Miracle-dz/UniFAR-FTUs huggingface dataset:
RNA sequencing for the study of splicing

Amongst the many processes that shape the final set of RNA molecules present in eukaryote cells, splicing emerges as the most prominent mechanism for message diversification. In recent years, applications of high throughput sequencing to RNA, known as RNA sequencing, have opened new avenues for the study of transcriptome composition, and have enabled further characterisation of such mechanism. In this thesis, I focus on the application of this technology to the study of human transcript diversity and its potential impact on the protein repertoire. In the first results chapter, I explore the extent of transcriptome diversity by asking whether there is a preference for the production of specific alternative transcripts within each given gene. I show that while many alternative transcripts can be detected, the expression of most protein coding genes tends to be dominated by one single transcript (major transcript). Such findings are validated in the second chapter, and are further used to explore changes in splicing patterns in a disease context. By analysing healthy and tumor samples from kidney cancer patients, I show that most of the detected splicing alterations do not lead to big changes in the relative abundance of major transcripts, at least in a recurrent manner. In addition, I introduce a framework to visualise the most extreme changes in splicing and to evaluate their potential functional impact. In the third chapter, I investigate the role of spliceosome assembly dynamics on the regulation of splice site choice. I show that depletion of PRPF8, a core spliceosomal component, leads to the preferential retention of a subset of introns with weaker splice sites, and also introduces alterations in the rate of co-transcriptional splicing. Finally, in the last chapter, I explore the validation of changes in alternative transcript abundance at the protein level, through the integration of results derived from RNA sequencing datasets with those obtained from proteomics experiments. Altogether, the findings described in this thesis provide a global picture on the extent of alternative splicing in the diversification of the transcriptome, expand current knowledge on the splicing reaction, and open new possibilities for the integration of transcriptomics and proteomics data.
Regulation of Endocytosis and Postendocytic Traffic in Polarized Epithelial Cells

The endocytic and postendocytic trafficking pathways in polarized epithelial cells was examined. First, sorting of fluid and membrane internalized from the apical plasma membrane was analayzed. Internalized fluid and membrane were intially delivered to apical early endosomes (AEE). Fluid remained in the AEE while membrane was rapidly sorted and delivered to the Rab11+ apical recycling endosome (ARE). The delivery of membrane markers to the ARE was microtubule-dependent. Transferrin, a marker of basolateral recycling pathway, had access to the AEE but not the ARE. Next, the role of Rac1 and RhoA in endocytosis and postendocytic was determined. Both Rac1 and RhoA were involved in regulation of endocytosis from both plasma membrane domains. Furthermore, Rac1 was implicated in regulation of apically targeted traffic from both the endocytic and secretory pathways. Expression of dominant active Rac1 (Rac1V12) caused formation of a central aggregate of membranes composed in part of the ARE. Markers targeted for the apical plasma membrane were trapped within this aggregate. RhoA was involved in the regulation of traffic from basolateral early endosomes (BEE). Expression of dominant active RhoA (RhoAV14) trapped ligands internalized from the basolateral plasma membrane in BEE that were also associated with filamentous actin (F-actin). A subset of BEE from control cells were also f-actin positive. Colocalization of BEE with proteins involved in actin polymerization based propulsion (APBP) and myosin motor-based propulsion was determined. Proteins involved in APBP were not associated with BEE bu MIc, a type I myosin, did colocalize with a subset of BEE. This suggests that BEE are transported along associated f-actin to the level of the stress fibers carried by MIc. Finally, the role of SNAP-23 in basolateral recycling of transferrin was determined. SNAP-23 was localized to the endosomes throughout the cell and to the basolateral plasma membrane. Treatment of permeabilized MDCK cells with botulinum neurotoxin E or addition of exogenous SNAP-23 or anti-SNAP-23 antibodies all inhibited transferrin recycling. This suggests that SNAP-23 is important for basolateral recycling in polarized epithelial cells.
CULTURA IN VITRO DE Solanum paludosum: REGENERAÇÃO

