Differential Trends in the Codon Usage Patterns in HIV-1 Genes

Host-pathogen interactions underlie one of the most complex evolutionary phenomena resulting in continual adaptive genetic changes, where pathogens exploit the host's molecular resources for growth and survival, while hosts try to eliminate the pathogen. Deciphering the molecular basis of host–pathogen interactions is useful in understanding the factors governing pathogen evolution and disease propagation. In host-pathogen context, a balance between mutation, selection, and genetic drift is known to maintain codon bias in both organisms. Studies revealing determinants of the bias and its dynamics are central to the understanding of host-pathogen evolution. We considered the Human Immunodeficiency Virus (HIV) type 1 and its human host to search for evolutionary signatures in the viral genome. Positive selection is known to dominate intra-host evolution of HIV-1, whereas high genetic variability underlies the belief that neutral processes drive inter-host differences. In this study, we analyze the codon usage patterns of HIV-1 genomes across all subtypes and clades sequenced over a period of 23 years. We show presence of unique temporal correlations in the codon bias of three HIV-1 genes illustrating differential adaptation of the HIV-1 genes towards the host preferred codons. Our results point towards gene-specific translational selection to be an important force driving the evolution of HIV-1 at the population level

VIBRATIONAL DEPENDENCE OF EXCITED STATE INTRAMOLECULAR PROTON TRANSFER IN 2-(2′^\prime-PYRIDYL)PYRROLE IN THE GAS PHASE VIA HIGH RESOLUTION ELECTRONIC SPECTROSCOPY

Work supported by NSF (CHE-0911117)Synthesis by Randolph P. Thummel, University of Houston, Houston, Texas 77204-5003Author Institution: Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260; Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, PolandRotationally resolved fluorescence excitation spectra of the S$_1\leftarrow$S$_0$ origin band and +144 cm\textsuperscript{-1} vibrational band transitions of 2-(2$^\prime$-Pyridyl)pyrrole (2PP) have been recorded in the collision free environment of a molecular beam. Analyses of these data provide new information about the changes in geometry that occur when 2PP absorbs light. Additionally, significant line broadening is observed in both spectra, which we attribute to an excited state intramolecular proton transfer (ESIPT) reaction. The dynamics and vibrational mode dependence of ESIPT in 2PP will be discussed

Excited-State Proton Transfer in <i>syn</i>-2-(2′-Pyridyl)pyrrole Occurs on the Nanosecond Time Scale in the Gas Phase

Microwave and UV excitation spectra of 2-(2′-pyridyl)pyrrole (2PP) have been recorded at high resolution in the gas phase. Analyses of these data show that the <i>syn</i> conformer of 2PP is a planar molecule in both the ground (S₀) and first excited (S₁) electronic states, and that the S₁ state undergoes a relatively slow excited-state proton transfer (ESPT) reaction when excited by light, as measured by the homogeneous line broadening that is observed in its UV spectrum. Apparently, excitation of the S₁ state moves electronic charge from the pyrrole ring to the pyridine ring, but the simultaneous transfer of the proton is inhibited by an unfavorably oriented dipole under solvent-free conditions. The rate of the ESPT reaction is enhanced by more than an order of magnitude with simultaneous excitation of a 144 cm^–1 in-plane vibrational mode