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At least 163 records · Page 9Linked to original sources
PubMed2006

Genomic organization of the rat Clock gene and sequence analysis in inbred rat strains.

While mutations in genes that function in the core molecular clock may disrupt circadian periodicity, their relevance to diurnal variation in metabolic, cardiovascular, and respiratory function is unknown. The circadian Clock gene product is an essential regulator of central and peripheral circadian rhythms in mammals. We have elucidated the complete exon-intron organization of the Clock gene in rat and have carried out an extensive search for single nucleotide polymorphisms (SNPs) in a panel of 12 inbred rat strains that exhibit diversity in studies of central and peripheral organ function and disease. The rat Clock gene consists of 23 exons spanning approximately 75 kb. Comparative sequence analysis identified 33 novel SNPs, including 32 that distinguish the Brown Norway (BN) rat from the other strains studied. Most notable were two novel mutations in the BN sequence at exon 8, Ile131Val and Ile132Val, occurring in a segment of the highly conserved PAS-A domain of the protein. These results afford the opportunity to assess the impact of genetic variation in Clock on central and peripheral functions subject to the core molecular clock and to test the importance of Clock variants in explaining diversity among rat strains in the expression of phenotypes, such as blood pressure, subject to circadian oscillation.

5' Untranslated Regions↗
PubMed1997

Elucidating the population histories and transmission dynamics of papillomaviruses using phylogenetic trees.

Using gene genealogies constructed from gene sequence data, we show that both the mucosal and cutaneous papillomaviruses (PV)-supergroups A and B-appear to have been transmitted through susceptible populations faster than exponentially. The data and methods involved (1) examining the PV database for phylogenetic signal in an L1 open reading frame (ORF) fragment and an E1 ORF segment, (2) demonstrating that the same two fragments have evolved in a way consistent with a molecular clock, and (3) applying methods of phylogenetic tree analysis that test different scenarios for the dynamics of viral transmission within populations. The results indicate increases in PV populations of both supergroups A and B in the recent past. This form of the increases, which fit a null model of population growth with an exponent increasing in time, is compatible with the fact that human populations have grown at a faster than exponential rate, thus increasing the numbers of susceptible hosts for HPVs. There are, however, indications that the population of supergroup A has now stopped increasing in size.

Codon↗
PubMed1992

[Lack of tolerance after administration of delayed-action isosorbide-5-mononitrate for 3 days in patients with exercise-induced silent ischemia: control with placebo].

In order to assess the development of tolerance we analyzed in a placebo-controlled study the effect of monotherapy with isosorbide-5-mononitrate (IS-5-MN) 60 mg in a controlled release formulation (Durules) once-a-day. The IS-5-MN was evaluated after the first dose and after once-a-day therapy for three days in 11 ambulatory patients (10 males, 1 female, aged 54 +/- 9 years) with stable exercise-induced silent myocardial ischaemia and significant coronary stenoses. The drug was given at 8 o'clock in the morning, and a bicycle ergometer exercise test was performed after 4 hours. The ST segment depression was evaluated by a computer-assisted system. Standing blood pressure decreased during all three periods of active treatment with IS-5-MN, (in comparison with placebo p < 0.001 and p < 0.01, p < 0.01 respectively). Heart rate did not change significantly. Compared with placebo baseline values, ischaemic threshold increased during the first day of treatment (188 sec, p < 0.0001 at 4 hours), and to a lesser extent both in second (103 sec, p < 0.003) and third day (116 sec, p < 0.003). The total exercise time increased during all three days of active therapy but significantly so only during the first day. The exercise stress test performed in the 5th day during placebo demonstrated a high reproducibility of ischaemic-threshold (235 vs 241 sec, p: ns), implying that the improvement during the active treatment with IS-5-MN was not due to a "training effect". Headache in 2 patients was the only significant side-effect.(ABSTRACT TRUNCATED AT 250 WORDS)

Delayed-Action Preparations↗
PubMed1998

Conserved regions of the timeless (tim) clock gene in Drosophila analyzed through phylogenetic and functional studies.

