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Acoustic startle modification and traditional psychoacoustic techniques for behavioral auditory phenotyping are compared.Non-auditory variables and influence of non-auditory inputs to the startle circuit must be taken into account.Acoustic startle modification procedures show low sensitivity compared to operant conditioning techniques.Acoustic startle modification is useful when testing mice with early-onset hearing loss or with learning impairments.Acoustic startle response (ASR) modification procedures, especially prepulse inhibition (PPI), are increasingly used as behavioral measures of auditory processing and sensorimotor gating in rodents due to their perceived ease of implementation and short testing times. In practice, ASR and PPI procedures are extremely variable across animals, experimental setups, and studies, and the interpretation of results is subject to numerous caveats and confounding influences. We review considerations for modification of the ASR using acoustic stimuli, and we compare the sensitivity of PPI procedures to more traditional operant psychoacoustic techniques. We also discuss non-auditory variables that must be considered. We conclude that ASR and PPI measures cannot substitute for traditional operant techniques due to their low sensitivity. Additionally, a substantial amount of pilot testing must be performed to properly optimize an ASR modification experiment, negating any time benefit over operant conditioning. Nevertheless, there are some circumstances where ASR measures may be the only option for assessing auditory behavior, such as when testing mouse strains with early-onset hearing loss or learning impairments.