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The six extraocular muscles (EOMs) are arranged around the eyeball as agonist-antagonist pairs performing the eye movements. The EOMs comprise a distinct muscle group that is fundamentally different from other skeletal muscle, which is reflected on many levels, such as functionality, anatomy as well as in their molecular make-up. Physiologically EOMs are considered superfast, high endurance muscles that are continuously active. In addition, EOMs contain unusual slow-tonic fibers that share features with amphibian and avian slow-tonic fibers. EOMs also express slow/cardiac isoforms of proteins and genes along with the typical isoforms of fast muscle fibers. Another striking hallmark of EOM is their differential involvement in a number of diseases. For instance, EOMs are preferentially spared in Duchenne Muscular Dystrophy (DMD). DMD is the most common fatal, genetic disease in males clinically characterized by progressive muscle wasting. Mutations in the dystrophin gene result in a destabilization of the muscle membrane causing muscle fiber damage. While all other skeletal muscles deteriorate the EOMs remain morphologically and functionally healthy. In the pathogenesis of DMD elevated Ca2+ levels are believed to be an early event and it has been shown that EOMs are protected from pharmacologically induced Ca2+ damage. The goal of this study was to characterize the spared EOMs, in particular their Ca2+ homeostasis, in the context of DMD pathology to reveal new potential therapeutic targets for the disease. A combination of physiological, molecular and biochemical methods was used to investigate the Ca2+ homeostasis of EOMs to demonstrate clear differences compared with the fast limb muscle tibialis anterior (TA). Ca2+ handling of stimulated cultured EOM myotubes suggested more efficient Ca2+ removal from the cytoplasm after induced Ca2+ influx compared with cultured myoblasts from TA. Subsequent mRNA and protein expression analyses of myoblasts and adult muscle tissue revealed high expression levels of many key Ca2+ regulating and buffering proteins in rodent EOMs compared with TA. Among these Ca2+ proteins were slow/cardiac proteins, which normally are not found in fast muscles. For instance, the sarcoplasmic Ca2+ ATPase SERCA2 was elevated along with its regulator phospholamban (PLN). Further, PLN was preferentially endogenously phosphorylated at Thr17 suggesting continuous activation of SERCA2 and possibly the fast isoform SERCA1, the main Ca2+ pumps responsible for removing Ca2+ from the cytoplasm after muscle contraction. Furthermore, Ca2+ buffers, such as calsequestrin (CASQ2) and parvalbumin (PARV) were elevated. These results suggest that EOMs are endowed with a unique and superior Ca2+ homeostasis that facilitates efficient Ca2+ buffering and removal from the cytoplasm. This is in agreement with their continuous and fast activation cycles, as well as with a potential protective mechanism in prevention of Ca2+ overload in DMD. The extreme activity patterns of EOM suggested that a high activity of store-operated Ca2+ entry (SOCE) plays a critical part to replenish Ca2+ for rapid and continuous cycles of contractions. To extend the data on general Ca2+ homeostasis and because of possible implications of store-operated Ca2+ influx and other Ca2+ influx pathways in DMD, the expression patterns of group 1 transient receptor potential (TRP) channels and the proteins Orai1 and STIM1 were studied. The TRP channels, TRPC1, TRPC6 and TRPV4 channel proteins in addition to STIM1 showed higher expression in EOM compared with TA. High TRPC1, TRPV4 and STIM1 levels could play a significant role in the high fatigue resistance, muscle differentiation and SOCE in EOM. In addition, tissue from the mdx mouse model of DMD was investigated. The only channels differentially expressed in mdx EOM compared with normal EOM were TRPM4 and TRPM7 (decreased in mdx EOM) and TRPV4 (increased in mdx EOM). Although, these changes in mdx EOM were of small magnitude, they could point toward subtle compensatory changes related to the disease process. In general, EOMs seem to be unaffected by the disease and inherently protected. In conclusion, the results in this thesis have improved the understanding of the Ca2+ homeostasis in EOMs and suggest that EOM may be better able to prevent prolonged elevation of cytoplasmic Ca2+ levels. These data may help to design new therapeutic approaches targeting Ca2+ handling proteins to ameliorate muscular dystrophy.