Postgraduate research supervision

Inhibitor of DNA binding 2 (ID2) is a helix-loop-helix transcriptional repressor rhythmically expressed in many adult tissues. Our earlier studies have demonstrated a role for ID2 in the input pathway, core clock function and output pathways of the mouse circadian system. We have also reported that Id2 null (Id2-/-) mice are lean with low gonadal white adipose tissue deposits and lower lipid content in the liver. These results coincided with altered or disrupted circadian expression profiles of liver genes including those involved in lipid metabolism. In the present phenotypic study we intended to decipher, on a sex-specific basis, the role of ID2 in glucose metabolism and in the circadian regulation of activity, important components of energy balance. We find that Id2-/- mice exhibited altered daily and circadian rhythms of feeding and locomotor activity; activity profiles extended further into the late night/dark phase of the 24-hr cycle, despite mice showing reduced total locomotor activity. Also, male Id2-/- mice consumed a greater amount of food relative to body mass, and displayed less weight gain. Id2-/- females had smaller adipocytes, suggesting sexual-dimorphic programing of adipogenesis. We observed increased glucose tolerance and insulin sensitivity in male Id2-/- mice, which was exacerbated in older animals. FDG-PET analysis revealed increased glucose uptake by skeletal muscle and brown adipose tissue of male Id2-/- mice, suggesting increased glucose metabolism and thermogenesis in these tissues. Reductions in intramuscular triacylglycerol and diacylglycerol were detected in male Id2-/- mice, highlighting its possible mechanistic role in enhanced insulin sensitivity in these mice. Our findings indicate a role for ID2 as a regulator of glucose and lipid metabolism, and in the circadian control of feeding/locomotor behavior; and contribute to the understanding of the development of obesity and diabetes, particularly in shift work personnel among whom incidence of such metabolic disorders is elevated.

The aim of this study was to analyse the circadian behavioural responses of mice carrying a functional knockout of the Per3 gene (P e r 3 - / -) to different light: dark (L: D) cycles. Male adult wild-type (WT) and P e r 3 - / - mice were kept under 12-hour light: 12-hour dark conditions (12L: 12D) and then transferred to either a short or long photoperiod and subsequently released into total darkness. All mice were exposed to both conditions, and behavioural activity data were acquired through running wheel activity and analysed for circadian characteristics during these conditions. We observed that, during the transition from 12L: 12D to 16L: 8D, P e r 3 - / - mice take approximately one additional day to synchronise to the new L: D cycle compared to WT mice. Under these long photoperiod conditions, P e r 3 - / - mice were more active in the light phase. Our results suggest that P e r 3 - / - mice are less sensitive to light. The data presented here provides further evidence that Per3 is involved in the suppression of behavioural activity in direct response to light. © 2014 D. S. Pereira et al.

Circadian rhythms in cardiac function are apparent in e.g., blood pressure, heart rate, and acute adverse cardiac events. A circadian clock in heart tissue has been identified, but entrainment pathways of this clock are still unclear. We cultured tissues of mice carrying bioluminescence reporters of the core clock genes, period 1 or 2 (per1(luc) or PER2(LUC)) and compared in vitro responses of atrium to treatment with medium and a synthetic glucocorticoid (dexamethasone [DEX]) to that of the suprachiasmatic nucleus (SCN) and liver. We observed that PER2(LUC), but not per1(luc) is rhythmic in atrial tissue, while both per1(luc) and PER2(LUC) exhibit rhythmicity in other cultured tissues. In contrast to the SCN and liver, both per1(luc) and PER2(LUC) bioluminescence amplitudes were increased in response to DEX treatment, and the PER2(LUC) amplitude response was dependent on the time of treatment. Large phase-shift responses to both medium and DEX treatments were observed in the atrium, and phase responses to medium treatment were not attributed to serum content but the treatment procedure itself. The phase-response curves of atrium to both DEX and medium treatments were found to be different to the liver. Moreover, the time of day of the culturing procedure itself influenced the phase of the circadian clock in each of the cultured tissues, but the magnitude of this response was uniquely large in atrial tissue. The current data describe novel entrainment signals for the atrial circadian clock and specifically highlight entrainment by mechanical treatment, an intriguing observation considering the mechanical nature of cardiac tissue.

