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Biology - Year 3 > Biological Rhythms > Flashcards

Biological Rhythms Flashcards

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1
Q

What is a period?

A

The time interval between one occurrence and the next of a specific point in the cycle

The length of time required to complete one cycle

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2
Q

What is a phase?

A

A defined point in a cycle

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3
Q

What is a diurnal rhythm?

What is a circadian rhythm?

A

An exogenous 24hr rhythm that responds to changes in in the environment. Is a passive response.

An endogenous 24hr rhythm generated by an internal mechanism

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4
Q

What are the properties of circadian rhythms?

A

They are driven by an internal mechanism and persist in constant conditions due to being caused by self sustaining oscillations

The endogenous period of a biological clock (τ) does not exactly equal the environmental cycle to which it is tuned

Can be synchronised to the environmental cycle upon exposure to specific environmental time cues

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5
Q

What is a Tau (τ)?

A

A free running period

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6
Q

Where is the SCN found?

A

Is part of the hypothalamus located just above where the optic chiasm crosses

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7
Q

What is a phase delay?

A

Shift later in time

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8
Q

What is a phase advance?

A

Shift earlier in time

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9
Q

What effect would light administered in the evening have on a circadian rhythm?

A

It would cause a phase delay

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10
Q

What effect would a lot of light in late night/early have on a circadian rhythm?

A

It would cause a phase advance

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11
Q

When do you need to take melatonin to get a phase advance?

A

Before the natural rise of melatonin

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12
Q

When do you need to take melatonin to get a phase delay?

A

When natural melatonin goes down

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13
Q

What neurotransmitter does the retinohypothalamic tract use to transfer light timing?

A

Glutamate

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14
Q

Is SCN activity the same between nocturnal and diurnal animals?

A

Yes, day and night activity is different in other regions of the brain but not in the SCN

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15
Q

How many period genes are there in mammals?

A

3, Per1, Per2 and Per3

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16
Q

What happens if you knock out period1?

What happens if you knock out period2?

What happens if you knock out both?

A

Mice with Targeted Disruption of mPer1 or mPer2 circadian behaviour is disrupted but not removed

mPer1/mPer2 double-mutant mice were immediately arrhythmic

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17
Q

Who did the Per gene KO study?

A

Bae et al. 2001

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18
Q

What are the regulators that make up the negative limb of the clock genes?

A

Cry and Per

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19
Q

What are the regulators involved in the positive limb of the clock genes?

A

Clock and Bmal1

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20
Q

Which is the most critical clock gene?

A

Bmal1, if this is knocked out then you loose all circadian rhythmicity

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21
Q

What is the main entrainment signal for mammals?

A

Light

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22
Q

Is slow wave activity higher at the beginning or end of sleep?

Is spindle activity higher at the beginning or end of sleep?

Is REM sleep higher at the beginning or end of sleep?

A

Beginning

End

End

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23
Q

What symptoms often manifest as a result of damage to the basal ganglia?

A

Movement problems/ disorders

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24
Q

What is the purpose of the blood brain barrier

A

Protects the CNS from potentially toxic chemicals, derived from e.g. diet, infection trauma

Maintains a highly controlled extracellular environment for neuronal function e.g. ion concentration

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25
Q

How do you calculate daily phase shift (Deltaφ)?

A

Deltaφ = τ - T

Where T = entraining cycle e.g. 24 hour L/D cycle, and τ = free running period

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26
Q

Briefly describe three studies that provide evidence for the SCN

A

Steven and Zucher (1972) - ablation of the SCN, found it abolishes circadian timing of behaviour showing SCN is related to circadian rhythms

Ralph et al. (1991) - transplantation studies, lesion the SCN in host, transplanted foetal SCN tissue into 3rd ventricle of host and assessed period, found this worked to restore rhythmicity

Welsh et al. 1995, rhythmicity in SCN slice in vitro, TTX inhibits sodium channels, even when SCN is prevented from outputting signal it continued to ‘tick’ and rhythm returns once inhibitor is removed

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27
Q

What is the name of the pathway that directly connects the eye to the SCN?

