Miracle-dz/UniFAR-FTUs huggingface dataset:
Games roots play: effects of soil volume and nutrients

1 A growing body of literature suggests that some plants may engage in a game of Tragedy of the Commons when competing for soil resources. Two annual plants sharing a whole space will produce more roots per individual and less reproductive yield per individual than one plant with half the space to itself. 2 Several papers have recently suggested that the increase in soil volume in going from a single plant to two competitor plants (as has been the case in empirical tests of the above prediction) may produce the increased root proliferation independent of the competitor. 3 We extend the Tragedy of the Commons model of Gersani et al. (2001 ) to explicitly consider the separate effects of volume per plant (V) and nutrient concentration per unit volume (N) on root proliferation and yield of plants that ‘own’ their space relative to plants that share their space with a competitor. We then use simulations resulting from the model to evaluate existing data and the new perspectives provided by recent challenges to the conceptual basis for the Tragedy of the Commons. 4 When N is held constant, increasing V should produce an almost linear increase in root proliferation and net nutrient profit for reproduction. The increase in roots should be more pronounced for two plants sharing their space, and the increase in yield should be more pronounced for plants with exclusive access to half the space. When V ¥ N is held constant, roots per plant should at first increase and then decline with increased volume. The difference between a plant that ‘owns’ its space vs. one that shares its space with a competitor should be less pronounced as V increases. 5 Synthesis. We use this model to help clarify some confusion surrounding the Tragedy of the Commons theory of below‐ground competition by showing how issues raised by others are not incompatible with the approach used to generate the Tragedy of the Commons theory and highlight future opportunities for research on root growth strategies.
Effects of 17β-Estradiol Metabolites on Cell Cycle Events in MCF-7 Cells

Different cell growth effects were observed in MCF-7 cells after six daily exposures to either 17 beta-estradiol (E2), 2-hydroxyestradiol (2-OHE2), or 2-methoxyestradiol (2-MeOE2) at 10 nM levels. 2-OHE2 enhanced cell growth significantly (P 220,000), were most prominently affected. In comparison, E2 and 2-OHE2 had little effect. We suggest that the enhanced 2-MeOE2-induced protein phosphorylation during S-phase may affect S-phase events, which subsequently causes inhibition of mitosis. Protein synthesis during G2/M transition was unexpectedly enhanced by 2-OHE2 and was not enhanced by E2. [35S]Methionine incorporation into proteins in the order of M(r) 32,000-46,000, 47,000-50,000, 58,000-67,000, and 83,000-89,000 was significantly (P < 0.05) increased. 2-MeOE2 had no effect. The results of this study indicate that 2-OHE2 may be the more potent mitogen, whereas 2-MeOE2 acts as a cytostatin.
Life histories of Neotropical butterflies from Trinidad 2. Antirrhaea philoctetes (Lepidoptera: Nymphalidae: Morphinae).

The life history of Antirrhaea philoctetes (Linnaeus) (Lepidoptera: Nymphalidae: Morphinae) is described from material reared on palms in the family Arecaceae (=Palmae). The hemispherical egg is yellowish light green and 2.5 mm in diameter. There are five larval instars. The mature larva differs from those of other described Antirrhaea species in its elaborate pattern of maroon and yellow patches. Each larval instar bears a pair of long whiplike tails that compose half the length of the body. The pupa is mottled and patterned with tan, brown, and some green, resembling a crumpled leaf. The complete life cycle takes 70 days at ambient temperatures in Trinidad (7 days in the egg stage, 50 days in five larval instars, and 13 days as a pupa).
Who’s at Fault? Tata Sons in 2012 or Mistry in 2016: A Case Study on Tata Group

Tata group is an Indian MNC founded in 1868 by Jamsetji Tata. His vision envisaged towards nation’s development to see India self-sufficient. The company was headed by JRD Tata during 1939-90. His tenure made a significant contribution towards the growth of the group. In 1991, Ratan Tata took over as a chairman of Tata group of companies. His clear vision and desire to achieve along with people’s support made the company grow 57 times from the year he was appointed. Since Tata lacked an heir, Cyrus Mistry, second largest shareholder in Tata sons who worked very closely with Ratan and ensured the best of his capabilities with a long term association and commitment, was appointed as the new chairman of Tata Group in 2012, after being on a position of Deputy Chairman for about a year. His leadership viewed major strategic decisions that affected Tata’s market image and growth, in the view of Tata trusts. In 2016, a sudden decision of Mistry’s exit raised several questions on the governance at the Tata group and the succession experiment that went wrong. The case also talks about the deviations in leadership style and reasons for the elevating trust deficit among the people concerned.
Functional Characterization of Plant Fatty Acid Amide Hydrolases