Circadian (approximately 24-hr) rhythms in Drosophila melanogaster depend upon cyclic expression of the period (per) and timeless (tim) genes, which encode interacting components of the endogenous clock. The per gene has been isolated from other insects and, more recently, a per ortholog was found in mammals where its expression oscillates in a circadian fashion. We report here the complete sequence of a tim gene from another species, Drosophila virilis. TIM is better conserved than the PER protein is between these two species (76 vs. 54% overall amino acid identity), and putative functional domains, such as the PER interaction domains and the nuclear localization signal, are highly conserved. The acidic domain and the cytoplasmic localization domain, however, are within the least conserved regions. In addition, the initiating methionine in the D. virilis gene lies downstream of the proposed translation start for the original D. melanogaster tim cDNA and corresponds to the one used by D. simulans and D. yakuba. Among the most conserved parts of TIM is a region of unknown function near the N terminus. We show here that deletion of a 32 amino acid segment within this region affects rescue of rhythms in arrhythmic tim01 flies. Flies carrying a full-length tim transgene displayed rhythms with approximately 24-hr periods, indicating that a fully functional clock can be restored in tim01 flies through expression of a tim transgene. Deletion of the segment mentioned above resulted in very long activity rhythms with periods ranging from 30.5 to 48 hr.

Amino Acid Sequence↗
PubMed2003

Molecular evolution of Pediculus humanus and the origin of clothing.

The human head louse (Pediculus humanus capitis) and body louse (P. humanus corporis or P. h. humanus) are strict, obligate human ectoparasites that differ mainly in their habitat on the host : the head louse lives and feeds exclusively on the scalp, whereas the body louse feeds on the body but lives in clothing. This ecological differentiation probably arose when humans adopted frequent use of clothing, an important event in human evolution for which there is no direct archaeological evidence. We therefore used a molecular clock approach to date the origin of body lice, assuming that this should correspond with the frequent use of clothing. Sequences were obtained from two mtDNA and two nuclear DNA segments from a global sample of 40 head and body lice, and from a chimpanzee louse to use as an outgroup. The results indicate greater diversity in African than non-African lice, suggesting an African origin of human lice. A molecular clock analysis indicates that body lice originated not more than about 72,000 +/- 42,000 years ago; the mtDNA sequences also indicate a demographic expansion of body lice that correlates with the spread of modern humans out of Africa. These results suggest that clothing was a surprisingly recent innovation in human evolution.

Africa↗
PubMed2001

Circadian clock regulation of pH in the rabbit retina.

Although it is generally accepted that the acid-base ratio of tissue, as represented by the pH, is strictly regulated to maintain normal function, recent studies in the mammalian nervous system have shown that neuronal activity can result in significant shifts in pH. In the mammalian retina, many cellular phenomena, including neuronal activity, are regulated by a circadian clock. We thus investigated whether a clock regulates retinal pH, using pH-sensitive microelectrodes to measure the extracellular pH (pH(o)) of the in vitro rabbit retina in the subjective day and night, that is, under conditions of constant darkness. These measurements demonstrated that a circadian clock regulates the pH(o) of the rabbit retina so that the pH(o) is lower at night than in the day. This day/night difference in retinal pH(o) was observed when the rabbits were maintained on a normal light/dark cycle and after they were maintained on a light/dark cycle that was phase-delayed by 9 hr. Continuous recordings of retinal pH(o) around subjective dusk indicated that the change from daytime to nighttime pH(o) is relatively fast and suggested that the clock that regulates pH(o) is located in the retina. The lowest pH(o) recorded in the retina in both the day and night was in the vicinity of the inner segments of photoreceptor cells, supporting the idea that photoreceptors serve as the primary source of protons. The circadian-induced shift in pH(o) was several times greater than light-induced pH(o) changes. These findings suggest that a circadian clock in the mammalian retina regulates retinal pH.

Animals↗
PubMed2005

Thinking clockwise.

