Miracle-dz/UniFAR-FTUs huggingface dataset:
Prehistoric Molluscan Faunas of the Yazoo River, Mississippi, USA: Archaeological Perspectives for Modern Conservation

ABSTRACT Archaeological faunal assemblages can provide data valuable to modern conservation ecology. For example, while freshwater mussels (Bivalvia: Unionidae, Margaritiferidae) are common constituents in the archaeological record of North America, today they are one of the world’s most imperiled faunal groups. Efforts to aid habitat restoration, population growth, and species reintroduction can be informed by studies of prehistoric mussel assemblages. These data can provide a historical perspective, cataloging communities as they existed prior to extensive modern impacts, thus representing an ecological baseline to be compared with modern populations. This study focuses on two late prehistoric (ca. 300–600 AD) sites on the Yazoo River, where nearly 24,000 freshwater mussel valves were recovered. Though modern data are extremely limited for the river, analysis revealed it once supported a diverse mussel community containing numerous species currently considered rare, endangered, or extinct in Mississippi. In total, the combined shell assemblages yielded 23 new river records for the Yazoo River. One species in particular, Quadrula fragosa, represents the second such occurrence in Mississippi, and bolsters its candidate status as a new state record, as argued in a recent report from a neighbouring river in the Yazoo Basin.
Towards high throughput and spatiotemporal proteomics : analytical workflows and quantitative label-free mass spectrometry

A large part of modern biology is dedicated to the functional annotation and interpretation of genetic information and its influence on the subject’s phenotype. Proteomics describes the state of the system from the perspective of expression, structure, localization, interaction and function of the proteins. It is a complex field which requires a combination of various disciplines such as cellular biology and biochemistry for sample preparation, analytical chemistry for sample measurement and bioinformatics for the processing of data. Different chapters of this thesis illustrate various aspects of the proteomics pipeline and emphasize the importance and connection between them. Therefore the information in this dissertation can be divided into three major parts depicting these aspects of a proteomics experiment. First, sample preparation for proteomics has been addressed through two studies aimed at decreasing sample complexity and increasing proteome coverage. The second part is dedicated mostly to the technical step of the mass spectrometry measurement and the analysis of obtained spectra. The final part describes example- and proof-of-principle applications.
Evaluating the Genetic Link between Autophagy and Parkinson's Disease in Budding Yeast Model

Parkinson’s disease (PD) is an incurable neurodegenerative disease characterized by the death of midbrain dopaminergic neurons. The suspected cause of PD is the misfolding and aggregation of a brain protein, α-synuclein. A popular hypothesis is that increasing degradation of α-synuclein may protect the cell from aggregation and toxicity. While strong pharmacological evidence indicates that autophagy is involved in the degradation of α-synuclein in PD, the genetic link remains weak. For my senior thesis, I evaluated the hypothesis that the lysosome is the route for α-synuclein degradation by the autophagy pathway. Specifically, I studied the genetic link between autophagy and α-synuclein using a budding yeast model. My results demonstrate four significant findings. First, through genetic evidence, my results support the hypothesis that α-synuclein is regulated by the autophagy pathway. Of the six autophagy genes that I evaluated, deletion of each altered one or more αsynuclein PD-related properties. Second, these deletion effects on α-synuclein were gene-specific, indicating substrate-specificity. Third, α-synuclein localization exhibited a range of cellular distributions depending on the deleted gene. Finally, I did not observe α-synuclein dependent toxicity. Our lab's cumulative data further supports the hypothesis that the lysosome is the route for α-synuclein degradation by the autophagy pathway.
Quantifying sea urchins covering behavior by image analysis

