Selectome update: quality control and computational improvements to a database of positive selection.

Selectome (http://selectome.unil.ch/) is a database of positive selection, based on a branch-site likelihood test. This model estimates the number of nonsynonymous substitutions (dN) and synonymous substitutions (dS) to evaluate the variation in selective pressure (dN/dS ratio) over branches and over sites. Since the original release of Selectome, we have benchmarked and implemented a thorough quality control procedure on multiple sequence alignments, aiming to provide minimum false-positive results. We have also improved the computational efficiency of the branch-site test implementation, allowing larger data sets and more frequent updates. Release 6 of Selectome includes all gene trees from Ensembl for Primates and Glires, as well as a large set of vertebrate gene trees. A total of 6810 gene trees have some evidence of positive selection. Finally, the web interface has been improved to be more responsive and to facilitate searches and browsing.

A circuit-based gatekeeper for adult neural stem cell proliferation: Parvalbumin-expressing interneurons of the dentate gyrus control the activation and proliferation of quiescent adult neural stem cells.

Newborn neurons are generated in the adult hippocampus from a pool of self-renewing stem cells located in the subgranular zone (SGZ) of the dentate gyrus. Their activation, proliferation, and maturation depend on a host of environmental and cellular factors but, until recently, the contribution of local neuronal circuitry to this process was relatively unknown. In their recent publication, Song and colleagues have uncovered a novel circuit-based mechanism by which release of the neurotransmitter, γ-aminobutyric acid (GABA), from parvalbumin-expressing (PV) interneurons, can hold radial glia-like (RGL) stem cells of the adult SGZ in a quiescent state. This tonic GABAergic signal, dependent upon the activation of γ(2) subunit-containing GABA(A) receptors of RGL stem cells, can thus prevent their proliferation and subsequent maturation or return them to quiescence if previously activated. PV interneurons are thus capable of suppressing neurogenesis during periods of high network activity and facilitating neurogenesis when network activity is low.

Calcium Microdomains Control Exo-Endocytosis of Synaptic-Like Microvesicles in Astrocytes

During the last decade, the discovery that astrocytes possess a nonelectrical form of excitability (Ca21-excitability) that leads to the release of chemical transmitters, an activity called ''gliotransmission'', indicates that these cells may have additional important roles in brain function. Elucidating the stimulus-secretion coupling leading to the exocytic release of chemical transmitters (such as glutamate, Bezzi et al., Nature Neurosci, 2004) may therefore clarify i) whether astrocytes represent in full a new class of secretory cells in the brain and ii) whether they can participate to the fast brain signaling in the brain. Here by using a recently developed approach for studying vesicle recycling dynamics at synapses (Voglmaier et al., Neuron, 2006; Balaji and Ryan, PNAS, 2007) combined with epifluorescence and total internal reflection fluorescence (TIRF) imaging, we investigated the spatiotemporal characteristics of stimulus-secretion coupling leading glutamate exocytosis of synaptic-like microvesicles (SLMVs) in astrocytes. We performed the analysis at both the whole-cell and single-vesicle levels providing the first system for comparing exo-endocytic processes in astrocytes with those in neurons. Both the time course and modalities of secretion in astrocytes present more similarities to neurons then previously expected. We found that 1. the G-protein-coupled receptor (GPCR)-evoked exocytosis reached the maximum on a ms time scale and that 2. ER tubuli formed sub-micrometer domains beneath the plasma membrane in close proximity to exocytic vesicles, where fusion events were spatiotemporally correlated with fast Ca21 events.

Antibacterial burst-release from minimal Ag-containing plasma polymer coatings.