Throughout the Animal Kingdom, the time of embryonic development is maintained and strictly controlled. Each step of the process is successful only when it occurs at the right time and place. This raises the question: how is time controlled during embryonic development? Time control is particularly crucial during embryo segmentation processes, where the number of generated segments, as well as the time of formation of each segment, is extraordinarily constant and specific for each species. Somitogenesis is the process through which the vertebrate presomitic mesoderm is segmented along its anterior-posterior axis into round-shaped masses of epithelial cells, named somites. In the chick embryo, a new pair of somites is formed every 90 min. The discovery that this clock-like precision is dictated by the somitogenesis molecular clock constituted a landmark in the Developmental Biology field. Several genes exhibit cyclic gene expression in the embryo presomitic mesoderm from which the somites arise, presenting a 90 min oscillation period, the time required to form a pair of somites. The combined levels of dynamic gene expression throughout the presomitic mesoderm enable cells to acquire positional information, thus giving them a notion of time. Anterior-posterior patterning of the vertebrate nervous system also involves partition into discrete territories. This is particularly evident in the hindbrain where overt segmentation occurs. Nevertheless, little is known about the segmentation genes and mechanisms that may be involved. This paper intends to describe the molecular clock associated with vertebrate somitogenesis, suggesting that it may be operating in many other patterning processes.

Animals↗
PubMed2001

Evidence for medial/lateral specification and positional information within the presomitic mesoderm.

In the vertebrate embryo, segmentation is built on repetitive structures, named somites, which are formed progressively from the most rostral part of presomitic mesoderm, every 90 minutes in the avian embryo. The discovery of the cyclic expression of several genes, occurring every 90 minutes in each presomitic cell, has shown that there is a molecular clock linked to somitogenesis. We demonstrate that a dynamic expression pattern of the cycling genes is already evident at the level of the prospective presomitic territory. The analysis of this expression pattern, correlated with a quail/chick fate-map, identifies a 'wave' of expression travelling along the future medial/lateral presomitic axis. Further analysis also reveals the existence of a medial/lateral asynchrony of expression at the level of presomitic mesoderm. This work suggests that the molecular clock is providing cellular positional information not only along the anterior/posterior but also along the medial/lateral presomitic axis. Finally, by using an in vitro culture system, we show that the information for morphological somite formation and molecular segmentation is segregated within the medial/lateral presomitic axis. Medial presomitic cells are able to form somites and express segmentation markers in the absence of lateral presomitic cells. By contrast, and surprisingly, lateral presomitic cells that are deprived of their medial counterparts are not able to organise themselves into somites and lose the expression of genes known to be important for vertebrate segmentation, such as Delta-1, Notch-1, paraxis, hairy1, hairy2 and lunatic fringe.

Animals↗
PubMed1986

Control of leech swimming activity by the cephalic ganglia.

We investigated the role played by the cephalic nervous system in the control of swimming activity in the leech, Hirudo medicinalis, by comparing swimming activity in isolated leech nerve cords that included the head ganglia (supra- and subesophageal ganglia) with swimming activity in nerve cords from which these ganglia were removed. We found that the presence of these cephalic ganglia had an inhibitory influence on the reliability with which stimulation of peripheral (DP) nerves and intracellular stimulation of swim-initiating neurons initiated and maintained swimming activity. In addition, swimming activity recorded from both oscillator and motor neurons in preparations that included head ganglia frequently exhibited irregular bursting patterns consisting of missed, weak, or sustained bursts. Removal of the two head ganglia as well as the first segmental ganglion eliminated this irregular activity pattern. We also identified a pair of rhythmically active interneurons, SRN1, in the subesophageal ganglion that, when depolarized, could reset the swimming rhythm. Thus the cephalic ganglia and first segmental ganglion of the leech nerve cord are capable of exerting a tonic inhibitory influence as well as a modulatory effect on swimming activity in the segmental nerve cord.

Action Potentials↗
PubMed2000

Somite formation and patterning.

As a consequence of their segmented arrangement and the diversity of their tissue derivatives, somites are key elements in the establishment of the metameric body plan in vertebrates. This article aims to largely review what is known about somite development, from the initial stages of somite formation through the process of somite regionalization along the three major body axes. The role of both cell intrinsic mechanisms and environmental cues are evaluated. The periodic and bilaterally synchronous nature of somite formation is proposed to rely on the existence of a developmental clock. Molecular mechanisms underlying these events are reported. The importance of an antero-posterior somitic polarity with respect to somite formation on one hand and body segmentation on the other hand is discussed. Finally, the mechanisms leading to the regionalization of somites along the dorso-ventral and medio-lateral axes are reviewed. This somitic compartmentalization is believed to underlie the segregation of dermis, skeleton, and dorsal and appendicular musculature.

