Miracle-dz/UniFAR-FTUs huggingface dataset:
Aminoacyl-ARNt synthétases mitochondriales humaines : aspects fondamentaux et contribution à la compréhension de pathologies reliées

Les aminoacyl-ARNt synthetases (aaRS) sont impliquees dans le mecanismes de la traduction. Dans les cellules humaines, il existe deux jeux de genes nucleaires codant pour les aaRS : un pour les aaRS cytosolique (cyt), le second pour les aaRS mitochondriales (mt). Les aaRS mt sont traduites dans le cytosole, adressees et importees dans la mitochondrie.Mutations dans 9 genes d’aaRS mt ont ete demontrees comme responsables de pathologies mitochondriales. Certaines des mutations n’affectent pas la propriete originelle d’aminoacylation. Il a ete propose que certaines de ces mutations puissent affecter des proprietes alternatives.Alors l’organisation des aaRS cyt est bien etudiee et que des implications dans des fonctions alternatives etablies pour certaines d’entre elles, les connaissances quant aux aaRS mt restent parcimonieuses. L’objectif principal de ce manuscrit de these est: (i) reveler d’organisation sous-mt de l’AspRS mt; (ii) etendre l’analyse de l’organisation sous-mt a l’ensemble des aaRS mt; et (iii) contribuer a la comprehension de mecanismes moleculaires sous-jacents a certaines pathologies. Ces travaux ouvrent la porte vers d’autres investigations de l’organisation des aaRS a l’interieur de la mitochondrie. Ces contributions seront utiles a la meilleure comprehension de mecanismes moleculaires sous-jacents a pathologies mitochondriales.
Método Molecular Para Estudos Ecológicos de Bactérias Diazotróficas do Gênero Paenibacillus em Amostras Ambientais

O objetivo deste trabalho foi desenvolver e testar um protocolo de PCR especifico para a amplificacao de especies de bacterias fixadoras de nitrogenio do genero Paenibacillus, utilizando-se a estrategia de clonagem e sequenciamento do gene nifH.
The use of neuroimaging in the assessment of brain size and social structure in odontocetes.

This study successfully utilised the non-invasive neuroimaging techniques of Computerised Tomography (CT) and Magnetic Resonance Imaging (MRI) to establish that dolphins have high relative brain size values, transcending the primate range for neocortex volume and neocortex ratio. Bottlenose dolphins superseded human values of the neocortex ratio and common dolphins marked the upper limit of the range for the dolphin species under investigation. In addition this study was the first to find a correlation between sociality and neocortex ratio in dolphins (R.I.M. Dunbar, pers.comm), which supports the hypothesis of neocortical development in relation to sociality/group size (Sawaguchi & Kudo 1990; Dunbar 1992) and social/Machiavellian intelligence (Byrne & Whiten 1988; Byrne 1995). The study devised new "measures of relative brain size, including the grey-white matter and higher cortical ratios and these require further research before verification of their efficacy. Equations were calculated to allow estimation of: (1) MRI values of total brain volumes from CT values, (2) total brain volume from cranial volume using CT, (3) cerebral cortex volume from cranial or total brain volume (CT) and (4) cerebral cortex and cerebellar cortex volume from total brain volume (MRI). The effects of freezing and defrosting on volume and density of CT and MRI values were investigated. Additionally, the relationship between relative brain size (Ea) and sociality was investigated for other dolphin research, using previously published figures, but no significant correlations were found. Finally, dolphin values were compared to primate values for neocortex volume and neocortex ratio with the finding that the only primate within the dolphin range of neocortex was the human, positioned higher than the solitary humpback dolphin, but below all of the other, more socially complex, dolphin species.
Faisabilité d'une sélection génétique sur la résistance aux strongles gastro-intestinaux chez les ovins laitiers dans les Pyrénées Atlantiques

