Browsing by Subject "Molecular"

Now showing 1 - 3 of 3

Open Access
Genome sequencing highlights the dynamic early history of dogs
(Public Library of Science, 2014) Freedman, A. H.; Gronau I.; Schweizer, R. M.; Ortega-Del Vecchyo, D.; Han, E.; Silva, P. M.; Galaverni, M.; Fan, Z.; Marx P.; Lorente-Galdos, B.; Beale, H.; Ramirez, O.; Hormozdiari, F.; Alkan C.; Vilà, C.; Squire K.; Geffen, E.; Kusak, J.; Boyko, A. R.; Parker, H. G.; Lee C.; Tadigotla, V.; Siepel, A.; Bustamante, C. D.; Harkins, T. T.; Nelson, S. F.; Ostrander, E. A.; Marques Bonet, T.; Wayne, R. K.; Novembre, J.
To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we generated high-quality genome sequences from three gray wolves, one from each of the three putative centers of dog domestication, two basal dog lineages (Basenji and Dingo) and a golden jackal as an outgroup. Analysis of these sequences supports a demographic model in which dogs and wolves diverged through a dynamic process involving population bottlenecks in both lineages and post-divergence gene flow. In dogs, the domestication bottleneck involved at least a 16-fold reduction in population size, a much more severe bottleneck than estimated previously. A sharp bottleneck in wolves occurred soon after their divergence from dogs, implying that the pool of diversity from which dogs arose was substantially larger than represented by modern wolf populations. We narrow the plausible range for the date of initial dog domestication to an interval spanning 11-16 thousand years ago, predating the rise of agriculture. In light of this finding, we expand upon previous work regarding the increase in copy number of the amylase gene (AMY2B) in dogs, which is believed to have aided digestion of starch in agricultural refuse. We find standing variation for amylase copy number variation in wolves and little or no copy number increase in the Dingo and Husky lineages. In conjunction with the estimated timing of dog origins, these results provide additional support to archaeological finds, suggesting the earliest dogs arose alongside hunter-gathers rather than agriculturists. Regarding the geographic origin of dogs, we find that, surprisingly, none of the extant wolf lineages from putative domestication centers is more closely related to dogs, and, instead, the sampled wolves form a sister monophyletic clade. This result, in combination with dog-wolf admixture during the process of domestication, suggests that a re-evaluation of past hypotheses regarding dog origins is necessary. © 2014.
Open Access
Molecular logic: from single logic gates to sophisticated logic circuits, from fundamental science to practical applications
(Wiley, 2017) Akkaya, E. U.; Katz, E.; Pischel, U.
Open Access
Raman enhancement on a broadband meta-surface
(American Chemical Society, 2012-07-30) Ayas S.; Güner, H.; Türker, B.; Ekiz, O. O.; Dirisaglik, F.; Okyay, Ali Kemal; Dâna, A.
Plasmonic metamaterials allow confinement of light to deep subwavelength dimensions, while allowing for the tailoring of dispersion and electromagnetic mode density to enhance specific photonic properties. Optical resonances of plasmonic molecules have been extensively investigated; however, benefits of strong coupling of dimers have been overlooked. Here, we construct a plasmonic meta-surface through coupling of diatomic plasmonic molecules which contain a heavy and light meta-atom. Presence and coupling of two distinct types of localized modes in the plasmonic molecule allow formation and engineering of a rich band structure in a seemingly simple and common geometry, resulting in a broadband and quasi-omni-directional meta-surface. Surface-enhanced Raman scattering benefits from the simultaneous presence of plasmonic resonances at the excitation and scattering frequencies, and by proper design of the band structure to satisfy this condition, highly repeatable and spatially uniform Raman enhancement is demonstrated. On the basis of calculations of the field enhancement distribution within a unit cell, spatial uniformity of the enhancement at the nanoscale is discussed. Raman scattering constitutes an example of nonlinear optical processes, where the wavelength conversion during scattering may be viewed as a photonic transition between the bands of the meta-material.