Many sea urchin species collect debris on their aboral surface, a behavior collectively described as “covering behavior”. In the Sultanate of Oman, the flower sea urchin, Toxopneustes pileolus, systematically shows this behavior, accumulating pieces of dead coral, pebbles, and fragments of various mollusks shells on its test. We compared the amount, size distribution, and relative volumetric mass of the covering material in three T. pileolus populations using both underwater image analysis and physical analysis of collected debris. The underwater photographic method to estimate test cover was a good predictor of the actual amount of debris on the test (R2 = 0.85). Toxopneustes pileolus, preferred covering itself with the largest pieces of debris available in the surface sediment, but did not select pieces according to relative density. There were no significant differences in percentage cover neither among urchins of different diameters nor among urchins collected in different populations. We discuss these results in relation to various advanced hypothesis on the function of the covering behavior. Résumé : Quantification du comportement de couverture chez les oursins par analyse d’image. Plusieurs espèces d’oursin accumulent sur la face aborale du test des débris divers: un comportement qualifié de “couverture”. Au Sultanat d’Oman, l’oursin Toxopneustes pileolus fait preuve de ce comportement de façon systématique et accumule sur son test des fragments de coquille de mollusque, des morceaux de corail mort ou de petits gravillons. Nous avons comparé la quantité, la distribution de taille et la masse volumique relative de ces matériaux dans trois populations de T. pileolus en utilisant d’une part une méthode de photographie sous-marine et d’autre part une analyse detaillée du matériel recolté au laboratoire. La méthode d’analyse photographique in situ s’est avérée un bon indicateur de la quantité de débris accumulés par les oursins (R2 = 0.85) malgré une tendance à la sous-estimation. Toxopneustes pileolous semble préférer les particules les plus grosses parmi celles se trouvant dans le sédiment voisin mais sans prendre en compte leur masse volumique. Nous n’avons observé de différence entre le niveau de couverture des oursins, ni entre populations, ni entre oursins de tailles différentes. Ces résultats sont mis en relation avec les différentes hypothèses avancées afin d’expliquer le “comportement de couverture”.
Molecular analysis of alternaria populations early blight causal agents in potato plants.

Early blight of potato can be caused by the two fungi Alternaria solani and Alternaria alternata, with significant impact observed on crop productivity in the field from the last past years in Europe. However, it is impossible to determine visually if the necrotic symptoms are caused by one or the other species. On the other hand, the differentiation of the two species based on the observation of the morphology of the spores is not considered as fully reliable because this spore diagnostic first means that the fungi remain alive despite of the collect conditions (treatments and drying situations) in the field. Secondly, Alternaria alternata differentiates spores much faster than Alternaria solani when isolated on artificial medium in Petri dish introducing a bias in this morphological diagnostic when both are present on the same sample. Finally the efficacy of fungicides has been demonstrated dependent on the fungal species especially for the QoI fungicides. In fact, the use during these last years of QoI fungicides has shown the development of resistance due to the respective F129L and G143A mutations according the species in the genes encoding the cytochrome bc1, Qo site of the respiration complex III. To improve the diagnostic of both Alternaria species and the detection of the point mutations conferring the resistance to the respiration complex III inhibitors, Bayer SAS has developed molecular tools to support Alternaria sp. monitoring and appropriate fungicide recommendation in the field. The fine analysis of the sequences of the genes encoding the cytochrome bc1 reveals the presence of not yet described sequences in the introns of several Alternaria isolates. The presence of these particular sequences will be discussed in term of Cyt bc1 gene organization, fungal population evolution, and horizontal gene transfer.
Analysis of the Ovine NEU1 Gene in a Unique Model of GM1 Gangliosidosis

4 INTRODUCTION . 6 LYSOSOMES . 6 LYSOSOMAL STORAGE DISORDERS . 7 GM-­‐1 GANGLIOSIDOSIS . 8 ANIMAL MODELS OF GM1 . 10 UNIQUE OVINE MODEL . 10 LYSOSOMAL MULTIENZYME COMPLEX . 11 ALPHA-­‐NEURAMINIDASE . 12 OBJECTIVES OF THIS STUDY . 14 METHODOLOGY . 16 MATERIALS AND METHODS . 18 GENOMIC DNA ISOLATION AND PURIFICATION . 18 ANALYSIS OF ISOLATED GENOMIC DNA . 19 PRIMER DESIGN FOR POLYMERASE CHAIN REACTION . 19 POLYMERASE CHAIN REACTION AMPLIFICATION . 19 AGAROSE GEL ELECTROPHORESIS . 19 EXTRACTION AND PURIFICATION OF FRAGMENTS FROM THE LOW MELT GEL . 20 DNA SEQUENCING AND ANALYSIS . 21 RESULTS . 21 GENOMIC DNA CONCENTRATION AND PURITY . 21 AGAROSE GEL ELECTROPHORESIS VISUALIZATION OF PCR PRODUCTS . 21 DNA SEQUENCE AND CHROMATOGRAM ANALYSIS . 22
The contents of amino acids and sterols in maize plants growing under different nitrogen conditions

