capturing circadian clocks from the perspective of phase
play

Capturing Circadian Clocks from the Perspective of Phase-Locked - PowerPoint PPT Presentation

Nov 16, 2022 •130 likes •505 views

Motivation Elementary Oscillators Low-Pass Filters Signal Comparator Discussion Capturing Circadian Clocks from the Perspective of Phase-Locked Loops Thomas Hinze Friedrich-Schiller-Universitt Jena Lehrstuhl Bioinformatik an der

  1. Motivation Elementary Oscillators Low-Pass Filters Signal Comparator Discussion Capturing Circadian Clocks from the Perspective of Phase-Locked Loops Thomas Hinze Friedrich-Schiller-Universität Jena Lehrstuhl Bioinformatik an der Biologisch-Pharmazeutischen Fakultät thomas.hinze@uni-jena.de Capturing Circadian Clocks from the Perspective of Phase-Locked Loops Thomas Hinze

  2. Motivation Elementary Oscillators Low-Pass Filters Signal Comparator Discussion Network Reconstruction: Complementary Strategies Top-down • From functional components to interacting network modules • Successive refinement • Identification, exploration and exchange of module candidates Bottom-up • From a monolithic behavioural specification to functional components • Successive modularisation • Identification of subnetworks acting as interfaced modules = ⇒ We introduce a top-down strategy inspired by control systems. Capturing Circadian Clocks from the Perspective of Phase-Locked Loops Thomas Hinze

  3. Motivation Elementary Oscillators Low-Pass Filters Signal Comparator Discussion Network Reconstruction: Complementary Strategies Top-down • From functional components to interacting network modules • Successive refinement • Identification, exploration and exchange of module candidates Bottom-up • From a monolithic behavioural specification to functional components • Successive modularisation • Identification of subnetworks acting as interfaced modules = ⇒ We introduce a top-down strategy inspired by control systems. Capturing Circadian Clocks from the Perspective of Phase-Locked Loops Thomas Hinze

  4. Motivation Elementary Oscillators Low-Pass Filters Signal Comparator Discussion Network Reconstruction: Complementary Strategies Top-down • From functional components to interacting network modules • Successive refinement • Identification, exploration and exchange of module candidates Bottom-up • From a monolithic behavioural specification to functional components • Successive modularisation • Identification of subnetworks acting as interfaced modules = ⇒ We introduce a top-down strategy inspired by control systems. Capturing Circadian Clocks from the Perspective of Phase-Locked Loops Thomas Hinze

  5. Motivation Elementary Oscillators Low-Pass Filters Signal Comparator Discussion Circadian Clocks: General Schematic Representation external one or several stimuli coupled (reference input) elementary oscillator(s) input path output path (upstream (downstream reaction network) reaction network) local feedback(s) Adapted from M.J. Gardner et al. How plants tell the time. Review in Biochem. J. 397 :15-24, 2006 Capturing Circadian Clocks from the Perspective of Phase-Locked Loops Thomas Hinze

  6. Motivation Elementary Oscillators Low-Pass Filters Signal Comparator Discussion Frequency Control Systems with Phase-Locked Loop external one or several stimuli coupled output (reference) elementary oscillator(s) signal tuning global feedback path signal signal comparator (loop filter for (phase difference or damping and delay) affects frequency deviation) frequency local feedback(s) error signal Adapted from J.L. Stensby. Phase-locked loops. CRC Press, 1997 Capturing Circadian Clocks from the Perspective of Phase-Locked Loops Thomas Hinze

  7. Motivation Elementary Oscillators Low-Pass Filters Signal Comparator Discussion Considering Elementary Oscillators external one or several stimuli coupled output (reference) elementary oscillator(s) signal tuning global feedback path signal signal comparator (loop filter for (phase difference or damping and delay) affects frequency deviation) frequency local feedback(s) error signal Collaboration with C. Bodenstein and B. Schau, FSU Jena Capturing Circadian Clocks from the Perspective of Phase-Locked Loops Thomas Hinze

