The Role of the Clock Gene in Protection Against Neural and Retinal

Degeneration

Jenny Yu

Senior Honors Thesis

Program in Biological Sciences
Northwestern University
Spring 2012

Principal Investigator: Dr. Ravi Allada

Research Advisor: Dr. Valerie Kilman
Abstract

In order to survive, organisms evolved to adapt to environmental changes, so it is unsurprising

that a biological system arose to deal with existence in a cycling 24-hour light and dark

environment. Gene expression and protein activity are regulated by the circadian system in

roughly twenty-four hour cycles to yield changes in behavior and activity of numerous biological

systems. The circadian system is an important focus of research, because it influences critical

processes, such as metabolism and sleep, and circadian rhythm disruption is observed in patients

with a variety of diseases, including neurodegenerative diseases such as Alzheimer’s and

Parkinson’s. Clock (Clk) is a primary circadian gene in both humans and Drosophila

melanogaster, more commonly known as the fruit fly. In mutant flies lacking functional Clk,

known as ClkJrk(Jrk) , one class of circadian neurons is absent. I show evidence that these

neurons develop normally but degenerate later in Jrk mutants and can be rescued by Clk

overexpression. Jrk mutants are also more susceptible to light-induced retinal degeneration. I

hypothesize that normal circadian rhythms resulting from Clk expression protect neurons from

daily, use-dependent damage. The underlying molecular mechanism of these results is still under

investigation, but my data suggests that Clk does not function by inhibiting the apoptosis

pathway. The results from this project will contribute to a greater understanding of the

relationship between neurodegenerative diseases and circadian rhythm disruption. The project

also has public health implications, because a large portion of the population, especially shift

workers, have disrupted circadian rhythms that may lead to increased risk of disease.

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Table of Contents:

I. Abstract……………………………………………………………………….…….…2

II. Introduction and Literature Survey……………………………………………………5

A. Circadian Rhythms………………………………………………………….…5

B. The molecular basis of the circadian system……………………………….....6

C. Disruption of the circadian system and disease…………………………….…8

D. Disruption of the circadian system and neurodegeneration………………...…9

E. Programmed cell death mechanisms…………………………………………11

F. Disruption of the circadian system and retinal degeneration………………...13

G. ClkJrk mutant as a model for elucidating Clk function…………….…………14

III. Materials and Methods……………………………………………………………….16

IV. Results………………………………………………………………………………..19

A. Clk overexpression in Jrk homozygotes……………………………………..19

B. Temperature-dependent induction of Clk overexpression…………………...22

C. Visualization sLNvs during various stages of development…………………25

D. cry13 expression……………………………………………………………..26

E. P35 and Diap1 overexpression in Jrk homozygotes………………………...30

F. Kir overexpression in Jrk homozygotes ………………………………….…35

G. Exposure of Jrk mutants to LL and DD conditions ……..…………………..37

H. Visualization of Jrk heterozygote retinas exposed to LL……….……...……40

V. Discussion……………………………………………………………………………42

VI. References……………………………………………………………………………46

VII. Acknowledgements………………………………………………………………..…51

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VIII. Curriculum Vitae …………………………….……..………………………………52

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Introduction and Literature Survey

A. Circadian rhythms

A circadian rhythm is an essential, daily cycling behavior thought to prepare organisms for daily

changes in their environment, such as light(Rosbash, 2009). Sleep, body temperature regulation,

and metabolism are examples of processes regulated by the circadian system in humans. The

molecular mechanisms of the circadian system are conserved between humans and numerous

other organisms, so findings from research conducted in model organisms can give insight into

the mechanisms of the human circadian system(Panda et al., 2002). This project focuses on the

circadian system of Drosophila melanogaster, also known as the fruit fly.

Circadian rhythms are regulated by specific neurons that function as endogenous clocks,

and these neurons communicate with each other and cells of other tissues to coordinate responses

and activity. These neurons are sensitive to changes in external time cues, such as light and

temperature, although they are capable of maintaining regular circadian rhythms in the absence

of these stimuli, such as during complete darkness. In humans, the superchiasmatic nucleus

(SCN) is the master clock, and it is sensitive to light stimulation received by the eyes as well as

other input(Blau et al., 2007). In fruit flies, six subsets of neurons in the brain are the main

circadian system controllers. They are the small ventral lateral neurons(sLNvs), the large ventral

lateral neurons(lLNvs), the dorsal lateral neurons(LNds), and three groups of dorsal

neurons(DNs)(Helfrich-Förster, 2003)(Figure 1). These neurons influence circadian behavior in

Drosophila. Flies exhibit two distinct peaks in locomotor activity during one 24-hour cycle of

light-dark, one peak occurs during the light to dark transition(morning) and the other peak occurs

during the dark to light transition(evening)(Stoleru et al., 2004). The LNvs are responsible for

regulation of morning activity and the LNds along with several other circadian neurons are

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responsible for regulation of the evening peak in activity(Stoleru et al., 2004). The two circadian

groups interact with each other but they can also function autonomously(Stoleru et al., 2004).

Figure 1. Anatomy of the circadian neurons in the brain of Drosophila

melanogaster(Helfrich-Förster, 2003).

B. The molecular basis of the circadian system

The basis of the circadian system lies in the regulation of gene expression in individual

cells(Benito et al., 2007). Specific portions of DNA called genes encode for the generation of

proteins, which carry out various functions in the cell and body as a whole. Cells regulate the

expression of genes by producing other proteins known as transcription factors. These

transcription factors bind to the DNA at specific sites in front of genes and can inhibit or

stimulate the transcription of the genes into RNA, which is then made into proteins.

In both mammals and fruit flies, the Clock gene is a major circadian system

regulator(Figure 2). In flies, the transcription factors, CLOCK (CLK) and CYCLE (CYC),

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combine and stimulate the transcription of the period (per) and timeless (tim) genes(Benito et al.,

2007). per and tim encode for the proteins, PERIOD(PER) and TIMELESS(TIM). The two

proteins bind together and enter the cell nucleus(Blau et al., 2007). Following entry, TIM begins

to degrade and the liberated PER interacts with CLK and CYC to prevent them from activating

gene expression(Blau et al., 2007). This halts the expression of per and tim, and the PER present

in the nucleus degrades(Blau et al., 2007). The light-sensitive protein, CRYPTOCHROME

(CRY), controls the rate of degradation of TIM and is one way by which the molecular clock

synchronizes with light cycles(Blau et al., 2007). The expression of Clk is both necessary and

sufficient to induce rhythms of gene expression that peak and fall at similar times each

day(Kilman and Allada, 2009). These gene rhythms drive daily cycles of behavior. This is true

even when Clk itself does not oscillate, though CLK’s phosphorylation state normally

does(Kilman and Allada, 2009). Clk’s prominent role in regulating the circadian system in both

mammals and flies is one reason why Clk is an attractive research subject.

Figure 2. Representation of the molecular circadian clock in Drosophila

melanogaster(Rosbash, 2009).

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C. Disruption of the circadian system and disease

There is mounting evidence associating morbidity of numerous diseases with misregulation of

the circadian system in humans, which is further supported by basic research investigating the

harmful effects of disrupted circadian systems. The increased prevalence of artificial light has

allowed humans to stay awake for longer periods, so it is important for researchers to understand

how these changes in the circadian rhythms can affect the body and overall health(Santhi et al.,

2011). The National Sleep Foundation claims that in the last century, Americans have decreased

their total sleep time by nearly two hours(National Sleep Foundation, 2003). In 2009, surveys

found that Americans were sleeping an average of 6.7 hours on weeknights and 7.1 on

weekdays(National Sleep Foundation, 2009). Shift workers, who make up a large portion of the

population, suffer from chronically disrupted circadian rhythms.

