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Sleep and waking are controlled by opposing interactions between circadian and homeostatic processes. A circadian process generated by the suprachiasmatic nucleus determines when sleep should occur, while a homeostatic process keeps track of time spent awake and asleep and signals sleep need or sleep propensity. Recent evidence indicates that these two processes employ many of the same set of genes. Herein, we review the basic concepts of the circadian and homeostatic regulation of sleep, and then outline the molecular components of circadian clock. We then discuss the evidence demonstrating a role of clock genes in sleep homeostasis in flies, mice, and humans. We conclude by suggesting that clock genes might be crucial for integrating homeostatic need, not only that of sleep but also of food intake and energy metabolism.

Rhythmic growth explained by coincidence between internal and external cues.

Most organisms use circadian oscillators to coordinate physiological and developmental processes such as growth with predictable daily environmental changes like sunrise and sunset. The importance of such coordination is highlighted by studies showing that circadian dysfunction causes reduced fitness in bacteria and plants, as well as sleep and psychological disorders in humans. Plant cell growth requires energy and water-factors that oscillate owing to diurnal environmental changes. Indeed, two important factors controlling stem growth are the internal circadian oscillator and external light levels. However, most circadian studies have been performed in constant conditions, precluding mechanistic study of interactions between the clock and diurnal variation in the environment. Studies of stem elongation in diurnal conditions have revealed complex growth patterns, but no mechanism has been described. Here we show that the growth phase of Arabidopsis seedlings in diurnal light conditions is shifted 8-12 h relative to plants in continuous light, and we describe a mechanism underlying this environmental response. We find that the clock regulates transcript levels of two basic helix-loop-helix genes, phytochrome-interacting factor 4 (PIF4) and PIF5, whereas light regulates their protein abundance. These genes function as positive growth regulators; the coincidence of high transcript levels (by the clock) and protein accumulation (in the dark) allows them to promote plant growth at the end of the night. Thus, these two genes integrate clock and light signalling, and their coordinated regulation explains the observed diurnal growth rhythms. This interaction may serve as a paradigm for understanding how endogenous and environmental signals cooperate to control other processes.

The phylogeography of an alpine leaf beetle: divergence within Oreina elongata spans several ice ages.

The genetic landscape of the European flora and fauna was shaped by the ebb and flow of populations with the shifting ice during Quaternary climate cycles. While this has been well demonstrated for lowland species, less is known about high altitude taxa. Here we analyze the phylogeography of the leaf beetle Oreina elongata from 20 populations across the Alps and Apennines. Three mitochondrial and one nuclear region were sequenced in 64 individuals. Within an mtDNA phylogeny, three of seven subspecies are monophyletic. The species is chemically defended and aposematic, with green and blue forms showing geographic variation and unexpected within-population polymorphism. These warning colors show pronounced east-west geographical structure in distribution, but the phylogeography suggests repeated origin and loss. Basal clades come from the central Alps. Ancestors of other clades probably survived across northern Italy and the northern Adriatic, before separation of eastern, southern and western populations and rapid spread through the western Alps. After reviewing calibrated gene-specific substitution rates in the literature, we use partitioned Bayesian coalescent analysis to date our phylogeography. The major clades diverged long before the last glacial maximum, suggesting that O. elongata persisted many glacial cycles within or at the edges of the Alps and Apennines. When analyzing additional barcoding pairwise distances, we find strong evidence to consider O. elongata as a species complex rather than a single species.

Power supply noise and logic error probability

Voltage fluctuations caused by parasitic impedances in the power supply rails of modern ICs are a major concern in nowadays ICs. The voltage fluctuations are spread out to the diverse nodes of the internal sections causing two effects: a degradation of performances mainly impacting gate delays anda noisy contamination of the quiescent levels of the logic that drives the node. Both effects are presented together, in thispaper, showing than both are a cause of errors in modern and future digital circuits. The paper groups both error mechanismsand shows how the global error rate is related with the voltage deviation and the period of the clock of the digital system.

Phylogenetic analysis of plastid and nuclear DNA sequences reveals a rapid late Miocene radiation of the temperate bamboo tribe Arundinarieae (Poaceae, Bambusoideae)

