Miracle-dz/UniFAR-FTUs huggingface dataset:
Composting of laying hen manure with the addition of a yeast probiotic

Abstract This study assessed the effect of inclusion of a yeast probiotic on the counts of lactobacilli, total aerobes (TA), total coliforms (TC), E. coli and Salmonella in the composting of laying hen manure. The yeast probiotic concentration (0, 7.5 and 15% wet basis) in the composting effect was defined as factor A and the fermentation time (FT) (0, 7 and 23 days) was defined as factor B. A completely randomised design with a factorial arrangement of 3 × 3 and four replicates was used. An interaction was found in Salmonella and pH (p < .0001). The lowest (p < .05) Salmonella counts were obtained at day 7 in the treatments with 7.5% and 15%, respect to the control. The lowest values (p < .05) for pH were obtained at day 23 in the treatments containing 0 and 15%. Lactobacilli, E. coli, TC, whereas TA counts were affected only by fermentation time (p < .05). In all treatments, lactobacilli increased (p < .05) by day 7. E. coli and TC counts decreased (p < .05) across the fermentation time and TA remained constant for the first seven days. (p < .05). Anaerobic fermentation of poultry litter over 23 days is sufficient to lower the pH and eliminate pathogenic microorganisms.
Females prefer cooperative males even when cooperative behavior is unobserved: evidence from the mound-building mouse, Mus spicilegus

Theoretical and empirical studies in humans suggest that cooperative behaviors may act as signals during mate choice. However, cooperation is not always observable by potential partners before mate choice. To address whether cooperative phenotypes are preferred based on cues different from cooperative behaviors per se, we designed an experimental paradigm using wild-born mound-building mice (Mus spicilegus), a species with biparental care. In this species, females cannot observe male cooperative behaviors: mate choice occurs in the spring, whereas mounds are cooperatively built in the fall. We first assessed the variation in mound building investment and identified males exhibiting high and low amounts of cooperation. Second, we presented these males to females during two-way choice tests. As offspring survival relies on mound protection, we hypothesized that mound building could be a form of paternal care and assessed whether cooperative males were more involved in offspring attendance using pup-retrieval experiments. Our results indicate that females were more attracted to highly cooperative males over less cooperative, even when they did not observe them build. This finding suggests that female mate choice is influenced either by cues of cooperativeness different than cooperative behaviors or by preferences for traits associated with cooperativeness. Moreover, male offspring attendance was negatively correlated with cooperativeness, suggesting the potential existence of two alternative paternal strategies in offspring care (mound building versus offspring attendance). Overall, our findings support the existence of preference for cooperative phenotypes in a non-human species and suggest that sexual selection might be involved in the evolution of cooperation.
Agricultural Intensification Can Preserve the Brazilian Cerrado: Applying Lessons From Mato Grosso and Goiás to Brazil’s Last Agricultural Frontier

Food security and climate change are two pressing issues shaping the future of tropical land use. Brazil, home to abundant land that is rich in carbon, water, and biodiversity and often cleared for agropastoral and renewable energy purposes, is the ideal location for studying socioeconomic and environmental trade-offs of land use dynamics. Here, I use recent (2000–2016) land-use land-cover change dynamics in the established agricultural states of Mato Grosso and Goiás to demonstrate how incentivizing intensive agricultural practices and improving degraded pastures may be a means by which Brazil can increase agricultural production while conserving the remainder of the Cerrado. I then discuss these outcomes with regard to agricultural expansion in the agricultural frontier region of Matopiba and briefly highlight contextual elements that need to be considered by other developing tropical countries looking toward Brazil as a model for agricultural and economic development.
Estimating cell type proportions in human cord blood samples from DNAm arrays

