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  1. AU=Rosensweig Clark
  2. AU="Leff, Jonathan D"
  3. AU="Akira Goto"
  4. AU="Javier Pizarro-Cerda"
  5. AU="Oakley, James V"
  6. AU="Wen, Teresa H"
  7. AU="Li, Huiyu"
  8. AU="Pannala, Ananth S"
  9. AU="Noda, K."
  10. AU="Almeida, Carolina Aparecida Faria"
  11. AU=Khoshakhlagh Arezou
  12. AU="Sofija Glamočlija"
  13. AU="Fleming, Sherry D"
  14. AU="Minkina, Tatiana M"
  15. AU="Fonseca, Danielle"
  16. AU="Maximilian, Carmen-Rodica"
  17. AU="Heuer, Lauren B"
  18. AU="Pan, Judy"
  19. AU="Doro, M."
  20. AU="Navarro-Zapata, Alfonso"
  21. AU="Martin, Emanuel H"
  22. AU="Biswas, Arnab"
  23. AU="Kurt Pfister"
  24. AU="Stefano Brignola"
  25. AU="Nierzwicki, Łukasz"
  26. AU="Benvin, Iva"
  27. AU="Sardesai, S. C."
  28. AU="Aldrees, Rana"

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  1. Artikel ; Online: SleepMat: a new behavioral analysis software program for sleep and circadian rhythms.

    Sisobhan, Shiju / Rosensweig, Clark / Lear, Bridget C / Allada, Ravi

    Sleep

    2022  Band 45, Heft 12

    Abstract: Study objectives: To develop a new publicly available software SleepMat that analyzes Drosophila Activity Monitoring system data.: Methods: The software is built on Matlab platform, employs an easy-to-use graphic user interface, and is highly ... ...

    Abstract Study objectives: To develop a new publicly available software SleepMat that analyzes Drosophila Activity Monitoring system data.
    Methods: The software is built on Matlab platform, employs an easy-to-use graphic user interface, and is highly flexible to customize data inputs.
    Results: This software provides large number of sleep and circadian parameters including period, actogram, anticipation, sleep amount, bout length, bout number, activity, sleep deprivation, latency, lifespan, and eduction results.
    Conclusions: This software will enable a user-friendly high throughput analysis of a broad range of sleep and circadian parameters that can be coupled to the power of Drosophila genetics.
    Mesh-Begriff(e) Animals ; Circadian Rhythm ; Sleep ; Sleep Deprivation ; Drosophila ; Software
    Sprache Englisch
    Erscheinungsdatum 2022-08-03
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 424441-2
    ISSN 1550-9109 ; 0161-8105
    ISSN (online) 1550-9109
    ISSN 0161-8105
    DOI 10.1093/sleep/zsac195
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  2. Artikel ; Online: Temperature-driven coordination of circadian transcriptional regulation.

    Xu, Bingxian / Hwangbo, Dae-Sung / Saurabh, Sumit / Rosensweig, Clark / Allada, Ravi / Kath, William L / Braun, Rosemary

    PLoS computational biology

    2024  Band 20, Heft 4, Seite(n) e1012029

    Abstract: The circadian clock is an evolutionarily-conserved molecular oscillator that enables species to anticipate rhythmic changes in their environment. At a molecular level, the core clock genes induce circadian oscillations in thousands of genes in a tissue- ... ...

    Abstract The circadian clock is an evolutionarily-conserved molecular oscillator that enables species to anticipate rhythmic changes in their environment. At a molecular level, the core clock genes induce circadian oscillations in thousands of genes in a tissue-specific manner, orchestrating myriad biological processes. While previous studies have investigated how the core clock circuit responds to environmental perturbations such as temperature, the downstream effects of such perturbations on circadian regulation remain poorly understood. By analyzing bulk-RNA sequencing of Drosophila fat bodies harvested from flies subjected to different environmental conditions, we demonstrate a highly condition-specific circadian transcriptome: genes are cycling in a temperature-specific manner, and the distributions of their phases also differ between the two conditions. Further employing a reference-based gene regulatory network (Reactome), we find evidence of increased gene-gene coordination at low temperatures and synchronization of rhythmic genes that are network neighbors. We report that the phase differences between cycling genes increase as a function of geodesic distance in the low temperature condition, suggesting increased coordination of cycling on the gene regulatory network. Our results suggest a potential mechanism whereby the circadian clock mediates the fly's response to seasonal changes in temperature.
    Sprache Englisch
    Erscheinungsdatum 2024-04-22
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1012029
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  3. Artikel ; Online: A subclass of evening cells promotes the switch from arousal to sleep at dusk.

