Miracle-dz/UniFAR-FTUs huggingface dataset:
Importance of release location on the mode of action of butyrate derivatives in the avian gastrointestinal tract

In the field of animal nutrition, butyrate is used as a zootechnical ingredient and can be used as an unprotected salt or in the form of protected derivatives such as butyrate glycerides or butyrate-loaded matrices. Dietary butyrate supplementation has been shown to improve growth performance and resilience of broiler chickens through distinct mechanisms, operating on both eukaryotic and prokaryotic cells. Firstly, butyrate influences endogenous avian cells in multiple ways: it is an agonist of free-fatty acid receptors, an inhibitor of pro-inflammatory pathways, an epigenetic modulating agent and acts as an energy source. Secondly, butyrate influences the microbiota residing in the avian gastrointestinal tract (GIT) as a result of its bacteriostatic properties. The responses, e.g. changes in growth performance, gut morphology, carcass traits or nutrient digestibility of chickens, to dietary butyrate supplementation are inconsistent with factors such as additive inclusion level, diet composition, age and health status of the bird modulating the effects of butyrate and its derivatives. For many derivatives, the precise GIT segment wherein butyrate is released is unclear. Release location may affect the observed responses to butyrate given the diversity of cell types and pH conditions encountered throughout the gastrointestinal tract of poultry, and the differences in microbiota composition in the different gut segments. As a consequence, our understanding of the mode of action of butyrate is hampered. Characterisation of existing derivatives and development of targeted-release formulations are, therefore, important to gain insight in the different physiological effects butyrate can elicit in broiler chickens.
Genetic diversity of antagonistic bacteria against sheath blight and bakanae rice disease by RAPD

In this research genetic diversity of 19 antagonistic bacterial strains were isolated from rice field contaminated with Rhizoctonia solani and Fusarium moniliforme. Based on morphological, biochemical, physiological and pathogenicity characteristics, total cellular protein profiles (SDS-PAGE) and PCR with specific primers the antagonistic strains were identified. The antagonistic strains of R.solani included B4, B6, B17, B18, B22, B24, B41 and B42 and that of F.moniliforme included F1, F6, F12, F15, F16, F18, F21, F24 were identified as Pseudomonas fluorescens and F14, F19, F32 and F35 were identified as Bacillus cereus. Out of fifteen RAPD primers, five primers were selected based on their ability to amplify all antagonistic strains. Twenteen strains were grouped based on RAPD analysis. Intra population gen diversity and distributed genetic diversity were assessed by POPGENE software. Nei’s genetic distance for A, B and C population is 0.22, 0.28 and 0.29 respectively. RAPD analysis revealed that strains B18 and F12 formed distinict group compared to other strains and showed maximum similarity with B24 and F18 strains. Other strains were placed in separated subgroups. Strains B41 and B6 showed maximum genetic distance. Molecular analysis using PCR based RAPD method is thus useful to differentiate such strains at the intra specific level.
Inhibition of skin tumors in DMBA-induced complete carcinogenesis system in mice by garlic (Allium sativum).

The chemopreventive action of garlic extract on DMBA-induced complete skin carcinogenesis system was studied in random bred, 6-7 weeks old, male Swiss albino mice. Topical weekly application of DMBA for 25 weeks at two dose levels, i.e. 200 nmol during the first week followed by 100 nmol during subsequent weeks, or 400 nmol during the first week followed by 200 nmol during subsequent weeks, resulted in 73.9% and 100% tumor incidences respectively. When garlic extract was topically applied twice daily for 3 days every week prior to above-stated dose schedules of DMBA, the incidences of tumors were reduced to 31.8% (P less than 0.01) and 43.4% (P less than 0.01) respectively.
ASPP2 regulating p63/p73 and Notch pathways in tumourigenesis