Epigenome-wide association studies are used to link patterns in the epigenome to human phenotypes and disease. These studies continue to increase in number, driven by improving technologies and decreasing costs. However, results from population-scale association studies are often difficult to interpret. One major challenge to interpretation is separating biologically relevant epigenetic changes from changes to the underlying cell type composition. This thesis focuses on computational methods for correcting cell type composition in epigenome-wide association studies measuring DNAm in blood. Specifically, we focus on a class of methods, called reference-based methods, that rely on measurements of DNAm from purified constituent cell types. Currently, reference-based correction methods perform poorly on human cord blood. This is unusual because adult blood, a closely related tissue, is a case-study in successful computational correction. Several previous attempts at improving cord blood estimation were only partially successful. We demonstrate how reference-based estimation methods that rely on for cord blood can be improved. First, we validated that existing methods perform poorly on cord blood, especially in minor cell types. Then, we demonstrated how this low performance stems from missing cell type references, data normalization and violated assumptions in signature construction. Resolving these issues improved estimates in a validation set with experimentally generated ground truth. Finally, we compared our reference-based estimates against reference-free techniques, an alternative class of computational correction methods. Going forward, this thesis provides a template for extending reference-based estimation to other heterogeneous tissues.
Mechanisms that maintain coexistence of antibiotic sensitivity and resistance also promote high frequencies of multidrug resistance

Antibiotic resistance, and in particular, multidrug resistance are public health concerns. Yet, there has been little theoretical work on the evolutionary dynamics of multidrug resistance (MDR). Here, we present a generic model of MDR inspired by two pervasive trends in resistance dynamics. The first trend is the robust coexistence of antibiotic sensitivity and resistance in multiple bacterial species and for numerous antibiotics. The second is that resistance to different antibiotics tends to be concentrated on the same strains, giving rise to high MDR frequencies. We argue that these two observations are linked: mechanisms that maintain coexistence also promote high MDR frequencies. This argument is based on the recognition that, in many of the most plausible models of coexistence, the coexistence-maintaining mechanism is fundamentally similar: either strain or host population structure stratifies the pathogen population into sub-populations and introduces variation in the fitness effect of resistance between these sub-populations. We show that this model structure also gives rise to high MDR frequencies, because resistance against all antibiotics is concentrated in the sub-populations where the fitness advantage gained from resistance is high. We test predictions from this model on two pneumococcal datasets and find predicted trends are qualitatively consistent with those observed in data. This model provides a parsimonious explanation for the pervasiveness of high MDR frequencies and allows us to reconcile this trend with observed long-term stability in the prevalence of resistance.
How feathered are birds? Environment predicts both the mass and density of body feathers

1.Studies modelling heat transfer of bird plumage design suggest that insulative properties can be attributed to the density and structure of the downy layer, whereas waterproofing is the result of the outer layer, comprised of contour feathers. In this study, we test how habitat and thermal condition affect feather mass and density of body feathers (contour, semiplume and downy feathers) measured on the ventral and dorsal sides of the body, using a phylogenetic comparative analysis of 152 bird species.2. Our results demonstrate that feather mass and the density of downy feathers are higher in species that inhabit colder environments, whereas total feather density is higher of species breeding under intermediate temperatures compared to the ones breeding under more extreme conditions. The density of contour feathers, depending on the body region, is either quadratically related or negatively correlated with minimum winter temperature.3. The density of contour and downy feathers, measured on both sides of the body, is higher in aquatic than in terrestrial birds. However, among the former, diving behaviour does not select for further increases in body feather mass or density.4. The results of this study provides key insights into how the plumage of birds is adapted to different environments and lifestyles and provides a basis for understanding the diverse range and the evolution of variation in these characteristics. (Less)
A propos de ceux cas de paludisme grave contractés sur le port de Marseille

Deux cas de paludisme a Plasmodium falciparum ont ete observes pendant l'ete 1993 chez des habitants d'un quartier du port de Marseille qui n'avaient jamais voyage outre-mer. Les resultats de l'enquete epidemiologique sont en faveur de l'importation par un bateau en provenance d'Afrique tropicale d'anopheles infestants qui, pendant leur transport et a leur arrivee, ont beneficie de conditions climatiques favorables a leur survie. L'attention des medecins de la ville a ete attiree sur la necessite d'evoquer le diagnostic de paludisme chez tout patient presentant une fievre d'origine indeterminee, particulierement en periode estivale et sans tenir compte d'un sejour eventuel en region d'endemie palustre.
Biosynthesis and Regulation of Phenylpropanoids in Plants

