption and ionization time of flight mass spectrometry (LDI-TOF). Integration of the results obtained by these techniques allowed the investigation of the nature and degree of change of the irradiated paint systems. These were observed to strongly depend on the type of paint system. © 2003 Éditions scientifiques et médicales Elsevier SAS. All rights reserved
Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes)
Recent development of deep sequencing technologies has facilitated de novo genome sequencing projects, now conducted even by individual laboratories. However, this will yield more and more genome sequences that are not well assembled, and will hinder thorough annotation when no closely related reference genome is available. One of the challenging issues is the identification of protein-coding sequences split into multiple unassembled genomic segments, which can confound orthology assignment and various laboratory experiments requiring the identification of individual genes. In this study, using the genome of a cartilaginous fish, Callorhinchus milii, as test case, we performed gene prediction using a model specifically trained for this genome. We implemented an algorithm, designated ESPRIT, to identify possible linkages between multiple protein-coding portions derived from a single genomic locus split into multiple unassembled genomic segments. We developed a validation framework based on an artificially fragmented human genome, improvements between early and recent mouse genome assemblies, comparison with experimentally validated sequences from GenBank, and phylogenetic analyses. Our strategy provided insights into practical solutions for efficient annotation of only partially sequenced (low-coverage) genomes. To our knowledge, our study is the first formulation of a method to link unassembled genomic segments based on proteomes of relatively distantly related species as references
Effects of salinity and drought on growth, ionic relations, compatible solutes and activation of antioxidant systems in oleander (Nerium oleander L.)
[EN] Nerium
oleander
is an
ornamental
species
of high
aesthetic
value,
grown
in arid
and
semi-
arid
regions
because
of its
drought
tolerance,
which
is also
considered
as
relatively
resistant
to salt;
yet
the
biochemical
and
molecular
mechanisms
underlying
oleander¿s
stress
toler-
ance
remain
largely
unknown.
To
investigate
these
mechanisms,
one-year-old
oleander
seedlings
were
exposed
to 15
and
30
days
of treatment
with
increasing
salt
concentratio
ns,
up
to 800
mM
NaCl,
and
to complete
withholding
of irrigation;
growth
parameters
and
bio-
chemical
markers
characteristic
of conserved
stress-response
pathways
were
then
deter-
mined
in stressed
and
control
plants.
Strong
water
deficit
and
salt
stress
both
caused
inhibition
of growth,
degradation
of photosynthetic
pigments,
a slight
(but
statistically
signifi-
cant)
increase
in the
leaf
levels
of specific
osmolytes,
and
induction
of oxidative
stress¿as
indicated
by
the
accumulation
of malondialdehyde
(MDA),
a reliable
oxidative
stress
marker
¿accompanied
by
increases
in the
levels
of total
phenolic
compounds
and
antioxidant
fla-
vonoids
and
in the
specific
activities
of ascorbate
peroxidase
(APX)
and
glutathione
reduc-
tase
(GR).
High
salinity,
in addition,
induced
accumulation
of Na
+
and
Cl
-
in roots
and
leaves
and
the
activation
of superoxide
dismutase
(SOD)
and
catalase
(CAT)
activities.
Apart
from
anatomical
adaptations
that
protect
oleander
from
leaf
dehydration
at moderate
levels
of
stress,
our
results
indicate
that
tolerance
of this
species
to salinity
and
water
deficit
is based
on
the
constitutive
accumulation
in leaves
of high
concentratio
ns
of soluble
carbohydrates
and,
to a lesser
extent,
of glycine
betaine,
and
in the
activation
of the
aforementioned
antiox-
idant
systems.
Moreover,
regarding
specifically
salt
stress,
mechanisms
efficiently
blocking
transport
of toxic
ions
from
the
roots
to the
aerial
parts
of the
plant
appear
to contribute
to a
large
extent
to tolerance
in
Nerium
oleanderThis work was financed by internal funds of the Polytechnic University of Valencia to Monica Boscaiu and Oscar Vicente. Dinesh Kumar’s stay in Valencia was financed by a NAMASTE fellowship from the European Union, and Mohamad Al Hassan was a recipient of an Erasmus Mundus pre-doctoral scholarship financed by the European Commission (Welcome Consortium).Kumar, D.; Al Hassan, M.; Naranjo Olivero, MA.; Agrawal, V.; Boscaiu, M.; Vicente, O. (2017). Effects of salinity and drought on growth, ionic relations, compatible solutes and activation of antioxidant systems in oleander (Nerium oleander L.). PLoS ONE. 12(9). doi:10.1371/journal.pone.0185017Se018501712
Sequencing of the Sea Lamprey (Petromyzon marinus) Genome Provides Insights into Vertebrate Evolution
Lampreys are representatives of an ancient vertebrate lineage that diverged from our own ∼500 million years ago. By virtue of this deeply shared ancestry, the sea lamprey (P. marinus) genome is uniquely poised to provide insight into the ancestry of vertebrate genomes and the underlying principles of vertebrate biology. Here, we present the first lamprey whole-genome sequence and assembly. We note challenges faced owing to its high content of repetitive elements and GC bases, as well as the absence of broad-scale sequence information from closely related species. Analyses of the assembly indicate that two whole-genome duplications likely occurred before the divergence of ancestral lamprey and gnathostome lineages. Moreover, the results help define key evolutionary events within vertebrate lineages, including the origin of myelin-associated proteins and the development of appendages. The lamprey genome provides an important resource for reconstructing vertebrate origins and the evolutionary events that have shaped the genomes of extant organisms
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