Circadian organization of the mammalian transcriptome is achieved by rhythmic recruitment of key modifiers of chromatin structure and transcriptional and translational processes. These rhythmic processes, together with posttranslational modification, constitute circadian oscillators in the brain and peripheral tissues, which drive rhythms in physiology and behavior, including the sleep-wake cycle. In humans, sleep is normally timed to occur during the biological night, when body temperature is low and melatonin is synthesized. Desynchrony of sleep-wake timing and other circadian rhythms, such as occurs in shift work and jet lag, is associated with disruption of rhythmicity in physiology and endocrinology. However, to what extent mistimed sleep affects the molecular regulators of circadian rhythmicity remains to be established. Here, we show that mistimed sleep leads to a reduction of rhythmic transcripts in the human blood transcriptome from 6.4% at baseline to 1.0% during forced desynchrony of sleep and centrally driven circadian rhythms. Transcripts affected are key regulators of gene expression, including those associated with chromatin modification (methylases and acetylases), transcription (RNA polymerase II), translation (ribosomal proteins, initiation, and elongation factors), temperature-regulated transcription (cold inducible RNA-binding proteins), and core clock genes including CLOCK and ARNTL (BMAL1). We also estimated the separate contribution of sleep and circadian rhythmicity and found that the sleep-wake cycle coordinates the timing of transcription and translation in particular. The data show that mistimed sleep affects molecular processes at the core of circadian rhythm generation and imply that appropriate timing of sleep contributes significantly to the overall temporal organization of the human transcriptome.

The effect of light on circadian rhythms and sleep is mediated by a multi-component photoreceptive system of rods, cones and melanopsin-expressing intrinsically photosensitive retinal ganglion cells. The intensity and spectral sensitivity characteristics of this system are to be fully determined. Whether the intensity and spectral composition of light exposure at home in the evening is such that it delays circadian rhythms and sleep also remains to be established. We monitored light exposure at home during 6-8?wk and assessed light effects on sleep and circadian rhythms in the laboratory. Twenty-two women and men (23.1?±?4.7?yr) participated in a six-way, cross-over design using polychromatic light conditions relevant to the light exposure at home, but with reduced, intermediate or enhanced efficacy with respect to the photopic and melanopsin systems. The evening rise of melatonin, sleepiness and EEG-assessed sleep onset varied significantly (P?0.01) across the light conditions, and these effects appeared to be largely mediated by the melanopsin, rather than the photopic system. Moreover, there were individual differences in the sensitivity to the disruptive effect of light on melatonin, which were robust against experimental manipulations (intra-class correlation?=?0.44). The data show that light at home in the evening affects circadian physiology and imply that the spectral composition of artificial light can be modified to minimize this disruptive effect on sleep and circadian rhythms. These findings have implications for our understanding of the contribution of artificial light exposure to sleep and circadian rhythm disorders such as delayed sleep phase disorder.

The aim of this handbook is to present an overview of the work on learning, written by leading scholars from all these different perspectives and disciplines.

Using positron emission tomography, we measured in vivo uptake of (18)F-fluorodeoxyglucose (FDG) in the brain and heart of C57Bl/6 mice at intervals across a 24-hour light-dark cycle. Our data describe a significant, high amplitude rhythm in FDG uptake throughout the whole brain, peaking at the mid-dark phase of the light-dark cycle, which is the active phase for nocturnal mice. Under these conditions, heart FDG uptake did not vary with time of day, but did show biological variation throughout the 24-hour period for measurements within the same mice. FDG uptake was scanned at different times of day within an individual mouse, and also compared to different times of day between individuals, showing both biological and technical reproducibility of the 24-hour pattern in FDG uptake. Regional analysis of brain FDG uptake revealed especially high amplitude rhythms in the olfactory bulb and cortex, while low amplitude rhythms were observed in the amygdala, brain stem and hypothalamus. Low amplitude 24-hour rhythms in regional FDG uptake may be due to multiple rhythms with different phases in a single brain structure, quenching some of the amplitude. Our data show that the whole brain exhibits significant, high amplitude daily variation in glucose uptake in living mice. Reports applying the 2-deoxy-D[(14)C]-glucose method for the quantitative determination of the rates of local cerebral glucose utilization indicate only a small number of brain regions exhibiting a day versus night variation in glucose utilization. In contrast, our data show 24-hour patterns in glucose uptake in most of the brain regions examined, including several regions that do not show a difference in glucose utilization. Our data also emphasizes a methodological requirement of controlling for the time of day of scanning FDG uptake in the brain in both clinical and pre-clinical settings, and suggests waveform normalization of FDG measurements at different times of the day.