ABSTRACT Phenylpropanoids are a large class of plant secondary metabolites derived from aromatic amino acids phenylalanine in most plants or tyrosine in partial monocots. It mainly includes flavonoids, monolignols, phenolic acids, stilbenes, and coumarins. Phenylpropanoids are widely distributed in the plant kingdom and play vital roles in plant development by acting as essential components of cell walls, protectants against high light and UV radiation, phytoalexins against herbivores and pathogens, floral pigments to mediate plant–pollinator interactions. In addition, phenylpropanoids possess diverse biological activities that are beneficial to human health. In the past decades, the structure and function of phenylpropanoids and the biosynthetic pathways of flavonoids, monolignols and phenolic acids have been extensively studied. Recent results showed that miR828, ta-siRNAs and R2R3-MYBs play critical regulatory roles in phenylpropanoid biosynthesis through two modes: either the miR828–MYB–phenylpropanoid biosynthesis cascade in which MYB transcripts are directly cleaved by miR828, or the miR828–ta-siRNA–MYB–phenylpropanoid biosynthesis cascade under the mediation of TAS4- or MYB-derived ta-siRNAs. In this review, we overview the structure, function and biosynthetic pathway of phenylpropanoids and summarize the complex regulatory mechanism of phenylpropanoid biosynthesis with a focus on the two cascades involving miR828, ta-siRNAs and MYBs.
Yeast Ecology of Fermented Table Olives: A Tool for Biotechnological Applications

The table olive is considered to be a traditional fermented vegetable in the Mediter­ ranean countries and its production and consumption is recently spreading all around the world. The presence of yeasts is very important during olive fermentation due to their double role. On one hand, yeasts maintain desirable biochemical activities (lipase, esterase, β-glucosidase, catalase, production of killer factors, etc.) with essen ­ tial technological applications in this fermented vegetable. On the other hand, spoil­ age activity may be shown. However, recent studies have reported that yeasts coming from table olives would be a new source of potential probiotics. Indeed, many yeast species found in table olive processing, have been reported to demonstrate such prop­ erties. Thus, starter cultures technology will play significant role, not only in olive fermentation by controlling the safety and the quality of the final product, but also in consumer’s
Etude des homologies phénotypiques et fonctionnelles des lymphocytes B en latence III de l'EBV avec les cellules B régulatrices, implication de l'axe PD-1/PD-L1

Le virus d’Epstein-Barr (EBV) est le premier virus transformant a avoir ete identifie chez l’Homme. Il infecte plus de 90% de la population adulte mondiale, persistant sous forme episomale dans le compartiment B memoire tout au long de la vie de l’hote. Lors de la primo-infection et lors de phases de reactivation du virus, les cellules B immortalisees sont en programme de latence III, aussi appelee phase de proliferation, ou l’ensemble des proteines de latence sont exprimees. Lorsque les hotes sont immunocompetents, un equilibre entre hote et virus s’etablit et la plupart des cellules B infectees sont eliminees par le systeme immunitaire de l’hote, principalement par les lymphocytes T cytotoxiques. En cas de deficit immunitaire, il peut y avoir emergence de lymphomes, tels que les desordres lymphoproliferatifs des patients immunodeprimes (PTLDs), les lymphomes non-Hodgkiniens (LNH) et Hodgkiniens (LH). Les travaux anterieurs du laboratoire ont permis de reveler que l’immuno-inhibiteur PD-L1/B7-H1/CD274 est surexprime a la surface des lymphocytes B en latence III de l’EBV. L’interleukine-10 (IL-10) est egalement secretee par ces cellules. Ces caracteristiques sont communes aux cellules B regulatrices (Bregs). Le but de ma these etait d’interroger les caracteristiques immuno-modulatrices des cellules B en latence III de l’EBV, dans le cadre des proprietes des Bregs. Nous montrons que les cellules B en latence III de l’EBV possedent les determinants antigeniques communs aux Bregs immatures (CD24High CD38High PD-L1High), associee a une surexpression des cytokines immunosuppressives cardinales des Bregs (IL-10, TGF-β1 et IL-35). Nous montrons que les cellules B en latence III de l’EBV peuvent conduire a la mort des cellules T CD4 autologues, ainsi qu’a l’inhibition de la proliferation des lymphocytes T CD4 et CD8, au profit de l’expansion de lymphocytes T regulateurs (Tregs). Nous avons trouve que cette expansion est mediee par l’axe PD-1/PD-L1. Ces travaux mettent en evidence un nouveau mecanisme de l’EBV concernant le detournement du systeme immunitaire de l’hote, augmentant ses capacites oncogeniques.
An investigation into the role of transglutaminase 2 in the uptake of cisplatin in parental and chemoresistant cancer cells

