Papers by Divya Sitaraman
Analysis of Sleep and Circadian Rhythms from Drosophila Activity-Monitoring Data Using SCAMP
PubMed, Feb 9, 2024
Sleep is a fundamental feature of life for virtually all multicellular animals, but many question... more Sleep is a fundamental feature of life for virtually all multicellular animals, but many questions remain about how sleep is regulated and what biological functions it plays. Substantial headway has been made in the study of both circadian rhythms and sleep in the fruit fly Drosophila melanogaster, much of it through studies of individual fly activity using beam break counts from Drosophila activity monitors (DAMs). The number of laboratories worldwide studying sleep in Drosophila has grown from only a few 20 years ago to hundreds today. The utility of these studies is limited by the quality of the metrics that can be extracted from the data. Many software options exist to help analyze DAM data; however, these are often expensive or have significant limitations. Therefore, we describe here a method for analyzing DAM-based data using the sleep and circadian analysis MATLAB program (SCAMP). This user-friendly software has an advantage of combining several analyses of both sleep and circadian rhythms in one package and produces graphical outputs as well as spreadsheets of the outputs for further statistical analysis. The version of SCAMP described here is also the first published software package that can analyze data from multibeam DAM5Ms, enabling determination of positional preference over time.
PubMed, 2018
A key element of laboratory courses introducing students to neuroscience includes behavioral exer... more A key element of laboratory courses introducing students to neuroscience includes behavioral exercises. Associative learning experiments often conducted in research laboratories are difficult to perform and time consuming. Commonly, these experiments cannot be performed without extensive instrumentation or animal care facilities. Here, we describe three distinct laboratory modules that build on simple chemosensory and memory assays in Drosophila larvae. Additionally, we describe open-ended research projects using these assays that can be developed into semester long independent research experiences. Given that Drosophila is a genetic model organism, these simple behavioral assays can be used to generate multiple hypothesis driven projects aimed at identifying a gene or class of neurons involved in appetitive and aversive learning. These lab modules are ideally suited for undergraduates at all levels to experience and can be incorporated in a lower/upper level neuroscience course or as a high school outreach exercise. Further, these modules enable students to collect their own data sets, work in groups in collating large data sets, performing statistical comparisons, and presenting results in the form of short research papers or traditional laboratory reports that include a short literature review.
Utilizing comparative models in biomedical research
Comparative Biochemistry and Physiology B, Aug 1, 2021
This review serves as an introduction to a Special Issue of Comparative Biochemistry and Physiolo... more This review serves as an introduction to a Special Issue of Comparative Biochemistry and Physiology, focused on using non-human models to study biomedical physiology. The concept of a model differs across disciplines. For example, several models are used primarily to gain an understanding of specific human pathologies and disease states, whereas other models may be focused on gaining insight into developmental or evolutionary mechanisms. It is often the case that animals initially used to gain knowledge of some unique biochemical or physiological process finds foothold in the biomedical community and becomes an established model. The choice of a particular model for biomedical research is an ongoing process and model validation must keep pace with existing and emerging technologies. While the importance of non-mammalian models, such as Caenorhabditis elegans, Drosophila melanogaster, Danio rerio and Xenopus laevis, is well known, we also seek to bring attention to emerging alternative models of both invertebrates and vertebrates, which are less established but of interest to the comparative biochemistry and physiology community.
Bio-protocol, 2019
Sleep is a conserved neurobehavioral state observed in animals with sufficiently complex nervous ... more Sleep is a conserved neurobehavioral state observed in animals with sufficiently complex nervous systems and is critical for survival. While the exact function of sleep remains unknown, the lack of sleep can have a range of physiological and behavioral effects. Studies in invertebrates and vertebrates have identified conserved neural mechanisms and cellular pathways in control of sleep, wakefulness and arousal. Methodologies to measure sleep have ranged from EEG recordings in humans and rodents to in-depth analysis of locomotor patterns in flies, fish and worms. Here we focus on sleep measurements using activity monitoring in the highly versatile experimental model system, Drosophila melanogaster, which is amenable to a number of genetic, physiological and behavioral manipulations. Further, we also describe methods used to manipulate sleep and wakefulness to understand the neural regulation of sleep and how organisms balance sleep, wakefulness and behavioral arousal. Sleep as a behavioral state is regulated by a number of factors including food, environmental conditions, and genetic background. The methodologies described here provide, a highthroughput approach to study neural regulation of sleep and factors that affect this complex behavior.
