397 research outputs found
ANALYSIS OF GENOMIC DATA IN RUMINANT SPECIES FOR PARENTAGE, PRODUCT TRACING AND POPULATION STRUCTURE STUDIES
The availability of genomic and high performance computing
technologies gave access to new approaches and methods to exploit the
high number of genetic information provided, even in livestock species.
These new tools can be used to unveil the relationships between different
populations or individuals, to understand the genetic background of breeds,
to define the genetic architecture of phenotypes or pathologies and to
detect selection signatures that shaped the cattle, sheep and goat reared
today.
In this context, these technologies may provide breeders and
breeders\u2019 associations with new tools that may be used in livestock
management. In fact, the estimation of genomic parentage among
individuals can help in defining the least related animals in case of identical
values of additive parentage and detect errors in pedigree declarations as
well. Moreover, since DNA is immutable within animal life but very
polymorphic between individuals, these tools may be of help in the
definition of the breed or the individual of origin, improving food safety.
In this thesis, I faced the complexity of genomic data in ruminant
species, focusing in particular on goats. I reported three studies with distinct
aims: i) study the signatures of selection in 369 animals of 16 Italian
populations, and then focusing on the Valdostana goat breed which
presents a breed-specific broad signature of selection in chromosome 7; ii)
define a new method to develop panels of SNPs for parentage assessment
that could be applied on species with unreliable genomic assembly; and iii)
study the selection signatures in 929 animals of 41 Pakistani and Italian goat
populations associated with a specific pigmentation pattern, the roan,
detecting a candidate gene important in understanding the coat color
genetics in goats and which could be also used as a marker for traceability
of breeds that carry this peculiar phenotypic pattern
Extremal functions for the anisotropic Sobolev inequalities
The existence of multiple nonnegative solutions to the anisotropic critical
problem - \sum_{i=1}^{N} \frac{\partial}{\partial x_i} (| \frac{\partial
u}{\partial x_i} |^{p_i-2} \frac{\partial u}{\partial x_i}) = |u|^{p^*-2} u
{in} \mathbb{R}^N is proved in suitable anisotropic Sobolev spaces. The
solutions correspond to extremal functions of a certain best Sobolev constant.
The main tool in our study is an adaptation of the well-known
concentration-compactness lemma of P.-L. Lions to anisotropic operators.
Futhermore, we show that the set of nontrival solutions \calS is included in
and is located outside of a ball of radius in
Asymptotic behaviour of a semilinear elliptic system with a large exponent
Consider the problem \begin{eqnarray*} -\Delta u &=& v^{\frac 2{N-2}},\quad
v>0\quad {in}\quad \Omega, -\Delta v &=& u^{p},\:\:\:\quad u>0\quad {in}\quad
\Omega, u&=&v\:\:=\:\:0 \quad {on}\quad \partial \Omega, \end{eqnarray*} where
is a bounded convex domain in with smooth boundary
We study the asymptotic behaviour of the least energy
solutions of this system as We show that the solution remain
bounded for large and have one or two peaks away form the boundary. When
one peak occurs we characterize its location.Comment: 16 pages, submmited for publicatio
AmelHap: Leveraging drone whole-genome sequence data to create a honey bee HapMap
Honey bee, Apis mellifera, drones are typically haploid, developing from an unfertilized egg, inheriting only their queen’s alleles and none from the many drones she mated with. Thus the ordered combination or ‘phase’ of alleles is known, making drones a valuable haplotype resource. We collated whole-genome sequence data for 1,407 drones, including 45 newly sequenced Scottish drones, collectively representing 19 countries, 8 subspecies and various hybrids. Following alignment to Amel_HAv3.1, variant calling and quality filtering, we retained 17.4 M high quality variants across 1,328 samples with a genotyping rate of 98.7%. We demonstrate the utility of this haplotype resource, AmelHap, for genotype imputation, returning >95% concordance when up to 61% of data is missing in haploids and up to 12% of data is missing in diploids. AmelHap will serve as a useful resource for the community for imputation from low-depth sequencing or SNP chip data, accurate phasing of diploids for association studies, and as a comprehensive reference panel for population genetic and evolutionary analyses.For the purpose of open access, the author has applied a Creative Commons Attribution (CC BY) licence to any Author Accepted Manuscript version arising from this submission. This work was supported by a grant from the CB Dennis British Beekeepers’ Research Trust awarded to MB and DW, and through strategic investment funding to the Roslin Institute from the Biotechnology and Biological Sciences Research Council (BBS/E/D/30002276). MP was supported by a Basque Government grant (IT1233-19)