A major problem in the successful treatment of cancer is a loss in the effectiveness of chemotherapeutic drugs, such as cisplatin, due to development of drug resistance by tumour cells. Such resistance necessitates prescription of higher and potentially toxic concentrations of drugs. The side-effects of such treatments therefore both reduces the quality of patients’ life, and also contributes to the failure of effective chemotherapy. At present, the mechanisms by which such drug resistance operates are not fully understood. However, candidate markers for drug resistance are emerging, one of which is transglutaminase 2 (TG2). TG2 is a ubiquitous, multifunctional enzyme that is implicated in several pathological and physiological processes, including the regulation of cell division and cell death. Two TG2 isoforms, TG2-L and TG2-S, have been characterised. The overexpression of TG2 has been observed in various aspects of cancer, including the development of drug-resistance and cell survival. However, the amount to which TG2 contributes to the cellular environment of normal and drug-resistant cancer cells is poorly understood and is still controversial. In order to establish whether TG2 is directly involved in drug resistance mechanisms, TG2 gene expression at the mRNA level and protein levels was modulated in the hepatocarcinoma (HepG2) cell line, and the effects were measured, using RT-PCR, Western blotting, flow cytometry, confocal microscopy, and a range of assays for determination of TG2-specific enzymatic activity. This study provides evidence that TG2 expression and its associated transamination activity are inhibited during the initiation of apoptosis by cisplatin, an observation that was reversed by increasing the expression of TG2 following the treatment of cells with retinoic acid. Single-dose treatment of HepG2 cells with IC80 concentrations of cisplatin generated drug-resistant progeny cells that exhibited reduced TG2 expression but increased enzyme activity, and this induced chemoresistance was accompanied by a reduced ability of cells to take up Alexa fluor 546/488-labelled cisplatin. Interestingly, treatment of cells with a classic TG2 inhibitor (cystamine), or treatment by TG2 mRNA silencing (siRNA), both reversed this effect and increased the level of uptake of fluorescent cisplatin in both parental and chemoresistant cancer cells. In conclusion, these results indicate that the presence of elevated levels of TG2 in hepatocellular carcinoma prevents and/or limits the entry of anti-cancer drugs. Thus, TG2 may represent a novel biomarker and possibly a therapeutic target for overcoming the chemotherapeutic resistance in hepatocarcinoma.
Studies on oxidative stress : activity levels of antioxidant enzymes in copper, zinc superoxide dismutase - deficient yeast cells expressing cloned Escherichia Coli iron superoxide dismutase

The Escherichia coli iron superoxide dismutase (FeSOD) gene was expressed, at two different levels (using episomal and centromeric plasmid systems), in Saccharomyces cerevi siae cells deficient in copper, zinc superoxide dismutase. Levels of antioxidant enzymes were studied in the recombinant strains in the presence and absence of 1 mM paraquat in minimal medium. Exposure to paraquat resulted in: (1) increase in the levels of total SOD, FeSOD, and catalase activities in both yeast strains expressing the FeSOD gene, and (2) decrease in the levels of glutathione reductase in yeast cells expressing the cloned FeSOD gene on the episo mal, but not on the centromeric, plasmid The increase in FeSOD activity suggested that there is stimulation of the yeast 3-phosphoglycerate kinase gene (PGK) promoter controlling the cloned FeSOD gene in the presence of paraquat This could be either due to the oxidative stress induced by paraquat, or as a result of an inherent effect of paraquat itself. This hypo thesis, that is, induction of the PGK promoter in S. cerevisiae under oxidative stress, is pre sently being studied in our laboratory. If confirmed, this finding would complement previous observations that transcription of S. cerevisiae PGK increases on heat-shock (Piper et al. (1986) Eur. 1. Bioc/zem. , 161,525-531). Thus the PGK gene could be implicated as being one of the genes that are induced as part of the general stress response of S. cerevisiae.
Grazer toxicity of littoral biofilms of diatoms