Resumo – Solanum paludosum, vulgarmente conhecida como Jurubeba roxa e uma especie da familia solanacea encontrada no Nordeste Brasileiro e rica em moleculas de interesse farmacologico. Entre estas moleculas destaca-se a solasodina que e um alcaloide esteroidal que se apresenta in natura na forma glicosidica e constitui-se em materia prima para a semi-sintese dos hormonios adrenocorticais e glicocorticais, usados como agentes contraceptivos e anti-inflamatorios. Neste trabalho mostram se os resultados de regeneracao a partir de explantes de folhas, fragmentos de hipocotilo e raiz cultivados em meios MS acrescido de diferentes reguladores de crescimento. Foram obtidas plantas em meios de cultura contendo diferentes combinacoes em reguladores de crescimento sendo a combinacao mais eficiente aquela que continha o acidoindlicoacetico (AIA 10-6) e benzilaminapurina (BAP 10-5 M). Palavras-chave: Solanump paludosum, hipocotilo , regeneracao
EL HALLAZGO DEL PRIMER NIDO DE DINOSAURIOS TRIASICOS, (SAURISCHIA, PROSAUROPODA), TRIASICO SUPERIOR DE PATAGONIA, ARGENTINA

Several in complete skeletons of juvenile Prosauropoda and two eggs were recovered from Upper Triassic beds of Southern Patagonia. The specimens are refered to a new genus and species, Mussaurus patagonicus, showing a mixed picture of anatomical affinities. Fore lirnbs, pelvis and hind limb are tipically Prosauropoda; the short cervical vertebrae resemble those of the Middle Triassic thecodont Lagosuchus, and some characters of the skull suggest relationships with both Prosauropoda and Sauropoda. Tentatively a new family of Prosauropoda is proposed to include this new species.
Extended Education in Switzerland: Values in Past, Present, and Future

It is only in recent years that extended education has been a topic of broader public interest in Switzerland. The impetuses for extended education were changes in social and family conditions, and PISA 2000. In 2007 under the HarmoS Intercantonal Agreement on Harmonization of Compulsory Schooling in Switzerland, all cantons that adopted the Har- moS Agreement are obligated to provide extended education offerings meeting the needs of children and to introduce canton-wide core times. The developments in recent years in two trailblazing cantons - Basel-Stadt and Bern - presented as examples will most likely show the way forward for the further development and expansion of extended education across Switzerland. This means that in the future, in addition to quantitative expansion there will probably be a main focus on qualitative expansion of extended education. In a long-term perspective, there may be a development in the direction of all-day school scheduling for all students: schools with all-day hours as the normal case.
Evolution and ecology of associations between Drosophila and their parasitic nematodes

In this dissertation, the evolutionary and ecological determinants of host range of nematode parasites (Tylenchida: Allantonematidae: Howardula, Parasitylenchus) of mushroom-breeding Drosophila (Diptera: Drosophilidae) are examined. These nematodes are horizontally transmitted, obligate parasites, often with severe effects on host fitness. Phylogenetic analysis of Drosophila and Howardula DNA sequences shows little congruence between host and parasite phylogenies. with frequent host colonizations and losses. Dro5op/j/7a-parasitic Howardula are not monophyletic. with host switches occurring between Drosophila and distantly related mycophagous sphaerocerid flies. Molecular analysis reveals eight new Howardula species. The ability of five nematode species to infect and develop in 24 ta. \onomically diverse Drosophila species is assessed. All nematode potential host ranges but one are large, even for host specialists. Novel hosts that are distantly related from the native host are less likely to be infected, but among closely related hosts there is variation in susceptibility. Potential host ranges differ greatly between related parasite species. Most novel infections do not cause reductions in host fecundity, with the exception of P. nearcticus. Thus, Drosophila-nematode associations are dynamic, and appear to be driven by a combination of repeated opportunities for host colonization due to shared mushroom breeding sites, and large nematode potential host ranges. Recent colonization of novel host species may explain the striking differences in virulence observed in natural Drosophila-nematode associations. For example, Nearctic
Photochemistry and the nucleic acids

The Photochemistry of Nucleic Acids Photosensitised Reactions of DNA: Cleavage and Addition Photoreactions of Nucleic Acids and their Constituents with Amino Acids and Related Compounds Applications of Psoralens as Probes of Nucleic Acid Structure and Function 4-Thiouridine as an Intrinsic Photaffinity Probe of Nucleic Acid Structure and Interactions.
Review of Architectural Flaws of the EMU: What Eurozone Crisis Lessons for the Proposed ‘Afrozone’?