  8. Motivation Elementary Oscillators Low-Pass Filters Signal Comparator Discussion Elementary Oscillators under Study • Sinusoidal function / Fourier series (dummy oscillator) • Goodwin oscillator (original form) • Goodwin oscillator with Michaelis-Menten degradation • First attempts towards Chlamydomonas core oscillator • Brusselator (autocatalysis, exclusively positive feedback loops) • Sirius oscillator (resonator, clock signal generator) • Repressilator (gene regulatory network, well-studied) • Suprachiasmatic nucleus (single neuron oscillator, well-studied) = ⇒ How to vary frequency? Obtaining response curves Capturing Circadian Clocks from the Perspective of Phase-Locked Loops Thomas Hinze

  9. Motivation Elementary Oscillators Low-Pass Filters Signal Comparator Discussion Elementary Oscillators under Study • Sinusoidal function / Fourier series (dummy oscillator) • Goodwin oscillator (original form) • Goodwin oscillator with Michaelis-Menten degradation • First attempts towards Chlamydomonas core oscillator • Brusselator (autocatalysis, exclusively positive feedback loops) • Sirius oscillator (resonator, clock signal generator) • Repressilator (gene regulatory network, well-studied) • Suprachiasmatic nucleus (single neuron oscillator, well-studied) = ⇒ How to vary frequency? Obtaining response curves Capturing Circadian Clocks from the Perspective of Phase-Locked Loops Thomas Hinze

  10. Motivation Elementary Oscillators Low-Pass Filters Signal Comparator Discussion Elementary Oscillators under Study • Sinusoidal function / Fourier series (dummy oscillator) • Goodwin oscillator (original form) • Goodwin oscillator with Michaelis-Menten degradation • First attempts towards Chlamydomonas core oscillator • Brusselator (autocatalysis, exclusively positive feedback loops) • Sirius oscillator (resonator, clock signal generator) • Repressilator (gene regulatory network, well-studied) • Suprachiasmatic nucleus (single neuron oscillator, well-studied) = ⇒ How to vary frequency? Obtaining response curves Capturing Circadian Clocks from the Perspective of Phase-Locked Loops Thomas Hinze

  11. Motivation Elementary Oscillators Low-Pass Filters Signal Comparator Discussion Elementary Oscillators under Study • Sinusoidal function / Fourier series (dummy oscillator) • Goodwin oscillator (original form) • Goodwin oscillator with Michaelis-Menten degradation • First attempts towards Chlamydomonas core oscillator • Brusselator (autocatalysis, exclusively positive feedback loops) • Sirius oscillator (resonator, clock signal generator) • Repressilator (gene regulatory network, well-studied) • Suprachiasmatic nucleus (single neuron oscillator, well-studied) = ⇒ How to vary frequency? Obtaining response curves Capturing Circadian Clocks from the Perspective of Phase-Locked Loops Thomas Hinze

  12. Motivation Elementary Oscillators Low-Pass Filters Signal Comparator Discussion Elementary Oscillators under Study • Sinusoidal function / Fourier series (dummy oscillator) • Goodwin oscillator (original form) • Goodwin oscillator with Michaelis-Menten degradation • First attempts towards Chlamydomonas core oscillator • Brusselator (autocatalysis, exclusively positive feedback loops) • Sirius oscillator (resonator, clock signal generator) • Repressilator (gene regulatory network, well-studied) • Suprachiasmatic nucleus (single neuron oscillator, well-studied) = ⇒ How to vary frequency? Obtaining response curves Capturing Circadian Clocks from the Perspective of Phase-Locked Loops Thomas Hinze

  13. Motivation Elementary Oscillators Low-Pass Filters Signal Comparator Discussion Elementary Oscillators under Study • Sinusoidal function / Fourier series (dummy oscillator) • Goodwin oscillator (original form) • Goodwin oscillator with Michaelis-Menten degradation • First attempts towards Chlamydomonas core oscillator • Brusselator (autocatalysis, exclusively positive feedback loops) • Sirius oscillator (resonator, clock signal generator) • Repressilator (gene regulatory network, well-studied) • Suprachiasmatic nucleus (single neuron oscillator, well-studied) = ⇒ How to vary frequency? Obtaining response curves Capturing Circadian Clocks from the Perspective of Phase-Locked Loops Thomas Hinze