Circadian rhythm disruption is evidenced by abnormal or varying sleep-wake cycles. The

categories of circadian rhythm and sleep disorders are separated into those that are voluntary or

environment-based and those that are intrinsic(Sack et al., 2007). Voluntary circadian rhythm

disorders, such as shift work disorder and jet lag disorder, are due to environmental

impositions(Sack et al., 2007). Intrinsic disorders, such as delayed sleep phase disorder and

restless leg syndrome, are caused by circadian system malfunctions(Sack et al., 2007). Short-

term consequences of sleep deprivation and disrupted circadian rhythms include increased risk of

injury or death, lower cognitive performance, and changes in metabolic hormones(Centers for

Disease Control and Prevention, 2011). Long-term sleep loss leads to increased risk of obesity,

diabetes, cancer, and possibly neurodegenerative diseases(Centers for Disease Control and

Prevention, 2011). There is a connection between arrhythmicity and neuronal diseases, such as

dementia and Alzheimer’s(Reddy and O'Neill, 2010).

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D. Disruption of the circadian system and neurodegeneration

Sleep disorders and irregular circadian behavior and neurodegenerative diseases, such as

Alzheimer’s and Huntington’s, often occur concurrently(Wulff et al., 2010). Patients afflicted

with neuronal diseases frequently exhibit arrhythmic behavior and have poor quality of

sleep(Cardinali et al., 2010). Alzheimer’s patients exhibit an abnormal circadian effect called

sundowning, where there is a regular and daily increase in agitated or abnormal behavior in the

late afternoon or evening(Cardinali et al., 2010). Alzheimer’s, the most common neurological

disorder associated with aging, is currently the fourth leading cause of death in the United

States(Hung et al., 2010). The occurrence of irregular circadian behavior makes vigilance more

difficult for caregivers and the irregular cycle is one reason why the elderly and people afflicted

with neuronal diseases are institutionalized(Reddy and O'Neill, 2010).

The direction of causality between circadian rhythm disruptions and neurodegenerative

diseases is currently inconclusive. In neurodegenerative diseases, there is extensive neuronal

loss, and the loss of neurons in brain regions responsible for circadian regulation may cause the

sleep disorders and disrupted circadian behavior(Jan et al., 2010). Neurodegeneration also leads

to changes in release of neurotransmitters, which would have the potential to affect input to the

central circadian pacemaker(Jan et al., 2010). There is evidence that sleep disorders exacerbate

symptoms of neurodegenerative diseases and contribute to the progression of these

diseases(Wulff et al., 2010). The relationship between circadian disorders and neurodegenerative

diseases is supported by the reduction in neurodegenerative symptoms when sleep and circadian

problems are treated. Therapeutic application of melatonin, an antioxidant substance with a role

in sleep regulation, can reduce the severity of Alzheimer’s and Parkinson’s symptoms(Cardinali

et al., 2010; Srinivasan et al., 2011). It is possible that there is a positive-feedback effect where

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existing sleep disorders and disruption to the sleep-wake system promote development of

neurological disorders that further worsen the sleep and circadian behavior due to extensive

neuronal loss.

The sleep-wake cycle may contribute to the development of Alzheimer’s disease by

influencing the fluctuations of amyloid-β protein(Aβ) in the brain interstitial fluid(Kang et al.,

2009). Aβ accumulation in the brain interstitial fluid(ISF) is a strong indicator of the onset of

Alzheimer’s disease(Kang et al., 2009). Fluctuations in Aβ are linked to the sleep-wake cycle in

both mice and humans, and acute sleep deprivation causes an increase in the Aβ levels in mice

that immediately decreased upon recovery sleep(Kang et al., 2009). When mice are chronically

sleep deprived, there are greater amounts of Aβ plaques, a component of the pathology of

Alzheimer’s disease, in the sleep-deprived mice compared to the control mice(Kang et al., 2009).

Orexin, a hormone that participates in control of wake and metabolism, is proposed to be

involved in the control of Aβ fluctuations, because treatment of orexin increases ISF Aβ

concentration and orexin receptor antagonists decrease ISF Aβ levels(Kang et al., 2009).

Components of the molecular circadian system may have roles in preventing the onset of

neurodegenerative diseases. per, one of the central circadian genes that are conserved between

species, may be involved in neuroprotection. Drosophila per null(per01) mutants have

accelerated aging and worsened neuron loss in a neurodegeneration-prone background(Krishnan

et al., 2011). Researchers observed shortened average lifespan and accelerated

neurodegeneration in double mutants of per01 and sniffer and in double mutants of per01 and

swiss cheese (Krishnan et al., 2011). sniffer is a loss of function mutation that leads to oxidative

stress-induced, age-related neuron degeneration and swiss cheese is a loss of function mutation

that results in age-dependent lesions of the neuropil and neuron cell death through

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apoptosis(Krishnan et al., 2011). The absence of per agonizes the propensity of the neuron

degeneration in sniffer and swiss cheese mutants, which suggests that appropriate regulation of

per can help protect cells against regulated cell death.

In Jrk mutants, I found a subset of circadian neurons disappeared after developing

normally, which led to the hypothesis that functional Clk expression may have a role in

protecting neurons from degeneration. Experiments focused on confirming the degeneration of

the neurons, determining the mechanism of action for CLK, and subsequently, Clk’s role in

activity-dependent retinal degeneration as a test of the generality of Clk’s protective function.

E. Programmed cell death mechanisms

One possible mechanism by which Clk could deter degeneration is if it blocks the

apoptosis pathway. Apoptosis is a well-known form of programmed cell death that is conserved

between species. Apoptosis can be triggered by a variety of intracellular or extracellular signals.

Intracellular signals from internal factors, such as excessive DNA damage, can activate the

apoptosis mechanism. Hormones or other signals from nearby cells can also communicate to a

cell to undergo apoptosis. For example, during metamorphoses in insects, a hormone called

ecdysone induces changes throughout the pupa to drive the transformation from the larval state

to an adult fly(Kirilly et al., 2011). It is known that there are massive alterations in organ

structure and drastic neural remodeling during metamorphoses, and this transition is aided by

apoptosis of select cells(Kirilly et al., 2011). The first step in the cell death process is the

reception of an intracellular or extracellular apoptosis signal. Various events occur in preparation

for the cell suicide: Ca2+ ions are released from the mitochondria and caspases are activated.

Anti-caspase proteins, such as P35 and DIAP1, can inhibit apoptosis. The circadian system

affects processes leading to programmed cell death, but the mechanism by which the circadian

11
system influences this pathway is still uncertain(Figure 3). For example, a mutation in cry causes

certain tumor cells to be more responsive to signals stimulating a specific apoptotic pathway(Lee

and Sancar, 2011).

Figure 3. Two proposed ways in which the mammalian circadian system is

connected to the DNA damage response and apoptosis in cells(Sancar et al.,
2010).

Another possible programmed cell death mechanism that Clk may inhibit is death caused

by prolonged overstimulation of neurons(Dong et al., 2009). This process of continued excitation

leading to cell death is called excitotoxicity. Neuronal excitotoxicity may play a role in the onset

of neurodegenerative diseases, such as Huntington’s, Alzheimer’s, and Parkinson’s(Dong et al.,

2009). When a neuron receives chronic overstimulation, the toxic levels of neurotransmitters and

ions induce a large influx of Ca2+, activating enzymes that lead the cell to undergo programmed

cell death.

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F. Disruption of the circadian system and retinal degeneration

Examining Clk’s function in protecting neurons led to additionally considering Clk’s role in the

retina. Fruit flies exposed to constant light stimulation undergo retinal degeneration due to the

inability of photoreceptors to turn off activity during light exposure(Dolph et al., 1993). If Clk

inhibits excitoxicity of neurons in the brain, then it may also work in the retinas to protect retinal

cells from overstimulation by light. The retina is constantly exposed to ultraviolet radiation in

nature and is proposed to display circadian-dependent protection against damage and cell death.