The skin is where two of the most common types of epithelial cancer, basal cell carcinoma (BCC) and squamous cell carcinoma (SCC), arise. In this work, we have investigated how ASPP2, a member of a family of proteins that interact with the p53 family, can affect skin tumourigenesis. We analysed the regulation of ASPP2 in pathways involved in the normal homeostasis of the epithelium, such as the p63 and Notch. Aberrant or misplaced activation of ΔNp63 in the epithelium is a known initiating cause for SCC and our results indicate that ASPP2 is important in limiting ΔNp63 expression in the differentiated epithelium, preventing cell proliferation in the skin. Additionally, we found that ASPP2 can cooperate with skin pro-differentiation pathways, such as Notch and p73. Overall, our results indicate a possible mechanism by which p63 expression can be regulated in the skin, and provide a new model for the spontaneous formation of SCC.
Développement d’une méthode bio-informatique permettant de relier les gènes aux métabolites

ii! Table des matières . iii! Liste des tableaux . vii! Liste des figures . viii! Liste des documents spéciaux . ix! Liste des sigles et abréviations . x! Remerciements . xii! Avant-Propos . xv! 1! Introduction . 1! 1.1! Dogme central de la biologie moléculaire . 1! 1.1.1! Avancées du dogme . 2! 1.2! Génomique . 4! 1.2.1! Variants génétiques et génome . 5! 1.2.2! Plateformes d’analyse . 6! 1.2.2.1! Génotypage par puce . 6! 1.2.2. 2! Séquençage . 7! Sanger . 7! Séquençage de nouvelle génération . 8! 1.2. 3! Études d’association pangénomique . 8! 1.2. 4! Applications de la génomique . 9! 1.2. 4.1! Traits monogéniques . 9! 1.2. 4.2! Traits complexes . 10! 1.3! Métabolomique . 11! 1.3. 1! Métabolites et métabolome . 11! 1.3. 2! Design expérimental . 14! 1.3. 2.1! Approches . 15!
Effect of red blood cell stroma on the reticuloendothelial system clearance and killing of Streptococcus pneumoniae.

Previous studies from this laboratory have shown that thermal injury can cause sufficient intravascular hemolysis to depress reticuloendothelial system (RES) phagocytic function and that the injection of red blood cell (RBC) stroma depresses RES function and increases susceptibility to experimental shock. The present study evaluated the effect of thermal injury and RBC stroma on susceptibility to infection with Streptococcus pneumoniae as well as the effect of RBC stroma on the RES clearance and killing of the bacteria. The mortality rate following pneumococcal infection was increased after thermal injury from 0% to 100% (P less than .01), and with the injection of RBC stroma (0.5 ml/100 g) mortality increased from 20% to 80% (P less than .01). Hepatic uptake of heat-killed S. pneumoniae was depressed from 64% to 44% of the injected dose following the injection of RBC stroma. RBC stroma depressed complement CH50 levels by 31%. The reduction in the number of viable S. pneumoniae present in the liver between 30 min and 4 hr following bacterial challenge was decreased in animals receiving RBC stroma. This was interpreted as an indication of impaired hepatic bactericidal function and was associated with an increase in the number of circulating viable S. pneumoniae. It is concluded that the increased susceptibility to pneumococcal infection induced by RBC stroma was probably due to an impairment in hepatic clearance and killing of the bacteria. The depressed bacterial clearance could have been contributed to by the stroma-induced decrease in complement levels. This study further supports the hypothesis that the intravascular hemolysis caused by thermal injury contributes to the increased susceptibility to infection following this form of injury.
Distribution, movements, and habitat use of small striped bass (Morone saxatilis) across multiple spatial scales

Distribution, movements, and habitat use of small (<46 cm, juveniles and individuals of unknown maturity) striped bass (Morone saxatilis) were investigated with multiple techniques and at multiple spatial scales (surveys and tag-recapture in the estuary and ocean, and telemetry in the estuary) over multiple years to determine the frequency and duration of use of non-natal estuaries. These unique comparisons suggest, at least in New Jersey, that smaller individuals (<20 cm) may disperse from natal estuaries and arrive in non-natal estuaries early in life and take up residence for several years. During this period of estuarine residence, individuals spend all seasons primarily in the low salinity portions of the estuary. At larger sizes, they then leave these non-natal estuaries to begin coastal migrations with those individuals from nurseries in natal estuaries. These composite observations of frequency and duration of habitat use indicate that non-natal estuaries may provide important habitat for a portion of the striped bass population.
Effects of neutrophil-mediated pulmonary endothelial injury on the localization and metastasis of circulating Walker carcinosarcoma cells.