Biomaterials releasing silver (Ag) are of interest because of their ability to inhibit pathogenic bacteria including antibiotic-resistant strains. In order to investigate the potential of nanometre-thick Ag polymer (Ag/amino-hydrocarbon) nanocomposite plasma coatings, we studied a comprehensive range of factors such as the plasma deposition process and Ag cation release as well as the antibacterial and cytocompatible properties. The nanocomposite coatings released most bound Ag within the first day of immersion in water yielding an antibacterial burst. The release kinetics correlated with the inhibitory effects on the pathogens Pseudomonas aeruginosa or Staphylococcus aureus and on animal cells that were in contact with these coatings. We identified a unique range of Ag content that provided an effective antibacterial peak release, followed by cytocompatible conditions soon thereafter. The control of the in situ growth conditions for Ag nanoparticles in the polymer matrix offers the possibility to produce customized coatings that initially release sufficient quantities of Ag ions to produce a strong adjacent antibacterial effect, and at the same time exhibit a rapidly decaying Ag content to provide surface cytocompatibility within hours/days. This approach seems to be favourable with respect to implant surfaces and possible Ag-resistance/tolerance built-up.

Functional Microdomains Control Glutamate Exocytosis from Astrocytes

The discovery that astrocytes possess a non-electrical form of excitability (Ca21-excitability) that leads to the release of chemical transmitters, an activity called ''gliotransmission'', indicates that these cells may have additional important roles in brain function. Elucidating the stimulus-secretion coupling leading to the exocytic release of chemical transmitters (such as glutamate, Bezzi et al., Nature Neurosci, 2004) may therefore clarify i) whether astrocytes represent in full a new class of secretory cells in the brain and ii) whether they can participate to the fast brain signaling in the brain. We have recently discovered the existence in astrocytes of functional sub-membrane microdomains of Ca21 release from the internal stores in response to mGluR5 activation (Marchaland et al., J of Neurosci., 2008). Such Ca21 microdomains control exocytosis of astrocytic glutamate signalling to neurons. Homer proteins are scaffold proteins controlling Ca21 signalling in different cellular microdomains, including dendritic spines in neurons (Sala et al., J of Neurosci., 2005). Thus, similarly to dendritic pines, Homer1 could be implicated in the coupling between astrocytic mGluR5 and IP3Rs on the ER. Here, by using a recently developed approach for studying vesicle recycling dynamics at synapses (Voglmaier et al., Neuron, 2006; Balaji and Ryan, PNAS, 2007) combined with epifluorescence and total internal reflection fluorescence (TIRF) imaging, we have investigated the involvement of Homer1 proteins in the Ca21-dependent stimulus-secretion coupling leading glutamate exocytosis of synaptic-like microvesicles (SLMVs) in astrocytes.

High speed release -mittausmenetelmän käyttäminen tarralaminaattiprosessin ohjaukses

Työn tavoitteena oli tutkia HSR(High Speed Release)-mittausmenetelmän käyttämistä tarralaminaattiprosessin ohjauksessa UPM Raflatacissa. Nykyisin käytössä olevaan LSR(Low Speed Release)-menetelmään verrattuna HSR-menetelmä kuvaa paremmin tarralaminaatin jatkojalostuksessa sekä etiketöinnissä tapahtuvaa irrotustyötä. Lisäksi työssä tutkittiin irrotusnopeuden vaikutusta HSR-arvoon. Työn kirjallisuusosassa perehdyttiin tarralaminaatin rakenteeseensekä valmistusprosessiin. Koska silikonin valinnalla on merkittävä vaikutus tarralaminaatin releasearvoon, kirjallisessa osassa syvennytään tarkastelemaan tarralaminaatin valmistuksessa käytettyjä silikoneja sekänäiden rakennetta. Kirjallisuusosassa on myös käsitelty muita releasetasoon vaikuttavia tekijöitä. Työn kokeellisessa osassa oli tarkoituksena tutkia HSR-mittausmenetelmän käytettävyyttä tarralaminaatin prosessinohjauksessa. Tätä tutkittiin selvittämällä nykyisin käytössä olevan LSR-menetelmän sekä HSR-menetelmän välistä korreloituvuutta. Mikäli näidenvälillä olisi korreloituvuutta, voitaisiin prosessinohjauksessa ajatella siirtyvän HSR-mittaukseen. Korrelaatiota näiden kahden menetelmän välille ei kuitenkaan löydetty. Työssä tutkittiin myös irrotusnopeuden vaikutusta tuotteen HSR-arvoon. Testeihin valittiin useita eri tuotteita useilta tuotantolaitoksilta. Kaikilla näillä tuotteilla releasearvo kasvoi irrotusnopeutta lisättäessä. Lisäksi työssä määritettiin uudet HSR-spesifikaatiot tietyille tuotteille. Kaikille UPM Raflatacin tuotteille on määritetty LSRspesifikaatiot, HSR-spesifikaatiot on asetettu vain tietyille tuotteille.