La resistance des nematodes gastro-intestinaux aux traitements anthelminthiques represente un reel probleme pour la production ovine. La situation de l’elevage ovin dans les Pyrenees Atlantiques est preoccupante en raison du climat tempere favorisant une forte pression parasitaire couple aux restrictions de traitements anthelminthiques specifiques a la production laitiere. L’utilisation quasi-exclusive de benzimidazoles pendant la lactation a ainsi entraine l’apparition de population de strongles digestifs resistants. Les methodes existant pour contourner ce probleme n’etant pas toujours adaptees aux pratiques courantes d’elevage, de nombreux efforts sont fournis actuellement autour de la selection d’animaux genetiquement resistants aux infestations par les nematodes gastro-intestinaux. Cette these expose les travaux experimentaux realises au Centre Ovin d’Ordiarp. L’etude de l’infestation de 51 mâles reproducteurs (de race Manech Tete Rousse) en attente de testage a permis de mettre en evidence de fortes variabilites individuelles et ainsi l’identification de beliers resistants et/ou resilients. La comparaison a la valeur genetique (index laitiers) des beliers permet d’envisager la selection d’individus resistants aux infestations parasitaires, a l’interieur des races ovines pyreneennes.
Assessment of the Activity of Antioxidant Enzymes

T he use of molecular oxygen to sustain life has as a metabolic byproduct the formation of superoxide and hydrogen peroxide. Glutathione (GSH)–dependent metabolism of hydrogen peroxide via GSH-dependent peroxidases is a vital process to prevent oxidative stress. These antioxidant enzymes in conjunction with glutathione reductase comprise the glutathione redox cycle (Reed, 1985, 1986). In conjunction with the superoxide dismutases, this cycle serves an essential role in limiting the production of hydroxyl radical and other reactive oxygen species that can cause indiscriminate damage to cellular constituents. As a substrate of several isoenzymes of glutathione peroxidases (UNIT 7.1), GSH is also used to limit the same oxidative events induced by organic hydroperoxides, including fatty acid hydroperoxides.
Gβ5γ2 Is a Highly Selective Activator of Phospholipid-dependent Enzymes*

In this study, Gβ specificity in the regulation of Gβγ-sensitive phosphoinositide 3-kinases (PI3Ks) and phospholipase Cβ (PLCβ) isozymes was examined. Recombinant mammalian Gβ1–3γ2 complexes purified from Sf9 membranes stimulated PI3Kγ lipid kinase activity with similar potency (10–30 nm) and efficacy, whereas transducin Gβγ was less potent. Functionally active Gβ5γ2 dimers were purified from Sf9 cell membranes following coexpression of Gβ5 and Gγ2-His. This preparation as well as Gβ1γ2-His supported pertussis toxin-mediated ADP-ribosylation of Gαi1. Gβ1γ2-His stimulated PI3Kγ lipid and protein kinase activities at nanomolar concentrations, whereas Gβ5γ2-His had no effect. Accordingly, Gβ1γ2-His, but not Gβ5γ2-His, significantly stimulated the lipid kinase activity of PI3Kβ in the presence or absence of tyrosine-phosphorylated peptides derived from the p85-binding domain of the platelet derived-growth factor receptor. Conversely, both preparations were able to stimulate PLCβ2 and PLCβ1. However, Gβ1γ2-His, but not Gβ5γ2-His, activated PLCβ3. Experimental evidence suggests that the mechanism of Gβ5-dependent effector selectivity may differ between PI3K and PLCβ. In conclusion, these data indicate that Gβ subunits are able to discriminate among effectors independently of Gα due to selective protein-protein interaction.
La importancia de la secuencia terminal repetida larga (LTR) en la patogenia del virus de la inmunodeficiencia humana

The importance of the long repeated terminal sequence (LTR) in the pathogeny of the human immunodeficeincy virus. The Long Terminal Repeat (LTR) of the human immunodeficiency virus genome functions as an essential site for the control of viral transcription. Although the LTR does not codify either structural or accessory proteins, its function is intimately linked to viral replication in response to mitogens, citokines and even other stimuli generated by opportunistic infectious agents. This revision attempts to describe the in vitro function of the LTR in viral replication and its importance in the pathogenesis of the acquired immunodeficiency syndrome.
Mapping QTLs for brown planthopper (BPH) resistance introgressed from Oryza officinalis in rice.

