Guidelines for Identifying Homologous Recombination Events in Influenza A Virus

The rapid evolution of influenza viruses occurs both clonally and non-clonally through a variety of genetic mechanisms and selection pressures. The non-clonal evolution of influenza viruses comprises relatively frequent reassortment among gene segments and a more rarely reported process of non-homologous RNA recombination. Homologous RNA recombination within segments has been proposed as a third such mechanism, but to date the evidence for the existence of this process among influenza viruses has been both weak and controversial. As homologous recombination has not yet been demonstrated in the laboratory, supporting evidence, if it exists, may come primarily from patterns of phylogenetic incongruence observed in gene sequence data. Here, we review the necessary criteria related to laboratory procedures and sample handling, bioinformatic analysis, and the known ecology and evolution of influenza viruses that need to be met in order to confirm that a homologous recombination event occurred in the history of a set of sequences. To determine if these criteria have an effect on recombination analysis, we gathered 8307 publicly available full-length sequences of influenza A segments and divided them into those that were sequenced via the National Institutes of Health Influenza Genome Sequencing Project (IGSP) and those that were not. As sample handling and sequencing are executed to a very high standard in the IGSP, these sequences should be less likely to be exposed to contamination by other samples or by laboratory strains, and thus should not exhibit laboratory-generated signals of homologous recombination. Our analysis shows that the IGSP data set contains only two phylogenetically-supported single recombinant sequences and no recombinant clades. In marked contrast, the non-IGSP data show a very large amount of potential recombination. We conclude that the presence of false positive signals in the non-IGSP data is more likely than false negatives in the IGSP data, and that given the evidence to date, homologous recombination seems to play little or no role in the evolution of influenza A viruses

Linear and nonlinear optical characterizations of a monomeric symmetric squaraine-based dye in solution

The photophysical properties of a symmetric squaryllium dye, namely, 2,4-bis[4-(N,N-dibutylamino)-2-hydroxyphenyl] squaraine (SQ), in its monomer form in acetone solution, have been thoroughly studied by means of one-photon absorption (1PA) and two-photon absorption (2PA), excitation anisotropy, fluorescence emission, fluorescence quantum yield, and excited state absorption. The results show that there is a strong one-photon allowed absorption band in the near IR region associated with intramolecular charge transfer. Higher one-photon allowed and forbidden singlet excited states were also revealed by absorption and excitation anisotropy. A relatively high fluorescence quantum yield (0.44) was measured for this dye. The nonlinear optical characterization of SQ in solution confirms the ability of squaraine dyes to be used as good two-photon absorbers. Additionally, it was found that this dye presents both saturable and reverse saturable absorption effects. Density functional theory calculations of the 1PA and 2PA electronic spectra of SQ were carried out to support the experimental data. A detailed analysis of the symmetry and energy of the orbitals involved in the lowest five electronic transitions is presented and discussed in relation to the behavior observed experimentally

From Gravitons to Giants

We discuss exact quantization of gravitational fluctuations in the half-BPS sector around AdS$_5 \times$S$^5$ background, using the dual super Yang-Mills theory. For this purpose we employ the recently developed techniques for exact bosonization of a finite number $N$ of fermions in terms of $N$ bosonic oscillators. An exact computation of the three-point correlation function of gravitons for finite $N$ shows that they become strongly coupled at sufficiently high energies, with an interaction that grows exponentially in $N$. We show that even at such high energies a description of the bulk physics in terms of weakly interacting particles can be constructed. The single particle states providing such a description are created by our bosonic oscillators or equivalently these are the multi-graviton states corresponding to the so-called Schur polynomials. Both represent single giant graviton states in the bulk. Multi-particle states corresponding to multi-giant gravitons are, however, different, since interactions among our bosons vanish identically, while the Schur polynomials are weakly interacting at high enough energies.Comment: v2-references added, minor changes and typos corrected; 24 pages, latex, 3 epsf figure