Miracle-dz/UniFAR-FTUs huggingface dataset:
Caractérisation biochimique et fonctionnelle de glutathion-S-transferases (GSTs) chez Phanerochaete chrysosporium

Phanerochaete chrysosporium est un champignon ligninolytique largement etudie pour ses capacites a degrader la lignine et certains xenobiotiques grâce a un important systeme d'enzymes extracellulaires. Son genome est entierement sequence et constitue un inventaire de sequences proteiques predites qui a permis la description de nombreuses superfamilles de proteines. Parmi elles, les Glutathion S-transferases sont essentiellement impliquees dans le metabolisme secondaire du champignon. Cependant, malgre les nombreux travaux montrant l'implication de ces enzymes dans la reponse aux stress, le developpement cellulaire et plus globalement dans certaines fonctions metaboliques, leurs reelles fonctions restent inconnues a cause de leur grande diversite et le manque de donnees concernant leurs specificites catalytiques. P. chrysosporium possede 27 isoformes de GSTs qui se regroupent en 7 classes. Parmi elles, 3 sont etendues chez les champignons saprophytes : les classes Omega, Ure2p et etherase. Deux membres de la classe Omega ont ete caracterises au niveau biochimique et montrent des specificites de substrat. En effet, PcGTO1 fait partie d'une nouvelle classe appelee S-glutathionyl-phydroquinone reductase, alors que PcGTO3 est plutot active avec le phenylacetophenone. La structure tridimensionnelle de PcGTO1 suggere que l'enzyme appartient egalement a une nouvelle classe structurale que nous avons appelee xi. La deuxieme classe majoritaire que nous avons etudiee est la classe des Ure2p qui est composee de 9 isoformes et se regroupent en 2 sous-classes. Trois isoformes ont ete etudiees au niveau transcriptionnel, biochimique et physiologique. PcUre2p4 et PcUre2p6 appartenant a la premiere sous-classe sont specifiquement exprimes dans des cultures fongiques en presence d'hydrocarbures aromatiques polycycliques et l'activite des proteines recombinantes correspondantes est classique des GSTs a savoir le transfert de glutathion sur un substrat hydrophobe. A l'inverse, PcUre2p1 qui appartient a la deuxieme sous-classe est exprime de maniere constitutive au niveau transcriptionnel et la proteine presente une activite thiol transferase comparable aux proteines de la classe Omega. Les analyses physiologiques menees grâce a la complementation de souche deficience de Saccharomyces cerevisiae ont montre que PcUre2p1, PcUre2p4 et PcUre2p6 n'avaient pas la meme fonction que l'isoforme de la levure puisqu'aucune complementation n'a ete detectee en ce qui concerne la resistance au stress ou la regulation du metabolisme azote. Ces resultats suggerent que les champignons, en particulier ceux qui presentent des proprietes saprophytes ont developpe des specificites de fonction de leur GSTs probablement en reponse a des contraintes environnementales.
Lipopolysaccharide Lewis Antigens

As determined by serological techniques, the O-antigen of lipopolysaccharide (LPS) of more than 80% of Helicobacter pylori strains tested worldwide express Lewis blood group antigens. Several host lectins are known to interact with host Lewis antigens; the same lectins may interact with H. pylori Lewis antigens. This chapter discusses phase variation of H. pylori LPS, including LPS biosynthesis and genetics; the biological significance of Lewis antigen mimicry; and the role of Lewis antigens in interactions of H. pylori with host lectins. Antigastric autoantibodies present in sera of H. pylori-infected patients are directed to gastric parietal canaliculi, but absorption with H. pylori does not diminish autoantibody reactivity. Selection and outgrowth of H. pylori Lex/y LPS variants would be driven by anti-Lex/y antibodies, and these are not found in infected patients. Studies on the biological role of H. pylori Lewis antigens have largely taken place through insertional mutagenesis of LPS biosynthesis genes. In summary, the mechanisms of H. pylori LPS phase variation are known in detail; knowledge of the biological role of Lewis antigens and phase variation therein is in its infancy, but a role in adhesion seems likely.
Adaptive immune response inhibits ectopic mature bone formation induced by BMSCs/BCP/plasma composite in immune-competent mice.