A hypothesis of the origins of the circadian system is that it developed evolutionarily to

help prepare and protect organisms from DNA damage caused by ultraviolet radiation(Rosbash,

2009). By cycling production of protective proteins, the cell can be safeguarded when necessary

and save resources and energy when defense is not required(Rosbash, 2009). Ultraviolet

radiation causes DNA damage in cells exposed to the sun and these damages can lead to DNA

mutations, development of cancer, or cell death. A DNA repair mechanism in mice displays

circadian cycling, so the probability of developing ultraviolet-induced skin cancer varies

according to the cycling efficiency of the DNA excision repair system(Gaddameedhi et al.,

2011). The susceptibility to light-induced retinal degeneration in diurnal rats is circadian-

dependent(Organisciak et al., 2000). Rats that were exposed to light during the nighttime had

significantly greater cell damage in the retinas than rats exposed to light during the daytime,

which suggests that a circadian-regulated mechanism in the retina renders cells less susceptible

to damage at certain time points(Organisciak et al., 2000). Clk controls the expression of

numerous genes, so it is likely that a normal level of functional Clk expression may be critical for

this protective effect.

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 Given the background information, this project aims to elucidate Clk’s role in protecting

against neural degeneration and retinal degeneration in fruit flies by examining the anatomy of

specific circadian neuron subsets in the brain and the anatomy of the retinal cells.

G. ClkJrk mutant as a model for elucidating Clk function

To determine the function of the Clk gene, the effects of the loss of Clk were examined. In fruit

flies, a null Clk mutant has not been isolated, so the ClkJrk(Jrk) mutant is the most similar

genotype to a Clk null. Jrk is a dominant negative mutation of Clk, meaning nonfunctional CLK

protein is produced that lacks the ability to activate genes and inhibits the ability of normal CLK

to function(Allada et al., 1998). Jrk mutants have negligible Clk-activated transcription.

In adult wild type flies, the lLNvs and all but one of the sLNvs produce pigment

dispersing factor (PDF), a neuropeptide transmitter critical to circadian molecular rhythms and

clock output(Helfrich-Förster, 1997;Blau and Young, 1999). These neurons display a

characteristic anatomy that can be visualized by using fluorescent markers to detect, or stain, for

the PDF protein, or by using genetic techniques to produce green fluorescent proteins(GFP) in

only these cells. The sLNvs and lLNvs are nearly the only cells in the brain that express PDF,

allowing detailed analysis of their structure with these methods.

The neuroanatomy of circadian pacemaker neurons in homozygote Jrk flies is

significantly different from the wild type neuroanatomy. In wild type and Jrk heterozygote flies,

both the large and small ventral lateral neurons(lLNvs and sLNvs) are visible when the brain is

stained for PDF(Helfrich-Förster, 1997). There are four to five lLNvs and four sLNvs in each

hemisphere of the brain(Figure 1)(Helfrich-Förster, 2003). The sLNvs also send axons towards

the upper portion of the brain(Figure 1). In Jrk homozygotes however, the sLNvs and their axons

are no longer visible using PDF staining and the lLNvs send aberrant projections upwards(Park

14
et al., 2000). In adult Jrk homozygotes, the sLNvs are not detectable with staining for PDF and

from in situ hybridization(Park et al., 2000). The lLNvs also have altered neuron structure

compared to those of wild type flies, sending aberrant projections upwards.

Jrk flies also have altered circadian behavior(Allada et al., 1998). Wild type flies show

anticipation of light changes and morning and evening peaks of activity with depression of

activity during the middle of the light period(Wheeler et al., 1993). Jrk homozygotes have no

anticipatory behavior of light changes in 12 hour cycles of light and dark(LD) (Allada et al.,

1998). When entrained wild type flies are placed in constant darkness(DD), the flies maintain

their rhythmic behavior(Allada et al., 1998). Jrk homozygotes are arrhythmic in DD after

entrainment(Allada et al., 1998).

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Materials and Methods:

Drosophila stocks

cry24G4;;Jrk, cry24G4, cry24G4;;GFPnlsJrk, cry24G4;;GFPnls, mGFP;cry13,

mGFP;cry13Jrk, cry13G4, cry13Jrk, ClkG4, UGFPnls, UmGFP;Jrk, UmGFP, Jrk iso, Jrk sib

ctrl, UKir2.1, UKir2.1Jrk, UP35, UP35;Jrk, tubG80ts, tubG80tsJrk, tubG80ts;UClk,

tubG80ts;UClkJrk, UClkJrk, UClk, UDiap1, UDiap1Jrk

Flies were raised at room temperature (~22°C) or at 25°C in 12 hour:12 hour light/dark

conditions(LD) unless otherwise stated.

GAL4/UAS system

GAL4-UAS is a binary tissue-specific expression system in flies. One transgene carries the yeast

GAL4 transcriptional activator driven by a fly tissue-specific promoter. Another transgene

carries a gene of interest to be expressed under the control of yeast UAS (upstream activating

sequence), the binding site for GAL4. Flies carrying both transgenes will express the gene of

interest only in the spatiotemporal pattern of the chosen tissue-specific promoter that drives

GAL4. Further temporal refinement of expression of specific genes was accomplished by using

the temperature sensitive GAL80 in conjunction with the GAL4-UAS system. Flies were placed

in 18°C and moved to 29°C at specific points in their life cycle depending on the experimental

group. Gal80 expression was under the control of the tubulin promoter. At 18°C, the GAL80

protein inhibits the GAL4-UAS system, blocking transgenic expression. At 29°C, GAL80

degrades, so the GAL4-UAS system was able to function and express the transgene.

Brain dissections

Brains were dissected in PBS(phosphate buffer saline) using forceps and a light microscope.

They were placed into fixative(4% formaldehyde with methanol in PBS) within 10 minutes after

16
dissection. Brains were fixed for approximately 30 minutes for adults and 20 minutes for larval

and pupal brains. Larval and pupal stages were determined according to the aging system of

Bainbridge and Bownes, 1981. The brains were washed 5 to 6 times in PBT(0.3% TritonX100 in

PBS). Then, the brains were incubated for one or two nights in a primary antibody solution (10%

goat normal serum in PBS with primary antibody) at 18°C or for at least four hours at room

temperature. For PDF staining, the primary antibody concentration was 0.125% by volume of

mouse anti-PDF (DSHB). For PER staining, the primary antibody concentration was 0.125% by

volume(Siwicki et al., 1988). The brains were washed in PBT 5 to 6 times after primary antibody

staining. If the brains were left in primary antibody for two nights, they were placed in PBT for

about 24 hours before washing. After washing, the brains were incubated in a secondary

antibody solution (10% goat normal serum in PBS with secondary antibody). The secondary

antibody concentrations were 0.083% by volume. The secondary antibodies used were Alexa

Fluor 594 donkey anti-mouse, Alexa Fluor 594 donkey anti-rabbit, and Cy5 donkey anti-mouse.

After another PBT washing cycle, the brains were washed using PBS 4 to 5 times. They were

then mounted on slides using 80% glycerol in PBS. The brains were imaged using a laser

scanning confocal microscope. ImageJ and Adobe Photoshop were used to edit images.

Retinal dissections

The head was separated into two halves using the forceps with brain tissue still connected to the

retinas. The heads were placed into a fixative solution(4% formaldehyde without methanol in

PBS) within 10 minutes of initial dissection. The heads were fixed for approximately half an

hour to 45 minutes before removal of the brain tissue, the exoskeleton surrounding the eyes, and

the lamina. The eyes were left in fixative for an additional half an hour, so the total fixing time

was about an hour to an hour and a half. The retinas were washed in PBT 4 to 5 times and then

17
PBS 4 to 5 times. They were placed in a phalloidin solution(0.2% of a 0.1mg/ml phalloidin stock

in PBS)overnight in an 18°C incubator. The retinas were washed in PBT 4 to 5 times and then

PBS 4 to 5 times. The retinas were mounted onto a glass slide using 80% glycerol in PBS with

the exoskeleton side facing downwards. The retinas were imaged using a laser scanning confocal

microscope.

