| Records |
| Author |
Peris, J.B.; Davis, P.; Cuevas, J.M.; Nebot, M.; Sanjuan, R. |
| Title |
Distribution of Fitness Effects Caused by Single-Nucleotide Substitutions in Bacteriophage f1 |
Type |
Journal Article |
| Year |
2010 |
Publication |
Genetics |
Abbreviated Journal |
Genetics |
| Volume |
185 |
Issue |
2 |
Pages |
603-U308 |
| Keywords |
|
| Abstract |
Empirical knowledge of the fitness effects of mutations is important for understanding many evolutionary processes, yet this knowledge is often hampered by several sources of measurement error and bias. Most of these problems can be solved using site-directed mutagenesis to engineer single mutations, an approach particularly suited for viruses due to their small genomes. Here, we used this technique to measure the fitness effect of 100 single-nucleotide substitutions in the bacteriophage f1, a filamentous single-strand DNA virus. We found that approximately one-fifth of all mutations are lethal. Viable ones reduced fitness by 11% on average and were accurately described by a log-normal distribution. More than 90% of synonymous substitutions were selectively neutral, while those affecting intergenic regions reduced fitness by 14% on average. Mutations leading to amino acid substitutions had an overall mean deleterious effect of 37%, which increased to 45% for those changing the amino acid polarity. Interestingly, mutations affecting early steps of the infection cycle tended to be more deleterious than those affecting late steps. Finally, we observed at least two beneficial mutations. Our results confirm that high mutational sensitivity is a general property of viruses with small genomes, including RNA and single-strand DNA viruses infecting animals, plants, and bacteria. |
| Address |
[Peris, Joan B.; Davis, Paulina; Cuevas, Jose M.; Sanjuan, Rafael] Univ Valencia, Inst Cavanilles Biodiversitat & Biol Evolut, Valencia 46980, Spain, Email: rafael.sanjuan@uv.es |
| Corporate Author |
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Thesis |
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| Publisher |
Genetics Soc Am |
Place of Publication |
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Editor |
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| Language |
English |
Summary Language |
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Original Title |
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| Series Editor |
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Series Title |
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Abbreviated Series Title |
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| Series Volume |
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Series Issue |
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Edition |
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ISSN  |
0016-6731 |
ISBN |
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Medium |
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| Area |
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Expedition |
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Conference |
|
| Notes |
ISI:000281905200017 |
Approved |
no |
| Is ISI |
yes |
International Collaboration |
no |
| Call Number |
IFIC @ elepoucu @ |
Serial |
383 |
| Permanent link to this record |
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| Author |
Sanjuan, R.; Nebot, M.; Chirico, N.; Mansky, L.M.; Belshaw, R. |
| Title |
Viral Mutation Rates |
Type |
Journal Article |
| Year |
2010 |
Publication |
Journal of Virology |
Abbreviated Journal |
J. Virol. |
| Volume |
84 |
Issue |
19 |
Pages |
9733-9748 |
| Keywords |
|
| Abstract |
Accurate estimates of virus mutation rates are important to understand the evolution of the viruses and to combat them. However, methods of estimation are varied and often complex. Here, we critically review over 40 original studies and establish criteria to facilitate comparative analyses. The mutation rates of 23 viruses are presented as substitutions per nucleotide per cell infection (s/n/c) and corrected for selection bias where necessary, using a new statistical method. The resulting rates range from 10(-8) to 10(-6) s/n/c for DNA viruses and from 10(-6) to 10(-4) s/n/c for RNA viruses. Similar to what has been shown previously for DNA viruses, there appears to be a negative correlation between mutation rate and genome size among RNA viruses, but this result requires further experimental testing. Contrary to some suggestions, the mutation rate of retroviruses is not lower than that of other RNA viruses. We also show that nucleotide substitutions are on average four times more common than insertions/deletions (indels). Finally, we provide estimates of the mutation rate per nucleotide per strand copying, which tends to be lower than that per cell infection because some viruses undergo several rounds of copying per cell, particularly double-stranded DNA viruses. A regularly updated virus mutation rate data set will be available at www.uv.es/rsanjuan/virmut. |
| Address |
[Sanjuan, Rafael] Univ Valencia, Inst Cavanilles Biodiversitat & Biol Evolutiva, Dept Genet, Valencia 46980, Spain, Email: rafael.sanjuan@uv.es |
| Corporate Author |
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Thesis |
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| Publisher |