Formation and Control of Trace Metal Emissions in Co-Firing of Biomass, Peat, and Wastes in Fluidised Bed Combustors

Environmentally harmful consequences of fossil fuel utilisation andthe landfilling of wastes have increased the interest among the energy producers to consider the use of alternative fuels like wood fuels and Refuse-Derived Fuels, RDFs. The fluidised bed technology that allows the flexible use of a variety of different fuels is commonly used at small- and medium-sized power plants ofmunicipalities and industry in Finland. Since there is only one mass-burn plantcurrently in operation in the country and no intention to build new ones, the co-firing of pre-processed wastes in fluidised bed boilers has become the most generally applied waste-to-energy concept in Finland. The recently validated EU Directive on Incineration of Wastes aims to mitigate environmentally harmful pollutants of waste incineration and co-incineration of wastes with conventional fuels. Apart from gaseous flue gas pollutants and dust, the emissions of toxic tracemetals are limited. The implementation of the Directive's restrictions in the Finnish legislation is assumed to limit the co-firing of waste fuels, due to the insufficient reduction of the regulated air pollutants in the existing flue gas cleaning devices. Trace metals emission formation and reduction in the ESP, the condensing wet scrubber, the fabric filter, and the humidification reactor were studied, experimentally, in full- and pilot-scale combustors utilising the bubbling fluidised bed technology, and, theoretically, by means of reactor model calculations. The core of the model is a thermodynamic equilibrium analysis. The experiments were carried out with wood chips, sawdust, and peat, and their refuse-derived fuel, RDF, blends. In all, ten different fuels or fuel blends were tested. Relatively high concentrations of trace metals in RDFs compared to the concentrations of these metals in wood fuels increased the trace metal concentrations in the flue gas after the boiler ten- to hundred-folds, when RDF was co-fired with sawdust in a full-scale BFB boiler. In the case of peat, lesser increase in trace metal concentrations was observed, due to the higher initial trace metal concentrations of peat compared to sawdust. Despite the high removal rate of most of the trace metals in the ESP, the Directive emission limits for trace metals were exceeded in each of the RDF co-firing tests. The dominat trace metals in fluegas after the ESP were Cu, Pb and Mn. In the condensing wet scrubber, the flue gas trace metal emissions were reduced below the Directive emission limits, whenRDF pellet was used as a co-firing fuel together with sawdust and peat. High chlorine content of the RDFs enhanced the mercuric chloride formation and hence the mercury removal in the ESP and scrubber. Mercury emissions were lower than theDirective emission limit for total Hg, 0.05 mg/Nm3, in all full-scale co-firingtests already in the flue gas after the ESP. The pilot-scale experiments with aBFB combustor equipped with a fabric filter revealed that the fabric filter alone is able to reduce the trace metal concentrations, including mercury, in the flue gas during the RDF co-firing approximately to the same level as they are during the wood chip firing. Lower trace metal emissions than the Directive limits were easily reached even with a 40% thermal share of RDF co-firing with sawdust.Enrichment of trace metals in the submicron fly ash particle fraction because of RDF co-firing was not observed in the test runs where sawdust was used as the main fuel. The combustion of RDF pellets with peat caused an enrichment of As, Cd, Co, Pb, Sb, and V in the submicron particle mode. Accumulation and release oftrace metals in the bed material was examined by means of a bed material analysis, mass balance calculations and a reactor model. Lead, zinc and copper were found to have a tendency to be accumulated in the bed material but also to have a tendency to be released from the bed material into the combustion gases, if the combustion conditions were changed. The concentration of the trace metal in the combustion gases of the bubbling fluidised bed boiler was found to be a summary of trace metal fluxes from three main sources. They were (1) the trace metal flux from the burning fuel particle (2) the trace metal flux from the ash in the bed, and (3) the trace metal flux from the active alkali metal layer on the sand (and ash) particles in the bed. The amount of chlorine in the system, the combustion temperature, the fuel ash composition and the saturation state of the bed material in regard to trace metals were discovered to be key factors affecting therelease process. During the co-firing of waste fuels with variable amounts of e.g. ash and chlorine, it is extremely important to consider the possible ongoingaccumulation and/or release of the trace metals in the bed, when determining the flue gas trace metal emissions. If the state of the combustion process in regard to trace metals accumulation and/or release in the bed material is not known,it may happen that emissions from the bed material rather than the combustion of the fuel in question are measured and reported.

