Miracle-dz/UniFAR-FTUs huggingface dataset:
Robustness and plasticity of epithelial cell state in development and malignancy

A better understanding of the molecular mechanisms that control pluripotency, differentiation and epithelial phenotypical plasticity is crucial for the development of the current knowledge in many general processes such as cell identity maintenance and cell fate decision-making. Embryonic stem cells (ESC) pluripotency maintenance and differentiation are of key importance to the embryonic development, as well as to the progress in stem cells technologies. The role of miR-290-295 cluster members in preserving the pluripotent state and differentiation potential of mouse ESC is well established. Nevertheless, the precise list of targets translating the microRNAs functionality is incomplete. In our study we, firstly, identified and validated miR-290 targets with high confidence. We further confirmed the expression variation of IRF2 in response to miRNAs’ depletion in ESC. Moreover, we revisited the involvement of nuclear factor kappa-B (NF-kB) pathway in the miRNA-dependent regulation in mESCs. Hence, our results provided new understanding of the role and mechanistic of miR-290-295 microRNAs involvement in ESC pluripotency and differentiation. In a similar fashion to ESC pluripotency and differentiation mechanisms, a globalanalysis-approach that compares and combines data from different epithelial to mesenchymal transition (EMT) models enabled us to construct a more detailed network of regulatory entities implicated in epithelial plasticity. The maintenance and plasticity of the epithelial cell phenotype are important events not only during normal embryonic development, but also to cancer progression and metastasis formation. Comparing this network between mouse and human, we identified a new transcription factor (TF) motif TFAP2A/C that is consistently involved in EMT. When applying the NMuMG cellular model of TGFβ-induced EMT, we found that the predicted activity of the TFAP2A/C is inversely correlated to the Tfap2a mRNA expression during the process. We have confirmed that TFAP2A directly binds to the promoter of Zeb2, a TF central to EMT. Thus, it regulates the expression of this gene. Furthermore, the TFAP2A overexpression in NMuMG cells modulates the cells’ epithelial phenotype and induces changes in cell adhesion and morphology. This overexpression was followed by increased mRNA levels of EMT master regulator TFs, together with an elevated expression of genes involved in cellular adhesion. Therefore, we identified a potentially new role of TFAP2A transcription factor, which suggests that elements of its regulatory function during neural crest development might operate in mechanisms controlling epithelial plasticity in normal breast and tumor tissues. Overall, we characterized another facet of microRNAs’ function in pluripotency and differentiation in ESC, as well as a new aspect of the implication of TFAP2A in epithelial cell state integrity and plasticity. Therefore we contributed to expanding our insight of how are regulated at molecular level the cell identity homeostasis and the unfolding of cellular phenotypical plasticity.
Les strongylidés du rhinocéros Africain (Rhinoceros bicornis)

Les parasites du rhinocéros africain, Rhinocéros bicornis, sont encore fort peu connus et, jusqu’ici, une seule espèce de Strongylidæ : Kiluluma stylosa (von Linstow, 1907), a été signalée chez ce grand mammifère (1). Les rhinocéros ne sont point, en effet, des animaux de capture courante, comme les éléphants que l’on chasse pour l’ivoire de leurs défenses ; s’ils sont tués par des indigènes ou par un sportsman, n’ayant d’autre but que d’ajouter un gibier rare à son tableau de chasse) ils ne sont, pas plus dans un cas que dans l’autre, l’objet de recherches parasitologiques et c’est ce qui explique pourquoi leur faune parasitaire a été si peu étudiée. Aussi, suis-je particulièrement reconnaissant à mon ami, le professeur E. Brumpt, d’avoir bien voulu me communiquer de nom­ breux échantillons de nématodes, recueillis par lui en 1902, dans la région du lac Rodolphe, à l’autopsie d’un rhinocéros, tué par le vicomte du Bourg de Bozas, dont il était le collaborateur scientifi­ que, au cours de sa mission en Afrique. Je tiens aussi à adresser mes remerciements au professeur Henry d’Alfort, qui a bien voulu me communiquer les riches documents de son laboratoire et dont les conseils m’ont été précieux. Tous les spécimens que j’ai examinés appartiennent à la famille des Strongylidæ; ce sont, pour la plupart, des genres nouveaux et, tous, des epèces nouvelles ; ils peuvent être répartis dans les trois sous-familles des Strongylinæ, des Bunostominæ et des Cylicostominæ, ainsi que dans une nouvelle sous-famille que j’appellerai les Amirinæ.
The complete mitogenome of ghost jellyfish Cyanea nozakii (Cnidaria, Semaeostomeae, Cyaneidae)

