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PubMed1985

Sign-tracking with an interfood clock.

Food was presented to pigeons, irrespective of their behavior. The fixed 60-s interfood interval was segmented into ten 6-s periods, each signaled by a distinctive stimulus color, ordered by wavelength. This "interfood clock" reliably generated and maintained successively higher rates of key pecking at stimuli successively closer to food. Under extinction, key pecking ceased. When the standard stimulus sequence was changed to a different sequence for each bird, accelerated responding again emerged and was sustained under each of the new color sequences. However, responding was neither maintained nor acquired when each successive interfood interval provided a different random sequence of the ten stimuli. Thus, the interfood clock generated and maintained sign-tracking under stimulus control, and the resulting behavior was attributable neither to stimulus generalization nor to a simple temporal gradient.

Journal Article↗

PubMed2005

Circadian clocks, clock networks, arylalkylamine N-acetyltransferase, and melatonin in the retina.

Circadian clocks are self-sustaining genetically based molecular machines that impose approximately 24h rhythmicity on physiology and behavior that synchronize these functions with the solar day-night cycle. Circadian clocks in the vertebrate retina optimize retinal function by driving rhythms in gene expression, photoreceptor outer segment membrane turnover, and visual sensitivity. This review focuses on recent progress in understanding how clocks and light control arylalkylamine N-acetyltransferase (AANAT), which is thought to drive the daily rhythm in melatonin production in those retinas that synthesize the neurohormone; AANAT is also thought to detoxify arylalkylamines through N-acetylation. The review will cover evidence that cAMP is a major output of the circadian clock in photoreceptor cells; and recent advances indicating that clocks and clock networks occur in multiple cell types of the retina.

Animals↗

PubMed2003

Pulmonary vein stenosis by ostial irrigated-tip ablation: incidence, time course, and prediction.

INTRODUCTION: The incidence of pulmonary vein (PV) stenosis and its time course for ostial trigger elimination in paroxysmal atrial fibrillation (PAF) is uncertain. In addition, the clinical value of serial computed tomographic (CT) scanning of the PV ostia and the predictive value of energy requirements for radiofrequency ablation have yet to be established. METHODS AND RESULTS: We performed irrigated-tip ablation in 37 patients with drug-resistant PAF. Serial spiral CT scans were taken prospectively in 34 patients the day before the procedure, at prehospital discharge, and at 3- and 6-month follow-up. Using a clock model, energy requirements were analyzed for every segment of the PV circumference. One hundred fifteen PVs were targeted in 57 procedures. Compared to baseline, 7 (6.08 %) of 115 PV showed minor (<50%) PV stenosis. Two severe (>90%) PV stenoses (1.73%) were detected with a mean follow-up of 275 +/- 100 days. Luminal narrowing occurred most frequently in the left inferior PV (6/9 stenosed PV). Minor stenosed PVs showed their maximal luminal regression within the 3-month follow-up. Two of two PVs with narrowing >50% at 3 months progressed to high-grade stenosis. Analysis of delivered energy showed no significant correlation with the degree of stenosis. However, for the left inferior PV, more energy was applied in the superior segment of a stenotic PV (6697 +/- 930 J vs 3555 +/- 380 J, P = 0.005). CONCLUSION: Assessment of PV diameter by serial spiral CT scanning shows a low incidence of severe stenosis. The left inferior PV is at higher risk. Minor stenosed PV showed no progression after 3 months. Occurrence of stenosis tended to be related to the amount of energy delivered.

Atrial Fibrillation↗

PubMed1995

Is proprioception important for the timing of motor activities?

This study tested whether a deafferented patient demonstrates impaired timing ability compared with four control subjects. By comparing normal subjects with the deafferented patient, some insight was expected on the importance of proprioception in timing of motor behavior. The protocol was set to enhance the strategy of the subjects in using feedbacks. Subjects had to synchronize finger taps with a sound produced at regular intervals. Once synchronized, the bips were muted and the subjects had to continue the tapping at the same pace. Interresponse interval (IRI) variability was measured under two feedback conditions: with and without vision and auditory feedback. The Wing and Kristofferson model (A.M. Wing and A.B. Kristofferson. Percept. Psychophys. 13(3): 455-460, 1973) was used to segment IRI variance into separate components: a central clock and a peripheral motor delay. When the deafferented patient saw and heard the outcome of her tapping movements, there was a greater variability in successive intervals between taps than when vison and hearing were blocked. We interpret this variability as indicating that the subject used auditory and visual feedback to maintain a correct overall rhythm. The patient may easily substitute visual and (or) auditory feedback for her defective proprioception for movement timing. However, this substitution proved to be inefficient in the limited training period provided in this experiment. The results suggest that the proprioceptive contribution to the time-keeping mechanism presumably depends on the presence of an efference copy signal.

