Miracle-dz/UniFAR-FTUs huggingface dataset:
Effet du liquide séminal sur l'infection par le VIH-1 dans des modèles cellulaires et tissulaires et recherche des facteurs modulateurs

Semen represents the main vector of HIV transmission. Several studies have recently shown that, in addition of being a carrier of HIV particles and infected cells, seminal fluid (SF) could modulate the efficiency of HIV infection of target cells through its intrinsic properties. These studies were all performed with SF from uninfected donors. But the composition of SF from HIV-infected men significantly differs from that of HIV-infected men, as demonstrated by studies on SF cytokines content, and microbiome. In addition, we showed that semen-producing organs are infected by HIV which most probably influences their seminal secretions. As a matter of fact, the volume of the ejaculate of HIV+ donors is generally less than that of uninfected men. In this context, my thesis was articulated around 2 axes: Effect of SF from HIV infected men on HIV-1 infection of Lymphocytes T CD4+: the effect of SF from HIV-infected men (HIV+SF) versus SF from uninfected donors (SF) on HIV infectivity of CD4+ T cells. We observed a significantly reduced infection of CD4+T cells by HIV-1 R5 in presence of HIV+SF as compared with SF, the latter displaying enhancing activity. This differential effect was not observed on the infectivity of the CD4+ cell line TZM-bl, or on PBMC infection by HIV-1 X4. We compared the composition of HIV+SF versus SF in terms of enhancing peptides, cytokines and prostaglandins, and investigated the impact of SF from both HIV-infected and uninfected men on CD4+T cell HIV receptors expression, activation and proliferation. HIV+SF vs HIV-SF was found to induce a significantly higher downmodulation of CCR5 expression shortly after exposure, which correlated with the concentrations of CCR5 ligands in semen. Effect of SF on HIV infection of cervix and colorectal tissues: the cervix and colorectal mucosa represent major front doors of the virus in the body and are thus particularly physiological models. We showed that the SF leads to a decrease of the infection ex vivo in exocervix tissues while no effect is observed on the infection of colorectal tissues. Fractionation of the seminal fluid and identification of factors with biologic activity on the HIV-1 infection : we had beginning a proteomic approach which allowed to decomplexified SF by successive HPLC, to select active biological fractions and to identify candidate proteins, by mass spectrometry, potentially responsible for an inhibitory effect on the infection by the HIV 1. Based on the literature and on our results, it clearly appears that SF is a complex biological fluid. Moreover, the effect of the semen on HIV-1 infection is dependent on the cellular or tissular model and on the HIV status of the donor. Indeed, the differences of composition (cytokines, antimicrobial peptides) between semen from infected men or SF from uninfected men lead to modifications of the modulation of HIV-1 infection by semen via direct or indirect mechanisms which which pave the way for further investigations.
Identification of ploidy level on varieties and hybrids of kiwifruit (Actinidia sp.).

The genus Actinidia includes over 66 species and over 118 taxon, that range in ploidy level from diploid to octoploid. Although there is basic information on ploidy levels of various species, sampling has been limited and little information on specific cultivars and hybrids is available. The objective of this research was to determine ploidy levels among a diverse collection of species, hybrids, and cultivars using flow cytometry. Nuclei were extracted, stained with propidium
A Mathematical Model for Estimation of Optimum Broiler Production Period under the Economic Conditions of Turkey

Abstract Oğuz, C. and Parlat, S.S. 2003. A mathematical model for estimation of optimum broiler production period under the economic conditions of Turkey. J. Appl. Anim. Res., 23: 195–199. A mathematical function is more suitable to determine the optimum production time. This has been shown by using the production data of a large broiler producing farm using a model. However, this model can be judged only after it is used frequently in experimental studies.
Mineral Nutrition of Plants: Principles and Perspectives