Amer Soc Microbiology |
Place of Publication |
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Editor |
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| Language |
English |
Summary Language |
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Original Title |
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| Series Editor |
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Series Title |
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Abbreviated Series Title |
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| Series Volume |
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Series Issue |
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Edition |
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| ISSN |
0022-538x |
ISBN |
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Medium |
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| Area |
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Expedition |
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Conference |
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| Notes |
ISI:000282641800008 |
Approved |
no |
| Is ISI |
yes |
International Collaboration |
yes |
| Call Number |
IFIC @ elepoucu @ |
Serial |
371 |
| Permanent link to this record |
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| Author |
Bernabeu, J.; Botella, F.J.; Nebot, M. |
| Title |
Novel T-Violation observable open to any pair of decay channels at meson factories |
Type |
Journal Article |
| Year |
2014 |
Publication |
Physics Letters B |
Abbreviated Journal |
Phys. Lett. B |
| Volume |
728 |
Issue |
|
Pages |
95-98 |
| Keywords |
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| Abstract |
Quantum entanglement between the two neutral mesons produced in meson factories has allowed the first indisputable direct observation of Time Reversal Violation in the time evolution of the neutral meson between the two decays. The exceptional meson transitions are directly connected to semileptonic and CP eigenstate decay channels. The possibility of extending the observable asymmetries to more decay channels confronts the problem of the “orthogonality condition”, which can be stated with this tonguetwister: Given a decay channel f, which is the decay channel f' such that the meson state not decaying to f is orthogonal to the meson state not decaying to f? In this Letter we propose an alternative T-Violation asymmetry at meson factories which allows its opening to any pair of decay channels. Instead of searching which is the pair of decay channels associated to the T-reverse meson transition, we build an asymmetry which tags the initial states of both the Reference and the T-reverse meson transitions. This observable filters the appropriate final states by means of two measurable survival probabilities. We discuss the methodology to be followed in the analysis of the new observable and the results expected in specific examples. |
| Address |
[Nebot, Miguel] Univ Valencia, Dept Fis Teor, CSIC, E-46100 Burjassot, Spain, Email: Jose.Bernabeu@uv.es; |
| Corporate Author |
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Thesis |
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| Publisher |
Elsevier Science Bv |
Place of Publication |
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Editor |
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| Language |
English |
Summary Language |
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Original Title |
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| Series Editor |
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Series Title |
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Abbreviated Series Title |
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| Series Volume |
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Series Issue |
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Edition |
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| ISSN |
0370-2693 |
ISBN |
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Medium |
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| Area |
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Expedition |
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Conference |
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| Notes |
WOS:000330556000017 |
Approved |
no |
| Is ISI |
yes |
International Collaboration |
no |
| Call Number |
IFIC @ pastor @ |
Serial |
1705 |
| Permanent link to this record |
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| Author |
Herrero-Garcia, J.; Nebot, M.; Rius, N.; Santamaria, A. |
| Title |
The Zee-Babu model revisited in the light of new data |
Type |
Journal Article |
| Year |
2014 |
Publication |
Nuclear Physics B |
Abbreviated Journal |
Nucl. Phys. B |
| Volume |
885 |
Issue |
|
Pages |
542-570 |
| Keywords |
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| Abstract |
We update previous analyses of the Zee-Babu model in the light of new data, e.g., the mixing angle On, the rare decay μ-> e gamma and the LHC results. We also analyze the possibility of accommodating the deviations in Gamma (H -> gamma gamma) hinted by the LHC experiments, and the stability of the scalar potential. We find that neutrino oscillation data and low energy constraints are still compatible with masses of the extra charged scalars accessible to LHC. Moreover, if any of them is discovered, the model can be falsified by combining the information on the singly and doubly charged scalar decay modes with neutrino data. Conversely, if the neutrino spectrum is found to be inverted and the CP phase delta is quite different from pi, the masses of the charged scalars will be well outside the LHC reach. |