Industrialisation greatly increased human night-time exposure to artificial light, which in animal models is a known cause of depressive phenotypes. Whilst many of these phenotypes are ?direct? effects of light on affect, an ?indirect? pathway via altered sleep-wake timing has been suggested. We have previously shown that the Period3 gene, which forms part of the biological clock, is associated with altered sleep-wake patterns in response to light. Here, we show that both wild-type and Per3-/- mice showed elevated levels of circulating corticosterone and increased hippocampal Bdnf expression after 3 weeks of exposure to dim light at night, but only mice deficient for the PERIOD3 protein (Per3-/-) exhibited a transient anhedonia-like phenotype, observed as reduced sucrose preference, in weeks 2-3 of dim light at night, whereas WT mice did not. Per3-/- mice also exhibited a significantly smaller delay in behavioural timing than WT mice during weeks 1, 2 and 4 of dim light at night exposure. When treated with imipramine, neither Per3-/- nor WT mice exhibited an anhedonia-like phenotype, and neither genotypes exhibited a delay in behavioural timing in responses to dLAN. While the association between both Per3-/- phenotypes remains unclear, both are alleviated by imipramine treatment during dim night-time light.

Circadian organisation of behavioural and physiological rhythms in mammals is largely driven by the clock in the suprachiasmatic nuclei (SCN) of the hypothalamus. In this clock, a molecular transcriptional repression and activation mechanism generates near 24 hour rhythms. One of the outputs of the molecular clock in specific SCN neurons is arginine-vasopressin (AVP), which is responsive to transcriptional activation by clock gene products. As negative regulators, the protein products of the period genes are thought to repress transcriptional activity of the positive limb after heterodimerisation with CRYPTOCHROME. When both the Per1 and Per2 genes are dysfunctional by targeted deletion of the PAS heterodimer binding domain, mice lose circadian organization of behaviour upon release into constant environmental conditions. To which degree the period genes are involved in the control of AVP output is unknown.

Sleep homeostasis and circadian rhythmicity interact to determine the timing of behavioral activity. Circadian clock genes contribute to circadian rhythmicity centrally and in the periphery, but some also have roles within sleep regulation. The clock gene Period3 (Per3) has a redundant function within the circadian system and is associated with sleep homeostasis in humans. This study investigated the role of PER3 in sleep/wake activity and sleep homeostasis in mice by recording wheel running activity under baseline conditions in wild-type (WT; n = 54) and in PER3-deficient (Per3(-/-); n = 53) mice, as well as EEG-assessed sleep before and after 6 hours of sleep deprivation in WT (n = 7) and Per3(-/-) (n = 8) mice. Whereas total activity and vigilance states did not differ between the genotypes, the temporal distribution of wheel running activity, vigilance states, and EEG delta activity was affected by genotype. In Per3(-/-) mice, running wheel activity was increased and REM sleep and NREM sleep were reduced in the middle of the dark phase, and delta activity was enhanced at the end of the dark phase. At the beginning of the baseline light period, there was less wakefulness and more REM and NREM in Per3(-/-) mice. Per3(-/-) mice spent less time in wakefulness and more time in NREM sleep in the light period immediately after sleep deprivation and REM sleep accumulated more slowly during the recovery dark phase. These data confirm a role for PER3 in sleep/wake timing and sleep homeostasis.

Light is the main entraining signal of the central circadian clock, which drives circadian organization of activity. When food is made available during only certain parts of the day, it can entrain the clock in the liver without changing the phase of the central circadian clock. Although a hallmark of food entrainment is a behavioral anticipation of food availability, the extent of behavioral alterations in response to food availability has not been fully characterized. The authors have investigated interactions between light and temporal food availability in the timing of activity in the common vole. Temporally restricted food availability enhanced or attenuated re-entrainment to a phase advance in light entrainment when it was shifted together with the light or remained at the same time of day, respectively. When light-entrained behavior was challenged with temporal food availability cycles with a different period, two distinct activity components were observed. More so, the present data indicate that in the presence of cycles of different period length of food and light, an activity component emerged that appeared to be driven by a free-running (light-entrainable) clock. Because the authors have previously shown that in the common vole altering activity through running-wheel availability can alter the effectiveness of food availability to entrain the clock in the liver, the authors included running-wheel availability as a parameter that alters the circadian/ultradian balance in activity. In the current protocols, running-wheel availability enhanced the entraining potential of both light and food availability in a differential way. The data presented here show that in the vole activity is a complex of individually driven components and that this activity is, itself, an important modulator of the effectiveness of entraining signals such as light and food.