A

Retinohypothalamic tract

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28
Q

What is the effect of glutamate on the SCN?

A

Ding et al. 1994

Glutamate early in the day = phase delay
Late in the day = advance

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29
Q

What pathway relays non-photic info to the SCN?

A

The GHT (geniculohypothalamic tract) that from the IGN (intergenticulate nucleus) and RN (raphe nuclei) utilises NPY and GABA as mediators

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30
Q

Who isolated the mammalian homologue of period?

A

Tei et al. (1997)

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31
Q

Who performed period gene KO studies?

A

Bae et al. 2001

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32
Q

What is the suspected role of Per3?

A

Linking circadian rhythmicity to sleep homeostasis

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33
Q

Who discovered the function of the cryptochrome genes?

What did they do?

What did they find?

A

Van der Horst et al. (1999)

Knocked out the cryptochrome genes

Found knocking out one affects the period similar to knocking out Per. KO of both Cry1 and Cry2 loses circadian rhythmicity

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34
Q

Who performed experiments to identify the positive regulators of the circadian clock?

How did they do this?

What did they find?

A

Takahashi et al.

Mutagenesis experiments in mice

Found one with a long period

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35
Q

What happens if you knock out Bmal1?

Who did this?

A

All rhythmicity is lost

Bunger et al. 2000

36
Q

Name three places where peripheral circadian oscilators have been found

A

hippocampus
cerebellum
motor cortex

37
Q

Where do Clock and Bmal1 bind?

A

The E-box

38
Q

What are the differences in light response of the visual and circadian systems?

A

The visual system responds to a broad range of light and takes into account the direction of light (radiance). It also responds to quick changes in light which is important for the detection of movement.

The circadian system does not require information about direction of light and just takes in irradiance information. It responds to a narrower range of light (is less sensitive to dim light) and responds to changes in light over a longer period of time. Don’t want the circadian system being affected by transient light changes, e.g. cloud covering the sun

39
Q

Who showed that rd/rd mice still phase shift?

A

Argamaso et al. 1995

40
Q

Who showed that rd/rd cl- mice still phase shift?

What are the features of the rd/rd cl- mice?

A

Freedman et al. 1999

They have no rods or cones, their photoreceptor layer is gone however they still have the pigment layer

41
Q

Who showed that rd/rd cl- mice supress melatonin in response to light?

A

Lucas et al. 2000

42
Q

What supports the fact the ganglion cells are involved in the pupil constriction reflex?

Which study covers this?

A

The ganglion cells connect to the lateral genticulate nucleus (LGN) which is the visual relay centre and the olivary pretectal nucleus (OPN). The connection from the OPN to they eye is involved in pupil reflex

Berson, 2003

43
Q

Who showed pupil constriction still occurs in rd/rd cl mice?

What did they find was different between the rd/rd cl mouse and the WT?

A

Lucas et al. 2001

That pupil constriction still occurred but not as much at low light levels

44
Q

What type of photopigment does the visual system have?

What does light do to retinal?

A

An g-protein coupled opsin photopigment that surrounds a light sensitive chromophore (retinal)

Changes it from 11-cis form to all-trans form

45
Q

Who showed action spectrum data in rodless/coneless mice?

What did they find?

A

Lucas et al. 2001

Rd/rd cl mice had very different peak to WT, template was similar to rhodopsin curve, max sensitivity at 480nm

46
Q

Who showed action spectra of melatonin sensitivity in humans?

What did they find?

A

Thapan et al. 2001

Max sensitivity at 468nm

47
Q

What is the effect of bright blue light on melatonin?

A

It suppresses it

48
Q

What are the cells that provide irradiance information to the SCN?

What percentage of the retina do these cells make up?