Activity eductions

Fly activity data was collected using the Drosophila Activity Monitoring(DAM) System and data

was processed using DAMFile Scan(Pfeiffenberger et al., 2010a). The computer programs

ClockLab and Counting Macro were used to analyze the data(Pfeiffenberger et al., 2010b).

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Results:

A. Clk overexpression in Jrk homozygotes

I confirmed previously published findings of the neuroanatomy of Jrk homozygotes using flies

from a uniform, or isogenic, genetic background(Figure 4A, B).

Clk was overexpressed in Jrk homozygotes by using cry24GAL4 to drive UASClk(UClk).

Clk overexpression was performed to confirm that the loss of sLNvs is due to loss of functional

CLK and that Clk expression is necessary for visualization of the sLNvs in adult brains. The

morphology of the cry24/+;;Jrk/UClkJrk brain is markedly different from that of a Jrk

homozygote brain. cry24/+;;Jrk/UClkJrk exhibit the same sLNv morphology as wild type brains

(Figure 4C).

The cry24 promoter is expressed in the PDF-positive neurons and drives Clk expression

strongly enough to successfully rescue the phenotype. The rescue of the wild type phenotype in

Jrk homozygotes when functional Clk expression is induced are evidence that the lack of

functional CLK is responsible for the loss of the sLNv PDF-staining and altered projections of

the lLNVs. The introduction of CLK is able to reverse the mutant phenotype by rescuing the

sLNvs.

The locomotor activities of the flies were also examined. As expected, the

cry24/+;;Jrk/Jrk and UClkJrk/Jrk flies showed activity characteristic of Jrk homozygotes, such

as lack of anticipation and nocturnal activity(Figure 5). When cry24 is used to overexpress Clk in

Jrk homozygotes, behavior is partially rescued. The anticipation of lights off is restored and flies

are less nocturnal, but anticipation of lights on and other characteristics of wild type behavior

still remain absent(Figure 5). The average period of rescued flies was 23.650±0.183 hours while

the average period of wild type flies was 24.591±0.113 hours(Table 1). The rescued flies were

19
moderately rhythmic in DD (P-S = 20.783±5.939)(Table 1). The partial rescue of behavior

despite the complete rescue in neuroanatomy suggests that gene oscillations, also dependent on

Clk, may remain aberrant.

Figure 4. Clk overexpression rescues PDF-stained sLNv morphology. A.

Wild type (Jrk sibling control) brains. sLNv somata and axons are visible as
indicated by arrows. B. Jrk homozygote brains. No sLNvs and lLNvs show
aberrant projections. C. cry24/+;;Jrk/UClkJrk adult brain. sLNv morphology
is rescued when Clk is overexpressed.

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 female_cry24_yw N = 8 female_yw_UclkJrk N = 7

cry24/+ UClkJrk/+
Percent of activity in L 66.6 Percent of activity in L 39.5

4.5 3
4
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female_cry24_fm7;Jrk_Jrk N = 7 female_cry24_fm7;Jrk_yw N = 8
Percent of activity in L 49.2 Percent of activity in L 44.6

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cry24/+;Jrk/Jrk 3
cry24/+;Jrk/+
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female_UclkJrk_Jrk N = 19 female_cry24_Uclk N = 7
Percent of activity in L 40.6 Percent of activity in L 75.1

1.8
UClkJrk/Jrk 3
cry24/+;UClk/+
1.6
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female_Jrk N = 8 female_cry24_fm7;Jrk_UclkJrk N = 19
Percent of activity in L 49.3 Percent of activity in L 50.6

2.5
Jrk/Jrk 2.5
cry24/+;Jrk/UClkJrk
2 2

1.5 1.5 *
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Figure 5. Activity eductions of experimental and control flies.

cry24/+;;Jrk/UClkJrk flies show rescue of anticipation of lights off (*).

21
 Average Period
Parental Cross SEM Average (P-S) SEM N
(hr)

cry24;Jrk x Jrk N/A N/A 0.376 ±0.834 21

UClkJrk x Jrk N/A N/A 0.226 ±0.226 18

cry24 x yw 24.591 ±0.113 60.817 ±14.673 15

cry24;Jrk x UClkJrk 23.650 ±0.183 20.783 ±5.939 24

cry24 x UClk 23.250 ±0.299 13.971 ±3.689 17

yw x UClkJrk 17.500 ±17.500 2.361 ±1.501 14

Jrk N/A N/A 0.359 ±0.332 14

cry24;Jrk x yw N/A N/A 0.564 0.500 16

Table 1. DD behavior for cry24-driven Clk rescue. (P-S) ≥10 indicates that the fly exhibited
rhythmic behavior and larger numbers indicate stronger rhythmicity.

B. Temperature-dependent induction of Clk overexpression

A temperature-sensitive repressor of GAL4 was used to induce Clk overexpression during

different stages of development in Jrk homozygotes in order to determine the critical period

when Clk expression can rescue sLNv anatomy. The tubG80ts driver was used to inhibit GAL4-

UAS system at 18°C and the GAL4-UAS system was disinhibited at 29°C. Initiating induction of

Clk overexpression during the larval or early pupal stage results in rescue of the sLNvs(Table 2,

Figure 6C, D). When Clk overexpression is first induced during adulthood however, the

phenotype cannot be rescued(Table 2, Figure 6E). Functional CLK is necessary during the early

developmental stages for proper maintenance of PDF-stained sLNvs.

22
18°C to
cry24/+;+/tubG80ts;Jrk/UClkJrk cry24/+;;Jrk/Jrk cry24/+;+/tubG80ts
29°C
L1 wild type(n=8) Jrk homozygote(n=6) wild type(n=9)
L2 wild type(n=5) Jrk homozygote(n=9) wild type(n=6)
early
wild type(n=6) Jrk homozygote(n=6) N/A(n=0)
L3
wild type(n=3),
late L3 Jrk homozygote(n=4) wild type(n=4)
Jrk homozygote(n=1)
Jrk homozygote(n=5), Jrk
pupal wild type(n=12)
partial rescue(n=4) homozygote(n=11)
adult Jrk homozygote(n=2) Jrk homozygote(n=1) wild type(n=15)

Table 2. The critical period of functional Clk expression for rescue of the PDF-
stained sLNvs is during the late L3 to pupal stages. Flies were moved from 18°C to
29°C at various developmental stages.

23
Figure 6. The critical period of
functional Clk expression for rescue of
the PDF-stained sLNvs is during the late
L3 to pupal stages. A. A
cry24/+;+/tubG80ts;Jrk/UClkJrk adult
brain when temperature-shifted at L1. B.
cry24/+;+/tubG80ts;Jrk/UClkJrk adult
brain when temperature-shifted at early
L3. C. cry24/+;+/tubG80ts;Jrk/UClkJrk
adult brains when temperature-shifted at
late L3. Left brain displays Jrk
homozygote phenotype and right brain
displays wild type phenotype. D.
cry24/+;+/tubG80ts;Jrk/UClkJrk adult B
brains when temperature-shifted as
pupae. Left brain displays Jrk
homozygote phenotype and right brain
displays wild type phenotype. E.
cry24/+;+/tubG80ts;Jrk/UClkJrk adult
brains when temperature-shifted 1 day
post-eclosion.

24
C. Visualization of sLNvs during various stages of development

There are three possible explanations for the disappearance of the PDF-stained sLNvs in adult

Jrk homozygote brains. First, CLK may be necessary during embryogenesis to allow

development of the sLNvs. The sLNvs may never develop in Jrk homozygotes. Second, the

sLNvs may develop properly in Jrk homozygote embryonic stages but degenerate when

functional Clk is not expressed in pupal life. A third possible explanation is that the sLNvs are

still present in adult brains, but they do not produce PDF and the PDF staining is unable to detect

the sLNvs.