There were evidence-prompted conclusions by many researches on the optimum currency area (OCA) theory that the European Monetary Union (EMU) is not an optimum currency area; and consequently, there were warnings about the dangers of a single monetary policy for the Eurozone because of the inability of the zone to fulfil the theoretical preconditions for an optimal currency area. The 2007 subprime crisis that transformed into global financial crisis ignited the Eurozone crisis of 2009 which substantially revealed some crucial flaws and inadequacies in the design of the Eurozone. This paper reviewed some literature on the original design of the European Monetary Union (EMU) and the post-financial crisis EMU (the Eurozone crisis), evaluated various debates on the sustainability of the EMU, identified the financial crisis-exposed defects in the design of Eurozone and well as the flaws inherent in the original optimum currency area (OCA) theory and its application to monetary integration, while making further efforts in highlighting lessons these have for the current monetary integration in the developing blocs of Africa and the proposed monetary integration of Africa. There has been the desire for the African Monetary Union which aims at the creation of a unified currency for the African continent. The 1991 Abuja treaty set out six stages in the process of achieving a monetary union and a single currency for Africa by 2028. The strategy for African monetary integration is based on progressive economic and monetary integration of African economic communities (ECOWAS, EAC, SADC etc) which are regarded as building blocks of Africa. This proposed African common currency is to be known as ‘afro’. This prompted this writer to tag the area that would eventually adopt this common currency as ‘Afrozone’ in this paper. Some of the major Eurozone design flaws identified in this paper as those exposed by the Eurozone crisis are: (i) the absence of effective economic governance mechanism; (ii) the retention of banking supervision and resolution at national levels; (iii) the lack of financial back-stops and crisis resolution mechanisms at the union level; and (iv) defects in the design of the Eurozone's common central bank. This paper highlights fifteen Eurozone crisis lessons for a complete and sustainable ‘Afrozone’ being proposed for the continent of Africa by 2028.
Low temperature induces oocytes p34^cdc2 synthesis and accumulation—the acquisition of competence to resume meiosis in toad oocytes

Full grown oocytes derived from Bufo Bufo gargarizans rearing at high temperature environment (24℃), never underwent GVBD after progesterone treatment.No p34^cdc2 Hl kinase activity was detected in the oocytes after progesterone stimulation or OA microinjection;Western blotting analysis showed that the level of p34^cdc2 and p33 in the oocytes are significantly lower than those in the oocytes derived from the hibernating toads (below 10℃). ^35S-Met incorporation analysis showed that when the oocytes were incubated at 6℃,synthesis of about thirty defferent polypeptides was promoted or induced,including p34^cdc2 and some other p13^suc1-binding proteins.All these results indicated that a low temperature environment is essential for the oocytes of Bufo Bufo gargarizans to express and stord some cell cycle drivers and its regulators,and to gain the maturation competence.These results will also provide a nwe clue for explaining the molecular mechanisms why gametogenesis of some organisms depends on a relative low temperature and how to maintain the geographical distribution of some animals.
Studies on the role of the Arabidopsis thaliana LATERAL ORGAN BOUNDARY DOMAIN (LBD) gene family