The effect of nitrogen nutrition on phytosterol and amino acid content in aboveground biomass of maize (Zea mays l.) was investigated in a pot experiment. For cultivation of maize plants nitrogen dose (2 or 4 g n/pot) was applied in the form of ammonium nitrate (an) for control treatments or urea ammonium nitrate solution (Uan). Uan solution was applied according to the CUltan method (Controlled Uptake long term ammonium nutrition). The content of amino acids as important nitrogen-containing compounds in plant biomass was affected by nitrogen nutrition. an increase of glutamine and asparagine levels in maize aboveground biomass was observed after Uan solution application. The results of free β-sitosterol analyses by HPlC showed its 94% increasing concentration after Uan application in contrast to an treatments. our results confirmed that sterol interconversions are controlled by environmental conditions and they are involved in the regulation of membrane properties in response to changing growth conditions.
The signature of human pressure history on the biogeography of body mass in tetrapods

Aim Examining the biogeography of body size is crucial for understanding how animal communities are assembled and maintained. In tetrapods, body size varies predictably with temperature, moisture, productivity seasonality and topographical complexity. Although millennial-scale human pressures are known to have led to the extinction of primarily large-bodied tetrapods, human pressure history is often ignored in studies of body size that focus on extant species. Here, we analyse 11,377 tetrapod species of the Western Hemisphere to test whether millennial-scale human pressures have left an imprint on contemporary body mass distributions throughout the tetrapod clade. Location Western Hemisphere. Time period Contemporary. Major taxa studied Tetrapods (birds, mammals, amphibians and reptiles). Methods We mapped the distribution of assemblage-level median tetrapod body mass at a resolution of 110 km across the Western Hemisphere. We then generated multivariate models of median body mass as a function of temperature, moisture, productivity seasonality and topographical complexity, as well as two variables capturing the history of human population density and human-induced land conversion over the past 12,000 years. We controlled for both spatial and phylogenetic autocorrelation effects on body mass–environment relationships. Results Human pressures explain a small but significant portion of geographical variation in median body mass that cannot be explained by ecological constraints alone. Overall, the median body mass of tetrapod assemblages is lower than expected in areas with a longer history of high human population density and land conversion, but there are important differences among tetrapod classes. Main conclusions At this broad scale, the effect of human pressure history on tetrapod body mass is low relative to that of ecology. However, ignoring spatial variation in the history of human pressure is likely to lead to bias in studies of the present-day functional composition of tetrapod assemblages, at least in areas that have long been influenced by humans.
Beyond predator satiation: Masting but also the effects of rainfall stochasticity on weevils drive acorn predation

Escaping seed predation is a classic “economy of scale” hypotheses (predator satiation hypothesis, Psh) to explain the selection for the synchronous production of massive and nil seed crops (masting) in plants. The Psh postulates that predator satiation occurs through a combination of (1) “functional satiation,” as not all seeds can be consumed during a massive crop, and (2) “numerical satiation,” as predator populations collapse during poor crop years. Many studies advocate for the Psh, but few have investigated the importance of masting compared to other factors for the control of predation extent. Namely, environmental cues prompting masting could also determine predator's success and, ultimately, influence directly and independently seed predation intensity. We explored this question in Mediterranean oaks, as they exhibit strong masting behavior; acorns are heavily predated upon by weevils; and rainfall stochasticity drives masting and the emergence of adult weevils from the soil. Results of two mid-term studies (4 and 11 yr) showed that acorn production and predation were highly variable across years, while the abundance of adult weevils was positively related to autumn rainfall and to the number of infested acorns the previous years. Ultimately, acorn predation was negatively influenced by inter-annual fluctuation of seed production (masting) yet, mainly and positively, prompted by autumn rainfall and acorn crop size (only in one site). Our results highlight the relevance of masting to reduce seed predation. Yet evidences that rainfall stochasticity directly determines the success of weevils, and it independently influences seed predation extent, indicate that environmental cues prompting masting may also fine-tune the output of this reproductive behavior. Additionally, local differences suggest that the relevance of masting may change with tree characteristics (low vs. high seed production) and landscape structure (isolated vs. dense forests). We also discuss what can be the effects of increasing drought in Mediterranean areas for this antagonistic interaction, triggered by rainfall.
Neotropical mycophagous drosophilids (Diptera: Drosophilidae): DNA barcoding as a way of overcoming the taxonomic impediment