: The lung, a frequent site of cancer metastases, is also a susceptible target in several models of endothelial injury. In previous studies we have demonstrated that such injury, induced by bleomycin or by exposure to high concentrations of atmospheric oxygen, can facilitate the localization and metastasis of circulating tumor cells. Here we have tested the hypothesis that neutrophil-mediated injury to pulmonary endothelium has a similar effect. In Sprague-Dawley rats, intravenous injection of cobra venom factor resulted in complement activation, rapid sequestration of neutrophils in the lung, and endothelial damage, demonstrated by morphology, and by increased protein content and leakage of intravenous 125I-albumin into bronchoalveolar lavage fluids. When 125I-iododeoxyuridine-labeled Walker carcinosarcoma cells were injected intravenously during the period of endothelial injury, the pulmonary capillaries contained aggregates of neutrophils and tumor cells 2 h later, and there was a 3-fold increase in pulmonary tumor cell localization after 24 h in treated animals, compared to controls. Enhancement of tumor cell localization was prevented by pretreatment of the rats with catalase or by antineutrophil antisera. When animals were examined 2 weeks after cell injection, treatment groups had significantly more metastatic tumor nodules and a greater area of lung tissue involved by metastatic tumors. We conclude that neutrophil-mediated damage to the pulmonary endothelium can significantly increase the trapping of circulating tumor cells, and is likely to be clinically important since the large vascular bed of the lung is susceptible to host-mediated injury.
The roles of vaccinia virus proteins in kinesin-dependent microtubule transport.

Vaccinia virus is a good model system for studying host cell biology and enhancing our understanding of microtubule-based transport. Whilst the key viral proteins involved in microtubule-based transport of intracellular enveloped virus (IEV) have been identified, their exact mechanistic relationship to each other and to microtubule motor proteins has not been fully established. This thesis aims to address how the viral protein F12L and kinesin-1 are recruited to IEV particles and how the viral proteins A33R and A36R are also involved in this process. It is known that the movement of IEV particles, from the perinuclear viral factories to the plasma membrane, is microtubule-dependent and involves the A36R protein as well as the recruitment of kinesin-l. At the plasma membrane, actin tail formation has been shown to be dependent on phosphorylation of A36R. However, A36R is dependent upon an interaction with the A33R protein in order to be recruited to the virion. It has also been shown that A33R is heavily phosphorylated at serine residues but its role is currently unknown. The initial part of my studies examined the potential role of phosphorylation of A33R and its effect on viral egress. No effect on viral transport was observed upon dephosphorylation of A33R. The viral protein F12L also has a proposed role in microtubule-dependent transport, as an accumulation of particles is observed in the region of the viral factories and transport to the cell surface does not occur in the absence of the protein. However, the mode of interaction of F12L with IEV and its association with kinesin-l is unclear. The precise structure of F12L is also unknown. In order to investigate the relationship between F12L, A36R, A33R and kinesin-l, a new range of tools was developed, including: a F12L antibody, GFP-F12L fusion constructs, deletion mutants to determine which regions of F12L are involved in virus transport, constructs to investigate whether F12L undergoes any post-translational modification event(s), as well as designing F12L and A33R recombinant viruses. No direct interaction has been established between F12L and A36R, or A33R, or kinesin-l.
Microhabitat use and social structure in Linnet Carduelis cannabina and Corn Bunting Miliaria calandra at a winter roost in central Spain