Detection of selection signatures for ear carriage in Maltese goat breed
Selection and breeding practices in goats have led to the fixation of several traits. This is probably due to the standardization of several peculiar morphological characteristics that have always been one of the major exclusion criteria of individuals from selection. Among these, ear carriage is one of the most ancient and considered a signature of domestication in several species, such as the dog, pig, sheep and goat (Boyko et al., 2010). The availability of improved genomic analyses tools for goats may provide useful information on genes involved in this trait. By studying, for example, the homozygosity decay of haplotypes (contiguous length of alleles) such information can be detected. In the current study, we focused on the Maltese goat, a breed showing floppy ears, in comparison with other Italian breeds using a goat medium density SNP chip (Nicoloso et al., 2015). A total 48,767 SNP markers for 369 animals belonging to 16 breeds or populations were analyzed. Genotypes were imputed within population excluding markers without known position on the current genome assembly (ARS1, Bickhart et al., 2017). Population analysis using MDS, ADMIXTURE and fastSTRUCTURE confirmed the good differentiation among the populations. Integrated Haplotype Score (iHS, Sabeti et al., 2007) was performed for each population, comparing the regions detected on the Maltese breed with the others considered to detect genes that may be involved into shaping ear morphology. These results may provide new insights into ear carriage phenotype by detecting genes that play a pivotal role in shaping the goat phenotypic diversity
Ground States for Diffusion Dominated Free Energies with Logarithmic Interaction
Replacing linear diffusion by a degenerate diffusion of porous medium type is
known to regularize the classical two-dimensional parabolic-elliptic
Keller-Segel model. The implications of nonlinear diffusion are that solutions
exist globally and are uniformly bounded in time. We analyse the stationary
case showing the existence of a unique, up to translation, global minimizer of
the associated free energy. Furthermore, we prove that this global minimizer is
a radially decreasing compactly supported continuous density function which is
smooth inside its support, and it is characterized as the unique compactly
supported stationary state of the evolution model. This unique profile is the
clear candidate to describe the long time asymptotics of the diffusion
dominated classical Keller-Segel model for general initial data.Comment: 30 pages, 2 figure
Ground state solutions to the nonlinear Schrodinger-Maxwell equations
We prove the existence of ground state solutions for the nonlinear
Schrodinger-Maxwell equations.Comment: 27 page
Sharp Global Bounds for the Hessian on Pseudo-Hermitian Manifolds
We find sharp bounds for the norm inequality on a Pseudo-hermitian manifold,
where the L^2 norm of all second derivatives of the function involving
horizontal derivatives is controlled by the L^2 norm of the sub-Laplacian.
Perturbation allows us to get a-priori bounds for solutions to sub-elliptic PDE
in non-divergence form with bounded measurable coefficients. The method of
proof is through a Bochner technique. The Heisenberg group is seen to be en
extremal manifold for our inequality in the class of manifolds whose Ricci
curvature is non-negative.Comment: 13 page
Short-Term Bisphosphonate Therapy Could Ameliorate Osteonecrosis: A Complication in Childhood Hematologic Malignancies
Osteonecrosis (ON) is a critical complication in the treatment of childhood leukemia and lymphoma. It
particularly affects survivors of acute lymphoblastic leukemia and non-Hodgkin lymphoma reflecting the
cumulative exposure to glucocorticosteroid therapy. ON is often multiarticular and bilateral, specially
affecting weight-bearing joints. A conventional approach suggests a surgical intervention even if
pharmacological options have also recently been investigated. We reported two cases of long time steroid-treated patients who underwent Bone Marrow Transplantation (BMT) for hematological disease. Both
patients developed femoral head osteonecrosis (ON) that was diagnosed by magnetic resonance imaging
(MRI) and the ON was also accompanied with pain and a limp. Despite of the conventional strategies of
therapy, we successfully started a short-term treatment with bisphosphonates in order to decrease the pain
and the risk of fracture
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