A combination of autologous bone marrow stromal cells (BMSCs) and biomaterials is a strategy largely developed in bone tissue engineering, and subcutaneous implantation in rodents or large animals is often a first step to evaluate the potential of new biomaterials. This study aimed at investigating the influence of the immune status of the recipient animal on BMSCs-induced bone formation. BMSCs prepared from C57BL/6 mice, composed of a mixture of mesenchymal stromal and monocytic cells, were combined with a biomaterial that consisted of biphasic calcium phosphate (BCP) particles and plasma clot. This composite was implanted subcutaneously either in syngenic C57BL/6 immune-competent mice or in T-lymphocyte-deficient Nude (Nude) mice. Using histology, immunohistochemistry, and histomorphometry, we show here that this BMSC/BCP/plasma clot composite implanted in Nude mice induces the formation of mature lamellar bone associated to hematopoietic areas and numerous vessels. Comparatively, implantation in C57BL/.
Ataxin-7 SUMOylation and its functional consequences in the spinocerebellar ataxia type 7 (SCA7) pathophysiology

Spinocerebellar ataxia type 7 (SCA7) is a neurodegenerative disease caused by a CAG expansion (polyQ) in the protein ataxin-7. SUMOylation, a post-translational modification that we identified to modulate mutant protein aggregation in a SCA7 cellular model, is facilitated by a SUMO E3 ligase. Here, we identified RanBP2 (Nup358), a nucleoporin belonging to the nuclear pore complex, as the major E3 enzyme implicated in ataxin-7 modification by SUMO-1. Indeed, RanBP2 silencing renders mutant ataxin-7 more prone to aggregation, thus demonstrating the implication of RanBP2 in SCA7 pathophysiology. We also show that endogenous ataxin-7 is a target for both SUMO-1 and -2 modification. Poly-SUMOylated ataxin-7 presents a docking site composed of SUMO2/3 chains for the recruitment of RNF4: this protein is a SUMO E3 ubiquitin ligase that mediates degradation of mutant ataxin-7 by the proteasome pathway. The degradation is abolished in presence of a mutant form of RNF4. In a SCA7 knock-in mouse model we quantified expression of SUMO-pathway related genes in cerebellum and retina, the most affected regions using quantitative RT-PCR. SUMO-related genes show expanded repeat-dependent alterations in expression patterns. At 6 months (before onset), deregulations begin to occur; by 12 months (late stage of disease), there is a statistically significant impairment in Sumo-1 levels in Atxn7100Q/5Q cerebellum. These results, together with the observation that SUMO-1 and RanBP2 protein accumulate abnormally in the cerebellum of a SCA7 patient, suggest that in vivo SUMO-modifying pathways may be perturbed in SCA7.
An investigation of the role of Notch signalling in germ cell development using mouse embryonic stem cells

xvii Chapter 1. Introduction. 18 1.1 Germ cell development: an overview.18 1.2 Spermatogenesis . 22 1.3 Notch signalling pathway.28 1.4 Research objectives . 34 Chapter 2. Materials and Methods. 35 2.1 Standard molecular biology techniques . 36 2.2 Histological techniques . 45 2.3 Animal techniques.48 2.4 Cell culture . 49 2.5 Computational analysis . 52 Chapter 3. Analysis of Notch signalling components in spermatogenesis . 53 3.
Reloading the revolver – male fitness as a simple explanation for complex reward partitioning in Nasa macrothyrsa (Loasaceae, Cornales)