The LATERAL ORGAN BOUNDARY DOMAIN (LBD) genes encode plant-specific DNA binding transcription factors. In A. thaliana, the LBD gene family is composed of 43 members. During the last years substantial progress has been made in uncovering the regulatory roles of LBD transcription factors and the LBD family members have been implicated in a variety of developmental processes. In this study, reverse genetic approaches were carried out in order to learn more about LBD gene functions. A functional characterization by phenotypic analysis of LBD gain and loss-of-function mutants turned out to be difficult, as LBD proteins contribute to complex regulatory networks. The results of this work show that the LBD family member JAGGED LATERAL ORGANS (JLO) is an important regulator of patterning processes in Arabidopsis. This is demonstrated by an aberrant embryonic development, defective lateral organ formation and separation, altered root architecture and a premature arrest of root and shoots meristem activity in jlo mutants. Some of these phenotypic aspects could be traced back to impaired auxin transport and signal transduction. Genetic studies, gene expression analyses and exogenous auxin treatment implicated a role for JLO in the transcriptional regulation of the auxin receptor TRANSPORT INHIBITOR RESPONSE 1 (TIR1). Reduced TIR1 expression in jlo mutants causes a stabilization of the Aux/IAA protein BODENLOS (BDL). The failure to release the ARF transcription factor MONOPTEROS (MP) from BDL repression is partially the cause for a misexpression of several auxin regulated genes in jlo mutants. These genes comprise members of the PINFORMED (PIN) and PLETHORA (PLT) family as well as AUXIN RESISTANT1 (AUX1) and WUSCHEL-RELATED HOMEOBOX 5 (WOX5). Therefore, JLO can be considered to be a central regulator of auxin signaling and distribution during Arabidopsis development. Furthermore, JLO was found to repress the expression of the class I KNOX genes SHOOT MERISTEMLESS (STM) and BREVIPEDICELLUS (BP) in lateral organs. Interaction studies and double mutant analyses provide evidence that JLO thereby acts in homomeric as well as in heteromeric complexes with ASYMMETRIC LEAVES 2 (AS2), another LBD protein. Moreover, AS2 can mediate an interaction between JLO and ASYMMETRIC LEAVES1 (AS1). This trimeric protein complex acts to promote organ development through restriction of BP expression from lateral organs. Interestingly, JLO and AS2 also jointly contribute to the regulation of PIN genes in roots. Again, both proteins function in a heteromeric complex, but also independently from each other. This indicates that JLO and AS2 act in a combinatorial fashion. Both LBD proteins integrate the regulation of KNOX expression with the control of hormonal signaling. In further studies, LBD31 was identified to interact with JLO as well as with AS2. This result opens up the possibility for different or higher order LBD complexes in Arabidopsis.
Adapting S. cerevisiae Chemical Genomics for Identifying the Modes of Action of Natural Compounds

Natural compounds have been largely excluded from characterization via high-throughput profiling strategies due to their limited abundance. Herein, I describe the modification of highthroughput yeast chemical genomic (CG) interaction profiling to permit identifying the modes of action of natural compounds. The previous assay proceeded by evaluating the genome-wide yeast deletion collection for drug-hypersensitivity in a volume of 0.7mL. Compound consumption was minimized with the adapted approach by reducing the assay volume 70% through simplifying the complexity of the yeast deletion pool screened. By recreating each yeast mutant in a drug-hypersensitive background, I created a novel resource that increases compound efficiency and further diminishes compound use. Evaluating a series of characterized compounds analyzed previously by the traditional CG approach validated the adaptations incorporated did not negatively affect the quality of data yielded. Ultimately, this modified strategy will be used to screen thousands of natural compounds contained within the RIKEN NPDepo library.
The Relationship between Employee Engagement and Corporate Social Responsibility: A Case Study of Car Dealership in Erbil, Kurdistan

The increasing awareness of the subject of corporate social responsibility has raised the questions about whether if there is a relationship between employee engagement and corporate social responsibility. Corporate Social Responsibility (CSR) is considering an important element of company's performance and its activities so employee‘s engagement will have its effects. The purpose of this research is to examine the relationship between employee engagement and corporate social responsibility. The study was carried out car dealerships in Erbil, Kurdistan. In total, 53 participants involved in this study. The findings of this study revealed that higher employee engagement level could be attained by higher level of corporate social responsibility, accordingly the research hypothesis supported. The limitation of this study was the small sample size; the researchers recommended obtaining bigger sample size for similar studies in the future.
Phenotyping of recombinant inbred lines for early blight resistance in tomato

