From biological clock to biological rhythms

The genetic and molecular analysis of circadian timekeeping mechanisms has accelerated as a result of the increasing volume of genomic markers and nucleotide sequence information. Completion of whole genome sequences and the use of differential gene expression technology will hasten the discovery of the clock output pathways that control diverse rhythmic phenomena.     

High-salt diet advances molecular circadian rhythms in mouse peripheral tissues

Most human somatic cells contain no or very low levels of telomerase. The over-expression of the catalytic subunit (hTERT) of human telomerase is a common method to generate cells with a greatly prolonged lifespan. These cells serve as models for cells that are either difficult to cultivate or have a limited lifespan in vitro. In addition, hTERT over-expressing cells are thought to be a useful resource for tissue engineering and regenerative medicine.While tumour suppressors and cell cycle checkpoints are maintained for an extended period in most hTERT over-expressing cells we found that there is a gradual change in gene expression over a range of 130 population doublings (PD) for the majority of genes analysed. Seven genes were significantly down-regulated with increasing population doublings (PDs), while only two were up-regulated. One gene, stanniocalcin 2, was highly expressed in parental fibroblasts but completely diminished as a consequence of hTERT transgene expression.These data demonstrate that in hTERT over-expressing cells two different types of expression changes occur: one can be directly associated with hTERT transgene expression itself, while others might occur more gradual and with varying kinetics. These changes should be taken into account when these cells are used as functional models or for regenerative purposes.     

Using variability to regulate long term biological rhythms

We present a model for the generation of precise, long term rhythms from a collection of imprecise, short term oscillators. The model uses variability between oscillators in conjunction with simple coupling rules to produce long term rhythms that are independent of rate equations (e.g. Arrhenius). The rhythms generated by the model are controlled by only two independent parameters and exhibit several physiologically interesting properties, including ready entrainment to external signals and splitting in response to strong constant signals. The model provides several predictions that can be tested in future experiments.     

Use of antisense oligodeoxynucleotides to study biological rhythms

Perturbation analysis has been crucial in the study of biological rhythms. Antisense technology provides investigators with new means to alter the internal milieu of the circadian clock itself. Practical aspects of the method and the theoretical background are presented in sufficient detail to enable others to design appropriate antisense oligodeoxynucleotides and use them for research purposes. This strategy will contribute substantially to the understanding of the influence of individual genes on rhythms in hormone secretion, metabolism, and behavior.     

Circadian rhythms: biological clocks work in phospho-time

The 24 hour molecular oscillator requires precisely calibrated degradation of core clock proteins, like PERIOD. New studies shed light on a sequential series of PERIOD phosphorylation events that first inhibits, then accelerates PERIOD degradation.     

Melatonin rhythms in the pineal and non-pineal tissues and their physiological implications in subtropical fish

Abstract

Melatonin (N-acetyl-5-methoxy tryptamine), following discovery from the extracts of bovine pineal gland, has been detected in the pineal as well as several extra-pineal tissues/organs of different vertebrates including fish. The unique feature of melatonin in the pineal gland is its rhythmic biosynthesis and release in blood in synchronization with the environmental light-–dark cycle. Accordingly, melatonin produced in the pineal of an animal living in a changing environment is implicated to the regulation of seasonal reproduction by acting as a hormone at one or more levels of hypothalamo-hypophyseal-gonadal axis. Additionally, melatonin is known to act as a potent free-radical scavenger or antioxidant to influence maturation of oocytes. However, possible relationship between extra-pineal melatonin and seasonality of reproduction in any animal remains enigmatic. Perhaps, carp is the only known animal in which temporal patterns of melatonin levels in the serum as well as in the extracts of pineal, retina, ovary, gut, and liver have been studied in relation to the reproductive events in an annual cycle. The purpose of current review is to bring those fascinating, and arguably most important data together to underline their significance in the control of seasonal reproduction in subtropical fish in general and in carp in particular.     

Glutamate signaling in peripheral tissues.

The hypothesis that l-glutamate (Glu) is an excitatory amino acid neurotransmitter in the mammalian central nervous system is now gaining more support after the successful cloning of a number of genes coding for the signaling machinery required for this neurocrine at synapses in the brain. These include Glu receptors (signal detection), Glu transporters (signal termination) and vesicular Glu transporters (signal output through exocytotic release). Relatively little attention has been paid to the functional expression of these molecules required for Glu signaling in peripheral neuronal and non-neuronal tissues; however, recent molecular biological analyses show a novel function for Glu as an extracellular signal mediator in the autocrine and/or paracrine system. Emerging evidence suggests that Glu could play a dual role in mechanisms underlying the maintenance of cellular homeostasis - as an excitatory neurotransmitter in the central neurocrine system and an extracellular signal mediator in peripheral autocrine and/or paracrine tissues. In this review, the possible Glu signaling methods are outlined in specific peripheral tissues including bone, testis, pancreas, and the adrenal, pituitary and pineal glands.     