Efferent Pathways↗

PubMed2005

The Mesp2 transcription factor establishes segmental borders by suppressing Notch activity.

The serially segmented (metameric) structures of vertebrates are based on somites that are periodically formed during embryogenesis. A 'clock and wavefront' model has been proposed to explain the underlying mechanism of somite formation, in which the periodicity is generated by oscillation of Notch components (the clock) in the posterior pre-somitic mesoderm (PSM). This temporal periodicity is then translated into the segmental units in the 'wavefront'. The wavefront is thought to exist in the anterior PSM and progress backwards at a constant rate; however, there has been no direct evidence as to whether the levels of Notch activity really oscillate and how such oscillation is translated into a segmental pattern in the anterior PSM. Here, we have visualized endogenous levels of Notch1 activity in mice, showing that it oscillates in the posterior PSM but is arrested in the anterior PSM. Somite boundaries formed at the interface between Notch1-activated and -repressed domains. Genetic and biochemical studies indicate that this interface is generated by suppression of Notch activity by mesoderm posterior 2 (Mesp2) through induction of the lunatic fringe gene (Lfng). We propose that the oscillation of Notch activity is arrested and translated in the wavefront by Mesp2.

Animals↗

PubMed1985

A biological clock in Drosophila.

The per locus plays a central role in the organization and function of the Drosophila biological clock. The gene has been mapped to a 7-kb DNA segment by physically locating the breakpoints of several chromosomal rearrangements that disrupt per function. This DNA contains a single transcription unit which produces a 4.5-kb poly(A)+ RNA. No oscillation in the synthesis of this transcript is detected when per expression is followed over a 24-hour cycle of light and dark. When wild-type DNA containing only this transcription unit is transferred to the genome of a per0 (arrhythmic) fly by P-element-mediated transformation, the 4.5-kb RNA is produced and rhythmic behavior is restored with high penetrance of the rhythmic phenotype. This transforming DNA will also complement chromosomal deletions that include the per locus and adjoining transcription units, indicating that only one gene in this chromosomal interval plays a measureable role in the production of circadian rhythms. Transformed flies having rhythms with longer than wild-type periodicity underproduce the 4.5-kb RNA. We suggest that the periodicity of circadian rhythms in Drosophila is determined by the level of expression of a per locus protein encoded by the 4.5-kb transcript. We have found DNA homologous to the per locus in several species of vertebrates. DNA exhibiting very high homology to a portion of the per locus has been cloned from the mouse and the DNA sequence of the conserved segment has been determined. Mouse and fly DNAs both appear to code for long protein segments composed exclusively of alternating threonine and glycine or serine and glycine residues.

Animals↗

PubMed2005

Phylogenetic evidence for the distinction of Saaremaa and Dobrava hantaviruses.

Dobrava virus (DOBV) and Saaremaa virus (SAAV) are two closely related hantaviruses carried by different rodent species. The distinction of these two viruses has been a matter of debate. While the phylogenies based on the viral M segment sequences were repeatedly showing monophyly of SAAV strains, some trees based on the S segment sequences were not, thus causing questions on the demarcation between these two viruses. In order to clarify this issue, the current collection of the virus S segment sequences was subjected to extensive phylogenetic analysis using maximum likelihood, maximum parsimony and distant matrix methods. In all inferred phylogenies, the SAAV sequences were monophyletic and separated from DOBV sequences, thus supporting the view that SAAV and DOBV are distinct hantavirus species. Since collection of the S segment sequences used in this study "obeyed" the molecular clock, calculations of the split of DOBV and SAAV were now repeated resulting in an estimation of 3.0-3.7 MYA that is very close to the values obtained earlier.