  14. Motivation Elementary Oscillators Low-Pass Filters Signal Comparator Discussion Elementary Oscillators under Study • Sinusoidal function / Fourier series (dummy oscillator) • Goodwin oscillator (original form) • Goodwin oscillator with Michaelis-Menten degradation • First attempts towards Chlamydomonas core oscillator • Brusselator (autocatalysis, exclusively positive feedback loops) • Sirius oscillator (resonator, clock signal generator) • Repressilator (gene regulatory network, well-studied) • Suprachiasmatic nucleus (single neuron oscillator, well-studied) = ⇒ How to vary frequency? Obtaining response curves Capturing Circadian Clocks from the Perspective of Phase-Locked Loops Thomas Hinze

  15. Motivation Elementary Oscillators Low-Pass Filters Signal Comparator Discussion Elementary Oscillators under Study • Sinusoidal function / Fourier series (dummy oscillator) • Goodwin oscillator (original form) • Goodwin oscillator with Michaelis-Menten degradation • First attempts towards Chlamydomonas core oscillator • Brusselator (autocatalysis, exclusively positive feedback loops) • Sirius oscillator (resonator, clock signal generator) • Repressilator (gene regulatory network, well-studied) • Suprachiasmatic nucleus (single neuron oscillator, well-studied) = ⇒ How to vary frequency? Obtaining response curves Capturing Circadian Clocks from the Perspective of Phase-Locked Loops Thomas Hinze

Recommend

Clocks Some clocks use motion to mark their intervals Others clocks dont appear to

Clocks Some clocks use motion to mark their intervals Others clocks dont appear to

Clocks 1 Clocks 2 Observations About Clocks They divide time into uniform intervals The measure time by counting those intervals Clocks Some clocks use motion to mark their intervals Others clocks dont appear to involve motion

305 views • 3 slides
3/2/19 Circadian rhythms (very brief) intro Rhythms and reward: Do circadian factors

3/2/19 Circadian rhythms (very brief) intro Rhythms and reward: Do circadian factors

3/2/19 Circadian rhythms (very brief) intro Rhythms and reward: Do circadian factors contribute to risk for adolescent substance use? Brant P Hasler, PhD, CBSM Organize physiological and behavioral processes for optimal interaction with

354 views • 8 slides
Sleep & Well-being Neuroscience of Sleep & Clocks Impact of Sleep Disruption

Sleep & Well-being Neuroscience of Sleep & Clocks Impact of Sleep Disruption

Sleep & Well-being Neuroscience of Sleep & Clocks Impact of Sleep Disruption Sleep in the Young Sleep Hygiene Mental Illness Discussion http://www.eye.ox.ac.uk/research/sleep- circadian-neuroscience-institute

943 views • 62 slides
Circadian Rhythms Controlling the timing of behaviour by anticipating the environment

Circadian Rhythms Controlling the timing of behaviour by anticipating the environment

Circadian Rhythms Controlling the timing of behaviour by anticipating the environment Circadian = circa + dium Exists in most if not all unicellular and multicellular organisms The Circadian Circuit Environmental Output Inputs

475 views • 36 slides
Phase-locked Loops for Chemical Control of Oscillation Frequency A prototype of biological clocks

Phase-locked Loops for Chemical Control of Oscillation Frequency A prototype of biological clocks

Motivation PLL Scheme Core Oscillator Signal Comparator Global Feedback Simul. Studies Generalisation Prospectives Phase-locked Loops for Chemical Control of Oscillation Frequency A prototype of biological clocks and their entrainment by

796 views • 58 slides
Continuous attractors as unreliable estimators Arvind Murugan Dept. of Physics Regression using

Continuous attractors as unreliable estimators Arvind Murugan Dept. of Physics Regression using

Continuous attractors as unreliable estimators Arvind Murugan Dept. of Physics Regression using attractors High dim config space Regression Attractor dynamics Circadian clocks as phase estimators External signal (Day-night cycle of light)

392 views • 17 slides
1 Sleep and Circadian Rhythms Functions of Sleep and Circadian Rhythm Functions of Sleep and