Animals↗
PubMedDate not supplied

[The studies of temporal and spatial characteristics of somitogenesis in fish embryos].

New data were obtained corroborating that somitogenesis is a rhythmic process, in which the time of somite formation is strictly constant. This constant (tau s) can be considered as a natural unit of developmental "biological clock" characterizing rhythmic processes. The constant tau s can be determined with an exceptional accuracy that has no analogs among the known biological processes. This fact alone suggests that the accuracy of developmental clock is very high. In addition to the constancy of tau s, all forming somites have equal linear size along the notochord axis. In the process with strictly constant temporal and spatial factors, time plays the leading role in triggering the formation of new somite. This became clear in studies of twin embryos. Both embryos had the same number of somites but they were shorter than in the normal embryos. Also, we measured the length of head and both segmented and unsegmented caudal parts of the trunk. Combined with the published data on somitogenesis, our results suggest that the previously proposed scheme for the role of developmental clock in embryogenesis predicts: (1) a possible loss of some embryonic stages without serious consequences for subsequent development and (2) periodic switching on/off any embryonic processes (at the molecular, cellular, or supercellular level) with intervals multiple to tau s.

Animals↗
PubMedDate not supplied

Oscillatory network with self-organized dynamical connections for synchronization-based image segmentation.

An oscillatory network of columnar architecture located in 3D spatial lattice was recently designed by the authors as oscillatory model of the brain visual cortex. Single network oscillator is a relaxational neural oscillator with internal dynamics tunable by visual image characteristics - local brightness and elementary bar orientation. It is able to demonstrate either activity state (stable undamped oscillations) or "silence" (quickly damped oscillations). Self-organized nonlocal dynamical connections of oscillators depend on oscillator activity levels and orientations of cortical receptive fields. Network performance consists in transfer into a state of clusterized synchronization. At current stage grey-level image segmentation tasks are carried out by 2D oscillatory network, obtained as a limit version of the source model. Due to supplemented network coupling strength control the 2D reduced network provides synchronization-based image segmentation. New results on segmentation of brightness and texture images presented in the paper demonstrate accurate network performance and informative visualization of segmentation results, inherent in the model.

Animals↗
PubMed2002

Catching a wave: the oscillator and wavefront that create the zebrafish somite.

Segmentation of the paraxial mesoderm is governed by an oscillator mechanism that creates a dynamic prepattern within the caudal presomitic mesoderm. The oscillator is comprised of genetic circuit involving the Notch signaling pathway and its target genes her1 and her7. The stabilization of the oscillating prepattern is antagonized by a gradient of Fgf signaling which is highest in the caudal presomitic mesoderm. Once the level of Fgf signaling declines in the rostral presomitic mesoderm, a wavefront mediated by the transcription factor fss/tbx24, stabilizes the prepattern and leads to the segmental expression of a number of genes which then establish segment polarity and initiate morphological somite formation.

Animals↗
PubMed2002

Virtual migration in tethered flying monarch butterflies reveals their orientation mechanisms.

A newly developed flight simulator allows monarch butterflies to fly actively for up to several hours in any horizontal direction while their fall migratory flight direction can be continuously recorded. From these data, long segments of virtual flight paths of tethered, flying, migratory monarch butterflies were reconstructed, and by advancing or retarding the butterflies' circadian clocks, we have shown that they possess a time-compensated sun compass. Control monarchs on local time fly approximately southwest, those 6-h time-advanced fly southeast, and 6-h time-delayed butterflies fly in northwesterly directions. Moreover, butterflies flown in the same apparatus under simulated overcast in natural magnetic fields were randomly oriented and did not change direction when magnetic fields were rotated. Therefore, these experiments do not provide any evidence that monarch butterflies use a magnetic compass during migration.