In vivo co-ordinated interactions between inhibitory systems to control glutamate mediated hippocampal excitability.

We present an overview of the long-term adaptation of hippocampal neurotransmission to cholinergic and GABAergic deafferentation caused by excitotoxic lesion of the medial septum. Two months after septal microinjection of 2.7 nmol a -amino-3-hydroxy-5-methylisoxazole-4-propionate (AMPA), a 220% increase of GABA A receptor labelling in the hippo- campal CA3 and the hilus was shown, and also changes in hippocampal neurotransmission characterised by in vivo microdialysis and HPLC. Basal amino acid and purine extra- cellular levels were studied in control and lesioned rats. In vivo effects of 100 m M KCl perfusion and adenosine A 1 receptor blockade with 1,3-dipropyl- 8-cyclopentylxanthine (DPCPX) on their release were also investigated. In lesioned animals GABA, glutamate and glutamine basal levels were decreased and taurine, adenosine and uric acid levels increased. A similar response to KCl infusion occurred in both groups except for GABA and glutamate, which release decreased in lesioned rats. Only in lesioned rats, DPCPX increased GABA basal level and KCl-induced glutamate release, and decreased glutamate turnover. Our results evidence that an excitotoxic septal lesion leads to increased hippocampal GABA A receptors and decreased glutamate neurotransmis- sion. In this situation, a co-ordinated response of hippocampal retaliatory systems takes place to control neuron excitability.

Losartan potassium dissolution test for drug release evaluation in pharmaceutical capsules using HPLC and UV spectrophotometry

This work describes the development and validation of a dissolution test for 50 mg losartan potassium capsules using HPLC and UV spectrophotometry. A 2(4) full factorial design was carried out to optimize dissolution conditions and potassium phosphate buffer, pH 6.8 as dissolution medium, basket as apparatus at the stirring speed of 50 rpm and time of 30 min were considered adequate. Both dissolution procedure and analytical methods were validated and a statistical analysis showed that there are no significant differences between HPLC and spectrophotometry. Since there is no official monograph, this dissolution test could be applied for quality control routine.

Weed control under integrated nutrient management systems in faba bean (Vicia faba) production in Egypt

Two field experiments were conducted in two successive seasons, 2005/2006 and 2006/2007, to determine whether management can improve faba bean competitiveness with weeds, thus helping to achieve its yield potential. The experiment included five treatments, composed of organic and mineral fertilizers, alone and mixed at different rates, along with a control and six weed control treatments, including oxadiargyl, prometryn, hand hoeing treatments alone or mixed with the herbicides, and a nonweeded treatment (control).The herbicide treatments were not superior to the two hand-hoeing treatments. Using compost favored growth and yield of faba bean more than of weeds. Adding fertilizer also improved most yield parameters. Application of compost alone or combined with 50 or 100% of the recommended NPK rate improved faba bean growth in terms of net assimilation rate, specific leaf area, and leaf weight ratio as components of relative growth rate. This improvement in growth resulted in increase of seed yield, yield components and protein of faba bean. Faba bean yield performance improved under interactive fertilizer effects and weed control treatments as growth improved, as a result of nutrient release from fertilizers and weed control.