PART I: ELEMENTS - Introduction and History - The Media of Plant Nutrition - Inorganic Components of Plants - PART II: TRANSPORT - Nutrient Absorption by Plants - Upward Movement of Water and Nutrients - Downward Movement of Food and Nutrients - PART III: METABOLISM AND GROWTH - Nitrogen and Sulfur: A Tale of Two Nutrients - Mineral Metabolism - Nutrition and Growth - PART IV: HEREDITY AND ENVIRONMENT - Physiological Genetics and Molecular Biology - Ecology and Environmental Stress - Big Picture: Past, Present, Future
The role of synaptogenic synaptic adhesion molecules in insulin secretion

Author(s): Suckow, Arthur T. | Abstract: The insulin secreting pancreatic [beta] cells, by virtue of their pattern of protein expression and the architecture of their secretory apparatus, share many features with neurons in the central nervous system (CNS). The work described throughout this dissertation arose from the observation that the [beta] cells' expression of the machinery necessary for GABAergic neurotransmission makes the [beta]-cell cellular "phenotype" very much resemble that of an inhibitory synapse. This observation led to the overarching hypothesis that key insights into the functional maturation of [beta] cells could be derived from existing knowledge of the development, differentiation and maintenance of GABAergic synapses in the CNS. [beta] cells contain synaptic-like microvesicles of which the origin, trafficking and role are poorly understood. Here, I demonstrate that the biogenesis of these vesicles in [beta] cells is driven by adaptor proteins that are important for the formation of vesicular GABA transporter-containing synaptic vesicles in the CNS. Additionally, high level expression of the vesicular GABA transporter is detected in both human and rat [beta] cells, and a novel glucose-regulated variant of this protein is described. These findings suggest that [beta]-cells and neurons share molecules and mechanisms important for mediating the neuron-specific GABAergic membrane trafficking pathways that underlie synaptic vesicle formation. The synaptogenic adhesion molecules, neuroligin and neurexin, drive synapse formation in vitro and regulate the differentiation of nascent synapses into either glutamatergic or GABAergic fully mature nerve terminals. Here, the expression of those neuroligin and neurexin family members important for the maturation of GABAergic synapses, and the expression of their intracellular, GABAergic binding partners, is demonstrated in [beta]-cells. Neuroligin expression is revealed to be important for glucose-stimulated insulin secretion and evidence is presented that it may drive the proper assembly of the insulin secretory apparatus. Neuroligin is found to affect insulin secretion through a neurexin- independent mechanism in rat [beta]-cells. Overall, these results indicate that knowledge of the pathways that guide GABAergic synapse formation and function will aid in our understanding of [beta]-cell development and functional differentiation, and may yield important targets for remedying some of the [beta]-cell dysfunction that occurs during the pathogenesis of diabetes
Drought Responses of Two Bambara Groundnut (Vigna subterranea L. Verdc.) Landraces Collected from a Dry and a Humid Area of Africa

Drought adaptation strategies of two bambara groundnut landraces, Uniswa Red and S19-3, collected from contrasting environments in Africa, were compared. Our objectives were to investigate the relative significance of effective stomatal control induced by the abscisic acid (ABA) signalling and osmotic adjustment in regulating plant water relations in general for this legume species. The ABA concentration [ABA] in the leaf increased linearly with declining relative leaf water content, and there were significantly higher [ABA] in Uniswa Red compared with S19-3 at the final harvest in the drought-stressed plants. Estimated by a linear-plateau model, S19-3 initiated the reduction in transpiration at a significantly lower soil water threshold (FTSW = 0.50 ± 0.024) than Uniswa Red (FTSW = 0.69 ± 0.023) indicating that the latter was more sensitive in reducing plant water use in response to soil drying. A similar trend was found for stomatal closure during soil drying, although the soil water thresholds at which relative stomatal conductance (gs) started to decline were not significantly different between the two landraces. By an early closure of stomata and hence an early reduction in transpiration rate during soil drying, Uniswa Red could be defined as a ‘water-saver’ such that it maintains leaf water status to a great extent of soil water deficit. This strategy is important for survival during intermittent drought. While S19-3 could be defined as a ‘water-spender’ with a late closure of stomata, hence a late declining of transpiration rate during soil drying allowed the landrace to maximize its water use despite giving up its leaf water relations. Such drought response together with a fast phenological development of S19-3 indicates that the landrace is capable of escaping from terminal drought while maximizing its water use and productivity when soil water is available.
Analyses and Comparison of Genomic Accuracy of Random Regression BLUP and Bayesian Ridge Regression

