55 research outputs found
La ionosfera: comunicare... naturalmente!
La ionosfera è la parte della media-alta atmosfera compresa tra i 60 e i 1000 km di quota. Essa è caratterizzata da una concentrazione di elettroni tale da modificare la propagazione delle onde radio che la attraversano
Effects of Surface Geology on Seismic Ground Motion Deduced from Ambient-Noise Measurements in the Town of Avellino, Irpinia Region (Italy)
The effects of surface geology on ground motion
provide an important tool in seismic hazard studies. It is well
known that the presence of soft sediments can cause amplification
of the ground motion at the surface, particularly when there is a
sharp impedance contrast at shallow depth. The town of Avellino is
located in an area characterised by high seismicity in Italy, about
30 km from the epicentre of the 23 November 1980, Irpinia
earthquake (M = 6.9). No earthquake recordings are available in
the area. The local geology is characterised by strong heterogeneity,
with impedance contrasts at depth. We present the results
from seismic noise measurements carried out in the urban area of
Avellino to evaluate the effects of local geology on the seismic
ground motion. We computed the horizontal-to-vertical (H/V)
noise spectral ratios at 16 selected sites in this urban area for which
drilling data are available within the first 40 m of depth. A Rayleigh
wave inversion technique using the peak frequencies of the
noise H/V spectral ratios is then presented for estimating Vs
models, assuming that the thicknesses of the shallow soil layers are
known. The results show a good correspondence between experimental
and theoretical peak frequencies, which are interpreted in
terms of sediment resonance. For one site, which is characterised
by a broad peak in the horizontal-to-vertical spectral-ratio curve,
simple one-dimensional modelling is not representative of the
resonance effects. Consistent variations in peak amplitudes are seen
among the sites. A site classification based on shear-wave velocity
characteristics, in terms of Vs30, cannot explain these data. The
differences observed are better correlated to the impedance contrast
between the sediments and basement. A more detailed investigation
of the physical parameters of the subsoil structure, together with
earthquake data, are desirable for future research, to confirm these
data in terms of site response
Expression of mitochondrial protein genes encoded by nuclear and mitochondrial genomes correlate with energy metabolism in dairy cattle
Background
Mutations in the mitochondrial genome have been implicated in mitochondrial disease, often characterized by impaired cellular energy metabolism. Cellular energy metabolism in mitochondria involves mitochondrial proteins (MP) from both the nuclear (NuMP) and mitochondrial (MtMP) genomes. The expression of MP genes in tissues may be tissue specific to meet varying specific energy demands across the tissues. Currently, the characteristics of MP gene expression in tissues of dairy cattle are not well understood. In this study, we profile the expression of MP genes in 29 adult and six foetal tissues in dairy cattle using RNA sequencing and gene expression analyses: particularly differential gene expression and co-expression network analyses.
Results
MP genes were differentially expressed (DE; over-expressed or under-expressed) across tissues in cattle. All 29 tissues showed DE NuMP genes in varying proportions of over-expression and under-expression. On the other hand, DE of MtMP genes was observed in < 50% of tissues and notably MtMP genes within a tissue was either all over-expressed or all under-expressed. A high proportion of NuMP (up to 60%) and MtMP (up to 100%) genes were over-expressed in tissues with expected high metabolic demand; heart, skeletal muscles and tongue, and under-expressed (up to 45% of NuMP, 77% of MtMP genes) in tissues with expected low metabolic rates; leukocytes, thymus, and lymph nodes. These tissues also invariably had the expression of all MtMP genes in the direction of dominant NuMP genes expression. The NuMP and MtMP genes were highly co-expressed across tissues and co-expression of genes in a cluster were non-random and functionally enriched for energy generation pathway. The differential gene expression and co-expression patterns were validated in independent cow and sheep datasets.
Conclusions
The results of this study support the concept that there are biological interaction of MP genes from the mitochondrial and nuclear genomes given their over-expression in tissues with high energy demand and co-expression in tissues. This highlights the importance of considering MP genes from both genomes in future studies related to mitochondrial functions and traits related to energy metabolism
Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals
peer-reviewedH.D.D., A.J.C., P.J.B. and B.J.H. would like to acknowledge the Dairy Futures
Cooperative Research Centre for funding. H.P. and R.F. acknowledge funding
from the German Federal Ministry of Education and Research (BMBF) within the
AgroClustEr ‘Synbreed—Synergistic Plant and Animal Breeding’ (grant 0315527B).
