Біблійні концепти і проповідницька традиція української літератури (на прикладі концепту води)

Clinical mastitis (CM) can be caused by a wide variety of pathogens and a farmer has to start treatment before the actual causal pathogen is known. Knowing the Gram-status of CM cases would aid in the decision for the most appropriate treatment. By providing a probability distribution for the Gram-status, rather than only providing the most likely Gram-status, the involved uncertainty is visible for a farmer, thereby allowing a more informed treatment decision. The objective of this study was to examine the value of providing probability distributions for the Gram-status of CM cases to a farmer to take a more informed treatment decision. A naive Bayesian network (NBN) based on data from 274 Dutch dairy herds in which the occurrence of CM was recorded over an 18-month period was constructed. The dataset contained 3,534 CM cases, all classified accordingto their Gram-status. Two-third of the dataset was used for the construction and one-third was retained for validation. Information usually available at a dairy farm was included in the NBN under construction (parity, month in lactation, season of the year, quarter position, somatic cell count history and CM history, being sick or not, and color and texture of the milk). For getting insight in the quality of the constructed NBN, the accuracy was determined. The accuracy of classifying CM cases into Gram-positive or Gram-negative pathogens was 73%. Because only CM cases with a high probability for Gram-negative or Gram-positive pathogens will be considered for specific treatment, it was interesting to have a closer look at CM cases with probabilities > 0.90. We foundthat the accuracy of the classification increased with the calculated probability for Gram-negative or Gram-positive pathogens. The probability distributions for the Gram-status provide the farmer with considerable additional information about the most likely Gram-status of a CM case and the uncertainty involved

Genetic associations for pathogen-specific clinical mastitis and patterns of peaks in somatic cell count

Genetic associations were estimated between pathogen-specific cases of clinical mastitis (CM), lactational average somatic cell score (LACSCS), and patterns of peaks in somatic cell count (SCC) which were based on deviations from the typical lactation curve for SCC. The dataset contained test-day records on SCC in 94 781 lactations of 25416 cows of different parities. Out of these 94 781 lactations, 41 828 lactations had recordings on occurrence of pathogen-specific CM and on SCC, and 52 953 lactations had recordings on SCC only. A total of 5 324 lactations with cases of CM were recorded. Analysed pathogens were Staphylococcus aureus, coagulase negative staphylococci, Escherichia coli, Streptococcus dysgalactiae, Streptococcus uberis, and culture-negative samples. Pattern definitions were based on three or five consecutive test-day recordings of SCC. They differentiated between short or longer periods of increased SCC, and also between lactations with and without recovery. Occurrence of pathogen-specific CM and presence of patterns of peaks in SCC were both scored as binary traits. Variance components for sire, maternal grandsire, and permanent animal effects were estimated using AS-REML. The estimated heritability for overall CM was 0.04, and similar heritabilities for pathogen-specific CM were estimated. Heritabilities for the patterns of peaks in SCC ranged from 0.01 to 0.06. Heritabilities for LACSCS were 0.07 to 0.08. Genetic correlations with patterns of peaks in SCC differed for each pathogen. Generally, genetic correlations between pathogen-specific CM and patterns of peaks in SCC were stronger than the correlations with LACSCS. This suggests that genetic selection purely on diminishing presence of peaks in SCC would decrease the incidence of pathogen-specific CM more effectively than selecting purely on lower LACSC

Influence of Ser and Thr residues in the geometry of transmembrane helices : implications on the structure and function of G protein-coupled receptors