Fatty acid amide hydrolase (FAAH) terminates the endocannabinoid signaling pathway that regulates numerous neurobehavioral processes in animals by hydrolyzing a class of lipid mediators, N-acylethanolamines (NAEs). Recent identification of an Arabidopsis FAAH homologue (AtFAAH) and several studies, especially those using AtFAAH overexpressing and knock-out lines suggest that a FAAH-mediated pathway exists in plants for the metabolism of endogenous NAEs. Here, I provide evidence to support this concept by identifying candidate FAAH cDNA sequences in diverse plant species. NAE amidohydrolase assays confirmed that several of the proteins encoded by these cDNAs indeed catalyzed the hydrolysis of NAEs in vitro. Kinetic parameters, inhibition properties, and substrate specificities of the plant FAAH enzymes were very similar to those of mammalian FAAH. Five amino acid residues determined to be important for catalysis by rat FAAH were absolutely conserved within the plant FAAH sequences. Site-directed mutation of each of the five putative catalytic residues in AtFAAH abolished its hydrolytic activity when expressed in Escherichia coli. Contrary to overexpression of native AtFAAH in Arabidopsis that results in enhanced seedling growth, and in seedlings that were insensitive to exogenous NAE, overexpression of the inactive AtFAAH mutants showed no growth enhancement and no NAE tolerance. However, both active and inactive AtFAAH overexpressors displayed hypersensitivity to ABA, suggesting a function of the enzyme independent of its catalytic activity toward NAE substrates. Yeast two-hybrid screening identified Arg/Ser-rich zinc knuckle-containing protein as a candidate protein that physically and domain-specifically interacts with AtFAAH and its T-DNA knock-out Arabidopsis was hypersensitive to ABA to a degree similar to AtFAAH overexpressors. Taken together, AtFAAH appears to have a bifurcating function, via NAE hydrolysis and protein-protein interaction, to control Arabidopsis growth and interaction with phytohormone signaling pathways. These studies help to functionally define the group of enzymes that metabolize NAEs in plants, and further will expand the knowledge-base of lipid metabolism and signaling for manipulation of various physiological processes important to plant growth and responses to environmental stress.
Growth performance and apparent nutrient digestibility in weaned piglets offered wheat-, barley- or sugar-beet pulp-based diets supplemented with food enzymes.

Pig studies on non-starch polysaccharides (NSPs) have mainly focused on finishing and breeding animals because their digestive capacity and ability to ferment fibre are considered greater than piglets. In this study, growth and nutrient digestibility, with particular reference to NSP constituent monomers, were evaluated in piglets offered contrasting sources of NSPs. The potential for enhancing growth performance and digestibility with exogenous food enzymes (xylanase, amylase, pectinase and beta-glucanase) was investigated. A total of 240 piglets weaned at 28 days of age, in groups of six, were allocated to six treatments in a 3×2 factorial design, diet type (W, B and SBP) by enzyme supplementation (– v . +). Diet W was wheat based and formulated to supply 14 MJ digestible energy (DE) per kg. In diets B and SBP, DE was reduced to 13·25 MJ/kg by replacing wheat with barley (708 g/kg) or with 185 g/kg dried unmolassed sugar beet pulp. Growth was monitored over 4 weeks. Digestibility of diets B–, B+, SBP– and SBP+ was evaluated in 16 piglets, in groups of four, using a 4×4 Latin-square design. In the growth study, mean initial and final piglet weights were 8·1 (s.e. 0·09) and 18·0 (s.e. 0·21) kg. Piglet health remained satisfactory and food intake averaged 523 (s.e. 6·7) g/day. There were no consistent and significant effects of diet type on food intake, live-weight gain or food conversion, except in week 1 when gain on diet W was higher than on diets B and SBP, 191 v. 150 v. 125 g/day, respectively (s.e. d. 20·0, P
Perturbations du métabolisme oxydatif induites par l’activation de PDGFRα : mécanismes et conséquences dans la leucémie chronique à éosinophiles FIP1L1-PDGFRA