Abstract The cnidarian jellyfishes are impressive organisms to show animal mitochondrial genomic diversities. Their mitogenome structure is linear and tRNA content has one or two in numbers, which is highly different than other metazoans. In this study, a complete mitogenome of the ghost jellyfish Cyanea nozakii (Cnidaria, Semaeostomeae, Cyaneidae) was sequenced and analyzed. The mitgenome is 17,381 bp long with 38.5% A, 16.0% C, 13.9% G, and 31.6% T nucleotide distributions. In addition, phylogenetic relationship of C. nozakii in the class Scyphozoa was investigated by using mitochondrial protein coding genes. Due to results, C. nozakii was positioned in the paraphyletic order Semaeostomeae. This is the first complete mitogenome from the genus Cyanea.
Microtubule binding by the formin Cappuccino and its implications for Drosophila oogenesis

Author(s): Roth-Johnson, Elizabeth Anne | Advisor(s): Quinlan, Margot E | Abstract: Coordination of actin and microtubule cytoskeletal networks is required for a number of fundamental cellular processes. Formin family actin nucleators are emerging coordinators of the actin and microtubule cytoskeletons, as they can both nucleate actin filaments and bind microtubules in vitro. To gain a more detailed mechanistic understanding of formin-microtubule interactions and formin-mediated actin-microtubule crosstalk, we studied microtubule binding by Cappuccino (Capu), a formin involved in regulating actin and microtubule organization during Drosophila oogenesis. We report that two distinct domains within Capu, FH2 and tail, work together to promote high-affinity microtubule binding. Microtubules potently inhibit Capu's actin nucleation activity but have little effect on Capu once bound to the barbed end of an elongating actin filament, supporting a model in which Capu does not simultaneously bind microtubules and assemble actin in vivo. After characterizing Capu-microtubule binding in vitro, we examined the localization of Capu and microtubules in S2 cells. We did not observe any obvious colocalization and conclude that S2 cells are not an ideal system for visualizing in vivo formin-microtubule interactions. To better understand Capu's mechanisms of action during oogenesis, we then systematically characterized several classical capu alleles. While all of these capu mutants exhibit severe developmental defects, they variably affect Capu's actin assembly activity in vitro. Together with our microtubule binding data, this indicates that Capu's physiological role extends beyond its ability to nucleate actin filaments. We therefore performed tandem affinity purification experiments to identify novel Capu binding partners and gain additional insight into Capu's role during oogenesis. We report several candidate binding partners involved in such diverse cellular processes as mitochondrial fission, endocytosis, and nuclear import. Though preliminary, these results suggest that Capu has additional uncharacterized functions in development; further investigation may help us uncover the physiological role of Capu-microtubule binding. Ultimately, our findings expand our understanding of Capu's role in Drosophila oogenesis and provide mechanistic insight into formins as coordinators of the actin and microtubule cytoskeletons.
Dodging the blades: new insights into three-dimensional area use of offshore wind farms by lesser black-backed gulls Larus fuscus

