VLANien käyttöönotto ja reititys kytkentäisessä lähiverkossa

Lähiverkkojen merkitys organisaatioiden toiminnassa on tänä päivänä tärkeämpi kuin koskaan aiemmin. Lähiverkot toimivat alustana useille tekniikoille ja palveluille. Lähiverkossa liikkuu dataliikenteen lisäksi myös puhetta ja kuvaa. Verkko mahdollistaa oheislaitteiden, kuten tiedostopalvelimien ja tulostimien, jakamisen ja käyttämisen koko verkon alueelta. Lähiverkkojen yhdistäminen voidaan toteuttaa teleoperaattoreiden toimesta, joten on vaikeaa enää määritellä lähiverkkoa tarkasti. Tämän diplomityön päätavoitteena oli muodostaa tehokas kytkentäinen lähiverkkoarkkitehtuuri. Keskeisenä osana työhön liittyy virtuaaliset lähiverkot, niiden käyttöönotto sekä reititys. Työn teoriaosassa käydään läpi lähiverkon ja tärkeimmän lähiverkkotekniikan, Ethernet-tekniikan peruselementit. Lisäksi käydään läpi TCP/IP- tekniikan periaate, sen keskeisimmät protokollat, VLAN-tekniikka sekä IP-reititys. Työosuudessa toteutettu Pilottiverkko muodostetaan Ciscon kytkin- ja reititinlaitteilla virtuaaliseen oppilaitosympäristöön. Pilottiverkon avulla esitetään vastaukset työn vaatimusmäärittelyihin, joita ovat verkon muunneltavuuden helppous, useiden broadcast-alueiden toteuttamisen mahdollisuus sekä käyttörajoituksiin perustuvan tietoturvan ja vikasietoisuuden mahdollistaminen verkossa.

Identification of neuronal network properties from the spectral analysis of calcium imaging signals in neuronal cultures

Neuronal networks in vitro are prominent systems to study the development of connections in living neuronal networks and the interplay between connectivity, activity and function. These cultured networks show a rich spontaneous activity that evolves concurrently with the connectivity of the underlying network. In this work we monitor the development of neuronal cultures, and record their activity using calcium fluorescence imaging. We use spectral analysis to characterize global dynamical and structural traits of the neuronal cultures. We first observe that the power spectrum can be used as a signature of the state of the network, for instance when inhibition is active or silent, as well as a measure of the network's connectivity strength. Second, the power spectrum identifies prominent developmental changes in the network such as GABAA switch. And third, the analysis of the spatial distribution of the spectral density, in experiments with a controlled disintegration of the network through CNQX, an AMPA-glutamate receptor antagonist in excitatory neurons, reveals the existence of communities of strongly connected, highly active neurons that display synchronous oscillations. Our work illustrates the interest of spectral analysis for the study of in vitro networks, and its potential use as a network-state indicator, for instance to compare healthy and diseased neuronal networks.

