Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Cloning and Characterization of the HOS1 Gene from 'Muscat Hamburg' Grapevine

A BSTRACT . Cold stress is an important factor that limits grape ( Vitis sp.) production around the world. The high expression of osmotically responsive genes 1 ( HOS1 ) protein acts as a repressor of cold-responsive genes in plants. To increase understanding of mechanism regulating cold tolerance in grape, we isolated and characterized a novel HOS1 gene, designated VvHOS1 from ‘Muscat Hamburg’ grapevine ( Vitis vinifera ). Real-time polymerase chain reaction (PCR) analysis revealed that the expression of VvHOS1 could be induced by the application of exogenous abscisic acid and various abiotic environmental conditions such as low temperature, drought, and salinity. Moreover, VvHOS1 expression could also be induced by cold plus drought conditions (4 8 C, 10% polyethylene glycol 6000). In addition, overexpression of VvHOS1 in arabidopsis ( Arabidopsis thaliana ) decreased the plants’ tolerance to cold, drought, and salt as well as negatively regulated the expression level of two stress-responsive genes, AtRD29A and AtCOR47 . The results obtained in this study should help us to elucidate the function of VvHOS1 and understand the cold-responsive pathway in grapevine.
Étude du réseau d'interactions entre les protéines du Virus de l'Hépatite C

Hepatitis C virus (HCV) infection is a public health problem affecting approximately 170 millions people worldwide. Infection, often asymptomatic, persists in 80 % of patients and can lead to liver cirrhosis or hepatocellular carcinoma. So far, the only treatment available is a PEG-interferon-a and ribavirin combination, which is efficient only for half of H CV infected persons. This thesis focuses on the characterization of interactions between HCV proteins that modulate the viral repli cation cycle through the formation of the replication complex. The bioluminescence resonance energy transfer (BRET) technique allows -the study of protein interactions in living eukaryotic cells. Our BRET experiments, coupled with subcellular localization analysis of viral proteins by fluorescence confocal microscopy in living cells, allowed us to confirm 14 interactions previously reported in literature and to identify 6 novel interactions, including the homo-oligomerization of NS3/4A protea~e. This interaction network allows us to elaborate a model of HCV replication complex. Combined with site directed mutagenesis, BRET studies allowed us to characterize homo-oligomerization interactions of NS4B and NS5A proteins, as weIl as their heterooligomerization. An important finding arising from our experiments is that amphipathic helix (AH) located in N-terminal of NS5A is essential for NS5A-NS5A and NS4B-NS5A interactions. Furthermore, fluorescence confocal microscopy revealed that this AH is located at the endoplasmic reticulum (ER), whereas the full-length NS5A was shown to be associated with lipid droplets (Shi et al., 2002). This divergence in localization of the AH and the full-length protein was also observed with NS4B, which is an integral ER protein, while expression of its N-terminal domain containing two AHs co-localized with mitochondria. These observations in NS4B and NS5A AHs localization, in addition to the fact that these proteins can interact together and that NS5A can modulate NS4B topology,
Complement-mediated microglial priming : an in vitro study