Background: Arundinarieae are a large tribe of temperate woody bamboos for which phylogenetics are poorly understood because of limited taxon sampling and lack of informative characters. Aims: This study assessed phylogenetic relationships, origins and classification of Arundinarieae. Methods: DNA sequences (plastid trnL-F; nuclear ITS) were used for parsimony and Bayesian inference including 41 woody bamboo taxa. Divergence dates were estimated using a relaxed Bayesian clock. Results: Arundinarieae were monophyletic but their molecular divergence was low compared to the tropical Bambuseae. Ancestors of the Arundinarieae lineage were estimated to have diverged from the other bamboos 23 (15-30) million years ago (Mya). However, the Arundinarieae radiation occurred 10 (6-16) Mya compared to 18 (11-25) Mya for the tropical Bambuseae. Some groups could be defined within Arundinarieae, but they do not correspond to recognised subtribes such as Arundinariinae or Shibataeinae. Conclusions: Arundinarieae are a relatively ancient bambusoid lineage that underwent a rapid radiation in the late Miocene. The radiation coincides with the continental collision of the Indo-Australian and Eurasian Plates. Arundinarieae are distributed primarily in East Asia and the Himalayas to northern Southeast Asia. It is unknown whether they were present in Asia long before their radiation, but we believe recent dispersal is a more likely scenario. Keywords: Arundinarieae; Bambuseae; internal transcribed spacer (ITS); molecular clock; phylogenetics; radiation; temperate bamboos; Thamnocalaminae; trnL-F

Testing of Access Network's Internet Protocol Television Features

Testaus on tänä päivänä olennainen osa tuotekehitysprosessia koko tuotteen elinkaaren ajan, myös tietoliikennetekniikassa. Tietoverkoille asetetut tiukat vaatimukset ympärivuorokautisen toimivuuden suhteen nostavatmyös niiden testauksen tason ja laadun merkitystä. Erityisesti verkkojen uudet toiminnallisuudet, joilla ei ole vielä vuosia kestäneen käytön ja kehityksen tuomaa varmuus- ja laatutasoa, tuovat haasteita testauksen toteutukselle. Televisiokuvan välityksen Internetin yli mahdollistavat ominaisuudet ovat esimerkki tällaisista toiminnallisuuksista. Tässä diplomityössä käsitellään Tellabs Oy:n tuotekehitysosastolla vuosina 2005 ja 2006 toteutetun, erään operaattorin laajakaistaliityntäverkon päivitysprojektin testausosuutta. Kattavamman tarkastelun kohteena ovat erityisesti verkkoon lisättyjen laajakaistatelevisio- eli IPTV-toiminnallisuuksien integraatio- ja systeemitestausmenetelmät.

Highly Available Enterprise-level Application Server Architecture

Korkeasaatavuus on olennainen osa nykyaikaisissa, integroiduissa yritysjärjestelmissä. Yritysten kansainvälistyessä tiedon on oltava saatavissa ympärivuorokautisesti, mikä asettaa yhä kovempia vaatimuksia järjestelmän yksittäisten osien saatavuudelle. Kasvava tietojärjestelmäintegraatio puolestaan tekee järjestelmän solmukohdista kriittisiä liiketoiminnan kannalta. Tässä työssä perehdytään hajautettujen järjestelmien ominaisuuksiin ja niiden asettamiin haasteisiin. Esiteltyjä teknologioita ovat muun muassa väliohjelmistot, klusterit ja kuormantasaus. Yrityssovellusten pohjana käytetty Java 2 Enterprise Edition (J2EE) -teknologia käsitellään olennaisilta osiltaan. Työssä käytetään sovelluspalvelinalustana BEA WebLogic Server -ohjelmistoa, jonka ominaisuudet käydään läpi hajautuksen kannalta. Työn käytännön osuudessa toteutetaan kahdelle erilaiselle olemassa olevalle yrityssovellukselle korkean saatavuuden sovelluspalvelinympäristö, joissa sovellusten asettamat rajoitukset on otettu huomioon.

The odd couple: contrasting phylogeographic patterns in two sympatric sibling species of woodlouse-­‐hunter spiders in the Canary Islands

Comparative phylogeography seeks for commonalities in the spatial demographic history of sympatric organisms to characterize the mechanisms that shaped such patterns. The unveiling of incongruent phylogeographic patterns in co-occurring species, on the other hand, may hint to overlooked differences in their life histories or microhabitat preferences. The woodlouse-hunter spiders of the genus Dysdera have undergone a major diversi cation on the Canary Islands. The species pair Dysdera alegranzaensis and Dysdera nesiotes are endemic to the island of Lanzarote and nearby islets, where they co-occur at most of their known localities. The two species stand in sharp contrast to other sympatric endemic Dysdera in showing no evidence of somatic (non-genitalic) differentiation. Phylogenetic and population genetic analyses of mitochondrial cox1 sequences from an exhaustive sample of D. alegranzaensis and D. nesiotes specimens, and additional mitochondrial (16S, L1, nad1) and nuclear genes (28S, H3) were analysed to reveal their phylogeographic patterns and clarify their phylogenetic relationships. Relaxed molecular clock models using ve calibration points were further used to estimate divergence times between species and populations. Striking differences in phylogeography and population structure between the two species were observed. Dysdera nesiotes displayed a metapopulation-like structure, while D. alegranzaensis was characterized by a weaker geographical structure but greater genetic divergences among its main haplotype lineages, suggesting more complex population dynamics. Our study con rms that co-distributed sibling species may exhibit contrasting phylogeographic patterns in the absence of somatic differentiation. Further ecological studies, however, will be necessary to clarify whether the contrasting phylogeographies may hint at an overlooked niche partitioning between the two species. In addition, further comparisons with available phylogeographic data of other eastern Canarian Dysdera endemics con rm the key role of lava ows in structuring local populations in oceanic islands and identify localities that acted as refugia during volcanic eruptions

Blood-Borne Circadian Signal Stimulates Daily Oscillations in Actin Dynamics and SRF Activity.