Tomato is one of the most remunerable and widely grown vegetables in the world. Early blight ( Alternaria solani ) is an important disease causing severe damage in tomato. Growing resistant varieties is the only effective, feasible technique for early blight management. More recent genetic studies on early blight resistance have been directed to the mapping and characterization of quantitative trait loci determining the resistance with the aid of molecular marker maps. A trial was conducted during rabi season, 2010-2011 to study phenotyping of recombinant inbred lines that have been developed for resistance against early blight of tomato caused by Alternaria solani . 179 recombinant inbred lines inoculated with 12 days old culture of Alternaria solani and disease severity was scored on a five-point scale. The frequency distribution curve of Area Under Disease Progress Curve predicted presence of major Quantitative Trait Loci.
Genetic engineering of the pancreatic β‐cell line MIN6 to express bacterial globin proteins protects cells from nitrosative stress

Susceptibility of pancreatic β‐cells to nitric oxide (NO) is a prime issue in type 1 diabetes mellitus. NO is produced by intraislet‐resident macrophages or by the β‐cells themselves after cytokine stimulation, leading to reduction of viability and apoptosis. We have previously demonstrated a potent NO detoxification activity of bacterial globin proteins. Unlike the mammalian counterparts, these proteins can possess an intramolecular reductase domain, which increases the catalytic NO turnover. Constitutive expression of either Ralstonia eutropha flavohemoglobin or Vitreoscilla hemoglobin increased the cellular viability of MIN6 β‐cell cultures exposed to the NO donor sodium nitroprusside (SNP) maximally by 42.8% and 33.8%, respectively, relative to the wild‐type MIN6 control. Addition of SNP to a final concentration of 100 μM induced caspase activity. Under these conditions, no significant induction of caspase activity was observed in the globin‐protected cells, whereas in the parental MIN6 cells, caspase activity was increased by 57 ± 2%. Treatment of β‐cells with a combination of interleukin‐1β, interferon‐γ, and tumor necrosis factor‐α stimulated the generation of NO in vivo, and the heterologous expression of globin proteins could protect β‐cells to a small extent from the cytokine challenge.
New Mapping Project Splits the Community

GENOMICSA new type of genomic map, known as the haplotype map, promises to speed the search for elusive genes involved in complex diseases. But to many biologists, it's an untested concept hardly worthy of the $110 million it will consume. Welcome to the haplotype map, a new type of genome map that, depending on where you look, is eliciting exuberance or exasperation.
A Comparative Study on Outbreak and Non-outbreak of Cochlodinium Polykrikoides Margalef in South Sea of Korea in 2007-2009

Harmful dinoflagellate, Cochlodinium polykrikoides, has always occurred in southern coastal waters every year during summer, but it did not occur in 2009. A comparative study on outbreak in 2007/2008 and non-outbreak of C. polykrikoides in 2009 was performed based on environmental parameters and phytoplankton appearances. Samples were obtained at 13 stations from Yeosu to Wando waters in 2007-2009. The heavy rainfall was associated with the decrease of surface water temperature below in July, the decrease of salinity below 31psu in August and increase of pH to 8.4 in Augus, 2009. concentration of DIN in 2009 was approximately too times as high as those of 2007 and 2008, and the ratioes of N:P and Si:N in 2009 showed Redfield ratio to be above the value of 16. This indicates that Redfield ratioes were significantly different between 2007/2008 and 2009. Dominant species during the field survey were shown to be Chaetoceros spp. , Skeletonema costatum and Thalassiosir spp. in diatoms and to be Ceratium spp. in dinoflagellate. In partiuclar, Gonyaulax polygramma occurred in August, 2009 instead of C. polykrikoides. Consequently, the massive rainfall and shortage of sunshine contributed to considerable variation in environmental parameters which were associated with delay in the timing of rapid growth phase of C. polykrikoides.
The Art of Morphogenesis: Cinema in and beyond the Capitalocene

The era of cinema, some have argued, is ending. As the photo-realist recording of reality, the capture of reflected light on photochemical film, cinema is already a thing of the past. Defined as the production of moving images, however—as animation and transformation, the continual generation of new forms from material that may be “real,” indexical and mimetic, or that may be entirely composed and composited, reproductions without an original—cinema is still very much alive. In this latter sense, cinema is about morphogenesis: the generation of new forms from old ones, reproduced, reassembled, recomposed, and reimagined.