The concept of microglial priming has developed through in vivo studies and is operationally defined as an exaggerated microglial production of soluble mediators (NO and cytokines e.g. IL-1β, TNF-α, IL-6) following a pro-inflammatory activation event (e.g. LPS-treatment). In practice microglial priming predisposes the brain to degeneration through the promotion of inflammatory mechanisms. In vivo studies of Crry (a major murine cell-surface C3-regulator) KO mice previously identified a novel role for C in the induction of the primed microglial phenotype, implicating iC3b ligation of microglial CR3. The purpose of this study was to further investigate C-dependent microglial priming and its mechanism(s) through study of microglia in isolation in vitro. Experiments using purified fluid-phase human iC3b failed to demonstrate any phenotypic effects of ligand exposure. Given the results of previous investigations concerning CR3 ligands, combined with the results of binding studies and sequence comparisons, it appears likely that, while still able to engage the cell-borne CR3, fluid-phase iC3b is incapable of exerting significant effects on the microglial phenotype. Studies using Zymsoan and C-fixing mAb-sensitised TC plastic as a means to generate ligands to investigate the consequences of microglial CR3 engagement by iC3b were confounded by the stimulatory effects of the C-activating agents (i.e. zymsoan or mAb) which prevented attempts to dissect the effects of the isolated interaction. Nonetheless, specific effects were attributable to the C3-derived CR3 ligands generated, which dramatically and significantly reduced the pro-inflammatory responses evoked by the C-activating agents. Investigations using C3-activation fragments immobilised on native (i.e. non-sensitised) TC plastic demonstrated phenotypic effects of microglial iC3b-CR3 ligation consistent with the previously reported mechanism of C-dependent microglial priming. Experiments using cultured Crry KO microglia demonstrated increased sensitivity to autologous C activation. Phenotyping experiments, however, failed to show any consequence of Crry expression status, even when the intrinsic sensitivity of Crry KO cells to C3 activation and deposition was effected, thus mimicking the in vivo scenario (including the potential for iC3b ligation of CR3). Data gathered from the several systems designed to ligate CR3 of microglial cells with C3-derived ligands highlight the broad range of potential cellular responses mediated by CR3 and emphasise the importance of context for the consequence of this interaction. In so doing, these data also further evidence that under certain circumstances, iC3b-CR3 binding can induce a primed microglial phenotype.
Functional Connectivity Dynamics of the Resting State across the Human Adult Lifespan

The aging brain undergoes alterations of Structural Connectivity (SC), but also transformations of the flexible interactions between brain regions during cognition, described by Functional Connectivity (FC). FC in the resting state (rs) displays a variety of age-related changes, but most studies do not address the spontaneous reorganization of FC across time. Here, we show by means of functional MRI (fMRI) human brain imaging that aging also profoundly impacts on the dynamics of this rs FC. Analyzing time-dependent correlations between human rs fMRI blood oxygen level dependent (BOLD) time series, we reveal a switching, markedly slowing down with age, between epochs of meta-stable FC and transients of fast network reconfiguration. Furthermore, we identify communities of functional links whose temporal fluctuations become increasingly anti-correlated in elderly subjects. This effect is stronger when the performance is reduced in cognitive screening tasks. Such remodeling of Functional Connectivity Dynamics (FCD) discloses qualitatively novel effects of aging that cannot be captured by variations of SC or static FC. Our new metrics manifest thus a strong biomarking potential, by achieving a quantitative parameterization of FCD variations across the human adult lifespan. Significance statement Aging alters the brain’s anatomical connectivity and inter-regional activity correlations (Functional Connectivity, or FC). Here we show that aging also affects the temporal remodeling of FC networks (Functional Connectivity Dynamics, or FCD) during the resting state. By analyzing human fMRI data, we find that the speed of FCD decreases with age. Furthermore FCD properties predict differences in cognitive performance between same-age subjects. This slowing down of FCD intriguingly parallels the reduction in information processing speed often invoked as a cause of age-related cognitive decline. We believe that FCD analyses will lead to better biomarkers of healthy and pathologic aging, since they avoid misinterpreting temporal as inter-subject variability.
Understanding the apoptotic signaling pathways in breast cancer using microarrays, proteomics and bioinformatics.

miRNAs are known to regulate gene expression and in the context of cancer have been shown to regulate metastasis, cell proliferation and cell death. In this report we describe potential miRNA regulatory roles with respect to induction of cell death by pharmacologic dose of Epidermal Growth Factor (EGF). Our previous work suggested that multiple pathways are involved in the induction of apoptosis, including interferon induced genes, cytokines, cytoskeleton and cell adhesion and TP53 regulated genes. Using miRNA time course expression profiling of EGF treated A431 cells and coupling this to our previous gene expression and proteomic data, we have been able to implicate a number of additional miRNAs in the regulation of apoptosis. Specifically we have linked miR-134, miR-145, miR-146b-5p, miR-432 and miR-494 to the regulation of both apoptotic and anti-apoptotic genes expressed as a function of EGF treatment. Whilst additional miRNAs were differentially expressed, these had the largest number of apoptotic and anti-apoptotic targets. We found 5 miRNAs previously implicated in the regulation of apoptosis and our results indicate that an additional 20 miRNAs are likely to be involved based on their correlated expression with targets. Certain targets were linked to multiple miRNAs, including PEG10, BTG1, ID1, IL32 and NCF2. Some miRNAs that target the interferon pathway were found to be down regulated, consistent with a novel layer of regulation of interferon pathway components downstream of JAK/STAT. We have significantly expanded the repertoire of miRNAs that may regulate apoptosis in cancer cells as a result of this work.
Exploring difference in subgingival microbial communities in dog and human periodontal diseases using DGGE technique