Harushima Y, Yano M, Shomura A, Sato M, Shimano T, Kuboki Y, Yamamoto T, Lin SY, Antonio BA, Parco A, Kajiya H, Huang N, Yamamoto K, Nagamura Y, Kurata N, Khush GS, Sasaki T. 1998. A high-density rice genetic map with 2275 markers using a single F2 population. Genetics 148:479-494. Huang N, McCouch S, Mew T, Parco A, Guiderdoni E. 1994. Development of an RFLP map from a doubled haploid population in rice. Rice Genet. Newsl. 11:34-137. Ishii T, Brar DS, Multani DS, Khush GS. 1994. Molecular tagging of genes for brown planthopper resistance and earliness introgressed from O. australiensis into cultivated rice, O. sativa. Genome 37:217-221. Jena KK, Pasalu IC, Krishnaiah K, Khush GS. 1998. A RAPD marker for the gene conferring resistance to Indian biotype of BPH. Rice Genet. Newsl. 15:133-134. Jeon YH, Ahn SN, Choi HC, Hahn TR, Moon HP. 1999. Identification of a RAPD marker linked to a brown planthopper resistance gene in rice. Euphytica 107:23-28. Kabir MA, Khush GS. 1988. Genetic analysis of resistance of brown planthopper in rice, Oryza sativa L. Plant Breed. 100:54-58. Khush GS, Brar DS. 1991. Genetics of resistance to insects in crop plants. Adv. Agron. 45:223-274. Kosambi DD. 1944. The estimation of map distances from recombination values. Ann. Eugen. 12:172-175. Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg AL. 1987. MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174-181. Michelmore RW, Paran I, Kesseli RV. 1991. Identification of markers linked to disease resistance gene by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc. Natl. Acad. Sci. USA 88:9828-9832. Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18:6531-6535.
The role of E-cadherin in modulating the behavioural characteristics of oral squamous carcinoma cells

The incipient invasion of epithelial tumour cells, characterised by disruption of normal cell-cell adhesion, marks the point of transition to malignancy. C-adherins are a family of calcium-dependent, transmembrane, cell-cell adhesion molecules whose function requires association with the actin cytoskeleton of the cell through cytoplasmic proteins called catenins. Oral keratinocytes express E-cadherin, which is considered a regulator of the epithelial phenotype. Loss of E-cadherin commonly is seen in oral squamous cell carcinoma (OSCC), particularly in poorly differentiated tumours, allowing cells to detach from the tumour mass, invade and metastasise. An E-cadherin negative OSCC cell line was identified where E-cadherin expression and function was restored through cDNA transfection resulting in functional cell surface expression of the protein and the formation of cell-cell attachments, with significant alteration in levels and distribution of catenins. Alteration of cell morphology, from a spindle to an epitheloid form, was observed. Additionally, restoration of E-cadherin showed a marked inhibition of the invasive potential of this OSCC cell line. These effects were not observed in the control cell line transfected with the expression vector containing antisense E-cadherin cDNA. Most findings in cell and molecular biology, presented in the literature, are based, primarily, on in vitro studies obtained from the culture of cells growing in 2-dimensional (2-D) tissue culture dishes. In this study I have investigated if E-cadherin plays a role in modulating tumour cell growth in a 3-D, as opposed to a 2-D, environment. Results showed that the epitheloid-like morphology brought about by E-cadherin expression under 2-D conditions allows differences in density dependent inhibition to occur accompanied by enhancement in the apoptotic capacity of the cells. However, where constraints of 3-D culture are imposed, these variations between E-cadherin expressing and non-expressing lines disappear. To explore the basis of these changes I have examined Western blot analysis of proteins known to play a role in mediating cell proliferation or regulation of apoptosis, such as Bcl-2, Akt-1, ILK and N-cadherin. I showed that changes in levels of expression of these proteins under 2-D conditions is markedly affected when cells were implanted in 3-D collagen I cultures. I also investigated the possible molecular cross talk between E-cadherin and the (34-integrin subunit. Results obtained from (34-knock-down experiments showed that (iH-integrin plays a role in the maturation of E-cadherin-dependent cell-cell contacts. I investigated the possible mechanisms of this apparent cadherin-integrin cross-talk and preliminary results showed that the function of (34-integrin was, potentially, executed through the Racl small Rho GTPase.
A Set of Allele-specific Markers Linked to L Locus Resistant to Tobamovirus in Capsicum spp.

