Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigating the differential instructive roles of WT1's isoforms

The Wilms’ tumour suppressor gene Wt1 is a key regulator of embryonic development and tissue homeostasis. In humans, mutation in the gene may lead to childhood kidney cancer, severe glomerular kidney diseases, gonadal dysgenesis and, in rare cases, heart diseases. The importance of WT1 in embryonic development is related to its crucial function in the regulation of two cellular plasticity processes: the epithelial to mesenchymal transition (EMT) and the reverse process, the mesenchymal to epithelial transition (MET). WT1 expression persists during the waves of EMT and MET that generate certain mesodermal tissues. In fact, WT1 is a major regulator of both transitions and it is essential for the survival of mesenchyme progenitors. Furthermore, it has been proposed that WT1 is required for the derivation of progenitors from different mesothelia, possibly through an EMT. Progenitors expressing WT1 are believed to differentiate into different cell types, giving rise to coronary vasculature, adipocytes and hepatic stellate cells. In my PhD I aimed to investigate the instructive role of different WT1 isoforms. To address this, the first goal was to generate a single plasmid that would accommodate all necessary components of an inducible system, in order to derive cellular models for the inducible expression of WT1 single isoforms. Second, I aimed to understand the processes that the single variants were sufficient to drive. Therefore, I started with the establishment of two cellular models for the inducible expression of the main four isoforms of WT1 (with or without the exon 5 and/or the KTS, here referred as +/+, +/-, -/+ and -/-). I cloned different plasmids carrying doxycycline inducible WT1 isoforms and derived single stable clones in two epithelial kidney cell lines that do not express WT1: the MDCK and the IMCD3 cells. I then analysed the expression profiles of the clones, using either microarray or RNA sequencing, and performed cellular assays to characterize the cells after WT1 induction.
Induction of Pro-Angiogenic Factors by Pregnancy-Specific Glycoproteins and Studies on Receptor Usage

Abstract : Pregnancy-specific glycoproteins (PSGs), also referred to as Schwangerschafts-protein 1(Sp1) or pregnancy-specific Beta1 glycoproteins, are a family of proteins secreted by the syncytiotrophoblast whose expression increases as pregnancy progresses and correlates with pregnancy success. Although PSGs have been identified for more than 30 years their functions have yet to be fully elucidated. PSGs belong to the carcinoembryonic antigen(CEA) family of proteins whose members have been implicated in the processes of angiogenesis, cell adhesion, immunomodulation and cell migration. The ability of humanPSG1, 6 and 11 and murine PSG17, 18 and 19 to induce anti-inflammatory cytokines has led to the hypothesis that these proteins may function to protect the fetus from a potential maternal immune attack. Recent reports demonstrated positive staining for murine PSGs lining the capillaries within the decidua at the implantation site, suggesting a possible role for PSGs in maternal vasculature remodeling.
Virulência de isolados de Puccinia coronata f. sp. avenae do Rio Grande do Sul.