Periodontal diseases are the most common infectious diseases of dogs. Up to now, the knowledge about periodontopathic bacteria in dogs remains sparse. The objectives of this study were to apply the Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) technique, cloning and 16S rRNA gene sequencing to the investigation into subgingival plaque bacteria from healthy and periodontitis dogs; and compare DGGE patterns from the subgingival plaque of dogs and humans. Sixty-eight bacterial species were detected from subgingival plaque of 12 Poodles in Thailand and the predominant genus was Porphyromonas (n=11). Porphyromonas gulae and Treponema denticola were the most common microflora in the periodontitis dog group. In addition, DGGE band patterns from the dogs’ subgingival plaque were compared with those of humans’ subgingival plaque. The DGGE results showed different bacterial community structures between the two species, which may influence pathogenesis. Therefore, because the pathogenesis of periodontal disease in dogs may not be the same as in human, employing dog as an animal model for studying this disease in human should be carefully analyzed.
Influence of Maturation, Pathology and Functional Lateralization on 3D Sulcal Morphology using MRI

Handedness, the preferred use of one hand for manual dexterity tasks, is associated with right-left asymmetries in the surface area and depth of the central sulcus with the dominant hemisphere showing a larger surface area and depth. It is less clear how right-left differences in manual dexterity are reflected in right-left asymmetries in the depth and surface area of the central sulcus. This study was designed to examine the relationship between the depth of the central sulcus and manual dexterity in consistently right-handed children and adolescents. We applied factor analysis as a observer-independent modeling of central sulcus depth. Central sulcus have been segmented from high-resolution structural magnetic resonance images (MRIs) in cohort of 51 typically-developing individuals. Right-left asymmetry in dexterity was assessed using a drawing task, which tested subject’s ability to draw superimposed circles in a regular fashion. All participants showed a strong preference for the right hand, avoiding any confound influence of differences in handedness. Factor analysis revealed 11 factors of which two were spatially expressed in the ’hand knob’ region of the primary motor cortex (M1-HAND). Only these two factors significantly predicted the right-left asymmetry in manual proficiency during a circle-drawing task. The deeper the left relative to the right central sulcus in M1-HAND, the stronger was the right-hand advantage in drawing performance. This effect was not related to age, gender, or the total cortical surface of the cerebral hemispheres. It also cannot be explained by handedness, because all participants were consistent right-handers. The results indicate that manual proficiency is associated with increased cortical folding, resulting in a deeper sulcus in the more proficient hemisphere.
The complete mitochondrial genome of the lesser sac-winged bat Saccopteryx leptura (Chiroptera: Emballonuridae) from Costa Rica

Abstract Here we present the first complete mitochondrial genome of the lesser sac-winged bat Saccopteryx leptura (Chiroptera: Emballonuridae) from Costa Rica, assembled from next-generation sequencing data. The mitogenome of Saccopteryx leptura measures 16,577 bp in length, and contains 13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes. A slight A + T bias was observed in the mitogenome of Saccopteryx leptura with an overall base composition of 31.5% A, 28.3% T, 25.8% C, and 14.2% G, and a GC content of 40.1%. The gene arrangement was identical to that of previously described bat mitogenomes.
Demography and Behavior of Western Sandpipers (Calidris mauri) Breeding on the Yukon-Kuskokwim River Delta, Alaska