Genomic selection can increase genetic gain per generation through early selection. Genomic selection is expected to be particularly valuable for traits that are costly to phenotype and expressed late in the life cycle of long-lived species. Accuracies of genomic evaluation applying Random Regression BLUP and Bayesian Ridge Regression in generation of 1001-1007, considering the number of markers 200, 800, 2000 and 10000 for the traits with heritability of 0.05, 0.1, 0.25 and 0.5 were compared. The results were shown that the genomic accuracy was higher in populations with more density marker genotyped in comparison to lower dense marker genotyped. Applying Bayesian Ridge Regression in comparison to RR-BLUP was resulted to higher accuracy of genomic evaluation as well as its persistency across generations.
Mapping PAMP Responses and Disease Resistance in Brassicas

The first layer of active defence in plants is based on the perception of pathogen-associated molecular patterns (PAMPs) leading to PAMP-triggered immunity (PTI). PTI is increasingly being investigated in crop plants, where it may have potential to provide durable disease resistance in the field. Limiting this work, however, is an absence of reliable bioassays to investigate PAMP responses in some species. Presented here is a series of methods to investigate PTI in Brassica napus. The assays allow measuring early cell signalling responses, gene expression changes, cell wall reinforcement, metabolome changes and scoring PAMP-Induced resistance. Illumina-based RNA sequencing analysis produced a genome-wide survey of transcriptional changes upon PAMP treatment seen in both the A and C genomes of the allotetraploid B. napus. Using these assays substantial variation in PAMP-responsiveness was observed amongst elite varieties of B. napus. Taking this further, a genome wide association study (GWAS) of the flg22 and elf18 triggered oxidative bursts, resistance to Pseudomonas syringae and Botrytis cinerea was carried out in a population of B. napus. A substantial number of molecular markers, covering both sequence and expression variation, have been identified as having significant association with these four traits. QTL mapping of the flg22 triggered oxidative burst in the ADxGD double haploid cross identified a major quantitative trait loci (QTL) on C9 of B. oleracea. mRNA-seq of the parents led to a non-synonymous single nucleotide polymorphism (SNP) list and enabled fine mapping through the addition of KASPar markers to the original map. This produced a relatively small list of candidate genes including CYLIC NUCLEOTIDE GATED ION CHANNEL 4 (CNGC4) also known as DEFENCE NO DEATH 2 (DND2). An insertion in Arabidopsis thaliana DND2 showed phenotypic difference in the oxidative burst between the insertion line and Col-0, potentially indicating a role for the gene in regulating early PTI.
A Review of the Impact of Accounting Information System for Effective Internal Control on Firm Performance

Businesses today operate in a highly competitive and changing global business environment and therefore require information system that provides speedy responses to the complex business issue. The rapid development in information technology (IT) has aided companies to generate and make use accounting information systems (AIS), and the qualitative characteristics of any accounting information system to make it effective can be sustained if there is proper internal control system. When companies and businesses adjust and regulate their computerized technique of internal control machinery according to accounting information system (AIS), there would be assurances of the reliability of financial information processes, the control measures of effectiveness and efficiency of the information reliability will be boasted, effectual and improved operative goals and enhanced performance. Therefore, this study focused and look at the influence of accounting information systems (AIS) for effective internal control on firm's performance and found out that when controls are operated efficiently and effectively, there will be improved performance, better accounting information reliability for better decision making for both the internal and external users.
Protein sequence-structure relationships