RESUMO: Nao existem estudos conclusivos sobre a variabilidade em virulencia de isolados de Puccinia coronata f. sp. avenae que ocorrem no Rio Grande do Sul. O principal objetivo do trabalho foi determinar o padrao de virulencia/avirulencia e a raca fisiologica de 46 isolados de Puccinia coronata f. sp. avenae coletados em tres municipios do Estado do Rio Grande do Sul com base na reacao em 25 linhas quase isogenicas portadoras de genes Pcs, utilizando o sistema norte-americano de nomenclatura e um novo sistema sugerido neste trabalho. Os isolados passaram por dois isolamentos monopustulares e posteriormente foram inoculados sobre plântulas portadoras dos genes Pcs sendo que a avaliacao foi efetuada 15 dias depois da inoculacao. Os resultados evidenciaram que os isolados sul-brasileiros apresentam elevada virulencia uma vez que 66% das inoculacoes resultaram em alto tipo de infeccao. Praticamente, cada isolado apresentou um padrao de virulencia/avirulencia, o que evidenciou a grande variabilidade do fungo na regiao. Entretanto, o sistema norte-americano de nomenclatura nao foi totalmente eficiente na determinacao das racas sul-brasileiras. Os genes Pc36, Pc53, Pc55 e Pc63 representam uma possivel combinacao de genes a ser incorporada ao sistema norte-americano de nomenclatura para uma caracterizacao mais eficiente das racas locais. ABSTRACT: There are no conclusive studies regarding the virulence variability of crown rusts strains that occur in southern Rio Grande do Sul. The main goal of this work was to determine the pattern of virulence/avirulence and the strain of 46 isolates of Puccinia coronata f. sp. avenae collected in three counties in the state of Rio Grande do Sul through the reaction under 25 Pcs genes by the North American system of nomenclature and by a new system suggested in this work. The isolates were subjected to two consecutive monopustular isolations and afterwards they were inoculated on seedlings of Pc near-isogenic lines, and fifteen days after the inoculation the reactions were scored. The results evidenced that the southern brazilian rust isolates presented a great virulence, since 66% of innoculations showed high infection type. In general, each isolate presented a different pattern of virulence/avirulence, which evidenced the large variability in virulence that the fungus presents in the target region. However, the North American system of nomenclature was not completely efficient in determining south-brazilian strains. Thus, the genes Pc36, Pc53, Pc55 and Pc 63, represent a possible gene combination to be incorporated to the North American system of nomenclature to a more accurate characterization of the local strains.
Novel Methods for Delivering and Promoting the Endosomal Escape of Nucleic Acid Based Drugs: Chiral Polyamines and Hydrophobic Nanoparticle-Containing Liposomes

Nucleic acid based drugs such as plasmid DNA (pDNA), small interfering RNA (siRNA), short hairpin RNA (shRNA), micro RNA (miRNA), and both antisense and antigene oligonucleotides, are potentially potent and specific compounds for therapeutic applications. Many major life threatening ailments might be treated using these molecules, and many polynucleotide products are currently in advanced clinical development. However, their successful therapeutic application is hindered due to limited delivery to their site of action in either the cytosol or the nucleus of a cell. Some of the barriers in the path of successful delivery of these biomolecules to their site of action have been addressed. However, endosomal entrapment followed by maturation to lysosomes and degradation of these compounds inside the cell is one remaining major hurdle. This dissertation describes two novel siRNA delivery techniques which present distinct advantages in their respective areas of application while, at the same time, constitute promising platforms for developing therapeutic biologicals. Chapter 2 focuses on liposomal delivery vehicles containing hydrophobic nanoparticles in their bilayers, which encapsulate the nucleic acid based drugs and promote endosomal escape by nanoparticle induced fusion with the endosomal membranes. Specifically we use metal nanoparticles in specialized liposomes for the efficient delivery of small interfering RNA (siRNA). Manuscript 2 focuses on novel chiral cationic polymers – polyethyleneimines (PEIs) – that form complexes with the negatively charged nucleic-acid based drugs and promote endosomal escape via a proton sponge effect. Specifically we use of chiral cationic polyamines for two intriguing applications: fabrication of chiral covalentlylinked microcapsules, and enantiospecific delivery of siRNA to Huh 7 cells. We found that two of the designed polymers improved transfection efficiency relative to commercially available transfection reagents with lower cell toxicity. In total this dissertation presents work that demonstrates novel and efficient delivery strategies that promote endosomal escape and enhance the intracellular activity of nucleic acid based drugs.
High‐throughput profiling and analysis of plant responses over time to abiotic stress

Sorghum (Sorghum bicolor (L.) Moench) is a rapidly growing, high-biomass crop prized for abiotic stress tolerance. However, measuring genotype-by-environment (G × E) interactions remains a progress bottleneck. Here we describe strategies for identifying shape, color and ionomic indicators of plant nitrogen use efficiency. We subjected a panel of 30 genetically diverse sorghum genotypes to a spectrum of nitrogen deprivation and measured responses using high-throughput phenotyping technology followed by ionomic profiling. Responses were quantified using shape (16 measurable outputs), color (hue and intensity) and ionome (18 elements). We measured the speed at which specific genotypes respond to environmental conditions, both in terms of biomass and color changes, and identified individual genotypes that perform most favorably. With this analysis we present a novel approach to quantifying color-based stress indicators over time. Additionally, ionomic profiling was conducted as an independent, low cost and high throughput option for characterizing G × E, identifying the elements most affected by either genotype or treatment and suggesting signaling that occurs in response to the environment. This entire dataset and associated scripts are made available through an open access, user-friendly, web-based interface. In summary, this work provides analysis tools for visualizing and quantifying plant abiotic stress responses over time. These methods can be deployed as a time-efficient method of dissecting the genetic mechanisms used by sorghum to respond to the environment to accelerate crop improvement.
Photosynthetic physiology of Scenedesmus sp. (Chlorophyceae) under photoautotrophic and molasses-based heterotrophic and mixotrophic conditions