Within Drosophilidae, the Zygothrica genus group corresponds to a speciose mycophagous group, which remains insufficiently investigated despite its potential for ecological and evolutionary studies. The recognised gap in the knowledge of species diversity and the threat provided by global warming due to niche conservatism and stringent temperature and humidity requirements make this group an excellent candidate for testing the implementation of DNA barcoding, which is the aim of this study. Extensive prospecting in various parts of Brazil provided 220 specimens. Considering both the morphological and molecular results, these individuals consisted of 56 species that could be distributed into three categories: 22 corresponded to previously described species, 24 very likely corresponded to undescribed species, and 10 uncertain cases corresponded mainly to one or a few females. Intra‐specific distances ranged from 0% to 5.3%, whereas inter‐specific congeneric and inter‐generic distances ranged from 2.4% to 21.7% and from 7.4% to 20% respectively. Moreover, all species were revealed as reciprocally monophyletic and presented positive barcoding gap values; 62.5% of them presented diagnostic characters. Although coalescent‐based methodologies suggested some additional splitting, species initially considered to be different were never lumped together. Therefore, in general, DNA barcoding of mycophagous drosophilids provided results that are largely congruent throughout different molecular approaches and also with morphological boundaries. Several putative new species were revealed, highlighting the potential of cytochrome c oxidase subunit I (COI) barcodes as a tool complementary to traditional taxonomy in unravelling cryptic diversity among Neotropical mycophagous drosophilids.
Effects non-digested and anaerobically digested farmyard manures on wheat crop cultivated in desert soil

Digesting animal manure anaerobically before applying it as fertilizer may be affected crop production differently compared to non-digested particularly in desert soils. A pot experiment was carried out to evaluate three non-digested (NDM) and digested (DM) farmyard manures (cattle, poultry, and sheep) and their combinations with urea on the wheat crop cultivated in desert soil. Fertilizers were applied at rates corresponding to 50, 150 and 250 kg Tot N ha -1 . During the growing period, seed germination percentage (SGP), plant height, plant tillering percentage (PTP) and deficiency symptoms were assessed. Furthermore, total biomass yield and relative yields of ear, straw and root fractions were measured at harvest. Results showed that high application of DM reduced SGP significantly (p<0.05), especially at the combination with urea. PTP was higher in non-digested manure treatments of sheep and poultry than DM, and also higher in digested cattle manure treatments than NDM, while it was zero in all urea treatments and control. Deficiency symptoms were seen in the treatments of low application rate as well as in all urea treatments and control. Plant height and biomass yield generally increased in NDM and DM treatments compared with urea treatments and the control. Beneficial of DM was seen in cattle and poultry manure treatments where they significantly (p<0.05) yielded higher root, ears, and total biomass compared to NDM. However, non-digested sheep and poultry manure yielded higher straw biomass than DM. The combination of non-digested and digested manure with urea gave the maximum biomass yield, especially in combination with digested poultry manure.
Études des interactions entre les immunoglobulines G et leurs récepteurs Fc gamma afin d'évaluer le patron de glycosylation des anticorps