Capsule Both species selected particular patches for roosting, and Linnets but not Corn Buntings showed a social structure with males occupying the preferred roosting positions. Aims To evaluate microhabitat preferences of Linnet and Corn Bunting within a winter communal roost, and to examine roost structure according to sex, age and body size. Methods We captured Linnets and Corn Buntings along a habitat gradient in a reed-bed in central Spain when they were coming to roost. Each bird was sexed, aged, and several body traits were measured. We also characterized the habitat patches where the birds were trapped and grouped patches according to their similarity. Results Three groups of patches were defined according to reed structure. Linnets preferred patches with low density of high and thick shoots, while Corn Buntings preferably used patches with intermediate values for these variables. Interspecific competition for preferred positions was not evident. Male Linnets were proportionately more abundant in the preferred patches, and individuals in lower body condition, independent of sex, age or body size, occupied the non-preferred patches. Male Corn Buntings were less abundant, bigger in size, and showed better condition than females, although differences in body size and condition were not apparent among patches within the roost. Conclusion Our results suggest that among-patch differences in structure and location within a reed-bed generate microhabitats that differ in quality for roosting passerines. This habitat heterogeneity in turn seems to be responsible for the social spatial structure observed in Linnets, in which females and individuals in poor physiological condition were displaced, possibly through competition, towards non-preferred positions. The relatively small body size of Linnets compared to Corn Buntings might explain Linnets' preference for patches that seem to provide more protection against harsh weather conditions.
MicroglialVEGFReceptorResponseIsanIntegral ChemotacticComponentinAlzheimer'sDiseasePathology

We hypothesize that microglial chemotactic responses to amyloid- peptide (A1‐42) serve as an early and integral component of inflammatoryresponseinAlzheimer’sdisease(AD)brain.Thisstudyreportsareceptorforvascularendothelialgrowthfactor(VEGF), termed VEGF-1 (Flt-1), subserves microglial chemotactic responses induced by A1‐42 stimulation, in vivo and in vitro. Expression of Flt-1 was significantly increased in tissue obtained from AD patients [compared with tissue from nondemented (ND) individuals], in A1‐42-injectedrathippocampus,andinpeptide-stimulatedhumanmicroglia.Singleanddoubleimmunohistochemicalstainingdemonstratedmarkedimmunoreactivity,forbothFlt-1anditsligandVEGF,inassociationwithmicrogliaandAdepositsinAD,butnotND, brain tissue. Functionally, treatment with anti-Flt-1 antibody was highly effective in inhibiting microglial mobility and chemotactic responsesmeasuredinvitrousingatranswellmigrationassay.Invivo,transplantedenhancedgreenfluorescentprotein(EGFP)-labeled microglia exhibited Flt-1-dependent chemotaxis induced by peptide injection with anti-Flt-1 effective in blocking migration of cells. Importantly, anti-Flt-1 reduction of microglial mobility was neuroprotective in peptide-injected hippocampus and associated with a significant increase in numbers of viable hippocampal neurons. The results of this study suggest critical functional roles for Flt-1 in mediatingmicroglialchemotacticinflammatoryresponseswhichcontributetopathologicalconditionsinADbrain.
The discovery and structural requirements of inhibitors of p-hydroxyphenylpyruvate dioxygenase

The benzoylcyclohexane-1,3-diones, the triketones, are potent bleaching herbicides whose structure-activity relationships and physical properties are substantially different from classical bleaching herbicides, which affect phytoene desaturase. The first clue to their unique mechanism of action was the discovery that rats treated with a triketone were found to be tyrosinemic. Additionally, examination of the rat urine revealed the accumulation of p-hydroxyphenylpyruvate (HPP) and p-hydroxyphenyllactate. These results suggested that this chemically induced tyrosinemia was the result of the inhibition of p-hydroxyphenylpyruvate dioxygenase (HPPD, EC 1.13.11.27), and this suggestion was confirmed when a triketone was shown to be a potent inhibitor of rat liver HPPD. In plants, HPPD is a component of the biosynthetic pathway to plastoquinone (PQ), which in turn is a key cofactor of phytoene desaturase. The expectation that triketone-treated plants should accumulate tyrosine while having reduced PQ levels was dramatically demonstrated in the meristematic tissue of ivyleaf morningglory. Plant HPPD, like the mammalian enzyme, was inhibited in vitro by triketones. These biochemical effects provide evidence that the triketone herbicidal mechanism of action is HPPD inhibition leading to a deficiency of PQ, a key cofactor for carotenoid biosynthesis. Other chemical classes of bleaching herbicides were also examined for their ability to elevate tyrosine and deplete PQ as a definitive means of establishing their mode of action and for delineating the structural and physical chemical requirements for an HPPD herbicide. Evidence is provided to support the claim that a 2-benzoylethen-1-ol substructure is the minimum substructure required for a potent HPPD inhibitor.
Selected observations on rickettsiae and their host cells.