Le rearrangement FIP1L1-PDGFRA (F/P), identifie de maniere recurrente dans les leucemies chroniques a eosinophiles, est a l’origine d’une activation constitutive de l’activite tyrosine kinase de la chaine α du recepteur au PDGFR. Les mecanismes concourant a la proliferation eosinophile exclusive et au profil de cytotoxicite specifique a cette leucemie sont encore mal elucides. Ce recepteur PDGFRα;, principalement exprime dans les cellules mesenchymateuses, y exerce des effets proliferatifs et chimiotactiques, en partie induits par la production intracellulaire de derives reactifs de l’oxygene (ROS). Ces constatations nous ont amene a etudier les perturbations du metabolisme oxydatif dans la leucemie F/P+, en utilisant une approche d’etude globale du proteome d’eosinophiles de sujets F/P+, compare a des eosinophiles de sujets controles. Dans ce travail, nous avons demontre qu’il existe, dans les eosinophiles F/P+, une deregulation de nombreuses proteines impliquees dans la signalisation redox intracellulaire. De plus, les modifications d’expression de certaines d’entre elles (peroxiredoxine-2, src-homology-2 domain containing tyrosine phosphatase-1 ou SHP-1), non retrouvees dans les eosinophiles de patients ayant un syndrome hypereosinophilique idiopathique, et identifiees dans une lignee cellulaire exprimant F/P, semblent specifiquement induites par F/P. L’activation du PDGFRα; dans les eosinophiles F/P+ est donc a l’origine d’un desequilibre du metabolisme oxydatif dont les consequences sur la differenciation vers le lignage eosinophile ou sur la cytotoxicite seront discutees.
Avian Influenza A Virus Infection among Workers at Live Poultry Markets, China, 2013–2016

We conducted a 3-year longitudinal serologic survey on an open cohort of poultry workers, swine workers, and general population controls to assess avian influenza A virus (AIV) seroprevalence and seroincidence and virologic diversity at live poultry markets (LPMs) in Wuxi City, Jiangsu Province, China. Of 964 poultry workers, 9 (0.93%) were seropositive for subtype H7N9 virus, 18 (1.87%) for H9N2, and 18 (1.87%) for H5N1. Of 468 poultry workers followed longitudinally, 2 (0.43%), 13 (2.78%), and 7 (1.5%) seroconverted, respectively; incidence was 1.27, 8.28, and 4.46/1,000 person-years for H7N9, H9N2, and H5N1 viruses, respectively. Longitudinal surveillance of AIVs at 9 LPMs revealed high co-circulation of H9, H7, and H5 subtypes. We detected AIVs in 726 (23.3%) of 3,121 samples and identified a high diversity (10 subtypes) of new genetic constellations and reassortant viruses. These data suggest that stronger surveillance for AIVs within LPMs and high-risk populations is imperative.
Analysis and Derivation of Continuum 3D Blebbing Model with Simulations

In this thesis we attempt to give a strong mathematical basis to cellular blebbing models. After outlining the biology and literature surrounding these phenomena we derive a continuum model for a 3D cell. This derivation results in a fourth order parabolic equation with nonlinear second and lower order terms. Using an operator splitting we obtain a system of second order equations. These can be approximated using only linear finite elements. The model generalizes to an abstract formulation. In this general semi-discrete scheme (continuous in time and discrete in space) we can show weak well posedness and show a priori error estimates. This includes formulating a finite element approximation, proving stability bounds then showing the convergence of the discrete to its limiting case. We formulate a fully discrete scheme and include a stability proof which allows us to implement the problem in Dune-fem. We can then showcase the implementation by showing the convergence rate of the error on two different surfaces. Finally, we round off the thesis by showing some more biologically focused examples. Here we use our implementation in two cases and look at the effects of parameters on potential bleb formulations. These use 3D surfaces with no restriction that they be of a certain shape. We also showcase the adaptability of our implementation by applying it to cell image data. We explain how this can be run using Dune-fempy software which offers a lower barrier for entry into creating and editing the scheme. This potentially gives a bridge to test how successful our model or similar models are in modelling blebs.
The Epigenetic Role of EGR1 during Postnatal Mammalian Brain Development