With several patents expiring within the next years, an increasing number of biopharmaceutical companies have started producing biosimilar antibodies. These therapeutic molecules must meet several criteria for health agencies, such as the obtainment of a “desirable” glycosylation pattern, which still represents a challenge for the industry in terms of control and characterization. It is in this context that the Canadian network MabNet, to which this project belongs, was born. This thesis is part of the analytical activities of the network and aims to develop a kinetic and/or reliable thermodynamic assay to evaluate the glycosylation profiles of different monoclonal antibodies. In this endeavour, the interactions between the extracellular domains of Fcγ receptors and monoclonal antibodies have been explored using a surface plasmon resonance (SPR)based biosensor. In an initial study, we have produced and purified the extracellular domains of both his-tagged FcγRI and FcγRIIIa receptors by transient transfection in mammalian cells. These receptors were used in an analytical surface plasmon resonance (SPR)-based assay to evaluate the glycosylation patterns and the aggregation state of the monoclonal antibodies. This work was published in the “Journal of Immunological Methods” in 2014. These results have also been presented during the “Canadian Conference of Chemical Engineering” in 2012 as the Keynote speaker (CSChE, Vancouver) and during the international conference named “Protein Expression in Animal Cell” in 2013 (PEACe, Kananaskis). More precisely, the comparison between the covalent immobilization of the receptors and their oriented capture via an anti-Histidine antibody (which associates with the his-tag) was performed by SPR. The non-oriented grafting of the receptor ectodomains was shown to generate complex kinetics, more likely due to the presence of several receptor populations at the biosensor surface as a result of the non-oriented chemical immobilization. A receptor capture approach based on anti-Histidine antibody greatly improved the assay, however, the kinetic still deviated from the Langmuir model (1:1). This deviation was due to the fact that, upon antibody binding, the affinity of the receptor ectodomain for the capture anti-His antibody diminished, resulting in receptor dissociation from the surface of the SPR instrument. These results suggest that capturing receptors via an anti-Histidine antibody is not ideal: another capture strategy should be considered to eliminate this artefact. This initial study also allowed us to highlight that a SPR assay is an interesting alternative to analytical ultracentrifugation analysis for the detection of aggregates
ELICITATION OF THERAPEUTIC POTENTIAL AND OXIDATIVE STRESS ASSESSMENT OF FENUGREEK SPROUTS UNDER UV IRRADIATION

Objective: To evaluate the effect of ultraviolet (UV) radiation on the therapeutical and oxidative stress status of fenugreek seedlings during the post-germination phase. Methods: The seeds of Trigonella foenum-graecum L. were subjected to UV radiation of different wavelengths UV 254 nm, UV 365 nm and the combination of 254 nm and 365 nm UV during the course of germination up to 96 h. Free radicals scavenging activity, in vitro antidiabetic activity as well as total phenol (TPC) and flavonoid (TFC) contents were evaluated up to four days of germination stages. Analysis of total activities of superoxide dismutase (SOD), peroxidase, catalase and NADPH oxidase (NOX) was conducted using non-denaturing polyacrylamide gel electrophoresis along with histochemical detection of H 2 O 2 and superoxide radical localisation, lipid peroxidation and plasma membrane integrity was also performed. Results: Overall it was observed that the sprouts exposed to UV 365 nm exhibited a significant enhancement in free radical scavenging as well as antidiabetic activity at the 48h stage of germination. Interestingly highest phenol and flavonol content were also stimulated at the same stage by UV 365 nm. The effect of UV irradiation was evident on the localisation of H 2 O 2 and superoxide radical. The on gel assay revealed that the total activities of the antioxidant enzymes were extensively elevated by UV irradiation. Conclusion: The results suggest that the UV irradiation technology can be implemented for the enhancement of nutraceutical properties of sprouts also UV exposure helps in the induction of the antioxidant enzyme system which may be beneficial for oxidative stress management in plants during germination phases.
Incipient capture myopathy as revealed by blood chemistry of chased zebras

Zebra (Equus zebra hartmannae and E. burchelli antiquorum) were subjected to stress which gave rise to elevation of cardiac rate, haematrocit, plasma osmolality and plasma levels of glucose, lactate and creatine kinase. These changes were very similar to those observed in animals actually suffering from capture myopathy. It was therefore tentatively concluded that incipient: signs of shock and therefore of capture myopathy were evident in the chased group of animals.