    Brown, Matthew P / Verma, Shubha / Palmer, Isabelle / Guerrero Zuniga, Adler / Mehta, Anuradha / Rosensweig, Clark / Keles, Mehmet F / Wu, Mark N

    Current biology : CB

    2024  

    Abstract: Animals exhibit rhythmic patterns of behavior that are shaped by an internal circadian clock and the external environment. Although light intensity varies across the day, there are particularly robust differences at twilight (dawn/dusk). These periods ... ...

    Abstract Animals exhibit rhythmic patterns of behavior that are shaped by an internal circadian clock and the external environment. Although light intensity varies across the day, there are particularly robust differences at twilight (dawn/dusk). These periods are also associated with major changes in behavioral states, such as the transition from arousal to sleep. However, the neural mechanisms by which time and environmental conditions promote these behavioral transitions are poorly defined. Here, we show that the E1 subclass of Drosophila evening clock neurons promotes the transition from arousal to sleep at dusk. We first demonstrate that the cell-autonomous clocks of E2 neurons primarily drive and adjust the phase of evening anticipation, the canonical behavior associated with "evening" clock neurons. We next show that conditionally silencing E1 neurons causes a significant delay in sleep onset after dusk. However, rather than simply promoting sleep, activating E1 neurons produces time- and light-dependent effects on behavior. Activation of E1 neurons has no effect early in the day but then triggers arousal before dusk and induces sleep after dusk. Strikingly, these activation-induced phenotypes depend on the presence of light during the day. Despite their influence on behavior around dusk, in vivo voltage imaging of E1 neurons reveals that their spiking rate and pattern do not significantly change throughout the day. Moreover, E1-specific clock ablation has no effect on arousal or sleep. Thus, we suggest that, rather than specifying "evening" time, E1 neurons act, in concert with other rhythmic neurons, to promote behavioral transitions at dusk.
    Sprache Englisch
    Erscheinungsdatum 2024-04-30
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 1071731-6
    ISSN 1879-0445 ; 0960-9822
    ISSN (online) 1879-0445
    ISSN 0960-9822
    DOI 10.1016/j.cub.2024.04.039
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  4. Artikel ; Online: Circadian programming of the ellipsoid body sleep homeostat in

    Andreani, Tomas / Rosensweig, Clark / Sisobhan, Shiju / Ogunlana, Emmanuel / Kath, William / Allada, Ravi

    eLife

    2022  Band 11

    Abstract: Homeostatic and circadian processes collaborate to appropriately time and consolidate sleep and wake. To understand how these processes are integrated, we scheduled brief sleep deprivation at different times of day ... ...

    Abstract Homeostatic and circadian processes collaborate to appropriately time and consolidate sleep and wake. To understand how these processes are integrated, we scheduled brief sleep deprivation at different times of day in
    Mesh-Begriff(e) Animals ; Circadian Clocks/genetics ; Circadian Rhythm/genetics ; Drosophila/metabolism ; Drosophila Proteins/metabolism ; Drosophila melanogaster/physiology ; Sleep/physiology
    Chemische Substanzen Drosophila Proteins
    Sprache Englisch
    Erscheinungsdatum 2022-06-23
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.74327
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  5. Artikel ; Online: Periodicity, repression, and the molecular architecture of the mammalian circadian clock.

    Rosensweig, Clark / Green, Carla B

    The European journal of neuroscience

    2018  Band 51, Heft 1, Seite(n) 139–165

    Abstract: Large molecular machines regulate daily cycles of transcriptional activity and help generate rhythmic behavior. In recent years, structural and biochemical analyses have elucidated a number of principles guiding the interactions of proteins that form the ...

    Abstract Large molecular machines regulate daily cycles of transcriptional activity and help generate rhythmic behavior. In recent years, structural and biochemical analyses have elucidated a number of principles guiding the interactions of proteins that form the basis of circadian timing. In its simplest form, the circadian clock is composed of a transcription/translation feedback loop. However, this description elides a complicated process of activator recruitment, chromatin decompaction, recruitment of coactivators, expression of repressors, formation of a repressive complex, repression of the activators, and ultimately degradation of the repressors and reinitiation of the cycle. Understanding the core principles underlying the clock requires careful examination of molecular and even atomic level details of these processes. Here, we review major structural and biochemical findings in circadian biology and make the argument that shared protein interfaces within the clockwork are critical for both the generation of rhythmicity and timing of the clock.
    Mesh-Begriff(e) ARNTL Transcription Factors ; Animals ; CLOCK Proteins/genetics ; Circadian Clocks ; Circadian Rhythm
    Chemische Substanzen ARNTL Transcription Factors ; CLOCK Proteins (EC 2.3.1.48)
    Sprache Englisch
    Erscheinungsdatum 2018-12-08
    Erscheinungsland France
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 645180-9
    ISSN 1460-9568 ; 0953-816X
    ISSN (online) 1460-9568
    ISSN 0953-816X
    DOI 10.1111/ejn.14254
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    Zs.A 2548: Hefte anzeigen Standort:
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  6. Artikel: Temperature-driven coordination of circadian transcriptome regulation.