Reward partitioning and replenishment and specific mechanisms for pollen presentation are all geared towards the maximization of the number of effective pollinator visits to individual flowers. An extreme case of an apparently highly specialized plant‐pollinator interaction with thigmonastic pollen presentation has been described for the morphologically complex tilt-revolver flowers of Caiophora arechavaletae (Loasaceae) pollinated by oligolectic Bicolletes pampeana (Colletidae, Hymenoptera). We studied the floral biology of Nasa macrothyrsa (Loasaceae) in the field and in the glasshouse, which has very similar floral morphology, but is pollinated by polylectic Neoxylocopa bees (Apidae, Hymenoptera). We investigated the presence of thigmonastic anther presentation, visitor behaviour (pollinators and nectar robbers), co-ordination of pollinator visits with flower behaviour and the presence of nectar replenishment. The aim of this study was to understand whether complex flower morphology and behaviour can be explained by a specialized pollination syndrome, or whether alternative explanations can be offered. The results showed that Nasa macrothyrsa has thigmonastic pollen presentation, i.e. new pollen is rapidly (<< 10 min) presented after a pollinator visit. Nectar secretion is independent of removal and averages 7‐14 m Lh ‐1 . The complex flowers, however, fail to exclude either native (hummingbirds) or introduced (honeybees) nectar robbers, nor does polylectic Neoxylocopa actively collect the pollen presented. The findings do not support a causal link between complex flower morphology and functionality in Loasaceae and a highly specialized pollination. Rapid pollen presentation is best explained by the pollen presentation theory: the large proportion of pollinators coming shortly after a previous visit find little nectar and are more likely to move on to a different plant. The rapid presentation of pollen ensures that all these valuable ‘hungry pollinators’ are dusted with small pollen loads, thus increasing the male fitness of the plant by increasing the likelihood of siring outcrossed offspring. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100, 124‐131.
Effect of microbial phytase on performance and apparent digestibility of amino acids in male broiler chickens

Effect of microbial phytase on performance and apparent digestibility of amino acids in male broiler chickens A. Hassanabadi, H. Nassiri Moghaddam and H. Kermanshahi 1 Department of Animal Science, college of Agriculture, University of Zanjan, Zanjan, Iran, Email: ha_ahmad@yahoo.com 2 Department of Animal Science, college of Agriculture, Ferdowsi University of Mashhad, P.O. Box 91775-1163, Mashhad, Iran.
Improving Traffic Participant Safety using Connected Active Safety Techniques and Collective Perception

The concurrent development of advanced driver assistance systems (ADAS), intelligent infrastructure, and vehicle-to-everything (V2X) collective perception messages (CPM) provide both means and structure for connected active safety that can benefit not only the occupants of newer vehicles, but also vulnerable road users (VRUs) and those in vehicles that are not equipped with the latest technologies.
Parentage determination in the freshwater prawn Macrobrachium rosenbergii De Man, 1879 using microsatellite markers

Macrobrachium rosenbergii is an important cultured species in India and other tropical and sub-tropical countries. Selective breeding and genetic improvement of this species poses a big challenge, due to the problems associated in the identification of the pedigree. Physical tagging of the progeny for pedigree identification is costly, and it takes long time and induces bias in the estimation of genetic parameters. Microsatellites are commonly used to detect parents and their offsprings in wild and captive populations, to assign parentage. In the present study. a total of 1788 specimens comprising 160 offsprings and 18 female parents were used for pedigree assigning. Four M. rosenbergii microsatelIites were selected for parentage assignment and CERVUS-3.0 software was used to determine the parentage. The average number of alleles per microsatellite marker was 3, with the allele size ranging from 184 to 246 bp, the polymorphic information content (PIC) was 0.412 and the observed average heterozygosity was 0.548. The combined exclusion probabilities for the first and second parent were 0.422 and 0.640, respectively. The success of assigning the offsprings to one parent was 69.23%. Results of the present study indicates that microsatellites can be employed to identify the parentage in M. rosenbergii. However, the number of loci needed and the type of microsatellites, needs to be standardised further for enhancing the rate of success.
Renal accumulation of macrophages in experimental polycystic kidney disease is reduced by bindarit

Renal interstitial accumulation of monocytes/macrophages driven by chemoattractants such as monocyte chemoattractant protein-1 (MCP-1)/CCL2, is a characteristic feature of polycistic kidney diseases (PKD). It has been suggested that infiltrating inflammatory cells contribute to promoting cyst growth and renal function impairment in PKD. Recently, we reported that in experimental PKD in PCK rats, bindarit, an inhibitor of MCP-1, effectively decreased the excessive renal expression of MCP-1, and limited interstitial infiltrates of monocytes/macrophages. The anti-MCP-1 therapy displayed an important antiproteinuric effect associated with amelioration of podocyte structure. In this highlight we describe bindarit’s effects on the evolution of PKD in PCK rats and on the activity of the drug in cultured podocytes to explain its antiproteinuric effect.
Bioclimatic evaluation of geographical range in Fragaria (Rosaceae): consequences of variation in breeding system, ploidy and species age