A

Retinal ganglion cells

~1%

49
Q

Who showed ipRGCs were sensitive to light?

A

Berson et al. 2002

50
Q

Where is melanopsin expressed in humans and who found this?

A

In the retina, Provencio et al. 2000

51
Q

Who looked at pupil constriction response in melanopsin KO mice?

What did they find?

A

Lucas et al. 2003

At low irradiance not much difference between WT and melanopsin KO, but at high irradiance, pupil constriction response is less in the melanopsin KO

52
Q

Who looked at phase shifting responses in melanopsin KO mice?

What did they find

A

Panda et al. 2002

In melanopsin KO animals get the same phase shift response but the size of the phase shift is reduced, get the biggest difference at low light levels

53
Q

Who made a triple rod/cone/melannopsin KO?

What did they find?

A

Hattar et al. 2003

there was no pupil constriction response in these mice and their circadian behaviour was completely arrhythmic

54
Q

Who did an experiment to show cells in the SCN respond to colour?

Briefly describe what they did.

A

Walmsley et al. 2015

  • replaced mouse green cone with human red cone so they could stimulate it with red light
  • exposed animals to either UV or long wavelength yellow light
  • measured neural activity in SCN cells
  • found could detect cells that respond to different colours in SCN cells. Some cells would turn on/respond to blue light stimulus.
55
Q

Are melatonin concentrations high or low during sleep?

A

High

56
Q

Breifly describe the two process model of sleep regulation.

A

Borbely, 1982

  • tracks the history of sleep and wakefullness
  • regualtes average level of sleep debt
57
Q

What markers were found for the two process model of sleep deprivation?

A

Dijk et al. 1999

Found more slow wave activity and longer sleep followed sleep deprivation in humans and rats. This was found in the frontal and parietal cortexes but not so much in the occipital region.

This suggests there is a sleep homeostatic process related in the sleep EEG and some areas of the brain may be more affected

58
Q

What happens to sleep homeostasis during partial sleep deprivation?

A

You loose mostly REM sleep so REM is recovered

Brunner et al. 1990

59
Q

What are some of the model organisms for clock genes?

A
  • Cyanobacteria
  • Neurospora (fungus)
  • Arabidopsis (plant)
  • Animals
  • Drosophila (fruitfly)
  • Vertebrates
  • Zebrafish
  • Mouse
  • (Human)
60
Q

What is classical forward genetics?

What is reverse genetics?

A

Starting with the phenotype — asking what gene is responsible

Starting with the gene — asking what it does

61
Q

What did Hall and Rosbash discover about the period gene?

A

that it accumulated during the night and was degraded during the day in sync with the circadian rhythm

62
Q

What does bHLH stand for?

What type of protein are they found on?

What are they for?

A

basic helix-loop-helix

Clock proteins

DNA binding region

63
Q

What recognises E-box motifs?

A

circadian clock proteins with bHLH DNA-binding regions

64
Q

What is Ohno’s 2R hypothesis>

A
  • two rounds of genome duplication that allowed blossoming of vertebrates with more complex physiology
  • rapid mutation rate in a duplicate version of the gene can cause it to either take on a related but different function or it can take on too many and loose function becoming a pseudogene
65
Q

What has been used as a proxy for circadian period length?

A

diurnal preference (chronotype)

66
Q

What is advanced sleep phase disorder (ASPD)?

A
  • Typical sleep time 1800 – 2100
  • Typical wake time 0200 – 0500
  • Characterised by early morning awakening/ sleep maintenance insomnia
  • Sleepiness in the afternoon
  • Differs from normal advance in sleep seen during ageing which tends to associate with sleep fragmentation
67
Q

What is delayed sleep phase disorder (DSPD)?

A
  • Typical sleep time: 0200 – 0600
  • Typical wake time 1000 – 1300
  • Characterised by daytime sleepiness, difficulty conforming to normal bed times and insomnia and difficulty waking up
  • High alertness in evening
68
Q

Which has a higher prevalence in the population ASPD or DSPD?