Using a micro-PET/CT scanner, we have measured (18)F-fluorodeoxyglucose uptake in interscapular brown adipose tissue (iBAT) in C57Bl/6 mice at intervals across a 24-hour light-dark cycle. Our data reveals a strong 24-hour profile of glucose uptake of iBAT, peaking at approximately 9 hours into the light phase of the 12 hour light, 12 hour dark day. BAT is increasingly gaining attention as being involved in metabolic phenotypes and obesity, where BAT, as observed by PET analysis, negatively correlates with obesity and age. Conversely, animals that show perturbations in circadian clocks, behavior and physiology show metabolic phenotypes. The observation of a 24-hour rhythm in glucose uptake in iBAT makes this tissue a candidate site of interaction between metabolic and circadian systems.

In humans, a primate-specific variable-number tandem-repeat (VNTR) polymorphism (4 or 5 repeats 54 nt in length) in the circadian gene PER3 is associated with differences in sleep timing and homeostatic responses to sleep loss. We investigated the effects of this polymorphism on circadian rhythmicity and sleep homeostasis by introducing the polymorphism into mice and assessing circadian and sleep parameters at baseline and during and after 12 h of sleep deprivation (SD). Microarray analysis was used to measure hypothalamic and cortical gene expression. Circadian behavior and sleep were normal at baseline. The response to SD of 2 electrophysiological markers of sleep homeostasis, electroencephalography (EEG) ¸ power during wakefulness and ´ power during sleep, were greater in the Per3(5/5) mice. During recovery, the Per3(5/5) mice fully compensated for the SD-induced deficit in ´ power, but the Per3(4/4) and wild-type mice did not. Sleep homeostasis-related transcripts (e.g., Homer1, Ptgs2, and Kcna2) were differentially expressed between the humanized mice, but circadian clock genes were not. These data are in accordance with the hypothesis derived from human data that the PER3 VNTR polymorphism modifies the sleep homeostatic response without significantly influencing circadian parameters.-Hasan, S., van der Veen, D. R., Winsky-Sommerer, R., Hogben, A., Laing, E. E., Koentgen, F., Dijk, D.-J., Archer, S. N. A human sleep homeostasis phenotype in mice expressing a primate-specific PER3 variable-number tandem-repeat coding-region polymorphism.

Currently, cell separation occurs almost exclusively by density gradient methods and by fluorescence- and magnetic-activated cell sorting (FACS/MACS). These variously suffer from lack of specificity, high cell loss, use of labels, and high capital/operating cost. We present a dielectrophoresis (DEP)-based cell separation method, using 3D electrodes on a low-cost disposable chip; one cell type is allowed to pass through the chip whilst the other is retained and subsequently recovered. The method advances usability and throughput of DEP separation by orders of magnitude in throughput, efficiency, purity, recovery (cells arriving in the correct output fraction), cell losses (those which are unaccounted for at the end of the separation) and cost. The system was evaluated using three example separations; live and dead yeast; human cancer cells/red blood cells; and rodent fibroblasts/red blood cells. A single-pass protocol can enrich cells with cell recovery of up to 91.3% at over 300,000 cells/second with >3% cell loss. A two-pass protocol can process 300,000,000 cells in under 30 minutes, with cell recovery of up to 96.4% and cell losses below 5%, an effective processing rate >160,000 cells/second. A three-step protocol is shown to be effective for removal of 99.1% of RBCs spiked with 1% cancer cells, whilst maintaining a processing rate of ~170,000 cells/second. Furthermore, the self-contained and low-cost nature of the separator device means that it has potential application in low-contamination applications such as cell therapies, where GMP compatibility is of paramount importance. Significance statement. Cell separation is a fundamental process in biomedicine, but is presently complicated, cumbersome and expensive. We present a technique that can sort cells at a rate equivalent to or faster than gold-standard techniques such as FACS and MACs, but can do label-free and with very low cell loss. The system uses dielectrophoresis (DEP) to sort cells electrostatically, using a novel electrode chip that eschews microfabrication in favour of a laminate drilled with 397 electrode-bearing wells. This high level of parallelisation makes the system immune to the bubbles that limit labs-on-chip, whilst also increasing capacity and throughput to unprecedented levels, whilst the chip is cheap enough to be disposable, preventing inter-separation contamination.