Effects of iron-ore particles on propagule release, growth and photosynthetic performance of Sargassum vulgare C. Agardh (Phaeophyta, Fucales)

The effect of iron-ore particles on the propagule release and growth of Sargassum vulgare C. Agardh was tested under treatments with different concentrations of iron-ore particles: 0.1, 1.0, 10.0 g.L-1 and a solution of 10.0 g.L-1 of filtered iron-ore. Filtered seawater was used as control. Photosynthesis vs. irradiance (P-I) curves were calculated for S. vulgare in the presence of iron-ore and in seawater. There was no significant difference in the number of propagules released by the receptacles or in the percentage of zygote formation among the treatments. The released propagules acted like aggregation centers for the particles, those more heavily coated with iron (10.0 g.L-1) exhibiting the highest sinking velocity (32.6 ± 9.8 mm.s-1). No difference in the percentage of embryo survival was detected during the first week in culture. After four weeks the embryos grew in all treatments. Maximum frond development (5.3 ± 0.8 mm) was observed in treatment of seawater enriched with Provasoli's medium (PES) while initial filoids did not develop in three treatments without PES and with iron-ore (0.1 g.L-1, 1.0 g.L-1 and 10.0 g.L-1). The values for Pmax, alpha and respiration showed no significant differences between the P-I curves. The calculated value for I K was 106.26 µmol.m-2.s-1 to the control curve and 981.49 µmol.m-2.s-1 to the iron-ore curve. The results indicate that the iron-ore particles in high concentration reduce the growth of S. vulgare as they recovered the embryos, juveniles and young plants. In contrast, the presence of the particles did not affect the release of gametes, percentage of zygote formation or the percentage of embryo survival.

The myth of nitric oxide in central cardiovascular control by the nucleus tractus solitarii

Considerable evidence suggests that nitroxidergic mechanisms in the nucleus tractus solitarii (NTS) participate in cardiovascular reflex control. Much of that evidence, being based on responses to nitric oxide precursors or inhibitors of nitric oxide synthesis, has been indirect and circumstantial. We sought to directly determine cardiovascular responses to nitric oxide donors microinjected into the NTS and to determine if traditional receptor mechanisms might account for responses to certain of these donors in the central nervous system. Anesthetized adult Sprague Dawley rats that were instrumented for recording arterial pressure and heart rate were used in the physiological studies. Microinjection of nitric oxide itself into the NTS did not produce any cardiovascular responses and injection of sodium nitroprusside elicited minimal depressor responses. The S-nitrosothiols, S-nitrosoglutathione (GSNO), S-nitrosoacetylpenicillamine (SNAP), and S-nitroso-D-cysteine (D-SNC) produced no significant cardiovascular responses while injection of S-nitroso-L-cysteine (L-SNC) elicited brisk, dose-dependent depressor and bradycardic responses. In contrast, injection of glyceryl trinitrate elicited minimal pressor responses without associated changes in heart rate. It is unlikely that the responses to L-SNC were dependent on release of nitric oxide in that 1) the responses were not affected by injection of oxyhemoglobin or an inhibitor of nitric oxide synthesis prior to injection of L-SNC and 2) L- and D-SNC released identical amounts of nitric oxide when exposed to brain tissue homogenates. Although GSNO did not independently affect blood pressure, its injection attenuated responses to subsequent injection of L-SNC. Furthermore, radioligand binding studies suggested that in rat brain synaptosomes there is a saturable binding site for GSNO that is displaced from that site by L-SNC. The studies suggest that S-nitrosocysteine, not nitric oxide, may be an interneuronal messenger for cardiovascular neurons in the NTS

Role of the hypothalamic pituitary adrenal axis in the control of the response to stress and infection