It is possible that although the sLNvs develop normally, they are not detected by

commonly used markers, because these markers are dependent on Clk expression. Transgenic

expression of GFP was used to resolve this uncertainty. I tested many different drivers to find

one that would continue to produce GFP in Jrk flies, allowing me to track these cells in the

absence of canonical clock markers (PER, TIM). cry24 was a strong driver of membrane GFP

expression(mGFP) in the PDF-positive neurons(data not shown). It was also shown in the

previous experiments that the cry24 driver is able to fully rescue anatomy and partially rescue

behavior. I first used cry24 to drive mGFP and examined the sLNvs in different stages of

development. These data show that the sLNv are present in Jrk larvae and develop relatively

normally(Figure 7A, B). Two sLNvs are labeled with nuclear GFP(GFPnls), and the sLNvs form

synaptic connections with two other neurons, the DN2s, which is consistent with previously

published data(Helfrich-Förster, 2003). At pupal stages however, cry24 expression becomes too

broad to definitively identify the sLNvs(data not shown). In addition, further rescue attempts

with an activity-inhibiting transgene resulted in lethality(discussed in section IV.F), limiting the

utility of cry24 for mechanistic studies.

25
cry24;;GFPnlsJrk
A B

C D
cry24;;GFPnls

Figure 7. sLNvs are present in Jrk homozygotes during L1 and L3.

GFPnls(green) and PDF(blue). A. cry24;;GFPnlsJrk homozygote L1 brain.
sLNvs indicated by arrows. B. cry24;;GFPnlsJrk homozygote L3 brain. sLNvs
indicated by arrows. C. cry24;;GFPnls homozygote L1 brain. sLNvs indicated
by arrows. D. cry24;;GFPnls homozygote L3 brain. sLNvs indicated by arrows.

D. cry13 expression

The Clk overexpression experiment was repeated using cry13 instead of cry24. cry13 expression

should also be retained in Jrk flies, but its expression is weaker and less broad, which would

allow us to distinguish the sLNv from other GFP-expressing cells. First, GFP expression was

examined at different developmental time points. The sLNvs are present during the larval stages

and pupal stages P1 to P4 in mGFP/+;Jrk/cry13Jrk flies, although there is no PDF staining of

the sLNvs(Figure 8.1C-F). The sLNvs do not show GFP expression in mGFP/+;+/cry13 larval

and early pupal brains, but they are labeled by PDF staining(Figure 8.1A, B). In Jrk mutants, cry

is upregulated, so the presence of GFP expression in the Jrk homozygote mutants but not in the

26
control is consistent with increased cry expression in Jrk homozygotes(Glossop et al., 2003).

The sLNvs are not visible using GFP during the P6 to P7 stages and during adulthood in

mGFP/+;Jrk/cry13Jrk(Figure 8.2F, H). The lLNvs do not appear until the late pupal stages and

they are visible using PDF staining(Figure 8.2D, H). The cry13-dependent expression of GFP in

late larval stages of Jrk flies suggested that this driver would be useful in dissecting the

molecular mechanisms of sLNv loss in Jrk.

27
 mGFP/+;+/cry13 mGFP/+;Jrk/cry13Jrk

*
*
* *

A C

*
*
* *

B D
Figure 8.1 sLNvs are present in *
mGFP/+;Jrk/cry13Jrk L3 to P4 brains. *
PDF(red) and GFP(green).
A. mGFP/+;+/cry13 L3 brain.
B. mGFP/+;+/cry13 P1 brain.
C. mGFP/+;Jrk/cry13Jrk L3 brain.
D. mGFP/+;Jrk/cry13Jrk P1 brain.
E. mGFP/+;Jrk/cry13Jrk P2 brain.
F. mGFP/+;Jrk/cry13Jrk P3-P4 brain. E

*
*

28
 mGFP/+;+/cry13 mGFP/+;Jrk/cry13Jrk

A E
PDF mGFP PDF mGFP

B F

C G
PDF mGFP PDF mGFP

D H H
Figure 8.2. sLNvs are not present in P6-P7 or adult Jrk brains. PDF(red) and GFP(green). A.
mGFP/+;+/cry13 P6-P7 brain. B. mGFP/+;+/cry13 P6-P7 LNvs. sLNvs are indicated by arrows.
C. mGFP/+;+/cry13 adult brain. D. mGFP/+;+/cry13 adult LNvs. sLNvs are indicated by arrows.
E. mGFP/+;Jrk/cry13Jrk P6-P7 brain. F. mGFP/+;Jrk/cry13Jrk P6-P7 LNvs.
G. mGFP/+;Jrk/cry13Jrk adult brain. H. mGFP/+;Jrk/cry13Jrk adult LNvs. 29
E. P35 and Diap1 overexpression in Jrk homozygotes

P35 and DIAP1 are anti-apoptosis proteins, so neuron-specific expression of P35 and Diap1

transgenes should inhibit death of sLNvs if they undergo apoptosis. P35 expression driven by

cry24 results in broad GFPnls expression in the sLNv region. This renders the experiment

uninterpretable because identification of the sLNvs relies on position and morphology in Jrk

flies. The cry13 driver was then used, because although it does not express as strongly as cry24,

it has a more restricted expression pattern and a cry13 line with mGFP was readily available.

The change from GFPnls to mGFP also aided in reducing the pan-neuronal presence of GFP seen

with the cry24-driven GFPnls. There is no rescue of the sLNv morphology in

mGFP/P35;cry13Jrk/Jrk(Figure 9G, H).

30
 A B

C D E F G H

Figure 9. P35 expression does not rescue the sLNvs in Jrk homozygotes. PDF(red)
and mGFP(green). A. mGFP/P35; cry13/+ brain. B. mGFP/P35;cry13Jrk/Jrk brain.
C. mGFP/P35; cry13/+ LNvs. D. PDF staining of mGFP/P35; cry13/+ brain. Arrow
indicates a sLNv. E. mGFP labeling of mGFP/P35; cry13/+ brain LNvs. Arrow
indicates sLNv. F. mGFP/P35;cry13Jrk/Jrk LNvs. G. PDF staining of
mGFP/P35;cry13Jrk/Jrk LNvs. H. mGFP labeling of mGFP/P35;cry13Jrk/Jrk LNvs.
No sLNvs are present.

To verify P35 expression in the P35;Jrk line, the presence of tritocerebral cells in older

adults was used as a marker of the anti-apoptotic activity of P35. Previously published data

indicates that PDF-positive tritocerebral cells degenerate a few days after eclosion(Helfrich-

Förster, 1997). When pdf homozygote, pdf/P35, and pdf/P35;+/Jrk brains were examined

however, the tritocerebral cells were still present in all groups 5 to 8 days after eclosion(Figure

10). Previous laboratory methods may have used ineffective methods of detecting the PDF-

positive tritocerebral cells, so the tritocerebral cells appeared to degenerate although they are still

31
present. Alternatively, this phenotype may occur in some genetic backgrounds and not others.

The rescue of PDF-positive tritocerebral cells is not a reliable marker of P35 expression, so there

is currently no positive control confirming that P35 is expressed at sufficient levels to prevent

apoptosis.

Figure 10. No degeneration of PDF-stained tritocerebral cells(*) after 5 to 8 days post-

eclosion. A. pdf/UP35 brain(7 to 8 days post-eclosion). B. pdf/UP35;+/Jrk brain(5 to 8
days post-eclosion). C. pdf homozygote brain(7 days post-eclosion).
32
 When Diap1 is expressed in the sLNvs using cry13, there is no rescue of the sLNvs. The

neuroanatomy of mGFP/+;cry13Jrk/Diap1Jrk is characteristic of Jrk homozygotes and no sLNvs

are present(Figure 11E, F). The results from the P35 and Diap1 experiments suggested that the

sLNvs do not undergo apoptosis. The sLNvs may degenerate by a different programmed cell

death mechanism, so the possibility of excitotoxicity-induced neurodegeneration was explored.