In peripheral tissues circadian gene expression can be driven either by local oscillators or by cyclic systemic cues controlled by the master clock in the brain's suprachiasmatic nucleus. In the latter case, systemic signals can activate immediate early transcription factors (IETFs) and thereby control rhythmic transcription. In order to identify IETFs induced by diurnal blood-borne signals, we developed an unbiased experimental strategy, dubbed Synthetic TAndem Repeat PROMoter (STAR-PROM) screening. This technique relies on the observation that most transcription factor binding sites exist at a relatively high frequency in random DNA sequences. Using STAR-PROM we identified serum response factor (SRF) as an IETF responding to oscillating signaling proteins present in human and rodent sera. Our data suggest that in mouse liver SRF is regulated via dramatic diurnal changes of actin dynamics, leading to the rhythmic translocation of the SRF coactivator Myocardin-related transcription factor-B (MRTF-B) into the nucleus.

Neuroligin-1 links neuronal activity to sleep-wake regulation.

Maintaining wakefulness is associated with a progressive increase in the need for sleep. This phenomenon has been linked to changes in synaptic function. The synaptic adhesion molecule Neuroligin-1 (NLG1) controls the activity and synaptic localization of N-methyl-d-aspartate receptors, which activity is impaired by prolonged wakefulness. We here highlight that this pathway may underlie both the adverse effects of sleep loss on cognition and the subsequent changes in cortical synchrony. We found that the expression of specific Nlg1 transcript variants is changed by sleep deprivation in three mouse strains. These observations were associated with strain-specific changes in synaptic NLG1 protein content. Importantly, we showed that Nlg1 knockout mice are not able to sustain wakefulness and spend more time in nonrapid eye movement sleep than wild-type mice. These changes occurred with modifications in waking quality as exemplified by low theta/alpha activity during wakefulness and poor preference for social novelty, as well as altered delta synchrony during sleep. Finally, we identified a transcriptional pathway that could underlie the sleep/wake-dependent changes in Nlg1 expression and that involves clock transcription factors. We thus suggest that NLG1 is an element that contributes to the coupling of neuronal activity to sleep/wake regulation.

Sustained sleep fragmentation induces sleep homeostasis in mice.

STUDY OBJECTIVES: Sleep fragmentation (SF) is an integral feature of sleep apnea and other prevalent sleep disorders. Although the effect of repetitive arousals on cognitive performance is well documented, the effects of long-term SF on electroencephalography (EEG) and molecular markers of sleep homeostasis remain poorly investigated. To address this question, we developed a mouse model of chronic SF and characterized its effect on EEG spectral frequencies and the expression of genes previously linked to sleep homeostasis including clock genes, heat shock proteins, and plasticity-related genes. DESIGN: N/A. SETTING: Animal sleep research laboratory. PARTICIPANTS: Sixty-six C57BL6/J adult mice. INTERVENTIONS: Instrumental sleep disruption at a rate of 60/h during 14 days. MEASUREMENTS AND RESULTS: Locomotor activity and EEG were recorded during 14 days of SF followed by recovery for 2 days. Despite a dramatic number of arousals and decreased sleep bout duration, SF minimally reduced total quantity of sleep and did not significantly alter its circadian distribution. Spectral analysis during SF revealed a homeostatic drive for slow wave activity (SWA; 1-4 Hz) and other frequencies as well (4-40 Hz). Recordings during recovery revealed slow wave sleep consolidation and a transient rebound in SWA, and paradoxical sleep duration. The expression of selected genes was not induced following chronic SF. CONCLUSIONS: Chronic SF increased sleep pressure confirming that altered quality with preserved quantity triggers core sleep homeostasis mechanisms. However, it did not induce the expression of genes induced by sleep loss, suggesting that these molecular pathways are not sustainably activated in chronic diseases involving SF.