A

DSPD

69
Q

What causes familial ASPD?

A

a missense mutation (A210G) found near a phosphorylation site on PER2

70
Q

What is likely to happen to peripheral clocks if the SCN is destroyed?

A

peripheral clocks are autonomous but without SCN will loose synchrony between tissues and even within individual cells

71
Q

Different studies have estimated different proportions of the transcriptome as being circadian. Why is this?

A

could be physiological differences between tissues, species, strains
the analysis method used

72
Q

Unlike the SCN peripheral clocks do not receive direct retinal input. What therefore happens following an abrupt change in the environmental light-dark cycle (i.e. as happens to cause jet lag)

A

peripheral clocks adapt more slowly than SCN - some thought to be quicker than others

called internal desynchroncy

73
Q

How were mammalian peripheral clocks detected before the advent of ‘clock gene analysis’?

A

before era of mammalian clock genes evidence for existence of peripheral clocks came from retinal culture studies

74
Q

Briefly describe the series of experiments that revealed molecular rhythms in peripheral tissues and cells

A

Balsalobre et al. 1998 - rat cells, serum pulse, found this caused rhtyhmicity, shows these signals exist outside the SCN

Yoo et al. 2004 - 24hr rhythm in SCN, also in tissues from other parts of the body, so must contain own clocks

Brown et al. 2005 - human cells, virus to introduce reporter gene, found rhythmicity in skin and hair cells

Welsh et al. 2004 - individual cells have different rhythms

75
Q

Explain the concept of the circadian timing system.

A

Acknowledges the existence of other clocks
Considers mammalian circadian biology as an orchestra with the SCN as the conductor and the periphery as musicians

Main function of SCN is to sync rhythms

76
Q

Briefly provide evidence of the functional roles(s) of peripheral clocks.

A

Storch et al. 2002 - Approx 10% of transcriptome under circadian control

Reddy et al. 2006 - 20% of liver proteins show circadian rhythmicity, in other animals many genes found to be rhythmic in one or more tissues

Marcheva et al. 2010 - tissue specific KO in pancreas, effects on glucose homestasis

77
Q

Briefly describe the interaction between timed feeding and circadian physiology.

A

Posparandial absorption varies with time of day - eating at night leads to higher TAG

timed feeding leads to a food anticipatory response that leads to behavioural and physiological changes

78
Q

What are some of the things that have linked circadian and metabolic physiology at the molecular level?

A

microarray and protein array studies that suggest 10% of the transcriptome is rhythmic

nuclear receptors are rhythmic

molecular metabolic sensors (AMPK and NAD)

clock mutant mouse - has metabolic effects

human clock gene polymorphisms - have metabolic effects

79
Q

What is torpor?

A

A period of greatly reduced metabolic activity

80
Q

What do orexigenic hormones do?

A

stimulates apetite

81
Q

What do anorexigenic hormones do?

A

suppresses appetite

82
Q

In 2009 what was the estimated cost of road and workplace accidents caused by excessive sleepiness?

A

$71 - $93 billion dollars per year

83
Q

What percentage of the working population is normally cited as being shiftworkers?

A

20-25% of working population in developed countries

84
Q

What is AANAT?

A

ralkylamine N-acetyltransferase

t is the penultimate enzyme in melatonin synthesis and controls the night/day rhythm in melatonin production in the vertebrate pineal gland

85
Q

What would be the effect of ganglionectomy (SCG) lesion on mammalian photoperiodism?

A

no circadian rhythm of melatonin secretion

86
Q

What effect does a long duration melatonin have on reproduction in:

  • Sheep (winter breeders)
  • Hamsters (spring-summer breeders)
A

long melatonin duration = winter so in sheep would stimulate reproduction

in hamsters it would inhibit reproduction

Biology - Year 3 (3 decks)

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