The release of adrenocorticotropin (ACTH) from the corticotrophs is controlled principally by vasopressin and corticotropin-releasing hormone (CRH). Oxytocin may augment the release of ACTH under certain conditions, whereas atrial natriuretic peptide acts as a corticotropin release-inhibiting factor to inhibit ACTH release by direct action on the pituitary. Glucocorticoids act on their receptors within the hypothalamus and anterior pituitary gland to suppress the release of vasopressin and CRH and the release of ACTH in response to these neuropeptides. CRH neurons in the paraventricular nucleus also project to the cerebral cortex and subcortical regions and to the locus ceruleus (LC) in the brain stem. Cortical influences via the limbic system and possibly the LC augment CRH release during emotional stress, whereas peripheral input by pain and other sensory impulses to the LC causes stimulation of the noradrenergic neurons located there that project their axons to the CRH neurons stimulating them by alpha-adrenergic receptors. A muscarinic cholinergic receptor is interposed between the alpha-receptors and nitric oxidergic interneurons which release nitric oxide that activates CRH release by activation of cyclic guanosine monophosphate, cyclooxygenase, lipoxygenase and epoxygenase. Vasopressin release during stress may be similarly mediated. Vasopressin augments the release of CRH from the hypothalamus and also augments the action of CRH on the pituitary. CRH exerts a positive ultrashort loop feedback to stimulate its own release during stress, possibly by stimulating the LC noradrenergic neurons whose axons project to the paraventricular nucleus to augment the release of CRH.

Neuroendocrine control of body fluid homeostasis

Angiotensin II and atrial natriuretic peptide (ANP) play important and opposite roles in the control of water and salt intake, with angiotensin II promoting the intake of both and ANP inhibiting the intake of both. Following blood volume expansion, baroreceptor input to the brainstem induces the release of ANP within the hypothalamus that releases oxytocin (OT) that acts on its receptors in the heart to cause the release of ANP. ANP activates guanylyl cyclase that converts guanosine triphosphate into cyclic guanosine monophosphate (cGMP). cGMP activates protein kinase G that reduces heart rate and force of contraction, decreasing cardiac output. ANP acts similarly to induce vasodilation. The intrinsic OT system in the heart and vascular system augments the effects of circulating OT to cause a rapid reduction in effective circulating blood volume. Furthermore, natriuresis is rapidly induced by the action of ANP on its tubular guanylyl cyclase receptors, resulting in the production of cGMP that closes Na+ channels. The OT released by volume expansion also acts on its tubular receptors to activate nitric oxide synthase. The nitric oxide released activates guanylyl cyclase leading to the production of cGMP that also closes Na+ channels, thereby augmenting the natriuretic effect of ANP. The natriuresis induced by cGMP finally causes blood volume to return to normal. At the same time, the ANP released acts centrally to decrease water and salt intake.

A brain microdialysis study on 5-HT release in freely moving rat lines selectively bred for differential 5-HT1A receptor function

Breeding for high and low hypothermic responses to systemic administration of a serotonin1A (5-HT1A) receptor agonist (8-hydroxy-2-(di-n-propylamino)tetralin, 8-OH-DPAT) has resulted in high DPAT-sensitive (HDS) and low DPAT-sensitive (LDS) lines of rats, respectively. These lines also differ in several behavioral measures associated with stress. In the present microdialysis study we observed that basal 5-HT concentrations in the prefrontal cortex and dorsal hippocampus did not differ significantly between HDS and LDS rats. Thus, behavioral differences between the HDS and LDS lines might not be attributed to differences in basal 5-HT release. However, both lines had lower basal levels of 5-HT release than their randomly bred control group (random DPAT-sensitive, RDS) in the prefrontal cortex (mean ± SEM, pg/20 µl, was 3.0 ± 0.4 for LDS, 3.8 ± 0.3 for HDS and 6.4 ± 0.6 for RDS; F(2,59) = 5.8, P<0.005). The administration of (±)-fenfluramine (10 mg/kg) induced a greater increase in hippocampal 5-HT levels in HDS rats (500%) as compared with LDS (248%) or RDS (243%) rats (P<0.0001). There were no significant differences in the prefrontal cortex among lines, with a fenfluramine-induced 5-HT increase of about 900% in the three groups. This differential response to fenfluramine may be due to functional alterations of hippocampal 5-HT reuptake sites in the HDS line.