Diurnal rhythms of autophagy: implications for cell biology and human disease

Autophagy is a key mechanism for cell survival under conditions of nutrient limitation. On the organismal level, autophagy is essential for survival of lower eukaryotes during extended periods of starvation, and it is induced in mammals during short-term starvation. As a consequence of the induction of autophagy during short periods of fasting, animals experience diurnal rhythms of autophagy in concert with their circadian cycle. Autophagy has also been identified as a component of the metabolic cycle of yeast, an ultradian rhythm that bears many similarities to the circadian rhythm of plants, flies and mammals. The circadian clock, which is present in almost all mammalian cell types studied to date, temporally regulates expression of multiple genes, gating cell processes such as nutrient uptake, glycolysis, and proliferation, to particular times of day. Whether the circadian clock directly regulates autophagy in mammalian cells, or whether autophagy may play a role in the cycling of mammalian cell clocks is not yet clear. Nevertheless, the relationship between circadian cycles and autophagy is an intriguing area for future study and has implications for multiple human diseases, including aging, neurodegeneration and cancer.     

The tau mutation in the Syrian hamster differentially reprograms the circadian clock in the SCN and peripheral tissues

The hypothalamic suprachiasmatic nuclei (SCN), the principal circadian oscillator in mammals, are synchronized to the solar day by the light-dark cycle, and in turn, they coordinate circadian oscillations in peripheral tissues. The tau mutation in the Syrian hamster is caused by a point mutation leading to a deficiency in the ability of Casein Kinase 1epsilon to phosphorylate its targets, including circadian PER proteins. How this accelerates circadian period in neural tissues is not known, nor is its impact on peripheral circadian oscillators established. We show that this mutation has no effect on per mRNA expression nor the nuclear accumulation of PER proteins in the SCN. It does, however, accelerate the clearance of PER proteins from the nucleus to an extent sufficient to explain the shortened circadian period of behavioral rhythms. The mutation also has novel, unanticipated consequences for circadian timing in the periphery, including tissue-specific phase advances and/or reduced amplitude of circadian gene expression. The results suggest that the tau mutation accelerates a specific phase, during mid-late subjective night of the SCN circadian feedback loop, rather than cause a global compression of the entire cycle. This reprogrammed output from the clock is associated with peripheral desynchrony, which in turn could account for impaired growth and metabolic efficiency of the mutant.     

A dynamic model for functional mapping of biological rhythms

Functional mapping is a statistical method for mapping quantitative trait loci (QTLs) that regulate the dynamic pattern of a biological trait. This method integrates mathematical aspects of biological complexity into a mixture model for genetic mapping and tests the genetic effects of QTLs by comparing genotype-specific curve parameters. As a way of quantitatively specifying the dynamic behavior of a system, differential equations have proven to be powerful for modeling and unraveling the biochemical, molecular, and cellular mechanisms of a biological process, such as biological rhythms. The equipment of functional mapping with biologically meaningful differential equations provides new insights into the genetic control of any dynamic processes. We formulate a new functional mapping framework for a dynamic biological rhythm by incorporating a group of ordinary differential equations (ODE). The Runge-Kutta fourth order algorithm was implemented to estimate the parameters that define the system of ODE. The new model will find its implications for understanding the interplay between gene interactions and developmental pathways in complex biological rhythms.     

Circadian performance rhythms: some practical and theoretical implications

Safety and productivity are low at night and this would appear to be because we are a diurnal species. This is reflected not only in our habitual sleep time, but also in our endogenous body clocks that, together with exogenous influences, such as the patterning of meals and activity, result in predictable circadian (24 h) rhythms in our physiological processes. Our performance capabilities also vary over the course of our waking period, with task demands affecting both the precise trend over the day, and the rate at which it adjusts to the changes in sleep timing occasioned by shift work. Studies designed to examine the reasons for this have shown that memory loaded performance may have a quite separate endogenous component to that responsible for more simple performance, suggesting that these two types of performance cannot be causally related. Furthermore, it would appear that the exogenous component of circadian rhythms may also differ across measures, and our attempts to model these endogenous and exogenous components have led us to re-examine the evidence on adjustment to night work. Our findings suggest that shiftworkers merely 'stay up late' on the night shift, rather than adjust to it, and that this is responsible for the reduced safety at night. It would seem that in situations where safety is paramount, the only solution to these problems is the creation of a nocturnal sub-society that not only always works at night but also remains on a nocturnal routine on rest days.     

Latitudinal clines: an evolutionary view on biological rhythms

Properties of the circadian and annual timing systems are expected to vary systematically with latitude on the basis of different annual light and temperature patterns at higher latitudes, creating specific selection pressures. We review literature with respect to latitudinal clines in circadian phenotypes as well as in polymorphisms of circadian clock genes and their possible association with annual timing. The use of latitudinal (and altitudinal) clines in identifying selective forces acting on biological rhythms is discussed, and we evaluate how these studies can reveal novel molecular and physiological components of these rhythms.     