GPS telemetry is improving our understanding of the way animals interact with their environment. Recent research has used this technology to assess the impact of offshore wind farms (OWFs) on seabirds, but few studies have collected fine-scale data from birds flying within OWFs. We use GPS telemetry to investigate movements of lesser blackbacked gulls Larus fuscus in relation to OWFs from a protected site with an active breeding colony. Individual birds varied considerably in their use of OWFs; 15 out of 24 birds visited them, and time spent in these areas was 1.3% of time budgets across all birds. Two birds, for which the most data was collected, frequently entered OWFs and flew at turbine blade height; however, their overlap with the spherical 3-dimensional rotor swept volume was significantly lower than a random distribution. Although preliminary, these tracking data suggest a lack of a macro-scale (wind farm-scale) avoidance for L. fuscus but a potential meso-scale (within wind farm-scale) avoidance of turbines. Such data are therefore important in improving our understanding of the implications of OWFs for seabirds. INTRODUCTION Technological advances are permitting ever more detailed insights into animal behaviour, ecology and conservation. A prime example is their application in the marine environment, where tracking has revolutionized the study of seabirds that spend much of their lives offshore where they are otherwise difficult to monitor (BirdLife International 2012). Marine areas are increasingly pressured by human activities, including fisheries, renewable energy developments (including offshore wind farms), pollution and climate change (Paleczny et al. 2015, Wright & Kyhn 2015). Consequently, it is imperative to identify the exposure of wildlife populations to such pressures. Offshore wind farms (OWFs) may affect seabirds directly through collision, presenting a barrier to movement, or displacing birds from foraging areas (Furness et al. 2013). GPS telemetry has been used to investigate the spatial overlap between OWFs and movements of species (e.g. Thaxter et al. 2015) and altitude of flight to inform collision risk modelling (Cleasby et al. 2015, Ross-Smith et al. 2016). However, to date, the fine-scale activity of birds within operational OWFs has not been fully explored. Such information could improve our understanding of collision risk through measuring the responses of
Genetic analysis for heterotic traits in bread wheat (Triticum aestivum L.) using six parameters model

The assessment of nature of gene effect for yield and its contributing traits and detection of epistasis in wheat was studied in five crosses involving seven parents through generation mean analysis. Scaling test and joint scaling test were showed significant for almost traits all crosses. Additive gene effects (d) were positively significant for days to maturity and tillers per plant in cross II; for seed per plant in cross IV. Dominance gene effects (h) were highly significant for days to 75% heading in cross II, III and IV; for days to maturity and grains per spike in cross II, for grain yield per plant and grains per spike in cross I. Additive x additive type of gene (i) were positive significant effect for days to 75% heading in cross II, III and IV; for days to maturity in cross II and grains per spike in crosses I, II; for 1000 grain weight in cross II and IV; for grain yield per plant in cross I. Additive x dominance type of gene effect (j) was positive significant for days to 75% heading in cross III; for days to maturity in cross II and III; for plant height in cross III; tillers per plant in cross II; for grain per spike and seed per plant in cross III and grain yield in cross IV. Dominance x dominance effect (l) were positively significant for days to 75% heading, plant height in cross I; for plant height in cross III, IV and V; for tillers per plant in cross II and for grains per spike in cross IV and V; seed per plant, grain yield in cross IV. Therefore, it has been suggested that selection of studied characters based on different gene action of generation mean to be used further crop improvement through ideal breeding programme.
Population Differentiation at the HLA Genes

Balancing selection is defined as a class of selective regimes that maintain polymorphism above what is expected under neutrality. Theory predicts that balancing selection reduces population differentiation, as measured by FST. However, balancing selection regimes in which different sets of alleles are maintained in different populations could increase population differentiation. To tackle this issue, we investigated population differentiation at the HLA genes, which constitute the most striking example of balancing selection in humans. We found that population differentiation of single nucleotide polymorphisms (SNPs) at the HLA genes is on average lower than that of SNPs in other genomic regions. However, this result depends on accounting for the differences in allele frequency between selected and putatively neutral sites. Our finding of reduced differentiation at SNPs within HLA genes suggests a predominant role of shared selective pressures among populations at a global scale. However, in pairs of closely related populations, where genome-wide differentiation is low, differentiation at HLA is higher than in other genomic regions. This pattern was reproduced in simulations of overdominant selection. We conclude that population differentiation at the HLA genes is generally lower than genome-wide, but it may be higher for recently diverged population pairs, and that this pattern can be explained by a simple overdominance regime.
Characterization of the complete chloroplast genome of the Eastern gamagrass, Tripsacum dactyloides