I conducted demographic and behavioral studies of Western Sandpipers (Calidris mauri) breeding on the Yukon-Kuskokwim River Delta, Alaska (1998–2005). In chapter one, I estimated apparent annual survival (product of true survival and site fidelity) while correcting for the probability of encounter for 237 males and 296 females. Overall return rates (individual returned to the site in a subsequent season) were lower for females (40%) than males (65%), as was apparent annual survival (± SE, females = 0.65 ± 0.05, males = 0.78 ± 0.03), and encounter rate (females = 0.51 ± 0.07, males = 0.74 ± 0.04). In chapter two, I examined the effects of mate and site fidelity on nesting success (N = 430 nests). Annual divorce rate ranged between 37– 83%, with 17–63% of pairs reuniting annually. Reuniting pairs initiated clutches earlier than newly formed pairs, and clutches that were initiated early in the season had higher nest success rates compared to late-season nests. When I controlled for clutch-initiation date, nests tended by individuals with prior breeding-site experience had higher daily survival rates compared to birds breeding at the site for the first time. The effect of site experience was greater for males than females. In chapter 3, I reported that Western Sandpipers exhibited aggregated breeding behavior on a 36 ha plot. Breeding aggregations occurred when dominant and/or older individuals excluded younger, subordinate individuals from preferred habitat. The pattern of habitat occupancy conformed to an ideal despotic distribution with aggregated nesting birds in less preferred habitat experiencing lower reproductive success. In chapter 4, I described and demonstrated the form and function of parent-chick communication in the Western Sandpiper. Through experimental playback of adult vocalizations to chicks in the field, I demonstrated: (1) chicks respond to the alarm call by vocalizing relatively less often and moving away from the signal source, (2) chicks respond to the gather call by vocalizing relatively more often and moving toward the signal source, (3) and chicks respond to the freeze call by vocalizing relatively less often and crouching motionless on the substrate for extended periods of time. I also describe two distinct chick vocalizations (chick-contact and chick-alarm calls).
Genetic Considerations in the Evolution of Sexual Dimorphism

Genetic Considerations in the Evolution of Sexual Dimorphism Minyoung Janet Wyman Doctor of Philosophy Graduate Department of Ecology & Evolutionary Biology University of Toronto 2012 Sexual differences are dramatic and widespread across taxa. However, a common genome between males and females should hinder phenotypic divergence. In this thesis I have used experimental, genomic, and theoretical approaches to study processes that can facilitate and maintain differences between males and females. I studied two mechanisms for the evolution of sexual dimorphism− condition-dependence and gene duplication. If sex-specific traits are costly, then individuals should only express such traits when they possess enough resources to do so. I experimentally manipulated adult condition and found that the sex-biased gene expression depends on condition. Second, duplication events can permit different gene copies to adopt sex-specific expression. I showed that half of all duplicate families have paralogs with different sex-biased expression patterns between members. I investigated how current sexual dimorphism may support novel dimorphism. With regards gene duplication, I found that related duplicates did not always have different expression patterns. However, duplicating a pre-existing sex-biased gene effectively increases organismal sexual dimorphism overall. From a theoretical perspective, I investigated how sexually dimorphic recombination rates allow novel sexually antagonistic variation to invade. Male and female recombination rates separately affect invasion probabilities of new alleles. ii Finally, I examined the assumption that a common genetic architecture impedes the evolution of sexual dimorphism. First, I conducted a literature review to test whether additive genetic variances in shared traits were different between the sexes. There were few significant statistical differences. However, extreme male-biased variances were more common than extreme female-biased variances. Sexual dimorphism is expected to evolve easily in such traits. Second, I compared these results to findings from the multivariate literature. In contrast to single trait studies, almost all multivariate studies of sexual dimorphism have found variance differences, both in magnitude and orientation, between males and females. Overall, this thesis concludes that sexual dimorphism can evolve by processes that generate novel sexual dimorphism or that take advantage of pre-existing dimorphism. Furthermore, a common genome is not necessarily a strong barrier if genetic variances differ between the sexes. It will be an exciting challenge to understand how mutation and selection work together to allow organisms differ in their ability evolve sexual dimorphism.
Detection of genetic diversity in Ocimum species using RAPD markers