Genes, Viral↗

PubMed2026

Spatiotemporal patterns of Rift Valley fever virus in Africa: a retrospective genomic epidemiology and phylodynamic modelling study.

BACKGROUND: Rift Valley fever virus (RVFV) is a mosquito-borne zoonotic pathogen causing outbreaks in humans and ruminants across Africa and the Arabian Peninsula. Originally restricted to the Great Rift Valley, RVFV has expanded geographically, prompting its classification by WHO as a pathogen of pandemic potential. We investigated the evolutionary and spatial dynamics of RVFV across Africa. METHODS: We used genomic data generated at the International Livestock Research Institute Nairobi genomic laboratory (BioProject PRJNA1106221) and combined with publicly available datasets retrieved from the National Center for Biotechnology (NCBI) GenBank nucleotide database. In retrieving RVFV genome sequences from the NCBI GenBank, we applied the search terms "Rift Valley fever virus segment L AND 6404[SLEN]", "Rift Valley fever virus segment M AND 3885[SLEN]", and "Rift Valley fever virus segment S AND 1520:1690[SLEN]" for L (Large), M (Medium), and S (Small) segments, respectively. For sequences without additional spatiotemporal information, we searched PubMed to extract the associated sequence metadata. We performed molecular clock analysis, phylogenetic inference, phylodynamic modelling (continuous phylogeographic reconstruction), and landscape phylogeography on the three RVFV genome segments (L, M, and S). We aimed to assess evolutionary rates, dispersal patterns, and environmental drivers. Focus was placed on lineage C, the most widely distributed variant. FINDINGS: The global dataset used in this study consisted of large (n=236), medium (n=237), and small (n=247), which were further filtered to exclude potential reassortants and vaccine strains. Genome sequences retrieved from NCBI GenBank database comprised large (n=180), medium (n=184), and small (n=202). The genome sequences from retrospective human and livestock isolates comprised large (n=56), medium (n=53), and small (n=45) collected in Burundi (2018), Kenya (2007, 2018, 2019, 2021, and 2022), and Rwanda (2018 and 2022). Our dataset revealed that RVFV exhibited low overall genetic diversity. Lineage C, however, showed evidence of active evolution, with substitution rates ranging from 3·58 × 10-4 to 9·76 × 10-4 substitutions per site per year. This lineage probably originated in Zimbabwe in the mid-1970s and has since expanded across eastern and southern Africa. Phylogeographic reconstructions revealed rapid spread, with diffusion coefficients exceeding 50 000 km2 per year. INTERPRETATION: Lineage C appears capable of establishing endemic transmission in new regions, with ongoing diversification observed during interepidemic periods. These observations reinforce the value of continuous genomic surveillance, particularly during cryptic transmission phases when adaptive mutations might emerge. Although further evidence is needed, observed trends in climate variability and land-use change point to the potential benefit of targeted surveillance in settings that could be at increased risk, including urban centres and wetlands. FUNDING: This work was supported by the German Federal Ministry for Economic Cooperation and Development, the Rockefeller Foundation, and the Africa Centres for Disease Control and Prevention.

Rift Valley fever virus↗

PubMed2003

The role of scleral buckle in experimental posterior penetrating eye injury.

PURPOSE: Although episcleral buckles are frequently placed as an additional procedure to vitreoretinal surgery, little is known about their independent effect after ocular trauma. The authors created a posterior penetrating ocular injury model to evaluate the isolated role of primary episcleral buckle placement. METHODS: Twenty eyes underwent surgery. The penetrating injury consisted of two 5-mm circumferential incisions placed five clock hours apart and 8 mm behind the limbus. A segmental episcleral buckle was placed over a randomly chosen injury site after wound closure. The degrees of fibrous proliferation, traction, and the presence of retinal detachment were evaluated on follow-up examinations. After enucleation and initial fixation, tissue sectioning was performed, and the greatest dimension of the fibrous proliferation at both wound sites was measured with a caliper. RESULTS: Two eyes were excluded from the study. Three eyes developed a retinal detachment; the remaining 15 eyes showed varying degrees of proliferation and traction on the retina. The greatest dimension of the fibrous proliferation at the buckle site (1.22 +/- 1 mm) was significantly different from that at the nonbuckle site (2 +/- 1.45 mm, P = 0.01). CONCLUSIONS: Primary episcleral buckle placement at the time of surgical repair reduces vitreous traction from the buckle site and decreases the degree of fibrovascular proliferation.