    Xu, Bingxian / Hwangbo, Dae-Sung / Saurabh, Sumit / Rosensweig, Clark / Allada, Ravi / Kath, William L / Braun, Rosemary

    bioRxiv : the preprint server for biology

    2023  

    Abstract: The circadian rhythm is an evolutionarily-conserved molecular oscillator that enables species to anticipate rhythmic changes in their environment. At a molecular level, the core clock genes induce a circadian oscillation in thousands of genes in a tissue- ...

    Abstract The circadian rhythm is an evolutionarily-conserved molecular oscillator that enables species to anticipate rhythmic changes in their environment. At a molecular level, the core clock genes induce a circadian oscillation in thousands of genes in a tissue-specific manner, orchestrating myriad biological processes. While studies have investigated how the core clock circuit responds to environmental perturbations such as temperature, the downstream effects of such perturbations on circadian regulation remain poorly understood. By analyzing bulk-RNA sequencing of
    Sprache Englisch
    Erscheinungsdatum 2023-11-01
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.1101/2023.10.27.563979
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  7. Artikel: A subclass of evening cells promotes the switch from arousal to sleep at dusk.

    Brown, Matthew P / Verma, Shubha / Palmer, Isabelle / Zuniga, Adler Guerrero / Rosensweig, Clark / Keles, Mehmet F / Wu, Mark N

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Animals exhibit rhythmic patterns of behavior that are shaped by an internal circadian clock and the external environment. While light intensity varies across the day, there are particularly robust differences at twilight (dawn/dusk). These periods are ... ...

    Abstract Animals exhibit rhythmic patterns of behavior that are shaped by an internal circadian clock and the external environment. While light intensity varies across the day, there are particularly robust differences at twilight (dawn/dusk). These periods are also associated with major changes in behavioral states, such as the transition from arousal to sleep. However, the neural mechanisms by which time and environmental conditions promote these behavioral transitions are poorly defined. Here, we show that the E1 subclass of
    Sprache Englisch
    Erscheinungsdatum 2023-08-29
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.1101/2023.08.28.555147
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  8. Artikel ; Online: Circadian programming of the ellipsoid body sleep homeostat in Drosophila

    Tomas Andreani / Clark Rosensweig / Shiju Sisobhan / Emmanuel Ogunlana / William Kath / Ravi Allada

    eLife, Vol

    2022  Band 11

    Abstract: Homeostatic and circadian processes collaborate to appropriately time and consolidate sleep and wake. To understand how these processes are integrated, we scheduled brief sleep deprivation at different times of day in Drosophila and find elevated morning ...

    Abstract Homeostatic and circadian processes collaborate to appropriately time and consolidate sleep and wake. To understand how these processes are integrated, we scheduled brief sleep deprivation at different times of day in Drosophila and find elevated morning rebound compared to evening. These effects depend on discrete morning and evening clock neurons, independent of their roles in circadian locomotor activity. In the R5 ellipsoid body sleep homeostat, we identified elevated morning expression of activity dependent and presynaptic gene expression as well as the presynaptic protein BRUCHPILOT consistent with regulation by clock circuits. These neurons also display elevated calcium levels in response to sleep loss in the morning, but not the evening consistent with the observed time-dependent sleep rebound. These studies reveal the circuit and molecular mechanisms by which discrete circadian clock neurons program a homeostatic sleep center.
    Schlagwörter circadian ; sleep homeostasis ; ellipsoid body ; Drosophila ; clock ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
    Thema/Rubrik (Code) 571
    Sprache Englisch
    Erscheinungsdatum 2022-06-01T00:00:00Z
    Verlag eLife Sciences Publications Ltd
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  9. Buch ; Online: Modeling Transient Changes in Circadian Rhythms

    Zhao, Ziyu / Hwangbo, Dae-Sung / Saurabh, Sumit / Rosensweig, Clark / Allada, Ravi / Kath, William L. / Braun, Rosemary

    2023  

    Abstract: The circadian clock can adapt itself to external cues, but the molecular mechanisms and regulatory networks governing circadian oscillations' transient adjustments are still largely unknown. Here we consider the specific case of circadian oscillations ... ...