The study of the interaction between rickettsiae and their host cells is in its infancy. Members of the genera Rickettsia, Coxiella and Rochalimaea show considerable diversity in host cell range (in vivo vs. in vitro), kind of association with host cell (pericellular, intracellular), mode of entry, interactions with various host cell membranes, intracellular localization (intraphagosomal, free in cytoplasm, intranuclear), adaptation to preferred microhabitat (e.g., optimal pH for enzymes), details of growth cycle, mechanisms of host cell damage. Quantitative in vitro methods exist for the study of infection cycles. Knowledge of nutritional requirements is almost non-existent. Host factors, (e.g., antibody, lymphokines, immune interferon) influence intracellular rickettsiae. Rickettsia-host cell interactions remain a fertile field for discovery.
The ecology and population genetics of introduced deer species

Deer have been introduced outside their native ranges numerous times worldwide, causing significant economic and environmental impacts. The scale of problems caused by some introduced deer species is expected to increase, while others are relatively harmless and may be important for conservation as their numbers decline in native regions. This thesis examines the factors promoting invasion in nonnative deer, and investigates the population genetics of two deer species introduced to Great Britain. Factors hypothesised to predict invasion success were tested using a comparative analysis of the outcomes of introductions of non-native deer populations. Two modelling approaches were taken to account for confounding effects in species-level and population-level analyses, and different factors were found to explain success at different stages of the invasion process. Populations of roe deer expanding from refugia and reintroductions were examined, and differences in genetic diversity between core and peripheral populations, alongside a decline in diversity with rate of expansion from the core were found. High levels of differentiation between and among core and peripheral populations suggest that genetic drift is the major factor causing these patterns. Using a genome scan of British and European roe deer, loci potentially under selection were identified. Association between some of these loci and environmental variables suggests that climatic extremes may have a role in exerting selective pressures on roe populations. The Chinese water deer is severely declining in range and number in its native habitat, but rapidly expanding after being introduced to Great Britain. Relatively high levels of diversity in native Chinese populations, and significant differentiation between the Chinese and British populations were found. The source population of the British deer is likely to be extinct, and the level of genetic structuring indicates that conserving populations across both ranges is important to maintaining their diversity.
RELATIONSHIP BETWEEN PROTEASE PRODUCTION AND CAPSULE SIZE IN CRYPTOCOCCUS NEOFORMANS

Objet. Cette etude a ete effectuee afin d'etablir une possible correlation entre la croissance, la taille de la capsule et la production de proteinase aux differentes temperatures des souches de Cryptococcus neoformans d'origine differente. Materiels et methodes. La croissance, la dimension de la capsule et la production de proteinase aux differentes temperatures ont ete examinees chez 40 differentes souches de C. neoformans provenant de malades atteints de SIDA (21 souches) et de fientes de pigeons (19 souches). L'activite proteasique a ete evaluee d'apres le diametre de proteolyse dans des milieux geloses chimiquement definis a temperatures differentes. Cette etude a ete effectuee afin d'etablir une possible correlation entre la production de proteinase et la production de la capsule de differentes souches de C. neoformans. Resultats. La plupart de souches etudiees ont produit une proteinase a 37 °C et a 28 °C. Il est possible d'emettre l'hypothese d'une correlation entre la production de proteinase et la dimension de la capsule des souches de C. neoformans provenant de malades atteints de SIDA, mais non pour les souches isolees des fiantes d'oiseaux.
Realized climatic niches are conserved along maximum temperatures among herpetofaunal invaders

The conservatism of the realized climatic niche is a pivotal assumption for predicting invasion risk under present and future climates. To date, however, no studies have identified the particular dimensions of realized climatic niches that are spatially and temporally conserved for a whole taxonomic group on a global scale. Understanding realized niche dynamics along each individual climatic variable separately is a key consideration for improving forecasts of invasive species distributions and anticipating future range expansions.