Biological oscillations with an ultradian time scale of 1 to several hours include cycles in behavioral arousal, episodic glucocorticoid release, and gene expression. Ultradian rhythms are thought to have an extrinsic origin because of a perceived absence of ultradian rhythmicity in vitro and a lack of known molecular ultradian oscillators. We designed a novel, non?spectral-analysis method of separating ultradian from circadian components and applied it to a published gene expression dataset with an ultradian sampling resolution. Ultradian rhythms in mouse hepatocytes in vivo have been published, and we validated our approach using this control by confirming 175 of 323 ultradian genes identified in a prior study and found 862 additional ultradian genes. For the first time, we now report ultradian expression of >900 genes in vitro. Sixty genes exhibited ultradian transcriptional rhythmicity, both in vivo and in vitro, including 5 genes involved in the cell cycle. Within these 60 genes, we identified significant enrichment of specific DNA motifs in the 1000 bp proximal promotor, some of which associate with known transcriptional factors. These findings are in strong support of instrinsically-driven ultradian rhythms and expose potential molecular mechanisms and functions underlying ultradian rhythms that remain unknown.

Under natural conditions, many aspects of the abiotic and biotic environment vary with time of day, season or even era, whilst these conditions are typically kept constant in laboratory settings. The timing information contained within the environment serve as critical timing cues for the internal biological timing system, but how this system drives daily rhythms in behaviour and physiology may also depend on the internal state of the animal. The disparity between timing of these cues in natural and laboratory conditions can result in substantial differences in the scheduling of behaviour and physiology under these conditions. In nature, temporal coordination of biological processes is critical to maximise fitness because they optimise the balance between reproduction, foraging, and predation risk. Here we focus on the role of peripheral circadian clocks, and the rhythms that they drive, in enabling adaptive phenotypes. We discuss how reproduction, endocrine activity and metabolism interact with peripheral clocks, and outline the complex phenotypes arising from changes in this system. We conclude that peripheral timing is critical to adaptive plasticity of circadian organisation in the field, and that we must abandon standard laboratory conditions to understand the mechanisms that underlie this plasticity which maximises fitness under natural conditions.

Metabolic profiling of individuals with type 2 diabetes mellitus (T2DM) has previously been limited to single-time-point samples, ignoring time-of-day variation. Here, we tested our hypothesis that body mass and T2DM affect daily rhythmicity and concentrations of circulating metabolites across a 24-h day in 3 age-matched, male groups?lean, overweight/obese (OW/OB), and OW/OB with T2DM?in controlled laboratory conditions, which were not confounded by large meals. By using targeted liquid chromatography/mass spectrometry metabolomics, we quantified 130 plasma metabolites every 2 h over 24 h, and we show that average metabolite concentrations were significantly altered by increased body mass (90 of 130) and T2DM (56 of 130). Thirty-eight percent of metabolites exhibited daily rhythms in at least 1 study group, and where a metabolite was rhythmic in >1 group, its peak time was comparable. The optimal time of day was assessed to provide discriminating biomarkers. This differed between metabolite classes and study groups?for example, phospholipids showed maximal difference at 5:00 AM (lean vs. OW/OB) and at 5:00 PM (OW/OB vs. T2DM). Metabolites that were identified with both robust 24-h rhythms and significant concentration differences between study groups emphasize the importance of controlling the time of day for diagnosis and biomarker discovery, offering a significant improvement over current single sampling.?Isherwood, C. M., Van der Veen, D. R., Johnston, J. D., Skene, D. J. Twenty-four-hour rhythmicity of circulating metabolites: effect of body mass and type 2 diabetes.