33
A D

B E

C F
Figure 11. No rescue of sLNvs in mGFP/+;cry13Jrk/Diap1Jrk. PDF(red) and
mGFP(green). A. mGFP/+;cry13/Diap1 brain. B. PDF staining of
mGFP/+;cry13/UDiap1 brain. C. mGFP labeling of mGFP/+;cry13/Diap1 brain. D.
mGFP/+;cry13Jrk/Diap1Jrk brain. E. PDF staining of mGFP/+;cry13Jrk/Diap1Jrk
brain. F. mGFP labeling of mGFP/+;cry13Jrk/Diap1Jrk.

34
F. Kir overexpression in Jrk homozygotes

Transgenic expression of the inward-rectifier K+ channel(Kir) causes silencing of

neurons(Nitabach et al., 2002). Kir expression provides a molecular method of selectively

inhibiting activity in neurons. In normal, rhythmic flies, the circadian clock drives 24-hour

oscillations of resting membrane potential and neural activity in clock neurons(Cao and

Nitabach, 2008). Unpublished work from the Allada lab also indicates that DN1 pacemaker

neurons are depolarized in Jrk(M. Flourakis, personal communication). If the sLNvs in Jrk

homozygotes degenerate due to excitotoxicity, then Kir-induced silencing of sLNvs will protect

the neurons from cell death.

Kir overexpression driven by cry13 in Jrk homozygotes does not rescue the sLNv

morphology. The sLNvs are not detectable using PDF staining and mGFP labeling(Figure 12E,

F). When cry24 was used to verify the results, it was discovered that cry24/+;;Kir/+ and

cry24/+;;KirJrk/Jrk genotypes are lethal. 4-1G4 is another driver that was used, but 4-

1/+;Jrk/KirJrk is also lethal.

Because many of the results with the cry13 transgene were unexpected, I tested whether

cry13-driven expression of Clk could rescue the sLNv. There was no rescue of Jrk homozygote

sLNv morphology, which did not agree with the results obtained using cry24. cry13 is more

weakly and narrowly expressed than cry24, so it is concluded that cry13 is not strongly

expressed enough or expressed early enough to drive sufficient Clk overexpression for rescue of

Jrk homozygotes. The data from experiments using cry13 above to test the role of apoptosis and

activity dependence are therefore inconclusive, because these transgenes may also have been

inadequately expressed. Further actions are being taken to confirm the results of the cry13-driven

experiments and will be elaborated upon in the Discussion section.

35
mGFP/+;cry13/Kir

A B C
mGFP/+;cry13Jrk/KirJrk

E F
D
Figure 12. No rescue of sLNvs with Kir expression in Jrk homozygote adult brains
dissected 4 to 6 days post-eclosion. A. PDF staining of mGFP/+;cry13/Kir brain. B.
PDF staining of mGFP/+;cry13/Kir LNvs. C. mGFP labeling of mGFP/+;cry13/Kir
LNvs. D. PDF staining of mGFP/+;cry13Jrk/KirJrk brain. E. PDF staining of
mGFP/+;cry13Jrk/KirJrk LNvs. F. mGFP labeling of mGFP/+;cry13Jrk/KirJrk LNvs

36
G. Exposure of Jrk mutants to LL and DD conditions

I used another approach to test for a role of Clk in activity-dependent apoptosis. CRY-positive

neurons, such as the LNvs, are sensitive to light entrainment, so they must receive light-input

that modifies their activity(Miyasako et al., 2007). To see if the sLNvs would undergo light-

dependent degeneration, adult flies were exposed to constant light(LL). For parallel experiments

to reduce light-dependent activation of the sLNvs, flies were raised from embryos in constant

dark (DD).

In Jrk heterozygote(cry24/+;;GFPnlsJrk/+) and wild type(cry24/+;;GFPnls/+) flies

raised in constant light (LL) at 29°C for approximately one month, the neuroanatomy has

significantly altered from those of wild type flies raised in LD. The flies were raised at 29°C to

exacerbate the LL effects and accelerate neurodegeneration. Jrk heterozygotes display wild type

neuroanatomy when raised in LD. When experimental and control flies were raised in LL, PDF-

stained LNvs disappear or fewer are present(Figure 13F, H). PDF expression in axons

transversing the optic lobe has decreased(Figure 13C, D). There are fewer LNvs in Jrk

heterozygote brains compared to wild type brains, which suggests that flies with reduced levels

of CLK are more susceptible to light-induced degeneration of the sLNvs. Broad GFPnls

expression makes it difficult to draw conclusions from GFP labeling, so cry13-driven mGFP

expression in flies raised at 25°C in LL is being investigated.

I also examined Jrk homozygote flies raised in DD to test whether reduction in sLNv

activation would rescue the sLNvs. The sLNvs are not rescued in Jrk homozygotes(Figure 14G,

H).

37
Figure 13. LNvs of Jrk heterozygotes are more susceptible to light-induced
excitotoxicity than LNvs of wild type flies. PDF(blue) and GFPnls(green). A.
cry24/+;;GFPnls/+ brain. B. cry24/+;;GFPnlsJrk/+ brain. C. PDF staining in
cry24/+;;GFPnls/+ brain. D. PDF staining of cry24/+;;GFPnlsJrk/+ brain. E.
cry24/+;;GFPnls/+ LNvs. F. PDF expression cry24/+;;GFPnls/+ LNvs. G.
cry24/+;;GFPnlsJrk/+ LNvs. H. PDF staining of cry24/+;;GFPnlsJrk/+ LNvs. No
sLNvs visible.

38
 B

A E

B C D F G H

Figure 14. Raising mGFP/mGFP;Jrk/cry13Jrk flies in DD does not rescue the sLNvs.
A. mGFP/mGFP; cry13/+ brain in LD. B. mGFP/mGFP;cry13/+ LNvs in LD. C. PDF staining of
mGFP/mGFP;cry13/+ LNvs in LD. Arrow indicates sLNvs. D. mGFP labeling of
mGFP/mGFP;cry13/+ LNvs in LD. Arrow indicates sLNvs. E. mGFP/mGFP;Jrk/cry13Jrk brain.
F. mGFP/mGFP;Jrk/cry13Jrk LNvs in DD. G. PDF staining of mGFP/mGFP;Jrk/cry13Jrk LNvs
in DD. H. mGFP labeling of mGFP/mGFP;Jrk/cry13Jrk LNvs in DD.

39
H. Visualization of Jrk heterozygote retinas in LL

An additional system for exploring Clk’s influence on excitotoxicity of cells is the retina. Retinal

cells modulate their activity based on changes in light exposure.

The Drosophila melanogaster retina is composed of an array of distinct units of eight

cells, called rhabdomeres. In a properly formed retina, seven of the eight cells can be clearly

visualized using whole mount staining and microscopy(Figure 15, 0 days LL). During LL, the

retinal cells exhibit constant activity and firing(Dolph et al., 1993). The chronically high levels

of activity cause degeneration of the retinal cells due to excitoxicity(Dolph et al., 1993). When

wild type(Jrk sib ctrl) flies and Jrk iso flies have not been exposed to LL conditions (0 days LL),

there is little difference between the retinal structure(Figure 15). The rhabdomeres are located in

the regular array, indicating healthy and intact retinal cells. In just two days under the LL

conditions, the retinal cells begin to exhibit degeneration(Figure 15). The cells are less distinct

and in some areas have lost the rigid array structure. The Jrk heterozygote retinas exhibit greater

progress of degeneration than the control retinas(Figure 15B). At five days under LL conditions,

the retinas in both genotypes have completely degenerated(Figure 15). The rhabdomeres are no

longer distinguishable and the actin structures of the cells have become irregular and

degenerated. The LL conditions are responsible for the degeneration of the retinal cells. When

the flies under LL for five days are compared with age-matched flies who were raised in LD for

five days, the LL fly retinas show degeneration while the LD flies show little change from flies

in LL for zero days(Figure 15). The LD retinas are still healthy and properly formed. This

experiment was independently repeated by a colleague and the results were consistent with my

work, showing an increase in susceptibility to light-induced degeneration in Jrk heterozygotes

(F. Xu, personal communication).

40
A B Figure 15. Jrk heterozygote
retinal cells are more
susceptible to light-induced
degeneration. A. Jrk sibling
control retinas. B. Jrk/+
retinas.