Päästökauppa ja sen vaikutukset Suomen terästeollisuuteen

Tässä työssä tavoitteena oli selvittää päästökaupan vaikutuksia Rautaruukin toimintaan ja kilpailukykyyn. Työssä tarkasteltiin tarkemmin Euroopan Yhteisöjen komission esittämää ehdotusta Euroopan Unionin laajuisesta päästökauppajärjestelmästä. Työssä selvitettiin Rautaruukin Raahen ja Koverharin terästehtaiden jo tehtyjen toimien vaikutus hiilidioksidipäästöihin sekä tulevaisuuden päästövähennysmahdollisuudet huomioiden eri päästöskenaariovaihtoehdot. Rautaruukki on saavuttanut tehdyillä toimenpiteillä huomattavia hiilidioksidipäästöjen vähenemiä. Ilman vuosien 1990-2001 välisenä aikana tehtyjä toimia olisivat hiilidioksidi-päästöt vuonna 2001 olleet noin 1 Mt suuremmat kuin ne todellisuudessa olivat. Myös tuulevaisuudessa Rautaruukilla on mahdollisuus vaikuttaa hiilidioksidipäästöihin. Laskelmien mukaan tunnistetuilla toimilla saavutettavat päästövähenemät vuonna 2005 voisivat olla noin 930 000 t ja vuonna 2008 960 00 t. Kuitenkin osa toimista on pitkäntähtäimen toimia, joiden toteuttaminen on vielä hyvin epätodennäköistä. Lisäksi toimien kustannuksista ei ole vielä tarkkaa tietoa. Päästökauppadirektiiviehdotuksen alkujaon merkitystä Rautaruukille on arvioitu vertailemalla eri alkujakovaihtoehtoja. Laskennassa on oletettu, että päästöoikeuksien ensimmäinen alkujako on ilmainen, jolloin kaikki vuoden 1990 päästöt saadaan ilmaiseksi. Näin Ollen vuonna 2005 kymmenen euron päästöoikeuden hinnalla tulee vuosittaiseksi kustannuksiksi noin 16 miljoonaa euroa. Toisella velvoitekaudella 90 % päästöoikeuksista jaetaan ilmaiseksi ja 10 % joudutaan ostamaan. Näin ollen vuonna 2008 kustannukset olisivat noin 69 miljoonaa euroa. Vastaavasti, jos huomioidaan tulevaisuuden investoinneilla saavutettavissa olevat hiilidioksidipäästöjen vähenemät, ovat kustannukset vuonna 2005 noin seitsemän miljoonaa euroa ja vuonna 2008 noin 59 miljoonaa euroa.

Teholähdesuunnittelu

Työssä vertaillaan massatuotannon näkökulmasta eri tehoalueille sopivia teholähteen toteuttamisvaihtoehtoja. Lisäksi esitellään standardien asettamia vaatimuksia teholähteille. Työssä käsitellään teholähdesuunnittelun eri osa-alueita ja niihin sopivien simulointityökalujen hyödyntämismahdollisuuksia suunnitteluprosessin osana. Simulointituloksia ja teoreettisia laskelmia vertaillaan prototyypistä suoritettuihin mittauksiin.

Puhelunohjaus Internetissä

Puhelunohjaus Internetissä ei sido käyttäjää tiettyyn paikkaan tai päätelaitteeseen. Käyttäjä voidaan paikantaa ja kommunikointi hänen kanssaan on mahdollista yhdistelemällä perinteisen puhelinverkon ja Internetin palveluita. Käyttäjä voi itse valita haluamansa palvelut aina tarpeensa mukaan. Tämä diplomityö esittelee Internet-puhelunohjauksen arkkitehtuurin ja tämän toteutuksen. Arkkitehtuurin perusosat kuvataan ja toteutuksen toimivuutta arvioidaan. Internet-puhelunohjaukseen liittyvät Internet-standardit esitellään ja niiden sopivuutta puhelunohjaukseen pohditaan. Aiheeseen liittyviä vaihtoehtoisia standardeja ja menetelmiä puhelunohjaukseen vertaillaan. Lisäksi työssä tutkitaan Necsom Oy:n Media Switch-reitittimen sopivuutta puhelunohjauksen laitealustaksi. Puhelunohjauksen arkkitehtuuri Internetissä mahdollistaa istuntojen muodostamisen ja ohjaamisen käyttäjäkohtaisen osoitteen perusteella. Muuta tietoa käyttäjästä ei tarvita istunnon aloitusvaiheessa. Työssä toteutettu puhelunohjausjärjestelmä on tehty Necsom Oy:n ja Lappeenrannan teknillisen korkeakoulun yhteishankkeena. Toteutuksesta saatujen tulosten perusteella Internet-puhelunohjaus on käyttökelpoinen tuotantokäytössä nyt ja tulevaisuudessa.

Single cell tuning of Myc expression by antigen receptor signal strength and interleukin-2 in T lymphocytes.