A dynamic model for functional mapping of biological rhythms

Functional mapping is a statistical method for mapping quantitative trait loci (QTLs) that regulate the dynamic pattern of a biological trait. This method integrates mathematical aspects of biological complexity into a mixture model for genetic mapping and tests the genetic effects of QTLs by comparing genotype-specific curve parameters. As a way of quantitatively specifying the dynamic behaviour of a system, differential equations have proved to be powerful for modelling and unravelling the biochemical, molecular, and cellular mechanisms of a biological process, such as biological rhythms. The equipment of functional mapping with biologically meaningful differential equations provides new insights into the genetic control of any dynamic processes. We formulate a new functional mapping framework for a dynamic biological rhythm by incorporating a group of ordinary differential equations (ODE). The Runge–Kutta fourth-order algorithm was implemented to estimate the parameters that define the system of ODE. The new model will find its implications for understanding the interplay between gene interactions and developmental pathways in complex biological rhythms.     

Limits to length asymmetry detection in starlings: implications for biological signalling

Fluctuating asymmetry has received considerable recent attention in evolutionary biology as these small developmental asymmetries can be related to biological fitness and, hence, could be used as a visual cue (or signal) of quality among individuals. The ability of signal receivers to detect and respond to small asymmetries is a fundamental assumption of the symmetry-signalling hypothesis, but has not been experimentally investigated. In this study I have investigated the perceptual threshold to detect and respond to paired-bar length asymmetry in a common bird, the European starling Sturnus vulgaris, by means of operant-learning techniques. The threshold indicates how large the length asymmetry must be to be reliably discriminated from symmetry; birds could not detect an asymmetry of 1.25%. In nature, many asymmetries can be smaller than 1.25%, hence this initial study suggests that caution should be used when trying to invoke symmetry-signalling in natural populations.     

Endogenous proteins controlling amyloid beta-peptide polymerization. Possible implications for beta-amyloid formation in the central nervous system and in peripheral tissues.

We report that certain plasma proteins, at physiological concentrations, are potent inhibitors of amyloid beta-peptide (Abeta) polymerization. These proteins are also present in cerebrospinal fluid, but at low concentrations having little or no effect on Abeta. Thirteen proteins representing more than 90% of the protein content in plasma and cerebrospinal fluid were studied. Quantitatively, albumin was the most important protein, representing 60% of the total amyloid inhibitory activity, followed by alpha1-antitrypsin and immunoglobulins A and G. Albumin suppressed amyloid formation by binding to the oligomeric or polymeric Abeta, blocking a further addition of peptide. This effect was also observed when the incorporation of labeled Abeta into genuine beta-amyloid in tissue section was studied. The Abeta and the anti-diabetic drug tolbutamide apparently bind to the same site on albumin. Tolbutamide displaces Abeta from albumin, increasing its free concentration and enhancing amyloid formation. The present results suggest that several endogenous proteins are negative regulators of amyloid formation. Plasma contains at least 300 times more amyloid inhibitory activity than cerebrospinal fluid. These findings may provide one explanation as to why beta-amyloid deposits are not found in peripheral tissues but are only found in the central nervous system. Moreover, the data suggest that some drugs that display an affinity for albumin may enhance beta-amyloid formation and promote the development of Alzheimer's disease.     

Thermodynamic response of soft biological tissues to pulsed infrared-laser irradiation.

The physical mechanisms that achieve tissue removal through the delivery of short pulses of high-intensity infrared laser radiation, in a process known as laser ablation, remain obscure. The thermodynamic response of biological tissue to pulsed infrared laser irradiation was investigated by measuring and analyzing the stress transients generated by Q-sw Er:YSGG (lambda = 2.79 microns) and TEA CO2 (lambda = 10.6 microns) laser irradiation of porcine dermis using thin-film piezoelectric transducers. For radiant exposures that do not produce material removal, the stress transients are consistent with thermal expansion of the tissue samples. The temporal structure of the stress transients generated at the threshold radiant exposure for ablation indicates that the onset of material removal is delayed with respect to irradiation. Once material removal is achieved, the magnitude of the peak compressive stress and its variation with radiant exposure are consistent with a model that considers this process as an explosive event occurring after the laser pulse. This mechanism is different from ArF- and KrF-excimer laser ablation where absorption of ultraviolet radiation by the collagenous tissue matrix leads to tissue decomposition during irradiation and results in material removal via rapid surface vaporization. It appears that under the conditions examined in this study, explosive boiling of tissue water is the process that mediates the ablation event. This study provides evidence that the dynamics and mechanism of tissue ablation processes can be altered by targeting tissue water rather than the tissue structural matrix.     

Optical clearing for multiscale biological tissues

Three‐dimensional reconstruction of tissue structures is essential for biomedical research. The development of light microscopes and various fluorescent labeling techniques provides powerful tools for this motivation. However, optical imaging depth suffers from strong light scattering due to inherent heterogeneity of biological tissues. Tissue optical clearing technology provides a distinct solution and permits us to image large volumes with high resolution. Until now, various clearing methods have been developed. In this study, from the perspective of the end users, we review in vitro tissue optical clearing techniques based on the sample features in terms of size and age, enumerate the methods suitable for immunostaining and lipophilic dyes and summarize the combinations with various imaging techniques. We hope this review will be helpful for researchers to choose the most suitable clearing method from a variety of protocols to meet their specific needs.