DNA methylation is an epigenetic mechanism critical for tissue development, cell specification and cellular function. Mammalian brains consist of millions to billions of neurons and glial cells that can be subdivided into many distinct types of cells. We hypothesize that brain methylomes are heterogeneously methylated across different types of cells and the transcription factors play key roles in brain methylome programming. To dissect brain methylome heterogeneity, in Chapter 2, we first focused on the identification of cell-subset specific methylated (CSM) loci which demonstrate bipolar DNA methylation pattern, i.e., hypermethylated in one cell subset but hypomethylated in others. With the genome-scale hairpin bisulfite sequencing approach, we demonstrated that the majority of CSM loci predicted likely resulted from the methylation differences among brain cells rather than from asymmetric DNA methylation between DNA double strands. Importantly, we found that putative CSM loci increased dramatically during early stages of brain development and were enriched for GWAS variants associated with neurological disorder-related diseases/traits. It suggests the important role of putative CSM loci during brain development, implying that dramatic changes in functions and complexities of the brain may be companied by a rapid change in epigenetic heterogeneity. To explore epigenetic regulatory mechanisms during brain development, as described in Chapter 3, we adopted unbiased data-driven approaches to re-analyze methylomes for human and mouse frontal cortices at different developmental stages. We predicted Egr1, a transcriptional factor with important roles in neuron maturation, synaptic plasticity, long-term memory formation and learning, plays an essential role in brain epigenetic programming. We performed EGR1 ChIP-seq and validated that thousands of EGR1 binding sites are with cell-type specific methylation patterns established during postnatal frontal cortex development. More specifically, the CpG dinucleotides within these EGR1 binding sites become hypomethylated in mature neurons but remain heavily methylated in glia. We further demonstrated that EGR1 recruits a DNA demethylase TET1 to remove the methylation marks at EGR1 binding sites and activate downstream genes. Also, we found that the frontal cortices from the knockout mice lacking Egr1 or Tet1 share strikingly similar profiles in both gene expression and DNA methylation. Collectively, the study in this dissertation reveals EGR1 programs the brain methylome together with TET1 during postnatal development. This study also provides new insights into how life experience and neuronal activity may shape the brain methylome. The Epigenetic Role of EGR1 during Postnatal Mammalian Brain Development
Caracterización de nidos de la Hormiga Arriera Atta cephalotes (Hymenoptera: Myrmicinae) en Cali (Colombia)

Nest sizes and infestation levels of the leaf-cutting ant, Atta cephalotes , were determined in urban areas of Cali, Colombia. A total of 143 green areas, consisting of parks, traffic islands, verges and other open spaces occupying a total of 1.276. 131 m2 was evaluated in March-April 2002. The highest proportion (89%) of the green areas showed low/medium infestations, i.e., with ant nests occupying less than 50% of the green space. The remaining 11% showed high infestations, with nests occupying more than half of their areas. Most (68%) of the nests were found on level natural spaces, the next most common habitat type being steep areas such as verges (27%). Few nests were found near human dwellings. Areas of the nests ranged from 1-211 m2. A direct correlation was found between number of quadrants needed to enclose 50% of the entrance of a nest and its total area (r= 0, 70). This methodology allows the level of infestation of areas affected by leaf-cutting ants to be estimated rapidly but accurately. This information would aid in setting up control or management programs for leaf-cutting ant infestations.
Fig trees and fig wasps: their interactions with non-mutualists

Non-mutualist species that interact with mutualists occur commonly in nature. Non-mutualists associated with the mutualism between fig trees and their pollinating fig wasps include mites and nematodes. This thesis focusses on the interaction of nematodes with fig trees and fig wasps in South Africa and Indonesia, with additional investigation on how mites, nematodes and fig pollination respond to highly seasonal environments. The reproduction of monoecious Ficus burtt-davyi in Grahamstown, South Africa slows down but does not stop in winter. There are fewer fig pollinating wasps Elisabethiella baijnathi flying in the air during winter, but most figs are probably pollinated by locally-produced fig wasps. Elisabethiella g5baijnathi females transport mites (Tarsonemella sp. nr. africanus) and nematodes (Parasitodiplogaster sp.) between figs. Contrasting dispersion patterns and relationships with fig wasp foundress numbers indicate that the mites, but not the nematodes, disperse between figs after being carried there by the pollinators. Three nematode species (Caenorhabditis sp., Schistonchus centerae, and S. guangzhouensis) developed inside both male and female figs of dioecious F. hispida tree in Sumatra, Indonesia. Caenorhabditis sp. was transferred between figs as juveniles, whereas Schistonchus spp. were transferred mostly as juveniles, and occasionally as adults. The nematode community of eight species in Sumatran monoecious F.racemosa was the most diverse recorded anywhere. No mites were found in both species of fig trees. Peak nematode populations occurred in D-phase figs, when the fig wasp offspring are ready to emerge. The nematodes attach themselves to newly-emerged female pollinators, which then carry them away. Usually more nematodes attached on the first fig wasps to emerge. Entry into figs by early-emerging pollinators resulted in higher numbers of the next generations of nematodes within the figs. Details of the ecology of each nematode species may be different, but as a group they did not seem to significantly affect seed and wasp development in both F. hispida and F. racemosa figs.
Mécanismes physiologiques et biologiques induits chez yarrowia lipolytyica en réponse à des modifications de l'environnement physico-chimique des cellules

