ORCID Profile
0000-0001-8876-1194
Current Organisations
Stony Brook University
,
University of Manchester
,
University of Glasgow
,
Universidad Politécnica de Madrid - Technical University of Madrid
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Publisher: Springer Science and Business Media LLC
Date: 14-09-2010
DOI: 10.1007/S00239-010-9385-4
Abstract: Early studies on the evolutionary dynamics of plant RNA viruses suggested that they may evolve more slowly than their animal counterparts, sometimes dramatically so. However, these estimates were often based on an assumption of virus-host co ergence over time-scales of many millions of years that is difficult to verify. An important ex le are viruses of the genus Tobamovirus, where the assumption of host-virus co ergence over 100 million years has led to rate estimates in the range of ~1 × 10(-8) nucleotide substitutions per site, per year. Such a low evolutionary rate is in apparent contradiction with the ability of some tobamoviruses to quickly overcome inbred genetic resistance. To resolve how rapidly molecular evolution proceeds in the tobomaviruses, we estimated rates of nucleotide substitution, times to common ancestry, and the extent of congruence between virus and host phylogenies. Using Bayesian coalescent methods applied to time-st ed sequences, we estimated mean evolutionary rates at the nucleotide and amino acid levels of between 1 × 10(-5) and 1.3 × 10(-3) substitutions per site, per year, and hence similar to those seen in a broad range of animal and plant RNA viruses. Under these rates, a conservative estimate for the time of origin of the s led tobamoviruses is within the last 100,000 years, and hence a far more recently than proposed assuming co ergence. This is supported by our cophylogeny analysis which revealed significantly discordant evolutionary histories between the tobamoviruses and the plant families they infect.
Publisher: Springer Science and Business Media LLC
Date: 02-2021
DOI: 10.1140/EPJC/S10052-020-08734-W
Abstract: Differential cross-section measurements are presented for the electroweak production of two jets in association with a Z boson. These measurements are sensitive to the vector-boson fusion production mechanism and provide a fundamental test of the gauge structure of the Standard Model. The analysis is performed using proton–proton collision data collected by ATLAS at $$\\sqrt{s}=13\\ \\hbox {TeV}$$ s = 13 TeV and with an integrated luminosity of $$139\\ \\hbox {fb}^{-1}$$ 139 fb - 1 . The differential cross-sections are measured in the $$Z\\rightarrow \\ell ^+\\ell ^-$$ Z → ℓ + ℓ - decay channel ( $$\\ell =e,\\mu $$ ℓ = e , μ ) as a function of four observables: the dijet invariant mass, the rapidity interval spanned by the two jets, the signed azimuthal angle between the two jets, and the transverse momentum of the dilepton pair. The data are corrected for the effects of detector inefficiency and resolution and are sufficiently precise to distinguish between different state-of-the-art theoretical predictions calculated using Powheg+Pythia8 , Herwig7+Vbfnlo and Sherpa 2.2. The differential cross-sections are used to search for anomalous weak-boson self-interactions using a dimension-six effective field theory. The measurement of the signed azimuthal angle between the two jets is found to be particularly sensitive to the interference between the Standard Model and dimension-six scattering litudes and provides a direct test of charge-conjugation and parity invariance in the weak-boson self-interactions.
Publisher: Springer Science and Business Media LLC
Date: 11-2017
Publisher: Springer Science and Business Media LLC
Date: 03-2018
Publisher: Springer Science and Business Media LLC
Date: 05-2017
Publisher: Wiley
Date: 05-12-2017
DOI: 10.1111/ELE.12890
Abstract: Accumulating evidence indicates that bio ersity has an important impact on parasite evolution and emergence. The vast majority of studies in this area have only considered the ersity of species within an environment as an overall measure of bio ersity, overlooking the role of genetic ersity within a particular host species. Although theoretical models propose that host genetic ersity in part shapes that of the infecting parasite population, and hence modulates the risk of parasite emergence, this effect has seldom been tested empirically. Using Rabies virus (RABV) as a model parasite, we provide evidence that greater host genetic ersity increases both parasite genetic ersity and the likelihood of a host being a donor in RABV cross-species transmission events. We conclude that host genetic ersity may be an important determinant of parasite evolution and emergence.
Publisher: Oxford University Press (OUP)
Date: 17-05-2013
Publisher: Springer Science and Business Media LLC
Date: 11-2020
DOI: 10.1140/EPJC/S10052-020-08509-3
Abstract: A search is presented for four-top-quark production using an integrated luminosity of 139 fb $$^{-1}$$ - 1 of proton–proton collision data at a centre-of-mass energy of $$13~\\text {TeV}$$ 13 TeV collected by the ATLAS detector at the LHC. Events are selected if they contain a same-sign lepton pair or at least three leptons (electrons or muons). Jet multiplicity, jet flavour and event kinematics are used to separate signal from the background through a multivariate discriminant, and dedicated control regions are used to constrain the dominant backgrounds. The four-top-quark production cross section is measured to be $$24^{+7}_{-6}$$ 24 - 6 + 7 fb. This corresponds to an observed (expected) significance with respect to the background-only hypothesis of 4.3 (2.4) standard deviations and provides evidence for this process.