Consultable des del TDXTítol obtingut de la portada digitalitzadaEn aquesta tesi s'apliquen eines bioinformàtiques a l'estudi de determinats sistemes biològics. En particular, l'estudi teòric de la influència de determinats aminoàcids sobre l'estructura i la dinàmica dels elements d'estructura secundària de les proteïnes s'aplica a la modelització per homologia dels receptors acoblats a proteïna G (GPCRs) i a l'estudi dels seus mecanismes d'activació. Se sap que determinats residus, com prolina, serina o treonina, provoquen distorsions locals en l'estructura de les hèlices a. L'anàlisi de bases de dades de seqüències de segments transmembrana mostra com certes combinacions d'aquests residus són més comunes que d'altres, i que algunes d'elles estan sobre-representades de manera significativa, mentre que d'altres estan clarament sots-representades. La restricció d'aquesta anàlisi de seqüències a la regió transmembrana dels GPCRs de la Classe A mostra com aquestes combinacions es troben en posicions específiques i, a més, es troben conservades en certes subfamílies de receptors. L'estructura i la dinàmica de les hèlices transmembrana que contenen aquestes combinacions de prolina i serina o treonina s'han estudiat mitjançant simulacions de dinàmica molecular en un entorn hidrofòbic explícit. Els resultats mostren com algunes d'aquestes combinacions indueixen distorsions importants en l'estructura de l'hèlix a, degut al seu efecte desestabilitzador de la xarxa de ponts d'hidrogen que dóna estabilitat a l'hèlix. Aquests resultats s'han aplicat a la construcció d'un model tridimensional del receptor de quimiocines CCR5 , utilitzant tècniques de modelització molecular per homologia. En aquest model es proposa que les hèlices transmembrana (TMH) 2 i 3 del receptor CCR5 són estructuralment diferents del patró de rodopsina. TMH2 està més doblegada degut a la presència d'un motiu Thr-X-Pro, que, a més, fa que aquesta hèlix es doblegui cap a TMH3. Així doncs, es proposa que, en aquest receptor, aquestes dues hèlices interaccionen. Aquesta interacció estaria mediada per la presència de residus hidrofòbics conservats i específics en les dues hèlices. Aquestes hipòtesis han estat posades a prova mitjançant experiments de mutagènesi dirigida, gràcies a la col·laboració amb l'Institut de Recherche Interdisciplinaire en Biologie Humaine et Nucléaire (IRIBHN), Université Libre de Bruxelles. Els resultats experimentals permeten establir la hipòtesi que la interfície TMH2-TMH3 participa en l'activació induïda per quimiocines del receptor CCR5. Com a conclusió, aquesta tesi pretén mostrar com, mitjançant la utilització d'eines bioinformàtiques, és possible traduir les seqüències primàries de proteïnes i les interaccions a nivell atòmic en estructures tridimensionals de proteïnes. A més, aquesta tesi mostra que, encara que l'estructura tridimensional de la rodopsina bovina és un patró útil per la modelització per homologia de GPCRs, s'han de tenir en compte de manera explícita les especificitats de seqüència de cada receptor per tal de construir models de receptors particulars. Aquestes especificitats de seqüència consisteixen en patrons de seqüència conservats en determinades famílies, que es tradueixen en divergències estructurals. Entre aquests patrons de seqüència, es proposa que els residus de serina i treonina, sols o combinats amb residus de prolina propers, poden modular la geometria de les TMHs, degut a la seva capacitat d'interferir amb la xarxa de ponts d'hidrogen que dóna estabilitat a les hèlices a. Finalment, es proposa que la influència dels motius de serina, treonina i prolina en l'estructura de les TMHs pot estar relacionada amb els processos d'activació dels GPCRs de la Classe A i, possiblement, d'altres proteïnes de membrana. En els GPCRs, aquests motius poden haver evolucionat per tal d'adaptar uns mecanismes d'activació conservats als lligands característics de cada família de receptors.This thesis is framed in the study of particular biological systems through the use of bioinformatics. In particular, the theoretical study of the influence of certain amino acids on the structure and dynamics of the secondary structure elements of proteins has been applied to homology modelling of G protein-coupled receptors (GPCRs) and to the study of their mechanisms of activation. Certain residues, as proline, serine or threonine, are known to induce local distortions in the a-helical structure. Analysis of sequence databases of transmembrane segments evidence that certain combinations of these residues are more common than others, and that some of them are significantly over-represented, while others are clearly under-represented. The focusing this sequence analysis on the transmembrane region of Class A GPCRs illustrates that these combinations are located in some specific locations and conserved within certain subfamilies of receptors. The structure and dynamics of transmembrane a-helices containing these combinations of proline and serine or threonine have been studied using molecular dynamics simulations in an explicit hydrophobic environment. The results show how some of these combinations induce significant distortions in the a-helical structure, due to their effect on the hydrogen bond network that stabilizes the helix. These results have been applied to the building of a three-dimensional model of the chemokine CCR5 receptor, using homology modelling techniques. In this model, transmembrane helices (TMH) 2 and 3 of CCR5 are proposed to be different from the bovine rhodopsin template. TMH2 is more bent due to the presence of a Thr-X-Pro motif, which, in turn, induces this helix to lean towards TMH3. As a consequence, an interaction between these two helices is proposed for this particular receptor. This interaction would be mediated through the presence of specific and conserved hydrophobic and aromatic residues in both helices. These hypothesis have been tested through site-directed mutagenesis experiments, thanks to a collaboration with the Institut de Recherche Interdisciplinaire en Biologie Humaine et Nucléaire (IRIBHN), Université Libre de Bruxelles. The experimental results let us to hypothesize that the TMH2-TMH3 interface is involved in the chemokine-induced activation of the CCR5 receptor. As a conclusion, this thesis aims to show how through the use of bioinformatics tools, primary sequences of proteins and interactions at an atomic level can be translated to three-dimensional protein structures. In addition, this thesis illustrates that, even though the three-dimensional structure of bovine rhodopsin is a very useful template for homology modelling of GPCRs, the sequence specificities of each receptor have to be explicitly taken into account in order to build models. These sequence specificities consist in sequence patterns conserved within certain families, which are translated into structural divergences. Among these sequence patterns, we hypothesize that serine and threonine, alone or combined with nearby proline residues, can modulate the geometry of TMHs, due to its capability to interfere with the hydrogen bond network that stabilize a-helices. Finally, we propose that the influence of serine, threonine and proline motifs in the structure of TMHs may be related to processes of activation in the Class A of GPCRs, and, possibly, other membrane proteins as well. In GPCRs, these motifs may have evolved in order to adapt a conserved mechanism of activation of the G protein to the cognate ligands of each receptor family

Knowledge gaps that hamper prevention and control of Mycobacterium avium subspecies paratuberculosis infection

In the last decades, many regional and country‐wide control programmes for Johne's disease (JD) were developed due to associated economic losses, or because of a possible association with Crohn's disease. These control programmes were often not successful, partly because management protocols were not followed, including the introduction of infected replacement cattle, because tests to identify infected animals were unreliable, and uptake by farmers was not high enough because of a perceived low return on investment. In the absence of a cure or effective commercial vaccines, control of JD is currently primarily based on herd management strategies to avoid infection of cattle and restrict within‐farm and farm‐to‐farm transmission. Although JD control programmes have been implemented in most developed countries, lessons learned from JD prevention and control programmes are underreported. Also, JD control programmes are typically evaluated in a limited number of herds and the duration of the study is less than 5 year, making it difficult to adequately assess the efficacy of control programmes. In this manuscript, we identify the most important gaps in knowledge hampering JD prevention and control programmes, including vaccination and diagnostics. Secondly, we discuss directions that research should take to address those knowledge gaps.http://wileyonlinelibrary.com/journal/tbed2019-05-01hj2018Veterinary Tropical Disease