    Abstract The circadian clock can adapt itself to external cues, but the molecular mechanisms and regulatory networks governing circadian oscillations' transient adjustments are still largely unknown. Here we consider the specific case of circadian oscillations transiently responding to a temperature change. Using a framework motivated by Floquet theory, we model the mRNA expression level of the fat body from Drosophila melanogaster following a step change from 25C to 18C. Using the method we infer the adaptation rates of individual genes as they adapt to the new temperature. To deal with heteroskedastic noise and outliers present in the expression data we employ quantile regression and wild bootstrap for significance testing. Model selection with finite-sample corrected Akaike Information Criterion (AICc) is performed additionally for robust inference. We identify several genes with fast transition rates as potential sources of temperature-mediated responses in the circadian system of fruit flies, and the constructed network suggests that the proteasome may play important roles in governing these responses.
    Schlagwörter Quantitative Biology - Molecular Networks ; Quantitative Biology - Quantitative Methods
    Thema/Rubrik (Code) 612
    Erscheinungsdatum 2023-04-14
    Erscheinungsland us
    Dokumenttyp Buch ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  10. Artikel ; Online: An evolutionary hotspot defines functional differences between CRYPTOCHROMES.

    Rosensweig, Clark / Reynolds, Kimberly A / Gao, Peng / Laothamatas, Isara / Shan, Yongli / Ranganathan, Rama / Takahashi, Joseph S / Green, Carla B

    Nature communications

    2018  Band 9, Heft 1, Seite(n) 1138

    Abstract: Mammalian circadian clocks are driven by a transcription/translation feedback loop composed of positive regulators (CLOCK/BMAL1) and repressors (CRYPTOCHROME 1/2 (CRY1/2) and PER1/2). To understand the structural principles of regulation, we used ... ...

    Abstract Mammalian circadian clocks are driven by a transcription/translation feedback loop composed of positive regulators (CLOCK/BMAL1) and repressors (CRYPTOCHROME 1/2 (CRY1/2) and PER1/2). To understand the structural principles of regulation, we used evolutionary sequence analysis to identify co-evolving residues within the CRY/PHL protein family. Here we report the identification of an ancestral secondary cofactor-binding pocket as an interface in repressive CRYs, mediating regulation through direct interaction with CLOCK and BMAL1. Mutations weakening binding between CLOCK/BMAL1 and CRY1 lead to acceleration of the clock, suggesting that subtle sequence divergences at this site can modulate clock function. Divergence between CRY1 and CRY2 at this site results in distinct periodic output. Weaker interactions between CRY2 and CLOCK/BMAL1 at this pocket are strengthened by co-expression of PER2, suggesting that PER expression limits the length of the repressive phase in CRY2-driven rhythms. Overall, this work provides a model for the mechanism and evolutionary variation of clock regulatory mechanisms.
    Mesh-Begriff(e) ARNTL Transcription Factors/chemistry ; ARNTL Transcription Factors/genetics ; ARNTL Transcription Factors/metabolism ; Allosteric Site/genetics ; Animals ; CLOCK Proteins/chemistry ; CLOCK Proteins/genetics ; CLOCK Proteins/metabolism ; Cell Line ; Circadian Clocks/genetics ; Cryptochromes/chemistry ; Cryptochromes/genetics ; Cryptochromes/metabolism ; Evolution, Molecular ; HEK293 Cells ; Humans ; Insect Proteins/chemistry ; Insect Proteins/genetics ; Insect Proteins/metabolism ; Mice ; Mice, Knockout ; Models, Molecular ; Period Circadian Proteins/chemistry ; Period Circadian Proteins/genetics ; Period Circadian Proteins/metabolism ; Protein Interaction Domains and Motifs/genetics ; Structural Homology, Protein
    Chemische Substanzen ARNTL Transcription Factors ; Cryptochromes ; Insect Proteins ; Period Circadian Proteins ; CLOCK Proteins (EC 2.3.1.48)
    Sprache Englisch
    Erscheinungsdatum 2018-03-19
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 2041-1723
    ISSN (online) 2041-1723
    DOI 10.1038/s41467-018-03503-6
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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