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The orientation of bacterichlorophyll c in green bacteria cells and cell fragments A.Dudkowiak1, T. Martynski1,2, J. Miyake2, D. Frackowiak1,2 1Institute of Physics, Poznan University of Technology, Piotrowo 3, 60-965 Poznan, Poland 2National Institute for Advanced Interdisciplinary Research, 1-1-4 Higashi, Tsukuba, Japan Introduction The green sulfur bacterium Prosthecochloris aestuarii (Chloropseudomonas ethylica) contains light-harvesting structures called chlorosomes. Chlorosomes are oblong bodies which contain the rod structures in their envelope [1,2]. The main pigment of these chlorosomes is bacteriochlorophyll (BChl) c, with small admixture of BChl a. Several models of the organization of the pigments into rod structures have been proposed [3-10]. These models were founded on the basis of the polarized light spectroscopy of the bacteria, the chlorosomes or the membranes fragments ordered in stretched polymers [11], squeezed gel [12-14] or in dried layers [10]. The polarization of light absorbed or emitted by the chlorosome structures located in organisms depends on the orientation of the pigment with respect to the rod axis; the orientation of the rod axis with respect to the longer axis of chlorosome; the orientation of chlorosome axis with respect to the long axis of bacterium, as well as the orientation of the long axis of organisms with respect to the matrix orientation axis. The results obtained on the basis of absorption and fluorescence anisotropy depend not only on the average angles of these orientations but also on the angular distribution functions of these axes of orientation. In the case of the orientation of isolated chlorosomes, the situation is simpler [11,13] but the results depend not only on the pigment orientation in chlorosome but also on the orientation of chlorosomes or their clusters in anisotropic matrix. In order to control the degree of orientation of the investigated macroscopic objects in the anisotropic polymer matrix, we apply, additionally to spectroscopic measurements, the observation of the sample in fluorescence microscope equipped with polarizers in exiting and observation light beams. From the photographs taken at various polarizations of these light beams and from the pictures taken in transmitted light the information about the orientation of investigated objects, can be obtained.