It is widely accepted that obesity is the main risk factor for type 2 diabetes mellitus (T2DM) (1). The progression from obesity to T2DM is largely a result of comorbidities, such as systemic inflammation and insulin resistance. Metabolic profiling by using targeted metabolomics, which enables the quantification of more than 100 low-MW intermediates of metabolism, is increasingly used to characterize (pre)diabetic phenotypes and has identified differences in metabolite profiles between those individuals who are obese and those with T2DM (2?5).

Recent work by our group and others has shown a 24-h variation in the human metabolome in healthy individuals, analyzed by using a range of analytical platforms (6?12), which has demonstrated that an estimated 15?20% of the metabolome is rhythmic in blood (6, 7). Transgenic mice that carry targeted genetic manipulation of circadian clock genes also exhibit a phenotype that involves defective metabolism, and associations between the circadian timing system and metabolic responses have been reported in humans (13). Reviews of these studies, including the higher incidence of obesity, T2DM, and related disorders in shift workers, have recently been published (14, 15).

Existing metabolomics studies in T2DM have been restricted to the analysis of single-time-point, mostly fasting, samples, which cannot characterize the effect of increased body mass and T2DM on rhythmic metabolites. Characterizing 24-h metabolite rhythms in T2DM compared with age- and body mass?matched controls may therefore provide novel insights into the etiology and progression of T2DM. Identification of the optimal time of day for blood sampling?when metabolite levels show the biggest difference between T2DM and controls?would also provide more discriminating diagnostic biomarkers, rather than taking a single morning fasting sample.

We thus assessed the effect of increased body mass [overweight/obese (OW/OB)] and T2DM on 24-h rhythms of circulating metabolites in men by using a quantitative targeted liquid chromatography/mass spectrometry (LC/MS) metabolomics approach. As T2DM is often accompanied by obesity, we set out to distinguish the effects of T2DM from those of increased body mass by incorporating both a lean and an OW/OB control group into the current study design.

Circadian rhythms enable organisms to synchronise the processes underpinning survival and reproduction to anticipate daily changes in the external environment. Recent work shows that daily (circadian) rhythms also enable parasites to maximise fitness in the context of ecological interactions with their hosts. Because parasite rhythms matter for their fitness, understanding how they are regulated could lead to innovative ways to reduce the severity and spread of diseases. Here, we examine how host circadian rhythms influence rhythms in the asexual replication of malaria parasites. Asexual replication is responsible for the severity of malaria and fuels transmission of the disease, yet, how parasite rhythms are driven remains a mystery. We perturbed feeding rhythms of hosts by 12 hours (i.e. diurnal feeding in nocturnal mice) to desynchronise the hosts' peripheral oscillators from the central, light-entrained oscillator in the brain and their rhythmic outputs. We demonstrate that the rhythms of rodent malaria parasites in day-fed hosts become inverted relative to the rhythms of parasites in night-fed hosts. Our results reveal that the hosts' peripheral rhythms (associated with the timing of feeding and metabolism), but not rhythms driven by the central, light-entrained circadian oscillator in the brain, determine the timing (phase) of parasite rhythms. Further investigation reveals that parasite rhythms correlate closely with blood glucose rhythms. In addition, we show that parasite rhythms resynchronise to the altered host feeding rhythms when food availability is shifted, which is not mediated through rhythms in the host immune system. Our observations suggest that parasites actively control their developmental rhythms. Finally, counter to expectation, the severity of disease symptoms expressed by hosts was not affected by desynchronisation of their central and peripheral rhythms. Our study at the intersection of disease ecology and chronobiology opens up a new arena for studying host-parasite-vector coevolution and has broad implications for applied bioscience.

Parkinson?s disease (PD) is a chronic disorder that presents a range of premotor signs, such as sleep
disturbances and cognitive decline, which are key non-motor features of the disease. Increasing
evidence of a possible association between sleep disruption and the neurodegenerative process
suggests that sleep impairment could produce a detectable metabolic signature on the disease. In
order to integrate neurocognitive and metabolic parameters, we performed untargeted and targeted
metabolic profiling of the rotenone PD model in a chronic sleep restriction (SR) (6 h/day for 21 days)
condition. We found that SR combined with PD altered several behavioural (reversal of locomotor
activity impairment; cognitive impairment; delay of rest-activity rhythm) and metabolic parameters
(branched-chain amino acids, tryptophan pathway, phenylalanine, and lipoproteins, pointing to
mitochondrial impairment). If combined, our results bring a plethora of parameters that represents
reliable early-phase PD biomarkers which can easily be measured and could be translated to human
studies.