Myc controls the metabolic reprogramming that supports effector T cell differentiation. The expression of Myc is regulated by the T cell antigen receptor (TCR) and pro-inflammatory cytokines such as interleukin-2 (IL-2). We now show that the TCR is a digital switch for Myc mRNA and protein expression that allows the strength of the antigen stimulus to determine the frequency of T cells that express Myc. IL-2 signalling strength also directs Myc expression but in an analogue process that fine-tunes Myc quantity in individual cells via post-transcriptional control of Myc protein. Fine-tuning Myc matters and is possible as Myc protein has a very short half-life in T cells due to its constant phosphorylation by glycogen synthase kinase 3 (GSK3) and subsequent proteasomal degradation. We show that Myc only accumulates in T cells exhibiting high levels of amino acid uptake allowing T cells to match Myc expression to biosynthetic demands. The combination of digital and analogue processes allows tight control of Myc expression at the population and single cell level during immune responses.

RasGAP Shields Akt from Deactivating Phosphatases in Fibroblast Growth Factor Signaling but Loses This Ability Once Cleaved by Caspase-3.

Fibroblast growth factor receptors (FGFRs) are involved in proliferative and differentiation physiological responses. Deregulation of FGFR-mediated signaling involving the Ras/PI3K/Akt and the Ras/Raf/ERK MAPK pathways is causally involved in the development of several cancers. The caspase-3/p120 RasGAP module is a stress sensor switch. Under mild stress conditions, RasGAP is cleaved by caspase-3 at position 455. The resulting N-terminal fragment, called fragment N, stimulates anti-death signaling. When caspase-3 activity further increases, fragment N is cleaved at position 157. This generates a fragment, called N2, that no longer protects cells. Here, we investigated in Xenopus oocytes the impact of RasGAP and its fragments on FGF1-mediated signaling during G2/M cell cycle transition. RasGAP used its N-terminal Src homology 2 domain to bind FGFR once stimulated by FGF1, and this was necessary for the recruitment of Akt to the FGFR complex. Fragment N, which did not associate with the FGFR complex, favored FGF1-induced ERK stimulation, leading to accelerated G2/M transition. In contrast, fragment N2 bound the FGFR, and this inhibited mTORC2-dependent Akt Ser-473 phosphorylation and ERK2 phosphorylation but not phosphorylation of Akt on Thr-308. This also blocked cell cycle progression. Inhibition of Akt Ser-473 phosphorylation and entry into G2/M was relieved by PHLPP phosphatase inhibition. Hence, full-length RasGAP favors Akt activity by shielding it from deactivating phosphatases. This shielding was abrogated by fragment N2. These results highlight the role played by RasGAP in FGFR signaling and how graded stress intensities, by generating different RasGAP fragments, can positively or negatively impact this signaling.

Defining ecologically relevant water quality targets for lakes in Europe

1. The implementation of the Water Framework Directive requires EU member states to establish and harmonize ecological status class boundaries for biological quality elements. In this paper, we describe an approach for defining ecological class boundaries that delineates shifts in lake ecosystem functioning and, therefore, provides ecologically meaningful targets for water policy in Europe. 2. We collected an extensive data set of 810 lake-years from nine Central European countries, and we used phytoplankton chlorophyll a, a metric widely used to measure the impact of eutrophication in lakes. Our approach establishes chlorophyll a target values in relation to three significant ecological effects of eutrophication: the decline of aquatic macrophytes, the dominance of potentially harmful cyanobacteria and the major functional switch from a clear water to a turbid state. 3. Ranges of threshold chlorophyll a concentrations are given for the two most common lake types in lowland Central Europe: for moderately deep lakes (mean depth 3–15 m), the greatest ecological shifts occur in the range 10–12 lg L 1 chlorophyll a, and for shallow lakes (<3 m mean depth), in the range 21–23 lg L 1 chlorophyll a. 4. Synthesis and applications. Our study provides class boundaries for determining the ecological status of lakes, which have robust ecological consequences for lake functioning and which, therefore, provide strong and objective targets for sustainable water management in Europe. The results have been endorsed by all participant member states and adopted in the European Commission legislation, marking the first attempt in international water policy to move from physico-chemical quality standards to harmonized ecologically based quality targets.