The resistance to Tobamovirus in Capsicum spp. has been known to be controlled by five different alleles (, , , , and ) of L locus on the telomere of long arm of pepper chromosome 11. To develop a set of molecular markers differentiating all the alleles of L locus, we used five pepper differential hosts including Capsicum annuum Early California Wonder (ECW, ), C. annuum Tisana (), C. annuum Criollo de Morelos 334 (CM334, ), Capsicum chinense PI 159236 (), and Capsicum chacoense PI 260429 (). Developing a series of CAPS or SCAR markers specifically linked to the alleles was allowed by the sequence comparison of PCR amplicons of the -linked markers (189D23M, A339, and 253A1R) and BAC sequences (FJ597539 and FJ597541) in the pepper differentials. Genotypes deduced by these markers in 48 out of 53 hybrids of commercial pepper varieties were consistent with their phenotypes by bioassay using Tobamovirus pathotypes (, , and ). Consequently, these markers can be useful to differentiate L alleles and for breeding Tobamovirus resistance in pepper with marker-assisted selection.
The effects of sintacidomix and sun drops P on the performance and presence of Salmonella spp. in broilers: (preliminary report).

The aim of our study was to investigate the effects of the commercial preparations (Sintacidomix granular and Sintacidomix granular combined with Sun Drops P (Sintofarm SPA)) added to standard broiler diets on average mortality, relevant production parameters and the presence of Salmonella spp. During the experiment, Cobb 500 broilers were randomly divided onto three farms. The first and the second experimental group of the broilers were fed with the addition of Sintacidomix granular and Sintacidomix granular combined with Sun Drops P, respectively. The broilers from the third, control group, were fed with standard diet without addition of commercial premix preparations.At the end of the breeding, better feed conversion and reduced mortality were observed in the broilers from both experimental groups, while the average body weight was observed to be higher in the second experimental group in comparison with the control one. Meconial and fecal samples of the broilers revealed no Salmonella spp during the experiment. With the use of the commercial premix preparations it was observed that in the first and the second experimental group Campylobacter caecal colonisation was postponed until the third week in comparison with the second week in the control group. Key words: broilers, production parameters, caecal colonisation
Comparative bacterial genomics

For the most part, diagnostic clinical microbiology still relies on 19th century ideas and techniques, particularly microscopy and laboratory culture. In this thesis I investigate the utility of a new approach, whole-genome sequencing (WGS), to tackle current issues in infectious disease. I present four studies. The first demonstrates the utility of WGS in a hospital outbreak of Acinetobacter baumannii. The second study uses WGS to examine the evolution of drug resistance following antibiotic treatment. I then explore the use of WGS prospectively during an international outbreak of food-borne Escherichia coli infection, which caused over 50 deaths. The final study compares the performance of benchtop sequencers applied to the genome of this outbreak strain and touches on the issue of whether WGS is ready for routine use by clinical and public health laboratories. In conclusion, through this programme of work, I provide ample evidence that whole-genome sequencing of bacterial pathogens has great potential in clinical and public health microbiology. However, a number of technical and logistical challenges have yet to be addressed before such approaches can become routine.
Genome Stability: DNA Repair and Recombination

Chapter 1: Restarting DNA Replication by Recombination Chapter 2. Double-strand Break Repair Pathways Chapter 3: RecA/Rad51 and the Search for Homology Chapter 4. Preparation of the RecA/Rad51 Filament Chapter 5. Single-Strand Annealing Chapter 6. Gene Conversion Chapter 7. In vivo Biochemistry: Recombination in Yeast Chapter 8: Break-induced Replication Chapter 9: Sister Chromatid Repair Chapter 10. Gene Targeting Chapter 11. Site-specific Recombination Chapter 12. Cytology and Genetics of Meiosis Chapter 13. Molecular Events During Meiotic Recombination Chapter 14 Holliday Junction Resolvases and Crossing-over Chapter 15. Nonhomologous End-joining Chapter 16. DNA Damage Checkpoints and Genome Instability
Physico-chemical and microbial factors affecting the operation of a package wastewater treatment plant