Sleep is essential for most living things to function. Many features of sleep are not yet understood however, mathematical models are playing an important role in developing our understanding of many of the physiological properties of sleep. We introduce the most well-known model of sleep regulation, the two process model which proposes that sleep-wake cycles can be modelled by the
interaction between two oscillators. This ostensibly simple model is an interesting example of a nonsmooth dynamical system whose rich dynamical structure has been relatively unexplored. A key aim of this work is to further understand how transitions between monophasic (one sleep a day) and polyphasic (many sleeps a day) sleep occur in the two process model.

The two process model can be framed as a one-dimensional map of the circle which, for some parameter regimes, has gaps. As is a feature of continuous circle maps the bifurcation set consists of saddle-node Arnold tongues. We show that border collision bifurcations that arise naturally in maps with gaps extend and supplement these tongues. We see how the periodic solutions that are created by saddle-node bifurcations in continuous maps transition to periodic solutions created by period-adding bifurcations as seen in maps with gaps. With this deeper understanding of the dynamics and bifurcation structure of the two process model we use modifiedý versions of the model to explain two experimental data sets.

An ultradian rhythm is a recurrent period or cycle which repeats multiple times across the day. We consider the sleep wake patterns of a the common vole, Microtus Arvalis, which has ultradian rest activity and feeding patterns. By deriving parameters for the two process model from EEG data and sleep/ wake onset times we are able to simulate with high accuracy the key features of spontaneous sleep-wake patterns in the voles. However, to explain phenomena seen in sleep deprivation experiments we include a high amplitude ultradian oscillation alongside the circadian, the results allow us to give some physiological insight into the internal mechanisms which drive sleep/wake onset times in the common vole.

Across the human lifespan there are many changes in the physiological properties of sleep, sleep timing and sleep duration. In adolescence sleep timing is delayed and there is a reduction in slow wave sleep which continues into old age as sleep timing gradually becomes earlier. Using a modified two process model which incorporates a van der Pol oscillator driven by external light signals into the circadian process we show that changes in sleep timing and duration across the lifespan can be explained by varying parameters. Model simulation show that these changes can be understood by a simultaneous reduction in the amplitude of the circadian oscillator and the upper asymptote of the homeostatic sleep pressure.

Infection can dramatically alter behavioural and physiological traits as hosts become sick and subsequently return to health. Such ?sickness behaviours? include disrupted circadian rhythms in both locomotor activity and body temperature. Host sickness behaviours vary in pathogen species-specific manners but the influence of pathogen intraspecific variation is rarely studied. We examine how infection with the murine malaria parasite, Plasmodium chabaudi, shapes sickness in terms of parasite genotype-specific effects on host circadian rhythms. We reveal that circadian rhythms in host locomotor activity patterns and body temperature become differentially disrupted and in parasite genotype-specific manners. Locomotor activity and body temperature in combination provide more sensitive measures of health than commonly used virulence metrics for malaria (e.g. anaemia). Moreover, patterns of host disruption cannot be explained simply by variation in replication rate across parasite genotypes or the severity of anaemia each parasite genotype causes. It is well known that disruption to circadian rhythms is associated with non-infectious diseases, including cancer, type 2 diabetes, and obesity. Our results reveal that disruption of host circadian rhythms is a genetically variable virulence trait of pathogens with implications for host health and disease tolerance.

Adipose tissues fulfil functions of energy storage and hormone secretion, many of which exhibit daily variations. Literature showed that approximately 20% of the murine adipose transcriptome exhibits daily oscillations, with 2-4% of the transcriptome rhythmic in constant conditions; in humans and mice. A disruption of circadian rhythms is associated with metabolic disturbances such as obesity and metabolic syndrome, highlighting the importance of understanding mechanisms of circadian metabolism. Published work identified energy substrates as biomarkers of insulin resistance and glucose intolerance in humans; hallmarks of obesity and diabetes, with unknown utilisation dynamics in vitro within adipocytes. My thesis aimed to provide a clearer view on circadian adipose biology using molecular, electrophysiological and metabolic approaches. I tested the hypotheses that an endogenous oscillator within pre-adipocytes was driving rhythmic utilisation of carbon sources involved in key metabolic pathways, that electrophysiological parameters in pre-adipocytes exhibited biological variations, and that bioluminescence rhythms of clock genes showed a reduced amplitude and faster damping in adipocytes in comparison to pre-adipocytes.