Abstract Tripsacum dactyloides, known as eastern gamagrass, is used as a donor of valuable traits. It grows naturally in the same region where maize is commercially cultured in the USA and has the ability to hybridize to maize. The wild genotype of eastern gamagrass is threaten by the gene flow from the transgenic maize. The circular genome is 141,050 bp in length and contains 120 genes, including 73 protein-coding genes (PCG), 39 transfer RNA genes (tRNA) and eight ribosomal RNA genes (rRNA). The overall nucleotide composition is: 30.8% A, 19.2% C, 19.3% G, 30.7% T, with a total G + C content of 38.5%. The phylogenetic tree was constructed to explore the taxonomic status of Tripsacum dactyloides, which contributes to phylogenetic studies and further conservation strategies for this species.
Development of a novel mouse model for the colorectal cancer risk locus at Xp22.2

iv Lay Summary . vi Abbreviations . viii List of Figures . xviii List of Tables. xx Chapter 1: Introduction . 1 1.1 Colorectal Cancer . 1 1.1.1 The large bowel . 1 1.1.2 The small intestine . 3 1.1.3 Epidemiology of colorectal cancer. 3 1.1.4 Environmental risk factors . 4 1.1. 5 Genetic risk factors . 5 1.1. 6 Classification of colorectal cancers . 10 1.1. 7 The molecular biology of sporadic CRC . 11 1.2 The SHROOM protein family . 13 1.2. 1 SHROOM2 . 13 1.2. 2 SHROOM3 . 18 1.2. 3 SHROOM1 . 19 1.2. 4 SHROOM4 . 19 1.3 GPR143 . 20 1.4 Mouse models . 20
Immunoregulatory activity of root bark of Cassia sieberiana D.C. in a modified adjuvant-induced arthritis in rat

The present study seeks to evaluate the immunoregulatory effects of extracts of the root bark of Cassia sieberiana, a plant used in Ghana for various painful inflammatory conditions, in a modified adjuvant arthritis model induced by administration of very low dose of Mycobacterium tuberculosis (MT) – carrageenan mixture in the rat. A volume of 0.1 mg kg -1 heat killed MT in paraffin oil was mixed with equal volume of 0.05% (w/v, normal saline) carrageenan. A single intraplantar dose of 0.1 ml of the MT carrageenan mixture was administered to experimental animals. Groups were administered extracts (20 to 200 mg kg -1 , p.o.), dexamethasone (0.3 mg kg -1 , p.o.) or vehicle an hour prior to the test and daily from test day till the 6th day. Paw volume (ml) of the injected hind limbs were measured using a plethysmometer, while paw withdrawal thresholds were determined using an analgesy meter. Serum levels of IL-1α, IL-6, IL-10 and TNF-α were determined via enzyme linked immunosorbent assay (ELISA). Results showed that the extracts attenuated the inflammation and hyperalgesia caused by the intraplantar injection of MT-carrageenan mixture in the rats in a dose-dependent fashion. Similarly, the extracts reduced the serum levels of IL-1α, IL-6 and TNFα while increasing the levels of IL-10. It can be concluded that the anti-inflammatory activity of extracts of root bark of C. sieberiana may be attributable to their immunomodulatory effects via suppression of pro-inflammatory cytokines, TNF-α, IL-1α and IL-6; and elevation of the anti-inflammatory cytokine, IL-10 levels, in serum.
Spanish wines in the US market: What attributes do US consumers look for in Spanish wines?

This paper analysed the impact of different attributes in Spanish quality wines on United States (US) demand behaviour. A hedonic price model was estimated in order to assess the values that US consumers give Spanish wines. The main results showed that the most influential factor on sale price was aging, which had a positive impact. US consumers valued the quality ratings provided by experts, especially in the upper price categories. The year of vintage and size of the winery were considered medium importance factors in decision-making, with the latest vintages and the smallest wineries receiving the highest ratings. Geographical origin (appellation) helped to explain consumer preferences. Although colour was the least important attribute in consumers’ purchase decisions, red wines were the most highly rated in this attribute.
Investigating the Effects of Spatial Confinement on Multicellular Morphogenesis