Animals↗

PubMed1988

Heat shock causes repeated segmental anomalies in the chick embryo.

A single heat shock, given to 2-day-old chick embryos, can generate multiple but discrete somite and skeletal anomalies. Each of these anomalies is restricted to one, or at the most two, consecutive segments. The anomalies are separated from each other by a distance of 6-7 somites or vertebrae, or a multiple of this distance. These results argue against the 'clock and wavefront' model; while they support the idea of a cellular clock, they are not consistent with a single propagating wave gating cells destined to form each segment. Heat shock also alters the size and number of segments, as well as the rostrocaudal proportions of the sclerotome. The results are consistent with the rostrocaudal fate of sclerotome cells being determined during segmentation. From our observations, we speculate on the implications for regionalization of the vertebral column.

Animals↗

PubMed2002

A dynamically coupled neural oscillator network for image segmentation.

We propose a dynamically coupled neural oscillator network for image segmentation. Instead of pair-wise coupling, an ensemble of oscillators coupled in a local region is used for grouping. We introduce a set of neighborhoods to generate dynamical coupling structures associated with a specific oscillator. Based on the proximity and similarity principles, two grouping rules are proposed to explicitly consider the distinct cases of whether an oscillator is inside a homogeneous image region or near a boundary between different regions. The use of dynamical coupling makes our segmentation network robust to noise on an image, and unlike image processing algorithms no iterative operation is needed for noise removal. For fast computation, a segmentation algorithm is abstracted from the underlying oscillatory dynamics, and has been applied to synthetic and real images. Simulation results demonstrate the effectiveness of our oscillator network in image segmentation.

Algorithms↗

PubMed2000

The development of the avian vertebral column.

Segmentation of the paraxial mesoderm leads to somite formation. The underlying molecular mechanisms involve the oscillation of "clock-genes" like c-hairy-1 and lunatic fringe indicative of an implication of the Notch signaling pathway. The cranio-caudal polarity of each segment is already established in the cranial part of the segmental plate and accompanied by the expression of genes like Delta1, Mesp1, Mesp2, Ulicx-1, and EphA4 which are restricted to one half of the prospective somite. Dorsoventral compartmentalization of somites leads to the development of the dermomyotome and the sclerotome, the latter forming as a consequence of an epithelio-to-mesenchymal transition of the ventral part of the somite. The sclerotome cells express Pax-1 and Pax-9, which are induced by notochordal signals mediated by sonic hedgehog (Shh) and noggin. The craniocaudal somite compartmentalization that becomes visible in the sclerotomes is the prerequisite for the segmental pattern of the peripheral nervous system and the formation of the vertebrae and ribs, whose boundaries are shifted half a segment compared to the sclerotome boundaries. Sclerotome development is characterized by the formation of three subcompartments giving rise to different parts of the axial skeleton and ribs. The lateral sclerotome gives rise to the laminae and pedicles of the neural arches and to the ribs. Its development depends on signals from the notochord and the myotome. The ventral sclerotome giving rise to the vertebral bodies and intervertebral discs is made up of Pax-1 expressing cells that have invaded the perinotochordal space. The dorsal sclerotome is formed by cells that migrate from the dorso-medial angle of the sclerotome into the space between the roof plate of the neural tube and the dermis. These cells express the genes Msx1 and Msx2, which are induced by BMP-4 secreted from the roof plate, and they later form the dorsal part of the neural arch and the spinous process. The formation of the ventral and dorsal sclerotome requires directed migration of sclerotome cells. The regionalization of the paraxial mesoderm occurs by a combination of functionally Hox genes, the Hox code, and determines the segment identity. The development of the vertebral column is a consequence of a segment-specific balance between proliferation, apoptosis and differentiation of cells.

Animals↗

PubMed2006

A pair-rule gene circuit defines segments sequentially in the short-germ insect Tribolium castaneum.