viii CHAPTER 1: INTRODUCTION 1 1.1 Designability 1 1.2 Contact potentials 4 1.3 A guide to the present study 5 CHAPTER 2: DESIGNABILITY OF LATTICE MODELS OF PROTEINS 8 2.1 Topology and designability of lattice conformations 9 2.1.1 Methods 10 2.1.1.1 Enumeration of compact conformations 10 2.1.1.2 Calculation of energy of conformations 11 2.1.1.3 Calculation of designability 15 2.1.1.4 Generation of contact graphs 15 2.1.1.5 Regression analysis 17 2.1.1.5 Naive Bayes prediction 17 2.1.2 Results 19 2.1.3 Discussion 24 2.1.3.1 Application to larger lattices and real protein structures 27 2.2 Sequence space diversity 28 2.2.1 Methods 28 2.2.2 Results 31 2.2.2.1 Extended set of conformations 31 2.2.2.2 Degeneracy 34 2.2.2.3 Reduced set of conformations 36 2.2.3 Discussion 37
Resource predictability and foraging behaviour facilitate shifts between nomadism and residency in the eastern grass owl

Population-level distribution strategies, such as migration, nomadism or residency, form often as a result of spatio-temporal resource dynamics. While commonly a species will adopt a single strategy across its range, occasionally multiple strategies can be observed. In Australia, the eastern grass owl Tyto longimembris is considered nomadic over most of its range. However, resident populations have been reported along the eastern coastal zone. We collected and analysed regurgitated pellets of a coastal resident population across three seasons in a single year. We compared these data with the availability of prey in the field to investigate whether resource predictability and foraging behaviour facilitate shifts between nomadism and residency. Many of the prey species consumed by the resident population display little spatial or temporal variation compared with prey consumed by nomadic populations. Temporal differences were observed in the diet with the main prey species (house mouse) declining from 88.9% in summer to 66.7% in winter and 40.0% in spring (Po0.01). Conversely, bird and rat consumption increased across the three seasons (16.3, 28.6 and 34.0% for birds, P = 0.08; and 15.0, 33.3 and 75.0% for rats, Po0.01; for summer, winter and spring, respectively). Trapping resulted in the capture of house mouse Mus domesticus only, which declined significantly from the first half to the second half of the year (Po0.01). These data indicate that the eastern grass owl in the coastal zone is a specialist predator of small rodents, but will broaden its diet to feed opportunistically on a range of other species when the preferred prey are less abundant. We conclude that the capacity to switch between specialized and opportunistic predation, combined with prey that are spatially and temporally more predictable, facilitates shifts between nomadism and residency in the eastern grass owl.
Distribution and condition of pueruli of the spiny lobster Jasus edwardsii offshore from north-east New Zealand

Pelagic spiny lobster, Jasus edwardsii, pueruli and phyllosomas were sampled on offshore transects from the south-east coast of the North Island of New Zealand in February 1998. Carapace length, weight, and total lipid content of pueruli (n = 360) were assessed; 33 pueruli had soft carapaces, indicative of recent metamorphosis from final-stage (stage 11) phyllosoma larvae. The recently metamorphosed pueruli occurred 24–216 km offshore, much farther offshore than has been previously suggested for the location of metamorphosis. Their distribution was compared to information on their size and condition, as well as their distance offshore, water depth, temperature and salinity, and estimates of phytoplankton biomass. The results indicate that a threshold of larval energy reserve is unlikely to trigger metamorphosis, but rather some exogenous trigger may be involved, or metamorphosis may be part of a programmed developmental process. The distribution and condition of the new pueruli suggest that about 84% had the energetic capacity to swim inshore to settle. This result may have important implications for patterns of puerulus settlement and subsequent recruitment of lobsters to coastal populations and their important associated fisheries. It may influence both the seasonal and interannual variability in settlement observed in this species.
Regulación genética en la respuesta al estrés calórico en Escherichia coli