H.P., R.F., R.E. and K.-U.G. acknowledge the Arbeitsgemeinschaft Süddeutscher
Rinderzüchter, the Arbeitsgemeinschaft Österreichischer Fleckviehzüchter
and ZuchtData EDV Dienstleistungen for providing genotype data. A. Bagnato
acknowledges the European Union (EU) Collaborative Project LowInputBreeds
(grant agreement 222623) for providing Brown Swiss genotypes. Braunvieh Schweiz
is acknowledged for providing Brown Swiss phenotypes. H.P. and R.F. acknowledge
the German Holstein Association (DHV) and the Confederación de Asociaciones
de Frisona Española (CONCAFE) for sharing genotype data. H.P. was financially
supported by a postdoctoral fellowship from the Deutsche Forschungsgemeinschaft
(DFG) (grant PA 2789/1-1). D.B. and D.C.P. acknowledge funding from the
Research Stimulus Fund (11/S/112) and Science Foundation Ireland (14/IA/2576).
M.S. and F.S.S. acknowledge the Canadian Dairy Network (CDN) for providing the
Holstein genotypes. P.S. acknowledges funding from the Genome Canada project
entitled ‘Whole Genome Selection through Genome Wide Imputation in Beef Cattle’ and acknowledges WestGrid and Compute/Calcul Canada for providing
computing resources. J.F.T. was supported by the National Institute of Food and
Agriculture, US Department of Agriculture, under awards 2013-68004-20364 and
2015-67015-23183. A. Bagnato, F.P., M.D. and J.W. acknowledge EU Collaborative
Project Quantomics (grant 516 agreement 222664) for providing Brown Swiss
and Finnish Ayrshire sequences and genotypes. A.C.B. and R.F.V. acknowledge
funding from the public–private partnership ‘Breed4Food’ (code BO-22.04-011-
001-ASG-LR) and EU FP7 IRSES SEQSEL (grant 317697). A.C.B. and R.F.V.
acknowledge CRV (Arnhem, the Netherlands) for providing data on Dutch and
New Zealand Holstein and Jersey bulls.Stature is affected by many polymorphisms of small effect in humans1. In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3. Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly associated genomic regions (P < 5 × 10−8) explained at most 13.8% of the phenotypic variance. Most of these variants were noncoding, including variants that were also expression quantitative trait loci (eQTLs) and in ChIP–seq peaks. There was significant overlap in loci for stature with humans and dogs, suggesting that a set of common genes regulates body size in mammals
Ancestral alleles defined for 70 million cattle variants using a population-based likelihood ratio test
Abstract Background The study of ancestral alleles provides insights into the evolutionary history, selection, and genetic structures of a population. In cattle, ancestral alleles are widely used in genetic analyses, including the detection of signatures of selection, determination of breed ancestry, and identification of admixture. Having a comprehensive list of ancestral alleles is expected to improve the accuracy of these genetic analyses. However, the list of ancestral alleles in cattle, especially at the whole genome sequence level, is far from complete. In fact, the current largest list of ancestral alleles (~ 42 million) represents less than 28% of the total number of detected variants in cattle. To address this issue and develop a genomic resource for evolutionary studies, we determined ancestral alleles in cattle by comparing prior derived whole-genome sequence variants to an out-species group using a population-based likelihood ratio test. Results Our study determined and makes available the largest list of ancestral alleles in cattle to date (70.1 million) and includes 2.3 million on the X chromosome. There was high concordance (97.6%) of the determined ancestral alleles with those from previous studies when only high-probability ancestral alleles were considered (29.8 million positions) and another 23.5 million high-confidence ancestral alleles were novel, expanding the available reference list to improve the accuracies of genetic analyses involving ancestral alleles. The high concordance of the results with previous studies implies that our approach using genomic sequence variants and a likelihood ratio test to determine ancestral alleles is appropriate. Conclusions Considering the high concordance of ancestral alleles across studies, the ancestral alleles determined in this study including those not previously listed, particularly those with high-probability estimates, may be used for further genetic analyses with reasonable accuracy. Our approach that used predetermined variants in species and the likelihood ratio test to determine ancestral alleles is applicable to other species for which sequence level genotypes are available
Validated lncRNA from blood stranded RNA-Seq that overlap with class 3 un-stranded lncRNA.
<p>Validated lncRNA from blood stranded RNA-Seq that overlap with class 3 un-stranded lncRNA.</p
Average number of differential expressed class 3 transcripts that are either upregulated or downregulated.
<p>This graph shows us the average number of class 3 putative lncRNA transcripts that are either upregulated (blue bars) or downregulated (red bars). We see that in the tissues kidney, liver and thymus there are, on average, more upregulated transcripts, while in the tissues leg muscle, ovaries, spleen and tongue there is, on average, more downregulated transcripts.</p
Number of unknown transcripts that pass the filtering pipeline, showing no coding potential.
<p>Number of unknown transcripts that pass the filtering pipeline, showing no coding potential.</p
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