In Drosophila, a hierarchy of maternal, gap, pair-rule, and segment polarity gene interactions regulates virtually simultaneous blastoderm segmentation. For the last decade, studies have focused on revealing the extent to which Drosophila segmentation mechanisms are conserved in other arthropods where segments are added sequentially from anterior to posterior in a cellular environment. Despite our increased knowledge of individual segmentation genes, details of their interactions in non-Drosophilid insects are not well understood. We analyzed the Tribolium orthologs of Drosophila pair-rule genes, which display pair-rule expression patterns. Tribolium castaneum paired (Tc-prd) and sloppy-paired (Tc-slp) genes produced pair-rule phenotypes when their transcripts were severely reduced by RNA interference. In contrast, similar analysis of T. castaneum even-skipped (Tc-eve), runt (Tc-run), or odd-skipped (Tc-odd) genes produced severely truncated, almost completely asegmental phenotypes. Analysis of interactions between pair-rule components revealed that Tc-eve, Tc-run, and Tc-odd form a three-gene circuit to regulate one another as well as their downstream targets, Tc-prd and Tc-slp. The complement of primary pair-rule genes in Tribolium differs from Drosophila in that it includes Tc-odd but not Tc-hairy. This gene circuit defines segments sequentially in double segment periodicity. Furthermore, this single mechanism functions in the early blastoderm stage and subsequently during germ-band elongation. The periodicity of the Tribolium pair-rule gene interactions reveals components of the genetic hierarchy that are regulated in a repetitive circuit or clock-like mechanism. This pair-rule gene circuit provides insight into short-germ segmentation in Tribolium that may be more generally applicable to segmentation in other arthropods.

Animals↗

PubMed2000

A clock and trail model for somite formation, specialization and polarization.

We present some theoretical considerations about the initial process of pre-patterning during embryonic segmentation, with particular reference to somite formation. We first suggest that the pre-pattern is a stable spatial sinusoidal (or, at least, periodic) wave. The periodic wave originates from an oscillator ("clock") in the proliferative region that gives rise to the cells. At the moment the cells leave the proliferative or "progress" zone, or somewhat later, a permanent record is made of the current state of the oscillation, which cells then keep during their pre-somitic phase, before explicit somite and somite boundary formation. Thus, a trail is left behind the progress zone in the form of a spatial sine wave. Second, we also observe that the factors involved in the progress-zone clock and its wave-like trail may form multimers, which will oscillate with higher space-time frequency and thus shorter wavelengths than the monomers. Whether or not our first suggestion is correct, this phenomenon may account for multiple wavelengths in somitogenesis, and may thus encompass somite formation, but also somite polarization (half-wavelength) into anterior and posterior halves, as well as the puzzling observation that expression of her1 in zebrafish is in primordia of alternating somites, i.e. it exhibits a 2-somite wavelength.

Animals↗

PubMed2002

Opsin-G11-mediated signaling pathway for photic entrainment of the chicken pineal circadian clock.

Light is a major environmental signal for entrainment of the circadian clock, but little is known about the intracellular phototransduction pathway triggered by light activation of the photoreceptive molecule(s) responsible for the phase shift of the clock in vertebrates. The chicken pineal gland and retina contain the autonomous circadian oscillators together with the photic entrainment pathway, and hence they represent useful experimental models for the clock system. Here we show the expression of G11alpha, an alpha subunit of heterotrimeric G-protein, in both tissues by cDNA cloning, Northern blot, and Western blot analyses. G11alpha immunoreactivity was colocalized with pinopsin in the chicken pineal cells and also with rhodopsin in the outer segments of retinal photoreceptor cells, suggesting functional coupling of G11alpha with opsins in the clock-containing photosensitive tissues. The physical interaction was examined by coimmunoprecipitation experiments, the results of which provided evidence for light- and GTP-dependent coupling between rhodopsin and G11alpha. To examine whether activation of endogenous G11 leads to a phase shift of the oscillator, Gq/11-coupled m1-type muscarinic acetylcholine receptor (mAChR) was ectopically expressed in the cultured pineal cells. Subsequent treatment of the cells with carbamylcholine (CCh), an agonist of mAChR, induced phase-dependent phase shifts of the melatonin rhythm in a manner very similar to the effect of light. In contrast, CCh treatment induced no measurable effect on the rhythm of nontransfected (control) cells or cells expressing G(i/o)-coupled m2-type mAChR, indicating selectivity of the G-protein activation. Together, our results demonstrate the existence of a G11-mediated opsin-signaling pathway contributing to the photic entrainment of the circadian clock.

