1,721,017 research outputs found
Proton translocation coupled to electron transfer reactions in terminal oxidases
No full textTerminal oxidases are the final proteins of the respiratory chain in eukaryotes and some bacteria. They catalyze most of the biological oxygen consumption on Earth done by aerobic organisms. During the catalytic reaction terminal oxidases reduce dioxygen to water and use the energy released in this process to maintain the electrochemical proton gradient by functioning as a redox-driven proton pump. This membrane gradient of protons is extremely important for cells as it is used for many cellular processes, such as transportation of substrates and ATP synthesis. Even though the structures of several terminal oxidases are known, they are not sufficient in themselves to explain the molecular mechanism of proton pumping. In this work we have applied a complex approach using a variety of different techniques to address the properties and the mechanism of proton translocation by the terminal oxidases. The combination of direct measurements of pH changes during catalytic turnover, time-resolved potentiometric electrometry and optical spectroscopy, made it possible to obtain valuable information about various aspects of oxidase functioning.
We compared oxygen binding properties of terminal oxidases from the distinct heme-copper (CcO) and cytochrome bd families and found that cytochrome bd has a high affinity for oxygen, which is 3 orders of magnitude higher than that of CcO. Interestingly, the difference between CcO and cytochrome bd is not only in higher affinity of the latter to oxygen, but also in the way that each of these enzymes traps oxygen during catalysis. CcO traps oxygen kinetically - the molecule of bound dioxygen is rapidly reduced before it can dissociate. Alternatively, cytochrome bd employs an alternative mechanism of oxygen trapping - part of the redox energy is invested into tight oxygen binding, and the price paid for this is the lack of proton pumping.
A single cycle of oxygen reduction to water is characterized by translocation of four protons across the membrane. Our results make it possible to assign the pumping steps to discrete transitions of the catalytic cycle and indicate that during in vivo turnover of the oxidase these four protons are transferred, one at a time, during the P→F, F→OH, Oh→Eh, and Eh→R transitions. At the same time, each individual proton translocation step in the catalytic cycle is not just a single reaction catalyzed by CcO, but rather a complicated sequence of interdependent electron and proton transfers. We assume that each single proton translocation cycle of CcO is assured by internal proton transfer from the conserved Glu-278 to an as yet unidentified pump site above the hemes. Delivery of a proton to the pump site serves as a driving reaction that forces the proton translocation cycle to continue.Terminaaliset oksidaasit ovat eukaryoottien ja joidenkin bakteerien hengitysketjujen viimeisiä proteiineja. Ne katalysoivat suurinta osaa aerobisten organismien biologisesta hapenkulutuksesta maapallolla. Katalyyttisen reaktion aikana terminaaliset oksidaasit pelkistävät molekulaarisen hapen vedeksi ja käyttävät prosessissa vapautuneen energian ylläpitääkseen elektrokemiallista protonigradienttia toimimalla protonipumppuina. Tämä protonien muodostama membraanigradientti on äärimmäisen tärkeä soluille, koska sitä käytetään hyväksi monissa solun toiminnoissa kuten substraattien kuljetuksessa ja ATP synteesissä. Vaikka useiden terminaalisten oksidaasien rakenteet tunnetaan, ne eivät itsessään riitä selittämään protonin pumppauksen molekulaarista mekanismia. Tässä työssä olemme käyttäneet monitahoista lähestymistapaa käyttäen erilaisia tekniikoita tutkiaksemme terminaalisten oksidaasien ominaisuuksia ja protonin pumppauksen mekanismia. Katalyyttisen reaktion aikana tapahtuvien pH:n muutosten mittaaminen sekä aikaerotteisen potentiometrisen elektrometrian ja optisen spektroskopian yhdistelmä mahdollisti arvokkaan tiedon keräämisen oksidaasien toiminnan eri osa-alueista.
Me kykenimme vertailemaan terminaalisten oksidaasien hapensitomisominaisuuksia hemi-kuparioksidaasi ja bd-oksidaasi entsyymiperheiden välillä ja havaitsimme, että kyseiset proteiinit käyttävät erilaisia mekanismeja hapen sitomisessa. Hemi-kupari oksidaasit sitovat hapen kineettisesti - sitoutunut happimolekyyli pelkistetään nopeasti ennen kuin se ehtii irrota aktiivisesta keskuksesta, kun taas bd-oksidaasi käyttää hapetus-pelkistus energiaa hapen tiukkaan sitomiseen, ja on siten kykenemätön pumppaamaan protoneja.
Yhden happimolekyylin pelkistäminen vedeksi mahdollistaa neljän protonin pumppaamisen kalvon yli. Tuloksemme mahdollistavat katalyyttisen kierron eri vaiheiden ja yksittäisten protoninpumppaus tapahtumien yhteen sovittamisen. Jokainen katalyyttisen kierron protonin pumppaus reaktio ei ole vain yksi entsyymin katalysoima reaktio, pikemminkin monimutkainen toisistaan riippuvaisten elektronin ja protonin siirtojen sarja. Oletamme, että jokainen protonin pumppaus reaktio varmistetaan proteiinin sisäisellä protoninsiirto reaktiolla vakioisesta glutamaatti tähteestä vielä tuntemattomaan pumppaus kohtaan . Protonin saapuminen pumppaus kohtaan toimii reaktion liikkeelle panevana voimana, joka pakottaa protonin pumppaus syklin jatkumaan.ei saavutettav
Large Spots DeepMIB project, synthetic dataset for testing 2D semantic segmentation
No full text<p>A complete DeepMIB project with a synthetic dataset generated for quick tests of semantic segmentation approaches.<br>The dataset includes a trained DeepLabV3-Resnet18 network for detection of large spots on a black background. </p><p>The network can be opened by loading "2D_LargeSpots_2cl_DeepLabV3.mibCfg" file by</p><ul><li><i>MIB->Menu->Tools->Deep learning segmentation->Options tab->Config files->Load </i></li><li>Drag and drop of the config file into DeepMIB window</li></ul><p> </p>
Large Spots DeepMIB project, synthetic dataset for testing 2D semantic segmentation
No full text<p>A complete DeepMIB project with a synthetic dataset generated for quick tests of semantic segmentation approaches.<br>The dataset includes a trained DeepLabV3-Resnet18 network for detection of large spots on a black background. </p><p>The network can be opened by loading "2D_LargeSpots_2cl_DeepLabV3.mibCfg" file by</p><ul><li><i>MIB->Menu->Tools->Deep learning segmentation->Options tab->Config files->Load </i></li><li>Drag and drop of the config file into DeepMIB window</li></ul><p> </p>
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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