Using 3T3-L1 pre-adipocytes, circadian rhythms of glucose utilisation were confirmed, with an acrophase for the first time demonstrated as similar or anti-phasic to an array of other carbon-based sources utilised in a circadian fashion. Other substrates exhibited steady-state utilisation patterns. Dielectrophoresis potential enabled the determination of circadian rhythms in cellular membrane capacitance, whilst membrane conductance exhibited rhythms of a shorter period. Finally, persistent anti-phasic circadian rhythms of bioluminescence driven by the promoters of Per2 and Bmal1 were characterised in pre-adipocytes and adipocytes, with Per2 pre-adipocytes presenting a higher amplitude than their adipocyte counterpart.

These data provide novel understanding of adipose circadian biology, especially revealing circadian rhythmicity of intermediates in key metabolic pathways strongly linked to the development of metabolic diseases. These findings could help explain metabolic pathways disruptions in obesity and related pathologies.

Electrical correlates of the physiological state of a cell, such as membrane conductance and capacitance, as well as cytoplasm conductivity, contain vital information about cellular function, ion transport across the membrane, and propagation of electrical signals. They are, however, difficult to measure; gold-standard techniques are typically unable to measure more than a few cells per day, making widespread adoption difficult and limiting statistical reproducibility. We have developed a dielectrophoretic platform using a disposable 3D electrode geometry that accurately (r2 > 0.99) measures mean electrical properties of populations of ~20,000 cells, by taking parallel ensemble measurements of cells at 20 frequencies up to 45 MHz, in (typically) ten seconds. This allows acquisition of ultra-high-resolution (100-point) DEP spectra in under two minutes. Data acquired from a wide range of cells ? from platelets to large cardiac cells - benchmark well with patch-clamp-data. These advantages are collectively demonstrated in a longitudinal (same-animal) study of rapidly-changing phenomena such as ultradian (2?3 hour) rhythmicity in whole blood samples of the common vole (Microtus arvalis), taken from 10 µl tail-nick blood samples and avoiding sacrifice of the animal that is typically required in these studies.

Polymorphisms in the human circadian clock gene PERIOD3 (PER3) are associated with a wide variety of phenotypes such as diurnal preference, delayed sleep phase disorder,
sleep homeostasis, cognitive performance, bipolar disorder, type 2 diabetes, cardiac
regulation, cancer, light sensitivity, hormone and cytokine secretion, and addiction.
However, the molecular mechanisms underlying these phenotypic associations remain
unknown. Per3 knockout mice (Per3

Objective. Circadian rhythms in cartilage homeostasis are hypothesized to temporally segregate and synchronize the
activities of chondrocytes to different times of the day, and thus may provide an efficient mechanism by which articular cartilage can recover following physical activity. While the circadian clock is clearly involved in chondrocyte homeostasis
in health and disease, it is unclear as to what roles it may play during early chondrogenesis. Design. The purpose of this study was to determine whether the rhythmic expression of the core circadian clock was detectable at the earliest stages of chondrocyte differentiation, and if so, whether a synchronized expression pattern of chondrogenic transcription factors and developing cartilage matrix constituents was present during cartilage formation. Results. Following serum
shock, embryonic limb bud?derived chondrifying micromass cultures exhibited synchronized temporal expression patterns of core clock genes involved in the molecular circadian clock. We also observed that chondrogenic marker genes followed a circadian oscillatory pattern. Clock synchronization significantly enhanced cartilage matrix production and elevated SOX9, ACAN, and COL2A1 gene expression. The observed chondrogenesis-promoting effect of the serum shock was likely attributable to its synchronizing effect on the molecular clockwork, as co-application of small molecule modulators
(longdaysin and KL001) abolished the stimulating effects on extracellular matrix production and chondrogenic marker gene expression. Conclusions. Results from this study suggest that a functional molecular clockwork plays a positive role in tissue homeostasis and histogenesis during early chondrogenesis.