0 days LL 0 days LL

2 days LL 2 days LL

5 days LL 5 days LL

5 days LD 5 days LD

41
Discussion

Overall mechanism of Clk function

Taken together, these data suggest Clk may have a function in neuroprotection. The sLNvs are

appropriately formed during early development. At a critical point during the mid-pupal stage,

functional Clk expression is necessary to protect the neurons from degenerating. Induction of Clk

expression after this critical period will not rescue the Jrk homozygote neuroanatomy because

the sLNvs have already degenerated or they have progressed too far in the degeneration process.

The neurons may undergo programmed cell death using a novel mechanism and not through a

caspase-dependent pathway. The data here regarding cell death mechanisms are not conclusive

however, due to possibly insufficient driver expression. The trigger or signal for degeneration in

the sLNvs may be excessive levels of neurotransmitters or possibly a specific hormone released

during the massive remodeling that occurs during the pupal stage.

Further confirmation of sLNv degeneration

As an alternative explanation for the inability to visualize the sLNvs using GFP expression, cry

promoter may be inactivated or expression reduced in adults so absence of GFP expression in the

sLNvs is due to insufficient activation by cry and not due to degeneration of the sLNvs. To

address this issue, a “memory” experiment will be performed. An actin^CD2^Gal4;UFlp;Jrk fly

will be produced to cross to a Gal4-GFP-Jrk containing fly. The GAL4 driver will only induce

expression of UFlp in specific cells and the FLP will cause GFP expression to be driven by the

actin promoter. This will allow GFP expression to be permanently expressed by the ubiquitous

actin promoter, independent of cry expression in adults, but spatially restricted to cells that

expressed Gal4, for instance cry24-specific cells. Currently, the fly lines necessary for this

experiment are being constructed using genetic crosses.

42
 Another method of confirming the degeneration of the sLNvs is dissecting pupae at

specific time intervals and imaging brains to visualize the degeneration of the sLNvs. The

dissections will be focused on flies in the P5 to P7 stage because the sLNvs are still present at P5

but gone by P6 or P7 in the mGFP/+;Jrk/cry13Jrk flies. Visual confirmation of the degeneration

process of the sLNvs will be significant evidence supporting the hypothesis of the

neuroprotective role of Clk expression. Propidium iodide staining is a commonly used technique

that distinguishes apoptotic or necrotic cells from normal cells(Riccardi and Nicoletti, 2006).

DNA in the nuclei is cleaved during apoptosis and necrosis. The propidium iodide binds to

DNA, and the appearance of the nuclei in apoptotic and necrotic cells differs from those in

normal cells due to the extensive DNA cleavage(Riccardi and Nicoletti, 2006). The propidium

iodide staining can confirm the degradation of the sLNvs when the time interval of degeneration

is established.

Modifications of P35, Kir, and Diap1 experiments

An immediate experiment that can be conducted to answer the question of the significance of the

Diap1 results is performing DIAP1 staining in mGFP/+;cry13/Diap1 and

mGFP/+;cry13Jrk/Diap1Jrk brains. If the cry13 promoter is driving Diap1 expression, then

DIAP1 will be detected in the sLNvs of larvae during staining. The staining protocol for DIAP1

is being developed and results of this experiment will be obtained by the end of the academic

year.

An initial experiment to verify the results of the P35 experiment is construction of the

P35;cry13Jrk line. The expression of two copies of cry13 may be able to drive sufficient P35

expression. Additionally, a method for verifying the P35 expression in the P35;Jrk line is still

being developed. It would be ideal to identify specific neurons that develop normally and then

43
degenerate at a later time point. These neurons would need to be easily detectable with available

markers. Rescue of these neurons using P35;Jrk would verify the function of the P35 transgene.

Another approach that will be performed is switching to the cry39 driver, a promoter that is more

strongly expressed than cry13 although its expression is still weaker than cry24. Reverting to

usage of cry24 is not ideal because construction of a cry24;mGFP;Jrk line will result in a fly

with transgenes on three chromosomes, which is difficult to produce and will not be a healthy

line. It is more efficient to examine cry39’s suitability before resorting to cry24. cry39-driven

Clk overexpression to rescue the Jrk homozygote neuroanatomy will be performed first in order

to ascertain whether cry39 has sufficient expression in the sLNvs. In case cry39 is found to be a

suitable driver, the mGFPcry39 and mGFPcry39;Jrk lines are being constructed and will be

used.

Further explorations of mechanisms of Clk function

The light-induced degeneration of the sLNvs experiment is currently being repeated under 25°C

to confirm the previously obtained results and to establish the time course of the neuron

degeneration. If neurons with reduced levels of CLK are more susceptible to excitotoxicity, it is

expected that the neurons of Jrk heterozygote flies will begin to degenerate before neurons of

wild type flies.

Ecdysone is a likely candidate for a cell death signal. It is a hormone that is released

during metamorphosis that triggers massive neural remodeling in the pupae in preparation for

adulthood. Drosophila neurons have been identified that under go caspase-dependent and

ecdysone-induced cell death. The Corazonin-positive group of peptidergic neurons in the

Drosophila larval ventral nerve cord degenerate during the pupal stage(Choi et al., 2006). The

44
cells can be rescued with dominant negative expression of a specific ecdysone receptor and they

are also rescued by expression of P35(Choi et al., 2006).

Significance and implications of results

The proposed molecular role of Clk in Drosophila is consistent with data obtained from

previously published research. This project suggests that Clk is important during developmental

periods for protection of specific neurons in the brain. Chronic sleep loss during critical

developmental periods in children can lead to cognitive impairment and impaired brain

development from widespread neuronal loss(Jan et al., 2010). Sleep in adolescent mice aids with

synaptic pruning and contributes to homeostasis of synaptic connections in the brain(Maret et al.,

2011). Wake favors the development of cortical spines and results in a net increase in cortical

spines while sleep favors the decrease of cortical spines in the adolescent mice(Maret et al.,

2011). This suggests that disruption of normal sleep-wake cycles in human adolescents may also

interfere with the normal fluctuations between neuron cortical spine growth and retraction during

a vulnerable period of brain development. Chronic insults to the sleep-wake system during

childhood and adolescence in humans may have irreversible and long-term consequences on the

developing brain. When the circadian system is disrupted, such as in Jrk mutants or in humans

with irregular sleep-wake cycles, neurons may be less protected against daily use-dependent

insults or less protected from the effects of normal cell pruning processes. Therefore, it would be

important to develop public health policies that encourage regular circadian behavior and

instigate changes in employment hours to mitigate potential negative effects arising from

disrupted circadian rhythms.

45
References

Allada, R., N. E. White, et al. (1998). "A Mutant Drosophila Homolog of Mammalian Clock

Disrupts Circadian Rhythms and Transcription of period and timeless." Cell 93(5): 791-

804.

Bainbridge, S. P. and M. Bownes (1981). "Staging the metamorphosis of Drosophila

melanogaster." Journal of Embryology and Experimental Morphology 66(1): 57-80.

Benito, J., H. Zheng, et al. (2007). "Transcriptional Feedback Loop Regulation, Function, and

Ontogeny in Drosophila." Cold Spring Harbor Symposia on Quantitative Biology 72:

437-444.

Blau, J. and M. W. Young (1999). "Cycling vrille Expression Is Required for a Functional

Drosophila Clock." Cell 99(6): 661-671.

Blau, J., F. Blanchard, et al. (2007). "What Is There Left to Learn about the Drosophila Clock?"

Cold Spring Harbor Symposia on Quantitative Biology 72: 243-250.

Cao, G. and M. N. Nitabach (2008). "Circadian Control of Membrane Excitability in Drosophila

melanogaster Lateral Ventral Clock Neurons." The Journal of Neuroscience 28(25):

6493-6501.

Cardinali, D.P., A. M. Furio, et al. (2010). "Clinical Aspects of Melatonin Intervention in

Alzheimers Disease Progression." Current Neuropharmacology 8(3): 218-227.