1 Sleep and Circadian Rhythms Functions of Sleep and Circadian Rhythm Functions of Sleep and

Disclosures Sleep-Circadian Rhythms in Aging and Women: Current research funding (Northwestern University) A Bi-directional Relationship? NIH (NHLBI, NIA) DARPA Jazz Alzheimers Association Dixon Family Foundation

466 views • 10 slides
Social (Media) Jet Lag: how usage of social technology can modulate and reflect circadian

Social (Media) Jet Lag: how usage of social technology can modulate and reflect circadian

Social (Media) Jet Lag: how usage of social technology can modulate and reflect circadian rhythms Elizabeth Murnane, Saeed Abdullah, Mark Matthews, Tanzeem Choudhury, Geri Gay Motivation Circadian-Aware Sensing and Intervention Sleep

1.22k views • 95 slides
Lab 11: Morning Lark or Night Owl? Circadian Clock Internal timekeeper that regulates the

Lab 11: Morning Lark or Night Owl? Circadian Clock Internal timekeeper that regulates the

NOTEBOOK Lab 11: Morning Lark or Night Owl? Circadian Clock Internal timekeeper that regulates the bodys physiology and behavior on a cycle that repeats each day Other animals, plants, fungi and unicellular organisms have circadian

279 views • 14 slides
Healthy Sleep Habits Homeostasis Homeostasis: Keeps track of need for sleep SAMANTHA

Healthy Sleep Habits Homeostasis Homeostasis: Keeps track of need for sleep SAMANTHA

10/27/2020 Circadian Rhythms: Internally driven cycles, bodys circadian clock Helps fall asleep and wake Circadian Rhythms are set by the light/dark Rhythms and cycle of the sun Healthy Sleep Habits Homeostasis Homeostasis:

314 views • 3 slides
Todays Topics Chapter 10. Clocks Physical Clocks. Synchronising physical clocks

Todays Topics Chapter 10. Clocks Physical Clocks. Synchronising physical clocks

Distributed Systems Lecture 3 1 Todays Topics Chapter 10. Clocks Physical Clocks. Synchronising physical clocks Logical Clocks Distributed Systems Lecture 3 2 What is time? What, then, is time? If no one asks me, I know

487 views • 22 slides
Question: Clocks Youre bouncing gently up and down at the end of a springboard, without

Question: Clocks Youre bouncing gently up and down at the end of a springboard, without

Clocks 1 Clocks 2 Question: Clocks Youre bouncing gently up and down at the end of a springboard, without leaving the boards surface. If you bounce harder, the time it takes for each bounce will become shorter become longer

501 views • 3 slides
Lamport Clocks Doug Woos Logistics notes Problem Set 1 due Friday Chandy-Lamport Snapshots

Lamport Clocks Doug Woos Logistics notes Problem Set 1 due Friday Chandy-Lamport Snapshots

Lamport Clocks Doug Woos Logistics notes Problem Set 1 due Friday Chandy-Lamport Snapshots thread up Today Lamport Clocks - Motivation - Basic ideas -Mutual exclusion - State machine replication Vector clocks Lamport Clocks Classic

743 views • 30 slides
Cold Atom Atom Clocks Clocks Cold Cold Atom Clocks and Fundamental Fundamental Tests Tests

Cold Atom Atom Clocks Clocks Cold Cold Atom Clocks and Fundamental Fundamental Tests Tests

Cold Atom Atom Clocks Clocks Cold Cold Atom Clocks and Fundamental Fundamental Tests Tests and and Fundamental Tests C. Salomon Laboratoire Kastler Brossel, Ecole Normale Suprieure, Paris

768 views • 38 slides
Numb3rs 11 2 10 3 The Chinese Remainder Theorem 9 4 8 5 7 6 Chiming Clocks Two clocks,

Numb3rs 11 2 10 3 The Chinese Remainder Theorem 9 4 8 5 7 6 Chiming Clocks Two clocks,

0 12 1 Numb3rs 11 2 10 3 The Chinese Remainder Theorem 9 4 8 5 7 6 Chiming Clocks Two clocks, with a hours and b hours on their dials 0 1 12 Say they both start at 0, and move one step every 2 11 10 3 minute 9 4 e.g.,