Cells of almost any organism respond to a sudden up-shift of temperature and to several other stress conditions, by a transient increase in the cellular concentration of a set of proteins, the heat- shock proteins (HSPs). The main HSPs, chaperones and proteases, are constituents of the cellular machin- ery of protein folding, translocation, repair and degradation. The bacteria Escherichia coli has been a paradigm regarding heat shock gene expression in prokaryotes. In this bacterium, the expression of the HSPs is regulated at the transcriptional level. The approximately 40 genes that encode the HSPs define the heat-shock stimulon. Most of these genes, including the main chaperone and protease genes, are under the positive control of σ σ 32 , encoded by rpoH, while approximately 10 genes, including rpoH and rpoE, are regulated by σ σ E , encoded by rpoE. The cytoplasmic response to heat is regulated by σ σ 32 , while that of the periplasm is regulated by σ E. The expression of both regulons is interconnecte d, since σ σ E regulates the transcription of rpoH at high temperatures. The ac tivity of these σ σ factors, under non-stress and stress conditions, depends upon negative and positive regulatory mechanisms acting at different levels: tran- scription, translation, half-life and activity of the factors. Models for the regulation of the cytoplasmic and periplasmic response to heat in E. coli are presented.
CD36 intestinal : un récepteur aux acides gras à longue chaîne qui contrôle l’hypertriglycéridémie post prandiale, l’endotoxémie et l’intégrité de l’épithélium intestinal

L’hypertriglyceridemie post prandiale constitue un facteur de risque des maladies cardiovasculaires et est presente en cas de syndrome metabolique, d’obesite et d’insulino-resistance. L’intestin conditionne la biodisponibilite des lipides et l’hypertriglyceridemie post prandiale. En effet, il controle la quantite et la qualite des chylomicrons secretes, en adaptant son metabolisme en fonction de la teneur en lipides du regime. Or a l’heure actuelle, le mecanisme de detection des lipides alimentaires par les enterocytes necessaire a cette adaptation, n’est pas elucide. Ce travail de these a permis de demontrer que la glycoproteine transmembranaire CD36, est un recepteur aux AGLC qui declenche l’activation des ERK1/2. Cette activation est responsable de l’induction du taux d’ARNm de 3 proteines cles de l’absorption des lipides (l’Apobec1, la Microsomal Triglyceride Transfer Protein (MTP), la Liver-Fatty Acid Binding Protein (L-FABP)) et de la degradation post prandiale de CD36. La pertinence physiologique de ce recepteur a ete evaluee chez des souris CD36 (-/-) soumises a un regime hyperlipidique riche en AGLC satures ou insatures. Nos donnees demontrent que CD36 intestinal est indispensable a l’absorption de forte quantite de lipides, au controle de l’hypertriglyceridemie post prandiale, de l’inflammation intestinale et de l’endotoxemie. Ces effets sont fortement aggraves en cas de regime hyperlipidique riche en AGLC insatures qui peuvent meme etre lethal. Le CD36 intestinal pourrait donc etre une cible therapeutique dans le traitement de l’hypertriglyceridemie et de l’endotoxemie post prandiales.
Mouse Hsp25, a small heat shock protein

Under conditions of cellular stress, small heat shock proteins (sHsps), e.g. Hsp25, stabilize unfolding proteins and prevent their precipitation from solution. 1H NMR spectroscopy has shown that mammalian sHsps possess short, polar and highly flexible C-terminal extensions. A mutant of mouse Hsp25 without this extension has been constructed. CD spectroscopy reveals some differences in secondary and tertiary structure between this mutant and the wild-type protein but analytical ultracentrifugation and electron microscopy show that the proteins have very similar oligomeric masses and quaternary structures. The mutant shows chaperone ability comparable to that of wild-type Hsp25 in a thermal aggregation assay using citrate synthase, but does not stabilize α-lactalbumin against precipitation following reduction with dithiothreitol. The accessible hydrophobic surface of the mutant protein is less than that of the wild-type protein and the mutant is also less stable at elevated temperature. 1H NMR spectroscopy reveals that deletion of the C-terminal extension of Hsp25 leads to induction of extra C-terminal flexibility in the molecule. Monitoring complex formation between Hsp25 and dithiothreitol-reduced α-lactalbumin by 1H NMR spectroscopy indicates that the C-terminal extension of Hsp25 retains its flexibility during this interaction. Overall, these data suggest that a highly flexible C-terminal extension in mammalian sHsps is required for full chaperone activity.