Riddle et al 2011 show that each TE family has a very complex epigenetic environment and very often, only a small percentage of the entire population of TEs harbor polymerase binding and permissive marks as H3K4me3. While such analysis may be more complex in D. melanogaster strains since the number of TE copies is high, D. simulans wild-type strains provide an excellent work model since they have lower copy number and fewer full-length putative active copies. Indeed, we have recently annotated these TE families and others in the D. simulans sequenced genome, and most of the copies are internally deleted in this species. However, the four TE families MDV3100 analyzed in this study present full-length elements and therefore putatively active copies in the D. simulans sequenced genome. We are currently trying to map all the copies from the four TEs analyzed here in the seven wild type strains, enabling comparison between common copies and insertionally polymorphic copies in different strains. While such analysis will give us a better view of the chromatin marks present in one strain, it will not elucidate the lack of correlation between TE expression and chromatin state as TEs are highly similar in Drosophila and hence transcripts are difficult to map at one single copy. Since laboratory breeding conditions are equal for all the strains, one could suggest that the original epigenetic differences between strains may no longer exist. However, we do observe such differences, suggesting that the laboratory conditions do not lead to an equivalent epigenome. We cannot assume that such differences arise with the inbreeding of the wild-type derived strains in the laboratory or are original epigenetic differences, maintained during breeding. Experiments using fresh collections of Drosophila populations should answer such question. While this report demonstrates the importance of studying natural populations, the perfect model system where one can control all the parameters is still not available, especially for modeling D. simulans populations. Neurofilaments are neuron-specific 10-nm intermediate filaments essential for radial growth of axons, and efficient propagation of electric impulses along axons. Various properties of NF composition, structure and dynamic behavior have been proposed to influence the accumulation of NF along axons that underlies caliber expansion and may determine shapes of other regions of the neuron. To achieve this stable geometry, axonally transported NF contribute to a large stationary cytoskeletal network, which also serves as a scaffold for the reversible docking of organelles and proteins, thereby regulating their activity, abundance, and trafficking. In serving these roles, different subunits of the NF bind to specific molecular motors, receptor proteins, and other cytoskeletal proteins. NFs are obligate heteropolymers composed of neurofilament heavy, medium, low and a-internexin in CNS axons. The exceptionally long NF-H and NF-M carboxyl terminal tail domains contain 51 and 7 phosphorylation sites, respectively within repeated serine-lysine-proline sequences, which are regulated by multiple protein kinases and multiple phosphatases. C-terminal domain phosphorylation straightens, aligns, and bundles NFs and extends C-terminal sidearms in vitro promoting cross bridge formation among NF and other cytoskeletal elements, and an increase in inter-filament spacing. The acquisition of phosphates on the C-terminal domains occurs mainly after NFs enter axons and coincides.