Frontiers in Neural Circuits, Dec 22, 2015
The citation for the first use of P2X2 as an exogenous chemogenetic neural activator (Lima and Mi... more The citation for the first use of P2X2 as an exogenous chemogenetic neural activator (Lima and Miesenbock, 2005
A biographical sketch of Troy D. Zars (1967–2018)
Journal of Neurogenetics, Jan 2, 2020
Abstract Troy D. Zars (1967–2018) was an American biologist. He studied the relationships between... more Abstract Troy D. Zars (1967–2018) was an American biologist. He studied the relationships between genes, neuronal circuits and behavior in the fruit fly Drosophila melanogaster. Zars co-pioneered the use of transgene expression to locally restore gene function in memory-defective fly mutants, an approach that provided breakthrough insights into the localization of memory traces in the fly brain. With ensuing refinements of the methods of transgene expression and the broadening in the range of transgenes to be expressed, this shaped the field of modern behavioral neurogenetics.
Frontiers in Neural Circuits, Nov 9, 2015
The Drosophila mushroom body (MB) is an associative learning network that is important for the co... more The Drosophila mushroom body (MB) is an associative learning network that is important for the control of sleep. We have recently identified particular intrinsic MB Kenyon cell (KC) classes that regulate sleep through synaptic activation of particular MB output neurons (MBONs) whose axons convey sleep control signals out of the MB to downstream target regions. Specifically, we found that sleep-promoting KCs increase sleep by preferentially activating cholinergic sleep-promoting MBONs, while wake-promoting KCs decrease sleep by preferentially activating glutamatergic wake-promoting MBONs. Here we use a combination of genetic and physiological approaches to identify wake-promoting dopaminergic neurons (DANs) that innervate the MB, and show that they activate wake-promoting MBONs. These studies reveal a dopaminergic sleep control mechanism that likely operates by modulation of KC-MBON microcircuits.
A biographical sketch of Troy D. Zars (1967–2018)
Journal of Neurogenetics, 2020
Abstract Troy D. Zars (1967–2018) was an American biologist. He studied the relationships between... more Abstract Troy D. Zars (1967–2018) was an American biologist. He studied the relationships between genes, neuronal circuits and behavior in the fruit fly Drosophila melanogaster. Zars co-pioneered the use of transgene expression to locally restore gene function in memory-defective fly mutants, an approach that provided breakthrough insights into the localization of memory traces in the fly brain. With ensuing refinements of the methods of transgene expression and the broadening in the range of transgenes to be expressed, this shaped the field of modern behavioral neurogenetics.
Neural Stimulation during Drosophila Activity Monitor (DAM)-Based Studies of Sleep and Circadian Rhythms in Drosophila melanogaster
PubMed, Feb 9, 2024
Sleep is a fundamental feature of life for virtually all multicellular animals, but many question... more Sleep is a fundamental feature of life for virtually all multicellular animals, but many questions remain about how sleep is regulated by circadian rhythms, homeostatic sleep drive that builds up with wakefulness, and modifying factors such as hunger or social interactions, as well as about the biological functions of sleep. Substantial headway has been made in the study of both circadian rhythms and sleep in the fruit fly Drosophila melanogaster, much of it through studies of individual fly activity using Drosophila activity monitors (DAMs). Here, we describe approaches for the activation of specific neurons of interest using optogenetics (involving genetic modifications that allow for light-based neuronal activation) and thermogenetics (involving genetic modifications that allow for temperature-based neuronal activation) so that researchers can evaluate the roles of those neurons in controlling rest and activity behavior. In this protocol, we describe how to set up a rig for simultaneous optogenetic or thermogenetic stimulation and activity monitoring for analysis of sleep and circadian rhythms in Drosophila, how to raise appropriate flies, and how to perform the experiment. This protocol will allow researchers to assess the causative role in the regulation of sleep and activity rhythms of any genetically tractable subset of cells.
Nature Communications, Jul 28, 2017
Animals execute one particular behavior among many others in a context-dependent manner, yet the ... more Animals execute one particular behavior among many others in a context-dependent manner, yet the mechanisms underlying such behavioral choice remain poorly understood. Here we studied how two fundamental behaviors, sex and sleep, interact at genetic and neuronal levels in Drosophila. We show that an increased need for sleep inhibits male sexual behavior by decreasing the activity of the male-specific P1 neurons that coexpress the sex determination genes fru M and dsx, but does not affect female sexual behavior. Further, we delineate a sex-specific neuronal circuit wherein the P1 neurons encoding increased courtship drive suppressed male sleep by forming mutually excitatory connections with the fru M-positive sleep-controlling DN1 neurons. In addition, we find that FRU M regulates male courtship and sleep through distinct neural substrates. These studies reveal the genetic and neuronal basis underlying the sex-specific interaction between sleep and sexual behaviors in Drosophila, and provide insights into how competing behaviors are co-regulated.
