It is not possible to visualize the interphase chromosomes with light microscopy; however, polytene chromosomes are giant interphase chromosomes visible under light microscopy. Therefore, polytene chromosomes of Drosophila melanogaster are unique materials for the observation and analysis of the genome and genetic organization of chromosomes in the interphase stage. Polytene chromosomes form through the sequential replication of the chromosomes of the diploid nucleus division of the cytoplasm following the replication. This way, a chromosome 70 to 110 time thicker than a typical metaphase chromosome and observable with light microscopy, appears. This interesting polyteny occurs within the cellular cycle, during the mid-phases of Drosophila melanogaster's embryogenesis under ecdysone, which is particularly important for the development of larva. Investigation of every aspect of polytene chromosomes is very useful for the analysis of chromosomal organization and genome as a whole [1,2].

The most detailed maps of the polytene chromosomes in salivary glands of Drosophila melanogaster were created by Bridges using light microscopy in 1930s and 1940s [3]. The stiffly packed and dense dark areas are called bands, and lighter and less dense areas are called interbands. Localization of RNA polymerase II and related transcription factors on interbands shows that active genes tend to locate on these band areas [4]. Furthermore, areas in the interbands that are swelled more densely and observed as puffed areas are called puffs. Typical feature of puff areas is that they are rather active gene areas with RNA synthesis in higher rates as compared to the other areas of the interphase chromosomes. So, model, sequence and timing of puffing in the polytene chromosomes can be considered as indicators of gene activity in the interphase nucleus. This way, it is possible to study the interphase nucleus with cytogenetic methods [5,6]. Changes in the puffing activity observed on polytene chromosomes constitute a series of events. This series of events occurring under the control of a set of gene complex provides opportunity to understand the regulation of development [7,8]. Changing environmental conditions cause occurrence of differences in the puffing model [6-9]. Polytene chromosomes of Drosophila larvae and puffing model constitute a useful model for the understanding of the effects of environmental factors on gene activity through cytologic observations. Changes in puffing models and in addition chromosomal abnormalities have been found in band regions as a result of administration of various toxic substances to Drosophila [1-12]. It can be said under the light of the data obtained that polytene chromosomes are good materials as a toxicology tool.

Puffs on the polytene chromosomes known as ecdysone puffs are located on 2B, 8EF, 10EF, 12DE, 13E, 21C, 22C, 23E, 27C, 28A, 29F, 42A, 43E, 44A, 46A, 46F, 47A, 47BC, 48B, 49E, 50CD, 50F, 62E, 63F, 67B, 70C, 70E, 72D, 73B, 74EF, 75B, 75D, 76A, 76D, 78C, 86E, 87F, 89B, 98F, 99Band 100E band areas [13]. Here are numerous studies on genes of such puff areas However, the understanding of localizations of genes on polytene chromosomes is not complete yet [14,15]. Therefore, elucidation of positions of genes on polytene chromosomes will ensure both a better understanding of interphase chromosomes and organization and operation of genes. We can say that, although investigators have been focused on polytene chromosomes since for almost 90 years, there is still must effort to be exerted on polytene chromosomes.