Sulautetun järjestelmän Web-käyttö

Diplomityössä on tutkittu sulautetun järjestelmän liittämistä Ethernet-verkkoon sekä TCP/IP-protokollapinoon kuuluvien tavallisimpien protokollien toimintaa. Työn tuloksien perusteella on suunniteltu harjoitustyö, jota voidaan käyttää sähkötekniikan osaston opetuksessa. Työssä hankittiin Atmelin sulautettu Web-serverikortti (EWS) ja STK500-kortti serverin ohjelmointiin. Serverin mukana tuli Internet-yhteyden mahdollistava TCP/IP-pinon lähdekoodi. Työssä selvitettiin TCP/IP:hen kuuluvien protokollien toimintaa teoriassa ja käytännön toteutusta EWS:n avulla. Lähdekoodiin lisättiin ominaisuudet, joiden avulla laite hakee kellonaikatiedot aikapalvelimelta time-protokollaa käyttäen ja lähettää sähköpostia määriteltyyn osoitteeseen sähköpostipalvelimen kautta. Laitetta käytettiin sekä palvelimena että asiakkaana. Työssä perehdyttiin sulautettujen järjestelmien yleisiin ominaisuuksiin ja erilaisiin verkonhallinnan apuohjelmiin. Työssä tutkittiin palvelin- ja asiakaskoneen välillä Ethernetissä kulkevaa verkkoliikennettä. Työssä minimoitiin protokollatiedostojen viemä tila prosessorin muistista ja tutkittiin Internet-yhteyden kuluttamien kellojaksojen määrää. Työssä selvitettiin tietoturva-kysymysten merkitystä ja toteutusta sulautetuissa järjestelmissä.

DNA barcoding of Corsican mayflies (Ephemeroptera) with implications on biogeography, systematics and biodiversity

Mayflies (Ephemeroptera) are known to generally present a high degree of insular endemism: half of the 28 species known from Corsica and Sardinia are considered as endemic. We sequenced the DNA barcode (a fragment of the mitochondrial COI gene) of 349 specimens from 50 localities in Corsica, Sardinia, continental Europe and North Africa. We reconstructed gene trees of eight genera or species groups representing the main mayfly families. Alternative topologies were built to test if our reconstructions suggested a single or multiple Corsican/Sardinian colonization event(s) in each genus or species group. A molecular clock calibrated with different evolution rates was used to try to link speciation processes with geological events. Our results confirm the high degree of endemism of Corsican and Sardinian mayflies and the close relationship between these two faunas. Moreover, we have evidence that the mayfly diversity of the two islands is highly underestimated as at least six new putative species occur on the two islands. We demonstrated that the Corsican and Sardinian mayfly fauna reveals a complex history mainly related to geological events. The Messinian Salinity Crisis, which is thought to have reduced marine barriers, thus facilitating gene flow between insular and continental populations, was detected as the most important event in the speciation of most lineages. Vicariance processes related to the split and rotation of the Corso-Sardinian microplate had a minor impact as they involved only two genera with limited dispersal and ecological range. Colonization events posterior to the Messinian Salinity Crisis had only marginal effects as we had indication of recent gene flow only in two clades. With very limited recent gene flow and a high degree of endemism, mayflies from Corsica and Sardinia present all the criteria for conservation prioritization.

Genetic dissection of sleep homeostasis.

Sleep is a complex behavior both in its manifestation and regulation, that is common to almost all animal species studied thus far. Sleep is not a unitary behavior and has many different aspects, each of which is tightly regulated and influenced by both genetic and environmental factors. Despite its essential role for performance, health, and well-being, genetic mechanisms underlying this complex behavior remain poorly understood. One important aspect of sleep concerns its homeostatic regulation, which ensures that levels of sleep need are kept within a range still allowing optimal functioning during wakefulness. Uncovering the genetic pathways underlying the homeostatic aspect of sleep is of particular importance because it could lead to insights concerning sleep's still elusive function and is therefore a main focus of current sleep research. In this chapter, we first give a definition of sleep homeostasis and describe the molecular genetics techniques that are used to examine it. We then provide a conceptual discussion on the problem of assessing a sleep homeostatic phenotype in various animal models. We finally highlight some of the studies with a focus on clock genes and adenosine signaling molecules.

Molecular phylogenetics and temporal diversification in the genus Aeromonas based on the sequences of five housekeeping genes

Several approaches have been developed to estimate both the relative and absolute rates of speciation and extinction within clades based on molecular phylogenetic reconstructions of evolutionary relationships, according to an underlying model of diversification. However, the macroevolutionary models established for eukaryotes have scarcely been used with prokaryotes. We have investigated the rate and pattern of cladogenesis in the genus Aeromonas (γ-Proteobacteria, Proteobacteria, Bacteria) using the sequences of five housekeeping genes and an uncorrelated relaxed-clock approach. To our knowledge, until now this analysis has never been applied to all the species described in a bacterial genus and thus opens up the possibility of establishing models of speciation from sequence data commonly used in phylogenetic studies of prokaryotes. Our results suggest that the genus Aeromonas began to diverge between 248 and 266 million years ago, exhibiting a constant divergence rate through the Phanerozoic, which could be described as a pure birth process.