Publisher: Elsevier BV
Date: 11-2017
Publisher: Microbiology Society
Date: 08-2012
Abstract: The genetic ersity present in populations of RNA viruses is likely to be strongly modulated by aspects of their life history, including mode of transmission. However, how transmission mode shapes patterns of intra- and inter-host genetic ersity, particularly when acting in combination with de novo mutation, population bottlenecks and the selection of advantageous mutations, is poorly understood. To address these issues, this study performed ultradeep sequencing of zucchini yellow mosaic virus in a wild gourd, Cucurbita pepo ssp. texana , under two infection conditions: aphid vectored and mechanically inoculated, achieving a mean coverage of approximately 10 000×. It was shown that mutations persisted during inter-host transmission events in both the aphid vectored and mechanically inoculated populations, suggesting that the vector-imposed transmission bottleneck is not as extreme as previously supposed. Similarly, mutations were found to persist within in idual hosts, arguing against strong systemic bottlenecks. Strikingly, mutations were seen to go to fixation in the aphid-vectored plants, suggestive of a major fitness advantage, but remained at low frequency in the mechanically inoculated plants. Overall, this study highlights the utility of ultradeep sequencing in providing high-resolution data capable of revealing the nature of virus evolution, particularly as the full spectrum of genetic ersity within a population may not be uncovered without sequence coverage of at least 2500-fold.
Publisher: Elsevier BV
Date: 06-2018
Publisher: Elsevier BV
Date: 04-2018
Publisher: American Society for Microbiology
Date: 05-2012
DOI: 10.1128/JVI.06050-11
Abstract: Although the rate at which proteins change is a key parameter in molecular evolution, its determinants are poorly understood in viruses. A variety of factors, including gene length, codon usage bias, protein abundance, protein function, and gene expression level, have been shown to affect the rate of protein evolution in a erse array of organisms. However, the role of these factors in viral evolution has yet to be addressed. The polar 3′-5′ stepwise attenuation of transcription in the Mononegavirales , a group of single-strand negative-sense RNA viruses, provides a unique system to explore the determinants of protein evolution in viruses. We analyzed the relative importance of a variety of factors in shaping patterns of sequence variation in full-length genomes from 13 Mononegavirales species. Our analysis suggests that the level of gene expression, and by extension the relative genomic position of each gene, is a key determinant of the protein evolution in these viruses. This appears to be the consequence of selection for translational robustness, but not for translational accuracy, in highly expressed genes. The small genome size and number of proteins encoded by these viruses allowed us to identify other protein-specific factors that may also play a role in virus evolution, such as host-virus interactions and functional constraints. Finally, we explored the evolutionary pressures acting on noncoding regions in Mononegavirales genomes and observed that, despite being less constrained than coding regions, their evolutionary rates are also associated with genomic position.
Publisher: Elsevier BV
Date: 09-2018
Publisher: Springer Science and Business Media LLC
Date: 02-2018
Publisher: Springer Science and Business Media LLC
Date: 03-2018
Publisher: Springer Science and Business Media LLC
Date: 11-2017
Publisher: Springer Science and Business Media LLC
Date: 06-2018
Publisher: Springer Science and Business Media LLC
Date: 14-08-2017
DOI: 10.1038/NPHYS4208
Publisher: American Society for Microbiology
Date: 15-06-2010
DOI: 10.1128/JVI.02160-09
Abstract: Despite their importance as agents of emerging disease, the time scale and evolutionary processes that shape the appearance of new viral species are largely unknown. To address these issues, we analyzed intra- and interspecific evolutionary processes in the Luteoviridae family of plant RNA viruses. Using the coat protein gene of 12 members of the family, we determined their phylogenetic relationships, rates of nucleotide substitution, times to common ancestry, and patterns of speciation. An associated multigene analysis enabled us to infer the nature of selection pressures and the genomic distribution of recombination events. Although rates of evolutionary change and selection pressures varied among genes and species and were lower in some overlapping gene regions, all fell within the range of those seen in animal RNA viruses. Recombination breakpoints were commonly observed at gene boundaries but less so within genes. Our molecular clock analysis suggested that the origin of the currently circulating Luteoviridae species occurred within the last 4 millennia, with intraspecific genetic ersity arising within the last few hundred years. Speciation within the Luteoviridae may therefore be associated with the expansion of agricultural systems. Finally, our phylogenetic analysis suggested that viral speciation events tended to occur within the same plant host species and country of origin, as expected if speciation is largely sympatric, rather than allopatric, in nature.
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
Location: Spain
No related grants have been discovered for JESUS ISRAEL PAGAN MUÑOZ.