The dynamics of coexistence: habitat sharing versus segregation patterns among three sympatric montane vipers

Contact zones of closely related and ecologically similar species constitute rare opportunities to study the evolutionary consequences of past speciation processes. They represent natural laboratories in which strong competition could lead to the exclusion of one species, or the various species may switch into distinct ecological niches. Alternatively, if reproductive isolation has not yet been achieved, they may hybridize. We elucidate the degree of taxon integrity by comparing genetics and habitat use of three similar-sized congeneric viper species, Vipera ammodytes, Viperaaspis, and Viperaberus, of Nadiza Valley in western Slovenia. No hybridization was detected for either mitochondrial or nuclear genomes. Similarly, external intermediacy by a single prestudy viper (probably V.ammodytesxV. aspis) indicates that hybridization occasionally occurs, but should be very rare. Populations of the three related viperids are partially allopatric in Nadiza Valley, but they also coexist in a narrow contact zone in the montane grassland along the south-exposed slope of Mount Stol (1673m a.s.l.). Here, the three species that occupy areas in or near patches of rocky microhabitats (e.g. stone piles, slides, and walls) live in syntopy. However, fine-scale measurements of structural components show partial habitat segregation, in which V.berus becomes more dominant at elevations above 1400m and occupies mostly the mountain ridge and north-exposed slopes of Mount Stol, V.aspis occurs below 1300m and is the only species to inhabit stoneless patches of grass and bushes around 1000m and lower, and V.ammodytes occurs at all elevations up to 1500m, but is restricted to a rocky microhabitat. We suggest that a high degree of microstructure divergence, slightly different environmental niches, and a generally favourable habitat for all three viper species, keep the pressure for mis-mating and hybridization low, although mechanisms such as reduced hybrid inferiority and temporal mating segregation cannot yet be excluded.

Postnatal β-cell maturation is associated with islet-specific microRNA changes induced by nutrient shifts at weaning.

Glucose-induced insulin secretion is an essential function of pancreatic β-cells that is partially lost in individuals affected by Type 2 diabetes. This unique property of β-cells is acquired through a poorly understood postnatal maturation process involving major modifications in gene expression programs. Here we show that β-cell maturation is associated with changes in microRNA expression induced by the nutritional transition that occurs at weaning. When mimicked in newborn islet cells, modifications in the level of specific microRNAs result in a switch in the expression of metabolic enzymes and cause the acquisition of glucose-induced insulin release. Our data suggest microRNAs have a central role in postnatal β-cell maturation and in the determination of adult functional β-cell mass. A better understanding of the events governing β-cell maturation may help understand why some individuals are predisposed to developing diabetes and could lead to new strategies for the treatment of this common metabolic disease.

One-seller assignment markets with multi-unit demands

We consider one-seller assignment markets with multi-unit demands and prove that the associated game is buyers-submodular. Therefore the core is non-empty and it has a lattice structure which contains the allocation where every buyer receives his marginal contribution. We prove that in this kind of market, every pairwise-stable outcome is associated to a competitive equilibrium and viceversa. We study conditions under which the buyers-optimal and the seller-optimal core allocations are competitive equilibrium payoff vectors. Moreover, we characterize the markets for which the core coincidences with the set of competitive equilibria payoff vectors. When agents behave strategically, we introduce a procedure that implements the buyers-optimal core allocation as the unique subgame perfect Nash equilibrium outcome.

Sex-Chromosome Homomorphy in Palearctic Tree Frogs Results from Both Turnovers and X-Y Recombination.

Contrasting with birds and mammals, poikilothermic vertebrates often have homomorphic sex chromosomes, possibly resulting from high rates of sex-chromosome turnovers and/or occasional X-Y recombination. Strong support for the latter mechanism was provided by four species of European tree frogs, which inherited from a common ancestor (∼5 Ma) the same pair of homomorphic sex chromosomes (linkage group 1, LG1), harboring the candidate sex-determining gene Dmrt1. Here, we test sex linkage of LG1 across six additional species of the Eurasian Hyla radiation with divergence times ranging from 6 to 40 Ma. LG1 turns out to be sex linked in six of nine resolved cases. Mapping the patterns of sex linkage to the Hyla phylogeny reveals several transitions in sex-determination systems within the last 10 My, including one switch in heterogamety. Phylogenetic trees of DNA sequences along LG1 are consistent with occasional X-Y recombination in all species where LG1 is sex linked. These patterns argue against one of the main potential causes for turnovers, namely the accumulation of deleterious mutations on nonrecombining chromosomes. Sibship analyses show that LG1 recombination is strongly reduced in males from most species investigated, including some in which it is autosomal. Intrinsically low male recombination might facilitate the evolution of male heterogamety, and the presence of important genes from the sex-determination cascade might predispose LG1 to become a sex chromosome.