The evaluation of the intrinsic and extrinsic forces that determine geographical range sizes and niche breadth is key to the understanding of species distributions and for informing the conservation of biodiversity. Fragaria (Rosaceae) contains the economically important cultivated strawberry (Fragaria × ananassa subsp. ananassa) and numerous wild species. Using georeferenced species records and global bioclimatic data, we describe the bioclimatic niches for 21 Fragaria spp. and investigate the relationship between their niches and geographical range size, breeding system, ploidy and time since divergence. We found no evidence of phylogenetic signal for bioclimatic niches. There was also no relationship between ploidy and geographical or bioclimatic range area, but geographical range area was significantly greater for species that were capable of self-fertilization. In addition, we found a significant decelerating relationship between species age and geographical range area. Overall, our results suggest that Fragaria spp. , although similar in morphology and life history, show high levels of divergence in bioclimatic niches and significant over-dispersion along some bioclimatic gradients, suggesting evolutionary lability in physiology and climate tolerance. As a consequence, wild species will remain a valuable resource for cultivated strawberry sustainability, especially under changing future climate. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176, 99–114.
POBREZA AGRARIA Y SHOCK DE INGRESOS EN PUNO: UN ANÁLISIS EN BASE A LA ENAHO

En este artículo se analiza la evolución de la pobreza monetaria en las unidades de agricultura familiar en Puno para el periodo 2007 al 2015 en base a datos de la ENAHO. La importante reducción de pobreza en la región entre 2007 y 2012 empieza a detenerse en 2013, y entre 2014 y 2015 se observa por primera vez un aumento en la tasa de pobreza general y en la de los hogares agropecuarios. Dada la forma que toma este incremento de pobreza, planteamos que se habría originado en un shock negativo de ingresos en las zonas urbanas afectadas por la desaceleración económica, el cual ha tenido efectos adversos en los ingresos agropecuarios, especialmente de los más articulados al mercado. Adicionalmente, generamos una estimación tipo Probit para analizar el perfil de pobreza de los hogares agropecuarios de Puno de acuerdo a características como rango de edad y tamaño, lengua materna, género y educación del jefe de hogar, entre otras variables. El análisis sugiere algunos temas a incorporar a la agenda de políticas para reducir de manera más efectiva y sostenible la pobreza en el campo de Puno en los próximos años.
Effect of umbilical cord blood regulatory T cells on natural killer cell differentiation and function

Graft versus Host Disease (GvHD) remains one of the main complications after haematopoietic stem cell transplantation (HSCT). Due to their ability to suppress effector cells, CD4+CD25highFoxp3high regulatory T (Treg) cells have been proposed as a cellular therapy to prevent GvHD. However it has been shown that Treg cells can inhibit natural killer (NK) cell functions. NK cells are key effectors of the Graft versus Leukaemia (GvL) effect post-transplant; therefore, it is plausible that a Treg cell therapy may impact on NK cell function and differentiation from haematopoietic stem cells (HSC). This study sought to elucidate the effects of Treg cells on NK cell function and differentiation using umbilical cord blood (CB) as a cell source. Herein, it is confirmed that CB CD4+CD25highFoxp3high Treg cells are fully functional and upon TCR-stimulation express CTLA-4 and LAP, and secrete TGF-β and IL-10. Also, they express receptors associated with trafficking to lymphoid tissues and the bone marrow, which are potential NK cell/Treg cell interaction sites. Furthermore, it is shown that CB Treg cells can suppress CB NK cell functions after TCR-stimulation in steady state but not in the presence of exogenous cytokines. Lastly, in an in vitro model of NK cell differentiation, a 90% reduction in total NK cells was observed when TCR-stimulated Treg cells were added at the time when HSC commitment to the NK cell lineage occurs. Interestingly, the few NK cells that developed in these cultures showed normal phenotype, IFN-γ secretion and cytotoxicity. Notably, the addition of human recombinant TGF-β to HSC cultures caused a similar reduction in NK cell differentiation as shown when TCRstimulated Treg cells were added to HSC cultures. Moreover, the Treg cellmediated effect was contact-dependent and cytokine competition-independent. Collectively, these results demonstrate for the first time that TCR-stimulated CB Treg cells inhibit NK cell differentiation through TGF-β, providing information for optimisation of the time of delivery for an adoptive Treg cell therapy post-HSCT to prevent GvHD.
Tree diversity enhances tree transpiration in a Panamanian forest plantation