310 views • 13 slides
Recall our discussion of time CS514: Intermediate Course Logical clocks: represent part of

Recall our discussion of time CS514: Intermediate Course Logical clocks: represent part of

Recall our discussion of time CS514: Intermediate Course Logical clocks: represent part of in Operating Systems relation, small overhead Vector clocks: accurately represent but more costly Professor Ken Birman Wall clocks:

388 views • 10 slides
Real clocks: a toy model for non-locality luis j. garay Universidad Complutense de Madrid

Real clocks: a toy model for non-locality luis j. garay Universidad Complutense de Madrid

Real clocks: a toy model for non-locality luis j. garay Universidad Complutense de Madrid NORDITA, Stockholm Non-locality: Aspects and Consequences 29 June 2012 Contents Non-ideal clocks Good clocks Evolution Loss of

622 views • 20 slides
A 40 Year Journey from Drosophila 's Clock Mutants to Human Circadian Disorders Mirabilis (Four

A 40 Year Journey from Drosophila 's Clock Mutants to Human Circadian Disorders Mirabilis (Four

A 40 Year Journey from Drosophila 's Clock Mutants to Human Circadian Disorders Mirabilis (Four OClocks) at 2pm Mirabilis (Four OClocks) at 6pm Hamster Activity Record Constant Darkness Hundreds of Genes Cycle with a Circadian Rhythm

265 views • 24 slides
Gravitational Physics Physics Gravitational with with Optical Clocks Clocks in in Space

Gravitational Physics Physics Gravitational with with Optical Clocks Clocks in in Space

Workshop on an Optical Clock Mission in ESAs Cosmic Vision Program Dsseldorf 8. - 9. 3. 2007 Gravitational Physics Physics Gravitational with with Optical Clocks Clocks in in Space Space Optical S. Schiller S. Schiller Heinrich-

691 views • 31 slides
Circadian Rhythms and Health March 8, 2018 Helen J. Burgess, Ph.D. Professor, Department of

Circadian Rhythms and Health March 8, 2018 Helen J. Burgess, Ph.D. Professor, Department of

Melatonin, Sleep, Circadian Rhythms and Health March 8, 2018 Helen J. Burgess, Ph.D. Professor, Department of Behavioral Sciences Co-Director, Sleep and Circadian Research Laboratory University of Michigan, Ann Arbor What is Melatonin?

509 views • 9 slides
Distributed Systems events vs. physical clocks : time of day Assume no central time source

Distributed Systems events vs. physical clocks : time of day Assume no central time source

Logical clocks Assign sequence numbers to messages All cooperating processes can agree on order of Distributed Systems events vs. physical clocks : time of day Assume no central time source Logical Clocks Each system maintains its

74 views • 5 slides
Time, Clocks, and State Machine Replication Dan Ports, CSEP 552 Todays question How

Time, Clocks, and State Machine Replication Dan Ports, CSEP 552 Todays question How

Time, Clocks, and State Machine Replication Dan Ports, CSEP 552 Todays question How do we order events in a distributed system? physical clocks logical clocks snapshots (break) application: state machine replication

1.06k views • 80 slides
Capturing data and use of GPS Capturing data GIS GPS Paper maps Coordinates Satellite images

Capturing data and use of GPS Capturing data GIS GPS Paper maps Coordinates Satellite images

Capturing data and use of GPS Capturing data GIS GPS Paper maps Coordinates Satellite images What is a GPS? Global Positioning System A network of satellites that continuosly transmit informations Making possible to identify locations How

579 views • 26 slides
Circadian rhythms and bipolar related phenotypes in UK Biobank Daniel Smith Professor of

Circadian rhythms and bipolar related phenotypes in UK Biobank Daniel Smith Professor of

Circadian rhythms and bipolar related phenotypes in UK Biobank Daniel Smith Professor of Psychiatry Circadian rhythms and mental health UK Biobank analyses Precision medicine for bipolar disorder Early to bed, early to rise makes a man

645 views • 40 slides

More recommend