Centers for Disease Control and Prevention. “Insufficient Sleep is a Public Health Epidemic.”

Accessed March 3, 2012. http://www.cdc.gov/Features/dsSleep/.

Choi, Y.-J., G. Lee, et al. (2006). "Programmed cell death mechanisms of identifiable peptidergic

neurons in Drosophila melanogaster." Development 133(11): 2223-2232.

46
Dolph, P., R. Ranganathan, et al. (1993). "Arrestin function in inactivation of G protein-coupled

receptor rhodopsin in vivo." Science 260(5116): 1910-1916.

Dong, X.-x., Y. Wang, et al. (2009). "Molecular mechanisms of excitotoxicity and their

relevance to pathogenesis of neurodegenerative diseases." Acta Pharmacologica Sinica

30(4): 379-387.

Gaddameedhi, S., C. P. Selby, et al. (2011). "Control of skin cancer by the circadian rhythm."

Proceedings of the National Academy of Sciences 108(46): 18790-18795.

Glossop, N. R. J., J. H. Houl, et al. (2003). "VRILLE Feeds Back to Control Circadian

Transcription of Clock in the Drosophila Circadian Oscillator." Neuron 37(2): 249-261.

Helfrich-Förster, C. (1997). "Development of pigment-dispersing hormone-immunoreactive

neurons in the nervous system of Drosophila melanogaster." The Journal of Comparative

Neurology 380(3): 335-354.

Helfrich-Förster, C. (2003). "The neuroarchitecture of the circadian clock in the brain of

Drosophila melanogaster." Microscopy Research and Technique 62(2): 94-102.

Hung, C.-W., Y.-C. Chen, et al. (2010). "Ageing and neurodegenerative diseases." Ageing

Research Reviews 9, Supplement(0): S36-S46.

Jan, J. E., R. J. Reiter, et al. (2010). "Long-term sleep disturbances in children: A cause of

neuronal loss." European Journal of Paediatric Neurology 14(5): 380-390.

Kang, J.-E., M. M. Lim, et al. (2009). "Amyloid-β Dynamics Are Regulated by Orexin and the

Sleep-Wake Cycle." Science 326(5955): 1005-1007.

Kilman, V. L. and R. Allada (2009). "Genetic Analysis of Ectopic Circadian Clock Induction in

Drosophila." Journal of Biological Rhythms 24(5): 368-378.

47
Kirilly, D., Jack Jing L. Wong, et al. (2011). "Intrinsic Epigenetic Factors Cooperate with the

Steroid Hormone Ecdysone to Govern Dendrite Pruning in Drosophila." Neuron 72(1):

86-100.

Krishnan, N., K. Rakshit, et al. (2011). "Loss of circadian clock accelerates aging in

neurodegeneration-prone mutants." Neurobiology of Disease(0).

Lee, J. H. and A. Sancar (2011). "Regulation of apoptosis by the circadian clock through NF-κB

signaling." Proceedings of the National Academy of Sciences 108(29): 12036-12041.

Maret, S., U. Faraguna, et al. (2011). "Sleep and waking modulate spine turnover in the

adolescent mouse cortex." Nat Neurosci 14(11): 1418-1420.

Miyasako, Y., Y. Umezaki, et al. (2007). "Separate Sets of Cerebral Clock Neurons Are

Responsible for Light and Temperature Entrainment of Drosophila Circadian Locomotor

Rhythms." Journal of Biological Rhythms 22(2): 115-126.

National Sleep Foundation. “2003 Sleep in America Poll.” Accessed March 3, 2012.

http://www.sleepfoundation.org/article/sleep-america-polls/2003-sleep-and-aging

National Sleep Foundation. “2009 Sleep in America Poll.” Accessed March 3, 2012.

http://www.sleepfoundation.org/sites/default/files/2009%20Sleep%20in%20America%20

SOF%20EMBARGOED.pdf

Nitabach, M. N., J. Blau, et al. (2002). "Electrical Silencing of Drosophila Pacemaker Neurons

Stops the Free-Running Circadian Clock." Cell 109(4): 485-495.

Organisciak, D. T., R. M. Darrow, et al. (2000). "Circadian-Dependent Retinal Light Damage in

Rats." Investigative Ophthalmology & Visual Science 41(12): 3694-3701.

Panda, S., J. B. Hogenesch, et al. (2002). "Circadian rhythms from flies to human." Nature

417(6886): 329-335.

48
Park, J. H., C. Helfrich-Förster, et al. (2000). "Differential regulation of circadian pacemaker

output by separate clock genes in Drosophila." Proceedings of the National Academy of

Sciences of the United States of America 97(7): 3608-3613.

Pfeiffenberger, C., B. C. Lear, et al. (2010a). "Locomotor Activity Level Monitoring Using the

Drosophila Activity Monitoring (DAM) System." Cold Spring Harbor Protocols

2010(11): pdb.prot5518.

Pfeiffenberger, C., B. C. Lear, et al. (2010b). "Processing Circadian Data Collected from the

Drosophila Activity Monitoring (DAM) System." Cold Spring Harbor Protocols

2010(11): pdb.prot5519.

Reddy, A. B. and J. S. O’Neill (2010). "Healthy clocks, healthy body, healthy mind." Trends in

Cell Biology 20(1): 36-44.

Riccardi, C. and I. Nicoletti (2006). "Analysis of apoptosis by propidium iodide staining and

flow cytometry." Nat. Protocols 1(3): 1458-1461.

Rosbash, M. (2009). "The Implications of Multiple Circadian Clock Origins." PLoS Biol 7(3):

e1000062.

Sack, R. L., D. Auckley, et al. (2007). "Circadian Rhythm Sleep Disorders: Part II, Advanced

Sleep Phase Disorder, Delayed Sleep Phase Disorder, Free-Running Disorder, and

Irregular Sleep-Wake Rhythm." Sleep 30(11): 1460-1483.

Sancar, A., L. A. Lindsey-Boltz, et al. (2010). "Circadian clock control of the cellular response to

DNA damage." FEBS Letters 584(12): 2618-2625.

Santhi, N., H. C. Thorne, et al. (2011). "The spectral composition of evening light and individual

differences in the suppression of melatonin and delay of sleep in humans." Journal of

Pineal Research: no-no.

49
Scheer, F. A. J. L., M. F. Hilton, et al. (2009). "Adverse metabolic and cardiovascular

consequences of circadian misalignment." Proceedings of the National Academy of

Sciences.

Siwicki, K. K., C. Eastman, et al. (1988). "Antibodies to the period gene product of drosophila

reveal diverse tissue distribution and rhythmic changes in the visual system." Neuron

1(2): 141-150.

Srinivasan, V., D. P. Cardinali, et al. (2011). "Therapeutic potential of melatonin and its analogs

in Parkinson’s disease: focus on sleep and neuroprotection." Therapeutic Advances in

Neurological Disorders 4(5): 297-317.

Stoleru, D., Y. Peng, et al. (2004). "Coupled oscillators control morning and evening locomotor

behaviour of Drosophila." Nature 431(7010): 862-868.

Wheeler, D. A., M. J. Hamblen-Coyle, et al. (1993). "Behavior in Light-Dark Cycles of

Drosophila Mutants That Are Arrhythmic, Blind, or Both." Journal of Biological

Rhythms 8(1): 67-94.

Wulff, K., S. Gatti, et al. (2010). "Sleep and circadian rhythm disruption in psychiatric and

neurodegenerative disease." Nat Rev Neurosci 11(8): 589-599.

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Acknowledgements

I am deeply grateful to Dr. Valerie Kilman for her three years of patient guidance and extensive
teaching as my research advisor and to Dr. Ravi Allada for giving me the valuable opportunity to
conduct research in his laboratory. This research was funded by a grant from the Brain Research
Foundation and summer undergraduate research grants from the Northwestern University
Program of Biological Sciences and Northwestern University Provost’s Office.

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