| Address |
[Herrero-Garcia, Juan; Rius, Nuria; Santamaria, Arcadi] Univ Valencia, Dept Fis Teor, E-46100 Burjassot, Valencia, Spain |
| Corporate Author |
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Thesis |
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| Publisher |
Elsevier Science Bv |
Place of Publication |
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Editor |
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| Language |
English |
Summary Language |
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Original Title |
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| Series Editor |
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Series Title |
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Abbreviated Series Title |
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| Series Volume |
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Series Issue |
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Edition |
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| ISSN |
0550-3213 |
ISBN |
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Medium |
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| Area |
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Expedition |
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Conference |
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| Notes |
WOS:000339598300025 |
Approved |
no |
| Is ISI |
yes |
International Collaboration |
yes |
| Call Number |
IFIC @ pastor @ |
Serial |
1858 |
| Permanent link to this record |
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| Author |
Botella, F.J.; Cornet-Gomez, F.; Miro, C.; Nebot, M. |
| Title |
New physics hints from τ scalar interactions and (g-2)e,μ |
Type |
Journal Article |
| Year |
2024 |
Publication |
Journal of Physics G |
Abbreviated Journal |
J. Phys. G |
| Volume |
51 |
Issue |
2 |
Pages |
025001 - 20pp |
| Keywords |
lepton sector; extended scalar sector; new physics signals |
| Abstract |
We consider a flavour conserving two Higgs doublet model that consists of a type I (or X) quark sector and a generalized lepton sector where the Yukawa couplings of the charged leptons to the new scalars are not proportional to the lepton masses. The model, previously proposed to solve both muon and electron g – 2 anomalies simultaneously, is also capable to accommodate the ATLAS excess in pp -> S -> tau(+)tau(-) with gluon-gluon fusion production in the invariant mass range [0.2; 0.6] TeV, including all relevant low and high energy constraints. The excess is reproduced taking into account the new contributions from the scalar H, the pseudoscalar A, or both. In particular, detailed numerical analyses favoured the solution with a significant hierarchy among the vevs of the two Higgs doublets, t(beta)similar to 10, and light neutral scalars satisfying m(A) > m(H) with sizable couplings to tau leptons. In this region of the parameter space, the muon g – 2 anomaly receives one and two-loop (Barr Zee) contributions of similar size, while the electron anomaly is explained at two loops. An analogous ATLAS excess in b-associated production and the CMS excess in ditop production are also studied. Further New Physics prospects concerning the anomalous magnetic moment of the tau lepton and the implications of the CDF M-W measurement on the final results are discussed. |
| Address |
[Botella, Francisco J.; Miro, Carlos; Nebot, Miguel] Univ Valencia, CSIC, Dept Fis Teor, E-46100 Burjassot, Spain, Email: Francisco.J.Botella@uv.es; |
| Corporate Author |
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Thesis |
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| Publisher |
IOP Publishing Ltd |
Place of Publication |
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Editor |
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| Language |
English |
Summary Language |
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Original Title |
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| Series Editor |
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Series Title |
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Abbreviated Series Title |
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| Series Volume |
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Series Issue |
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Edition |
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| ISSN |
0954-3899 |
ISBN |
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Medium |
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| Area |
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Expedition |
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Conference |
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| Notes |
WOS:001132956900001 |
Approved |
no |
| Is ISI |
yes |
International Collaboration |
yes |
| Call Number |
IFIC @ pastor @ |
Serial |
5877 |
| Permanent link to this record |