ii Statement of Originality . iii Other Contributions . v Statements of Contributions . vi Ackknowledgments . vii List of Abbreviations . xii List of Figures . xiii List of Tables . xvi Chapter 1 | Introduction . 1 1.1 The cell, in a filament nutshell . 1 1.2 The path to cell sensing . 4 1.3 The influence of the physical microenvironement on the cell . 8 1.4 Embryonic stem cell growth in confinement . 11 1.5 Understanding cell-cell interactions through cocultured systems . 14 1.6 Conclusion . 16 1.7 Motivation and approach . 16 2 | Patterned cell type seperation in cocultured cell mixtures in vitro . 20 2.1 Abstract . 20 2.2 Introduction . 20 2.3 Results . 23 2.3. 1 The role of the cytoskeleton in cocultured cell type separation . 23 2.3. 2 Cell substrate binding affinity in cocultured cells . 26 2.3. 3 Simulating Patterned Adhesion . 27 2.4 Discussion . 32 2.5 Materials and Methods . 35 2.5. 1 Cell culture and drug studies . 35
Sublethal effect of Ethephon pesticide on carcass composition of rosy barb, Puntius conchonius (Hamilton, 1822)

Experiment on bioassay was undertaken to find out the toxic effect of ethephon on proximate composition of rosy barb (Puntius conchonius). The 96 hrs LC50 of ethephon for rosy barb fish was found to be 64.034 mgl. During sublethal exposures for a period of 28 days, two concentrations were selected i.e. 1/10 and 1/5 of LC50 such as of 12.81 and 6.40 mgl. At the end of exposure periods of 7, 14, 21 and 28 days i.e., after every seven days, ten fingerlings were sacrificed for carcass biochemical analysis such as moisture content, crude protein, crude fat, total ash content and carbohydrate. Crude protein significantly decreased from 60.08 ±0.05 on 1 day to 53.38±0.05 on 28 day; crude fat significantly decreased from 10.07 ± 0.05 on 1 day to 8.08±0.02 on 28 day of the study. Whereas, carbohydrate increased from 10.06±0.02 on 1 day to 12.02±0.02 on 28 day, ash content increased significantly from 9.94 ±0.05 on 1 day to 11.08±0.01 on 28 day and moisture content also increased from 9.79 ± 0.03 to on 1 day to 12.30±0.02 on 28 day respectively. All the estimated parameters showed significant alteration during exposure period indicated toxicity of ethephon pesticide to the rosy
Análises moleculares em Melipona rufiventris e Melipona mondury (Hymenoptera: Apidae)

ix Introdução. 01 1. Abelhas sem ferrão. 01 2. Análises moleculares. 04 3. Análise do conteúdo de DNA em insetos. 09 Referências Bibliográficas. 13 Capítulo 1: Caracterização de locos microssatélites para a abelha sem ferrão Melipona rufiventris (Hymenoptera: Apidae) . 21 Capítulo 2: Nota científica sobre a caracterização de locos microssatélites para Melipona mondury (Hymenoptera: Apidae). 28 Capítulo 3: Estudo comparativo do uso de primers microssatélites específicos e heterólogos em M. rufiventris e M. mondury (Hymenoptera: Meliponini). 35 Resumo. 36 Introdução. 37 Material e Métodos. 38 Resultados e Discussão. 39 Referências. 42 Tabelas e Figuras. 46 Capítulo 4: Diferenciação genética de espécies de Melipona do grupo rufiventris por análise de DNA mitocondrial. 49 Resumo. 50 Introdução. 51 Material e Métodos. 52 Resultados. 54 Discussão. 55 Referências. 58
Restoration of plant species and genetic diversity depends on landscape‐scale dispersal

In the era of ongoing global change, it is highly important that restoration efforts lead to functioning, self‐sustainable ecosystems that are resilient to disturbance and resistant to environmental changes. Therefore, it is necessary that restoration aims at achieving high genetic diversity of plant populations in addition to the recovery of characteristic species composition and diversity. Nevertheless, species‐ and gene‐level biodiversity are rarely examined together in the context of restoration, although high genetic diversity of plant populations is a fundamental factor ensuring long‐term success of restoration. Landscape‐scale dispersal is the key process linked to the recovery of vegetation and maintaining both species and genetic diversity following restoration. In fragmented landscapes, dispersal of seeds and genetic material is often disrupted, leading to failure in spontaneous recovery of species richness as well as in establishment and maintenance of genetically diverse populations. Here, we review the linkages between landscape‐scale dispersal of plants and the recovery of species richness and genetic diversity of plants during habitat restoration. We propose recommendations for restoration planners and practitioners to consider while aiming to restore self‐sustainable ecosystems with high species‐ and gene‐level biodiversity.