Animals↗

PubMed1980

Leucokinetic study. Morphology of the bone marrow and blood after experimental induction of marrow hypoplasia by cyclophosphamide in laboratory rats.

Experimental hypoplasia of femoral bone marrow in rats was induced by cyclophosphamide, injected i.p. at various clock hours (08.00, 12.00, 16.00, 20.00, 24.00, and 04.00). Cyclophosphamide-induced neutropenia persisted for six days and was followed by transitory granulocytosis with subsequent decrease in the cont of circulating mature granulocytes. The absolute counts of circulating segmented neutrophils changed in parallel with the absolute counts of segmented neutrophils in the bone marrow. The count of circulating neutrophils was not essentially influenced by the clock hour of cyclophosphamide injection. The toxic action of cyclophosphamide upon the bone marrow exhibited a circadian rhythmicity: the greatest decrease in the count of nucleated marrow cells was found in the morning, and the least, in the evening. The minimal compartment transit times of the development stages of bone-marrow neutrophils, and the daily granulocyte production in the rat were calculated.

Animals↗

PubMed2004

Segmentation and zooid formation in animals with a posterior growing region: the case for metabolic gradients and Turing waves.

The discovery of periodic propagation of anteriorly moving pulses/stripes of gene expression in the presomitic mesoderm (PSM) of vertebrates has given new life to the clock and wavefront model, and other models of morphogenesis based on a molecular oscillator where the time periodicity is translated into spatial periodicity. Instead we suggest that segmentation, somitogenesis and metamerism in vertebrates and in invertebrates with a posterior growing region are based on a Turing-Child metabolic gradient that is progressively shifted posteriorly with the PSM as elongation, segmentation and somitogenesis proceed. This gradient corresponds to anteriorly propagating metabolic front in the PSM that drives the anteriorly propagating mRNA synthesis and which, together with mRNA degradation, explains stripe formation and spatial periodicity.The process of segmentation has been compared to zooid formation. We show that for annelids the metabolic profile behaves as a Turing field in the sense that an increase in the length of the system or a decrease of the Turing wavelength results in an additional peak in the posterior growing region as predicted by Turing theory. In particular, it is shown that the metabolic gradient that drives the segmentation is based on a Turing system.

Animals↗

PubMed1996

Maximum-Likelihood Models for Combined Analyses of Multiple Sequence Data

Abstract. Models of nucleotide substitution were constructed for combined analyses of heterogeneous sequence data (such as those of multiple genes) from the same set of species. The models account for different aspects of the heterogeneity in the evolutionary process of different genes, such as differences in nucleotide frequencies, in substitution rate bias (for example, the transition/transversion rate bias), and in the extent of rate variation across sites. Model parameters were estimated by maximum likelihood and the likelihood ratio test was used to test hypotheses concerning sequence evolution, such as rate constancy among lineages (the assumption of a molecular clock) and proportionality of branch lengths for different genes. The example data from a segment of the mitochondrial genome of six hominoid species (human, common and pygmy chimpanzees, gorilla, orangutan, and siamang) were analyzed. Nucleotides at the three codon positions in the protein-coding regions and from the tRNA-coding regions were considered heterogeneous data sets. Statistical tests showed that the amount of evolution in the sequence data reflected in the estimated branch lengths can be explained by the codon-position effect and lineage effect of substitution rates. The assumption of a molecular clock could not be rejected when the data were analyzed separately or when the rate variation among sites was ignored. However, significant differences in substitution rate among lineages were found when the data sets were combined and when the rate variation among sites was accounted for in the models. Under the assumption that the orangutan and African apes diverged 13 million years ago, the combined analysis of the sequence data estimated the times for the human-chimpanzee separation and for the separation of the gorilla as 4.3 and 6.8 million years ago, respectively.

Journal Article↗