Literature DB >> 21556016

Understanding systems-level properties: timely stories from the study of clocks.

John B Hogenesch1, Hiroki R Ueda.   

Abstract

After several decades dominated by reductionist approaches in biology, researchers are returning to the study of complex biology with a litany of new and old techniques--this paradigm has been termed systems biology. Here we detail how systems biology is being used to uncover complex systems-level properties of the circadian clock. These properties include robustness, periodicity and temperature compensation. We describe how clock researchers are using systems-biology techniques, such as genetic perturbations, kinetic luminescence imaging, synthetic biology and mathematical modelling, to untangle these complex properties in mammals, fungi and bacteria. The strategies developed in the context of circadian clocks may prove useful for tackling similar problems in other systems.

Mesh:

Year:  2011        PMID: 21556016     DOI: 10.1038/nrg2972

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  79 in total

1.  Nucleotide binding and autophosphorylation of the clock protein KaiC as a circadian timing process of cyanobacteria.

Authors:  T Nishiwaki; H Iwasaki; M Ishiura; T Kondo
Journal:  Proc Natl Acad Sci U S A       Date:  2000-01-04       Impact factor: 11.205

2.  Estimation of mean body temperature from mean skin and core temperature.

Authors:  Rainer Lenhardt; Daniel I Sessler
Journal:  Anesthesiology       Date:  2006-12       Impact factor: 7.892

3.  Temperature Compensation of Circadian Period Length in Clock Mutants of Neurospora crassa.

Authors:  G F Gardner; J F Feldman
Journal:  Plant Physiol       Date:  1981-12       Impact factor: 8.340

4.  Studying genetic regulatory networks at the molecular level: delayed reaction stochastic models.

Authors:  Rui Zhu; Andre S Ribeiro; Dennis Salahub; Stuart A Kauffman
Journal:  J Theor Biol       Date:  2007-02-06       Impact factor: 2.691

5.  Peripheral circadian oscillators require CLOCK.

Authors:  Jason P DeBruyne; David R Weaver; Steven M Reppert
Journal:  Curr Biol       Date:  2007-07-17       Impact factor: 10.834

6.  A sequential program of dual phosphorylation of KaiC as a basis for circadian rhythm in cyanobacteria.

Authors:  Taeko Nishiwaki; Yoshinori Satomi; Yohko Kitayama; Kazuki Terauchi; Reiko Kiyohara; Toshifumi Takao; Takao Kondo
Journal:  EMBO J       Date:  2007-08-23       Impact factor: 11.598

7.  Differential functions of mPer1, mPer2, and mPer3 in the SCN circadian clock.

Authors:  K Bae; X Jin; E S Maywood; M H Hastings; S M Reppert; D R Weaver
Journal:  Neuron       Date:  2001-05       Impact factor: 17.173

8.  A clock shock: mouse CLOCK is not required for circadian oscillator function.

Authors:  Jason P Debruyne; Elizabeth Noton; Christopher M Lambert; Elizabeth S Maywood; David R Weaver; Steven M Reppert
Journal:  Neuron       Date:  2006-05-04       Impact factor: 17.173

9.  A role for casein kinase 2 in the mechanism underlying circadian temperature compensation.

Authors:  Arun Mehra; Mi Shi; Christopher L Baker; Hildur V Colot; Jennifer J Loros; Jay C Dunlap
Journal:  Cell       Date:  2009-05-15       Impact factor: 41.582

10.  CKIepsilon/delta-dependent phosphorylation is a temperature-insensitive, period-determining process in the mammalian circadian clock.

Authors:  Yasushi Isojima; Masato Nakajima; Hideki Ukai; Hiroshi Fujishima; Rikuhiro G Yamada; Koh-hei Masumoto; Reiko Kiuchi; Mayumi Ishida; Maki Ukai-Tadenuma; Yoichi Minami; Ryotaku Kito; Kazuki Nakao; Wataru Kishimoto; Seung-Hee Yoo; Kazuhiro Shimomura; Toshifumi Takao; Atsuko Takano; Toshio Kojima; Katsuya Nagai; Yoshiyuki Sakaki; Joseph S Takahashi; Hiroki R Ueda
Journal:  Proc Natl Acad Sci U S A       Date:  2009-09-02       Impact factor: 11.205

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  62 in total

Review 1.  Paradoxical and bidirectional drug effects.

Authors:  Silas W Smith; Manfred Hauben; Jeffrey K Aronson
Journal:  Drug Saf       Date:  2012-03-01       Impact factor: 5.606

2.  Photoreceptor phagocytosis is mediated by phosphoinositide signaling.

Authors:  Debarshi Mustafi; Brian M Kevany; Christel Genoud; Xiaodong Bai; Krzysztof Palczewski
Journal:  FASEB J       Date:  2013-08-02       Impact factor: 5.191

3.  Transcriptional regulation of LUX by CBF1 mediates cold input to the circadian clock in Arabidopsis.

Authors:  Brenda Y Chow; Sabrina E Sanchez; Ghislain Breton; Jose L Pruneda-Paz; Naden T Krogan; Steve A Kay
Journal:  Curr Biol       Date:  2014-06-19       Impact factor: 10.834

4.  Dynamic fluctuations lubricate the circadian clock.

Authors:  Ming-Tao Pai; Charalampos Kalodimos
Journal:  Proc Natl Acad Sci U S A       Date:  2011-08-23       Impact factor: 11.205

5.  Prevalence of cycling genes and drug targets calls for prospective chronotherapeutics.

Authors:  Nimish D Kathale; Andrew C Liu
Journal:  Proc Natl Acad Sci U S A       Date:  2014-11-03       Impact factor: 11.205

6.  It is time to take timing seriously in clinical genetics.

Authors:  György Kosztolányi
Journal:  Eur J Hum Genet       Date:  2014-12-24       Impact factor: 4.246

7.  Rhythmic ring-ring stacking drives the circadian oscillator clockwise.

Authors:  Yong-Gang Chang; Roger Tseng; Nai-Wei Kuo; Andy LiWang
Journal:  Proc Natl Acad Sci U S A       Date:  2012-09-11       Impact factor: 11.205

Review 8.  Nuclear magnetic resonance spectroscopy of the circadian clock of cyanobacteria.

Authors:  Yong-Gang Chang; Roger Tseng; Nai-Wei Kuo; Andy LiWang
Journal:  Integr Comp Biol       Date:  2013-05-10       Impact factor: 3.326

9.  Circadian Rhythm Disruption Aggravates DSS-Induced Colitis in Mice with Fecal Calprotectin as a Marker of Colitis Severity.

Authors:  Joseph Amara; Youakim Saliba; Joelle Hajal; Viviane Smayra; Jules-Joel Bakhos; Raymond Sayegh; Nassim Fares
Journal:  Dig Dis Sci       Date:  2019-05-21       Impact factor: 3.199

Review 10.  The clock shop: coupled circadian oscillators.

Authors:  Daniel Granados-Fuentes; Erik D Herzog
Journal:  Exp Neurol       Date:  2012-10-23       Impact factor: 5.330

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