Animals↗
PubMed2005

Bursts of information: coordinating interneurons encode multiple parameters of a periodic motor pattern.

The limbs on different segments of the crayfish abdomen that drive forward swimming are directly controlled by modular pattern-generating circuits. These circuits are linked together by axons of identified coordinating interneurons. We described the distributions of these neurons in each abdominal ganglion and monitored their firing during expression of the swimming motor pattern. We analyzed the timing, the numbers of spikes, and the duration of each burst of spikes in these coordinating neurons. To see what information these neurons encoded, we correlated these parameters with the timing, durations, and strengths of bursts of spikes in motor axons from the same modules. During the power-stroke phase of each output cycle, the anterior-projecting neurons fired bursts of spikes that encoded information about the start-time, duration, and strength of each burst of spikes in power-stroke motor neurons from the same module. When the period and intensity of the motor output fluctuated, the bursts of spikes in these neurons tracked these fluctuations accurately. Each additional spike in these neurons signified an increase in the strength of the power-stroke burst. The posterior-projecting neurons that fired during the return-stroke phase encoded similar information about the return-stroke motor neurons. Although homologous neurons from different ganglia were qualitatively similar, neurons from posterior ganglia fired significantly more spikes per burst than those from more anterior ganglia, a segmental gradient that correlates with the normal posterior-to-anterior phase progression of limb movements. We propose that this gradient and a similar gradient in the durations of bursts in power-stroke motor neurons might reflect a hitherto-undetected difference in the excitation or intrinsic excitability of swimmeret modules in different segments.

Action Potentials↗
PubMed2002

Cellular oscillators in animal segmentation.

Kinetic modeling of developmental dynamics requires detailed knowledge about genetic and metabolic networks that underlie developmental processes. However, such knowledge is not available for a vast majority of developmental processes. Here, we present an coarse-grained, phenomenological model of periodic pattern formation in multicellular organisms based on cellular oscillators (CO) that can be applied to systems for which little or no molecular data is available. An oscillatory process within cells serves as a developmental clock whose period is tightly regulated by cell-autonomous and non-autonomous mechanisms. A spatial pattern is generated as a result of an initial temporal ordering of the cell oscillators freezing into spatial order as the clocks slow down and stop at different times or phases in their cycles. When applied to vertebrate somitogenesis, the CO model can reproduce the dynamics of periodic gene expression patterns observed in the presomitic mesoderm. Different somite lengths can be generated by altering the period of the oscillation. There is evidence that a CO-type mechanism might also underlie segment formation in certain invertebrates, such as annelids and short germ insects. This suggests that the dynamical principles of sequential segmentation might be equivalent throughout the animal kingdom although most of the genes involved in segment determination differ between distant phyla.

Algorithms↗
PubMed2006

Period2 expression pattern and its role in the development of the pineal circadian clock in zebrafish.

In zebrafish, pineal arylalkylamine-N-acetyltransferase (zfaanat2) mRNA expression begins at 22 h post-fertilization (hpf), and the clock-controlled rhythm of its transcript begins on the third day of development. Here we describe the role of light and of the clock gene, period2 (zper2) in the development of this rhythm. In 1-day-old zebrafish embryos, zper2 expression is transiently up-regulated by light in the pineal gland and, to a lesser extent, in other areas of the brain. Expression of zper2 that was not affected by light occurred in the olfactory placode and lactotroph cells of the pituitary primordium. Circadian analysis of pineal zfaanat2 mRNA expression indicated that light exposure is required for proper development of the circadian clock-controlled rhythmic expression of this gene. Knockdown of zPER2 using antisense technology abolished the effect of light on development of the zfaanat2 rhythm in the pineal gland, corroborating the role of zper2 in light entrainment of the circadian oscillator in zebrafish. Further analysis of zper2 expression at earlier stages of development revealed that light exposure at the blastula to mid-segmentation stages also caused a transient increase in zper2 expression. At mid-segmentation, before pineal differentiation, light-induced zper2 expression was enhanced in pineal progenitor cells. Thus, a possible role for early photoreception and light-induced zper2 expression in the development of clock-controlled rhythms remains to be investigated.

Animals↗