Summary 1. Tree plantations play an important role in meeting the growing demand for wood, but there is concern about their high rates of water use. Recent approaches to reforestation in the tropics involve the establishment of multispecies plantations, but few studies have compared water use in mixed vs. monospecific stands. 2. We hypothesized that tree species diversity enhances stand transpiration. Tree water use rates were estimated in monocultures (n = 5), two-species mixtures (n = 3), three-species mixtures (n = 3) and five-species mixtures (n = 4). Sap flux densities were monitored with thermal dissipation probes in 60 trees for 1 year in a 7-year-old native tree plantation in Panama. We also estimated changes in the amount of wood produced per unit water transpired (i.e. water use efficiency, WUEwood). 3. Annual stand transpiration rates in two- ⁄ three-species mixtures (464 ± 271 mm year )1 )a nd five-species mixtures (900 ± 76 mm year )1 ) were 14% and 56% higher than those of monocultures (398 ± 293 mm year )1 ), respectively. Trees growing in mixtures had larger diameters, conductive sapwood and basal area than those in monocultures, which partly explained the enhanced stand transpiration in mixtures. 4. The five-species mixtures maintained equally high stand transpiration rates during wet (2AE64 ± 0AE30 mm day )1 ) and dry seasons (2AE51 ± 0AE21 mm day )1 ), whereas monocultures and two-species mixtures had significantly lower transpiration rates during the dry season, because of the presence of dry season deciduous species. 5. The WUEwood of the five-species mixtures (2AE1 g DM kg )1 H2O) was about half that of either monocultures, two- or three-species mixtures. 6. The comparably high stand transpiration rates in the five-species plots may arise from enhanced vegetation-atmosphere-energy exchange through higher canopy roughness and ⁄ or complementary use of soil water. 7. Synthesis and applications. Stand transpiration increased linearly with tree species richness and basal area in monocultures, two- and three-species mixtures, but the ratio of stand transpiration to basal area was larger for five-species mixtures. In conclusion, species selection and consideration of species richness and composition is crucial in the design of plantations to maximize wood production while conserving water resources.
The molecular and functional genetics of Bardet-Biedl Syndrome

Bardet-Biedl Syndrome (BBS) is a rare genetic disease comprising obesity, retinal dystrophy, Polydactyly and renal abnormalities. When this study began there were six known loci for BBS, only one of which, BBS6, had been identified. The initial aims of the project were to find BBS genes by screening of candidate genes within the known intervals and performing a genome wide screen using previously unlinked patients. During the time of this project three of the known BBS loci {lcub}BBSI, 2 and 4) have been identified and a further two novel genes (BBS7 and 8) have also been cloned. BBS was previously thought to be a recessive disease, but through mutation screening of all BBS genes in our cohort of 160 patients we have found evidence for complex inheritance involving the requirement for three mutations a homozygous mutation in one BBS gene and a further heterozygous mutation at a second BBS locus, to manifest disease in some families. As a quick and cheap alternative to sequencing for mutation detection, I developed the technique of multiplex capillary heteroduplex analysis (MCHA) which is now in routine use for screening new BBS cases. To determine the possible function of the BBS4 protein, a yeast-two-hybrid screen was undertaken to identify interactors of BBS4. Pericentriolar Material 1 (PCM1), one of the potential interactors, also co-localises with the protein at the centriolar satellites of centrosomes and basal bodies of primary cilia. The BBS8 protein, which shares homology with BBS4 also localises to the basal body and, from immunohistochemistry experiments using the BBS8 antibody, has been shown to be expressed in ciliated tissues such as kidney, retina, brain and spermatids, implicating basal body dysfunction in the aetiology of BBS. During the course of my studies, we have progressed from a handful of genetic loci to the determination of the putative protein function which may pave the way to the design of future therapies.