The Biologically Engineered Single Sludge Treatment (BESST) system is a small package wastewater treatment plant, which is designed to reduce influent concentrations of ammoniacal nitrogen, biochemical oxygen demand and total suspended solids, to a standard fit for discharge into controlled waterways. This thesis examines the treatment performance of the BESST, while operating under steady state and disruptive conditions, and assesses the contribution of physicochemical and microbiological factors to treatment efficacy. The design of the BESST was based on principles of activated sludge processes, and comprised of an anoxic area, an aerobic area, and an upflow clarifier. In each area of the system, physico-chemical and microbiological profiles were distinct from the other areas. The influent delivered to the system was municipal sewage, delivered from the start of the wastewater treatment works within which the prototype BESST was located. The influent was generally high in concentrations of biochemical oxygen demand, and was highly variable in nature. At times, this was reflected in effluent quality, particularly when disruptive events were occurring, such as mechanical failure. However, good levels of reduction in concentrations of ammoniacal nitrogen, biochemical oxygen demand and total suspended solids were observed throughout the treatment period, and the system demonstrated a good level of robustness with regard to mechanical failure and experimental changes to sewage control parameters. Transformations of nitrogen and phosphorus were performed by bacteria in the biomass of the system, and were analysed throughout the sampling period by qualitative, culture based and molecular microbiological methods. Culture based techniques were shown to be a valuable monitoring tool, but were not representative of the actual community in the BESST. Molecular methods provided a higher resolution of microbial populations present during treatment, but it was not possible to correlate data obtained from culture based methodology with that obtained using molecular techniques. Enhanced phosphorus removal trials were performed during the study period, in order to facilitate the production of an effluent very low in concentrations of total phosphorus. The trial suggested that enhanced removal of phosphorus was possible in the BESST, and found the most dominant morphotype accumulating polyphosphate, to be that of filamentous bacteria. The study produced a large and complex dataset, which presented difficulties in the analysis of interactions between variables. Suggestions are presented to overcome such difficulties. The BESST is presented in this study as a package wastewater system which is able to successfully perform biological nutrient removal in a robust manner, the interrogation of which has led to a greater contribution to knowledge of small wastewater treatment systems and the reactive nature of the chemical and biological processes occurring within them.
Mechanisms of outer membrane protein folding: effects of the lipid environment and periplasmic chaperones

In contrast with the wealth of information on the folding of soluble, cytosolic proteins, little is known about the folding of integral membrane proteins. The outer membrane proteins (OMPs) of Gram-negative bacteria have a β-barrel structure and are essential for cell survival. The mechanisms of OMP transport across the periplasm and how these proteins subsequently fold and insert into the outer membrane remain to be elucidated. The work presented herein examines the folding and membrane insertion of four different OMP constructs. Two homologous bacterial OMPs, OmpT and OmpP, were cloned, over-expressed and purified before biochemical and biophysical methods were employed to examine their folding properties. This work demonstrates that small differences in primary sequence can have large effects on folding efficiency and stability. In spite of both OmpT and OmpP being able to fold under a variety of conditions, it was not possible to establish conditions under which folding was completely reversible. Examination of the origins of irreversible OMP folding was carried out using OmpT, as well as both hexa-histidine tagged and untagged constructs of the outer membrane acyltransferase enzyme, PagP. This study revealed evidence that lipid adhesion of the protein in the unfolded state may be important in preventing aggregation and promoting reversibility. Finally, conditions were established to promote the folding of untagged PagP in low urea concentrations to allow the study of OMPs in the presence of the periplasmic chaperones, SurA and Skp. SurA was shown to have little effect on the folding of PagP into liposomes with zwitterionic or negatively charged membrane surfaces, while Skp was shown to exhibit holdase activity and to modulate PagP folding rate, dependent on the lipid composition. The results present the first detailed insights into the mechanism by which Skp and SurA act to facilitate PagP folding in vitro.