Proceedings of the National Academy of Sciences of the United States of America, Apr 8, 2008
Journal of Comparative Physiology A-neuroethology Sensory Neural and Behavioral Physiology, Jun 6, 2007
Apparently unpaired exposure to appetitive or aversive stimuli can suppress or enhance later asso... more Apparently unpaired exposure to appetitive or aversive stimuli can suppress or enhance later associative learning. While the suppressive eVect has been found in both vertebrate and invertebrate animals, it is not clear if the enhancing eVect is restricted to the vertebrates. Additionally, whether Drosophila associative learning can be inXuenced in either direction is open. To address these questions, we examined the eVects of pre-exposing Xies to a high temperature negative reinforcer in the heat-box placelearning paradigm. We found that pre-exposing Xies to an unavoidable high temperature enhanced later associative conditioning that uses mild increases in temperature. This enhancement lasts at least 20 min, does not depend on changes in the straightforward avoidance behavior of a high temperature source, and is independent of the antennal thermosensor. We thus provide an example of enhanced associative learning after unpaired exposure to a typical reinforcer in an invertebrate animal, suggesting the conservation of this component of learning.
Genetics, Apr 1, 2008
The ad hoc genetic correlation between ethanol sensitivity and learning mechanisms in Drosophila ... more The ad hoc genetic correlation between ethanol sensitivity and learning mechanisms in Drosophila could overemphasize a common process supporting both behaviors. To challenge directly the hypothesis that these mechanisms are singular, we examined the learning phenotypes of 10 new strains. Five of these have increased ethanol sensitivity, and the other 5 do not. We tested place and olfactory memory in each of these lines and found two new learning mutations. In one case, altering the tribbles gene, flies have a significantly reduced place memory, elevated olfactory memory, and normal ethanol response. In the second case, mutation of a gene we name ethanol sensitive with low memory (elm), place memory was not altered, olfactory memory was sharply reduced, and sensitivity to ethanol was increased. In sum, however, we found no overall correlation between ethanol sensitivity and place memory in the 10 lines tested. Furthermore, there was a weak but nonsignificant correlation between ethanol sensitivity and olfactory learning. Thus, mutations that alter learning and sensitivity to ethanol can occur independently of each other and this implies that the set of genes important for both ethanol sensitivity and learning is likely a subset of the genes important for either process.
Journal of Neurogenetics, Dec 27, 2019
Current Biology, Jul 1, 2017
Highlights d DH44-R1 functions in hugin + neurons to regulate rest:activity rhythms d A neuromedi... more Highlights d DH44-R1 functions in hugin + neurons to regulate rest:activity rhythms d A neuromedin U ortholog, Hugin, is a circadian output molecule d An LNv/DN1/DH44 PI/Hugin SEZ/VNC circuit links the clock to motor output d The DH44 PI-Hugin SEZ circuit regulates locomotor activity, but not feeding rhythms
Neural circuits involved in regulation of sleep play a critical role in sleep-wake transition and... more Neural circuits involved in regulation of sleep play a critical role in sleep-wake transition and ability of an organism to engage in other behaviors critical for survival. The fruit fly, Drosophila melanogaster is a powerful system for the study of sleep and circuit mechanisms underlying sleep and co-regulation of sleep with other behaviors. InDrosophila, two neuropils in the central brain, mushroom body (MB) and central complex (CX) have been shown to influence sleep homeostasis and receive neuromodulator input critical to sleep-wake switch.Dopamine neurons (DANs) are the primary neuromodulator inputs to the MB but the mechanisms by which they regulate sleep- and wake-promoting neurons within MB are unknown. Here we investigate the role of subsets of DANs that signal wakefulness and project to wake-promoting compartments of the MB. We find that inhibition of specific subsets of PAM and PPL1 DANs projecting to the MB increase sleep in the presence of strong wake-inducing stimuli th...
BIO-PROTOCOL, 2019
Sleep is a conserved neurobehavioral state observed in animals with sufficiently complex nervous ... more Sleep is a conserved neurobehavioral state observed in animals with sufficiently complex nervous systems and is critical for survival. While the exact function of sleep remains unknown, the lack of sleep can have a range of physiological and behavioral effects. Studies in invertebrates and vertebrates have identified conserved neural mechanisms and cellular pathways in control of sleep, wakefulness and arousal. Methodologies to measure sleep have ranged from EEG recordings in humans and rodents to in-depth analysis of locomotor patterns in flies, fish and worms. Here we focus on sleep measurements using activity monitoring in the highly versatile experimental model system, Drosophila melanogaster, which is amenable to a number of genetic, physiological and behavioral manipulations. Further, we also describe methods used to manipulate sleep and wakefulness to understand the neural regulation of sleep and how organisms balance sleep, wakefulness and behavioral arousal. Sleep as a behavioral state is regulated by a number of factors including food, environmental conditions, and genetic background. The methodologies described here provide, a highthroughput approach to study neural regulation of sleep and factors that affect this complex behavior.
Journal of Neurogenetics, 2019
selection in Drosophila
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Papers by Divya Sitaraman