Ocimum is an important member of Lamiaceae and the genus is an important source of many essential oils and aroma chemicals in perfumery and cosmetic industries. Ocimum species are Used as pot herbs and find diverse uses in the indigenous system of medicine of many Asian and African countries, from industrial point of view. Ocimum species with oil rich in camphor, citral, geraniol, linalool, linalylacetate and methyl etc., are important and can be harnessed for successful utilization in industry. There is a variation in the production of these products among different species of Ocimum. Therefore, precise characterization of promising species and determination of genetic variation among those are felt necessary. Until recently, ever-promising species released formally are characterized based on morphological data, organic content and yield potential. These characters differ under varying environmental condition thereby nosing problem in proper identification of species. Unlike morphological markers, cytological (chromosome number, nuclear DNA content) and molecular markers (RAPD, AFLP, ISSR etc., ) are not prone to environmental influences and accurately characterize the plants portraying the extent of genetic diversity among the taxa. Of the different markers RAPD has been widely used in the last decade in species identification programme and in accessing genetic variations among different taxa at DNA level because of its cost effectiveness and simple operation without requiring prior knowledge of species DNA sequences. RAPDs reveal similar patterns of genetic diversity when compared with other markers type, can be performed more rapidly than most other methods, and can provide vital information for the development of genetic, sampling, conservation and improvement strategies. Random amplified Random amplified polymorphic DNA (RAPD) markers were employed to study the genetic relationships between six Ocimum species. Of the 80 random primers screened 10 primers resulted in 73 RAPD bands of good amplification. The data structure included a total of 100 to 1000 base pair marker levels. A dendrogram was constructed using Euclidean distances by Ward’s method. Based on the number of bands all the species were grouped into three clusters and the dendrogram maximum similarity between the Ocimum species.
Isolation of a Quercetin-metabolizing Bacterium 19-20 from Human Feces

Much attention has been focused on the potential health-promoting effects of quercetin, a flavonoid that is metabolized by the intestinal microbiota. However, there are few reports on the intestinal bacteria that degrade quercetin. We isolated the quercetin-degrading bacterium strain 19 _ 20 (Accession no: LC175305) from human feces. Based on comparative 16S rRNA gene sequence analysis, the bacterium exhibits 100% similarity to Clostridium orbiscindens (Accession no: Y18187). Quercetin degradation was observed to increase in a time-dependent manner when co-incubated with strain 19 _ 20 in vitro; the majority of quercetin was degraded within 24 hr. Strain 19 _ 20 quercetin degradation was inhibited by resveratrol. Co-incubation of quercetin and resveratrol significantly reduced strain 19 _ 20 quercetin degradation. This is the first report of the inhibitory effect of resveratrol on quercetin degradation by intestinal bacteria.
The ectoparasite community of Liza ramada : population interactions and variable environments

In the Vaccares lagoon (Rhone delta, Camargue, France), mullets of the species Liza ramada (Pisces, Teleostei) are parasitized by seven metazoan species, ectoparasites of gills : six Monogenea and one Copepoda. The spatial and temporal structures of this parasite community were analysed. The host migrates within this delta in the course of the seasons, and its parasites are potentially affected by the fluctuating environmental constraints. The crossed effects between the structure of the parasite infrapopulations and some environmental characteristics were studied with a co-inertia analysis. This study emphasizes the interactions between the populations structures and the environment, and their consequences on local biodiversity.
Effect of Selenium Yeast and Vitamin E Supplementation on Growth, Nutrient Utilization and Immunity in Male Kids (Capra hircus)

An experiment aimed to observe the effects of supplementation of selenium yeast and/or vitamin E on their growth, nutrient utilization and immune response. 24 male kids (2-3 months) were divided into Group I (control; without any supplementation), II (0.3 mg selenium kg-1DM as Se-yeast), III (100 mg of vitamin E as DL-α-tocopheryl acetate ) and IV (combination of II and III) along with a basal diet (concentrate mixture and oat straw) to meet their nutrient requirement for 180days. No significant (P>0.05) effect of selenium yeast and/or vitamin E supplementation on average daily gain, digestibility of nutrients, retention of nitrogen, calcium and phosphorus. Highest (P