Molecular mechanism of a green-shifted, pH-dependent red fluorescent protein mKate variant.

Fluorescent proteins that can switch between distinct colors have contributed significantly to modern biomedical imaging technologies and molecular cell biology. Here we report the identification and biochemical analysis of a green-shifted red fluorescent protein variant GmKate, produced by the introduction of two mutations into mKate. Although the mutations decrease the overall brightness of the protein, GmKate is subject to pH-dependent, reversible green-to-red color conversion. At physiological pH, GmKate absorbs blue light (445 nm) and emits green fluorescence (525 nm). At pH above 9.0, GmKate absorbs 598 nm light and emits 646 nm, far-red fluorescence, similar to its sequence homolog mNeptune. Based on optical spectra and crystal structures of GmKate in its green and red states, the reversible color transition is attributed to the different protonation states of the cis-chromophore, an interpretation that was confirmed by quantum chemical calculations. Crystal structures reveal potential hydrogen bond networks around the chromophore that may facilitate the protonation switch, and indicate a molecular basis for the unusual bathochromic shift observed at high pH. This study provides mechanistic insights into the color tuning of mKate variants, which may aid the development of green-to-red color-convertible fluorescent sensors, and suggests GmKate as a prototype of genetically encoded pH sensors for biological studies.

Spontaneous cell polarization: Feedback control of Cdc42 GTPase breaks cellular symmetry.

Spontaneous polarization without spatial cues, or symmetry breaking, is a fundamental problem of spatial organization in biological systems. This question has been extensively studied using yeast models, which revealed the central role of the small GTPase switch Cdc42. Active Cdc42-GTP forms a coherent patch at the cell cortex, thought to result from amplification of a small initial stochastic inhomogeneity through positive feedback mechanisms, which induces cell polarization. Here, I review and discuss the mechanisms of Cdc42 activity self-amplification and dynamic turnover. A robust Cdc42 patch is formed through the combined effects of Cdc42 activity promoting its own activation and active Cdc42-GTP displaying reduced membrane detachment and lateral diffusion compared to inactive Cdc42-GDP. I argue the role of the actin cytoskeleton in symmetry breaking is not primarily to transport Cdc42 to the active site. Finally, negative feedback and competition mechanisms serve to control the number of polarization sites.

Signs of a vector's adaptive choice: on the evasion of infectious hosts and parasite-induced mortality

Laboratory and field experiments have demonstrated in many cases that malaria vectors do not feed randomly, but show important preferences either for infected or non-infected hosts. These preferences are likely in part shaped by the costs imposed by the parasites on both their vertebrate and dipteran hosts. However, the effect of changes in vector behaviour on actual parasite transmission remains a debated issue. We used the natural associations between a malaria-like parasite Polychromophilus murinus, the bat fly Nycteribia kolenatii and a vertebrate host the Daubenton's bat Myotis daubentonii to test the vector's feeding preference based on the host's infection status using two different approaches: 1) controlled behavioural assays in the laboratory where bat flies could choose between a pair of hosts; 2) natural bat fly abundance data from wild-caught bats, serving as an approximation of realised feeding preference of the bat flies. Hosts with the fewest infectious stages of the parasite were most attractive to the bat flies that did switch in the behavioural assay. In line with the hypothesis of costs imposed by parasites on their vectors, bat flies carrying parasites had higher mortality. However, in wild populations, bat flies were found feeding more based on the bat's body condition, rather than its infection level. Though the absolute frequency of host switches performed by the bat flies during the assays was low, in the context of potential parasite transmission they were extremely high. The decreased survival of infected bat flies suggests that the preference for less infected hosts is an adaptive trait. Nonetheless, other ecological processes ultimately determine the vector's biting rate and thus transmission. Inherent vector preferences therefore play only a marginal role in parasite transmission in the field. The ecological processes rather than preferences per se need to be identified for successful epidemiological predictions.