The zone of photosynthetic production by phytoplankton in lakes typically extends to a depth of several meters. Simply expressed, in photoautotrophic biofilms, this zone is condensed to a few millimeters in which steep gradients of photon flux density, oxygen concentration and nutrient availability are observed (e.g. KüHL et al. 1996). The physic<rehemical and biotic regulatory factors for biofilms are the same as for the pelagic phytoplankton. Because high densities of biomass are concentrated on a surface when biofilms develop, this energy and carbon source would be an ideal habitat for grazers. The question arises as to how defense mechanisms have been developed by biofilm microorganisms to reduce the grazing pressure. The growth habitat (e.g. the surface of stones, mud and living matter) attracts grazers which are not found, or are of minor imponance, in free water, such as snails, worms, larvae of insects, water fowl, ete. In addition, the animal groups that are effective grazers of the phytoplankton are also active in the upper stories of the biofilms (BARNES & MINSHALL 1983, STEVENSON et al. 1996). Astonishingly, extended photoautotrophic epilithic biofilms are observed during most periods of the year on stones in the littoral zone of many Central European lakes. This makes the existence of protection mechanisms rather likely. Diatom-dominated biofilms that develop every year in winter and spring in Lake Zürich (Switzerland) were investigated to determine whether they contain components that may be suitable for chemical defense from grazers. Acute grazer toxicity of the crustacean Thamnocephalus platyurus was used as a measure of this feature.
IN SILICO STUDIES FOR VARIOUS ANTIBACTERIAL BENZIL AND ITS SUBSTITUTED ANALOGS

Objective: The antibacterials have moved on to low levels by more challenges toward antibacterial discovery of drug over an earlier period of 30 years. The resistance pathogens such as Staphylococcus aureus , Mycobacterium tuberculosis (MTB), and Streptococcus pneumoniae are nowadays facing difficulty in effective treatment. This leads to the necessary for the new discovery of drugs for antibacterial activity. The foremost disease in the world among all the infectious disease is found to tuberculosis (TB) which causes high proportions of mortality. Hence, we have decided on identifying the leads for the target of enzymes of infectious disease TB. Methods: The new leads for MTB have been discovered using computer-aided drug design docking tool. The new compounds identified were made to dock into the enzyme active site retrieved from protein data bank. Results: After three different docking strategies, the score was found to be 4.558 kcal mol−1 for the compound 2’-chloro-4-methoxy-3-nitro benzyl in structure activity relationship and docking studies. Conclusion: The molecule shows valuable interactions and also it is found to be surrounded by non-polar amino acids. On further analyzing the compound it is found to be potent to antibacterial drug discovery.
Effect of loach paste on the liver and immune organs of D-galactose-induced ageing mice

ABSTRACT We examined the effects of loach paste (LP) on liver and immune organs of d-galactose (DG)-induced aging mice. The results showed that LP can alleviate the atrophy of spleen and thymus, and restore the blood glucose levels. LP was particularly beneficial to liver. Liver indices and activities of aspartate aminotransferase, alanine aminotransferase, and alkaline phosphatase reduced with high doses of LP. Moreover, LP can improve the antioxidant system in liver by increasing the activities of total superoxide dismutase, glutathione peroxidase, and catalase, reducing malondialdehyde concentration. Furthermore, LP can improve immunity and reduce the inflammation of liver. The swelling of liver cells was alleviated and the cell arrangement returned to normal in the LP group. In addition, gene expressions of HSP70 and tumour necrosis factor-α (TNF-α) in liver which can promote inflammatory cytokine decreased significantly. Thus, regular LP intake effectively relieved DG-induced oxidative stress and alleviated liver and immune organs damage.