Les composes hydrophobes sont connus comme des sources de carbone qui peuvent etre utilisees par les levures comme Yarrowia lipolytica pour de multiples applications. Ces composes causent parfois des perturbations aux levures mais sont aussi rapportes comme conferant aux cellules une certaine resistance contre les stress environnementaux. Dans le cadre de cette these, nous avons etudie le role de l'oleate de methyle comme source de carbone sur la resistance de la levure Y. lipolytica en reponse au choc d’un compose amphiphile, la -dodecalactone, et au stress thermique. Les resultats obtenus montrent que les cellules ayant pousse sur oleate sont beaucoup plus resistantes au choc lactone ainsi qu’au stress thermique que les cellules ayant pousse sur glucose. L’action de la lactone se trouve au niveau de la membrane ou elle cause une fluidification membranaire et une depletion de sterols qui sont consideres comme la cause de la mort cellulaire. Ce travail met en evidence le role des corps lipidiques dans la reponse cellulaire qui se manifeste de differentes manieres en reponse a ces stress. Une accumulation des corps lipidiques est importante pour la resistance de la cellule aux stress. Les cellules ayant pousse sur glucose transforment leur sterol libre en esters de steryle pour former les corps lipidiques en reponse au choc lactone, ce qui augmente leur sensibilite. Tandis que les cellules ayant pousse sur oleate qui ont accumule des corps lipidiques pendant leur croissance ont tendance a convertir leurs esters de steryle en sterol libre pour compenser la depletion de sterol membranaire causee par la lactone ce qui diminue leur sensibilite. L'homeostasie de l'ergosterol, liee a la presence de corps lipidiques, semble donc jouer un role cle dans la resistance cellulaire a ces stress. Ce travail releve aussi que la presence de lipides modifie le processus de mort cellulaire programmee de Y. lipolytica en reponse a un stress thermique.
Untersuchung der Photodynamischen Inaktivierung von Dermatophyten mit dem Photosensibilisator Curcumin

Dermatophyten sind keratinophile Fadenpilze (Hyphomycetes). Sie infizieren keratinhaltige Strukturen wie das Stratum corneum sowie Haare und Nagel. Durch Dermatophyten verursachte Infektionen (Dermatophytosen) gehoren zu den haufigsten Erkrankungen weltweit. Die vorliegende Arbeit untersuchte den Einfluss von Curcumin in Kombination mit einer Bestrahlung auf das Wachstumsverhalten der 6 Dermatophytenarten Trichophyton (T.) rubrum, T. interdigitale, T. terrestre, Microsporum (M.) canis, M. gypseum und Epidermophyton (E.) floccosum. Die Konidien dieser 6 Dermatophytenarten wurden mit in Dimethylsulfoxid (DMSO) gelostem Curcumin versetzt und nach einer Inkubationszeit von 20 Minuten mit einer Dosis von 5 J/cm² und einer Peakwellenlange von 367 nm bestrahlt. Abschliesend wurden die Konidien in Sabouraud Dextrose Losung lichtgeschutzt inkubiert. Das Wachstum der Dermatophyten wurde uber 96 Stunden regelmasig durch photometrische Extinktionsmessungen und mikroskopische Kontrollen erfasst. Die Ergebnisse zeigten, dass photodynamisch aktiviertes Curcumin das Wachstum aller 6 untersuchten Dermatophytenarten uber 96 h signifikant mit hoher Effektivitat inhibierte. Dabei wurde das Wachstum von T. rubrum und E. floccosum vollstandig gehemmt, das Wachstum von T. interdigitale, M. gypseum, M. canis und T. terrestre wurde um 91,1%, 43,5%, 99,6% und 91,8% reduziert. Durch die Versuche konnte ein bereits zuvor beschriebener wachstumsinhibierender Effekt von belichtetem Curcumin auf T. rubrum bestatigt werden und des Weiteren erstmalig eine wachstumsinhibierende Wirkung von photodynamisch aktiviertem Curcumin auf die Dermatophytenarten E. floccosum, T. interdigitale, M. gypseum, M. canis und T. terrestre nachgewiesen werden.