Abstract: Heterotrophically grown cells of a newly isolated strain of Scenedesmus sp. retained their photosynthetic pigment content after prolonged darkness. When these cells had reached an apparent stationary phase and were subsequently exposed to light (mixotrophy), growth rapidly resumed and the biomass increased by 5.5-fold relative to photoautotrophically grown cultures and doubled compared with heterotrophic cultures. Although it is expected, and supported by the majority of reports in the literature, that dark acclimation of algal cultures should lead to eventual loss of photosynthetic pigments, some algae defy these expectations and synthesize and retain their photosynthetic pigments independent of light, despite the high associated maintenance costs. Here we examined the photosynthetic activity of heterotrophically grown cells in an attempt to explain this variance, using Scenedesmus sp. as a model organism. The photosynthetic capacity of heterotrophically grown cells was comparable with that of autotrophically grown cultures, associated with an interesting set of changes to the photosynthetic apparatus that includes lower nonphotochemical quenching, chlorophyll content, absorption cross-sectional area, higher connectivity between reaction centers, higher electron transport flux per reaction center, and probability at t = 0 that a trapped exciton moves an electron into the electron transport chain beyond the primary quinone electron acceptor, and performance index. As a result, when these heterotrophically grown cultures were transferred back to light, they were still able to perform photosynthesis and enhance overall growth, which was otherwise limited in complete darkness.
Biological nitrogen fixation by irrigated dry bean (Phaseolus vulgaris L.) genotypes

Abstract: Dry bean (Phaseolus vulgaris L.) is usually considered to be poor at biological nitrogen fixation (BNF), but large variations in this trait have been observed among bean genotypes. We evaluated 16 bean genotypes for N2 fixation ability in four N treatments: (i) uninoculated in low-N soil (30 kg N ha-1), (ii) inoculated with commercial Rhizobium leguminosarum bv. phaseoli inoculant Nitrastik-D® in low-N soil, (iii) inoculated with commercial R. leguminosarum bv. phaseoli inoculant Nodulator® in low-N soil, and (iv) uninoculated in high-N soil (100 kg N ha-1). There were differences between genotypes in all the plant parameters that were measured, but only nodulation was affected by N treatment. The 100 kg N ha-1 treatment suppressed nodulation. Seven genotypes nodulated well with either inoculant, two genotypes nodulated better with Nitrastik-D than with Nodulator, three nodulated better with Nodulator than with Nitrastik-D, and four nodulated poorly with either inoculant. Cultivars AC Redbond, Island, and Resolute, all currently commercially grown, did not fix much N2 at flowering (4–8 kg N ha-1) or maturity (19–34 kg N ha-1). By contrast, germplasm lines PI 136692 (red bean), GH-196 (pinto bean), and LEF2RB (carioca bean) had high BNF capability at flowering (10–11 kg N ha-1) and especially at maturity (60–72 kg N ha-1), in addition to high seed yield (2778–2897 kg ha-1), indicating their superior ability to support both of these economically important traits throughout plant growth. These three genotypes would be valuable to breeders for the genetic improvement of BNF in dry bean cultivars.
PENGARUH VARIASI KONSENTRASI INDOLE ACETID ACID (IAA) TERHADAP PERTUMBUHAN TUNAS PISANG BARANGAN (Musa acuminata L. triploid AAA.) DALAM KULTUR IN VITRO

Penelitian ini bertujuan untuk mengetahui pengaruh variasi konsentrasi Indole Acetid Acid (IAA) terhadap pertumbuhan tunas pisang Barangan (Musa acuminate L. triploid AAA.) serta konsentrasi yang optimum dalam kultur in vitro. Penelitian ini dilakukan di Kebun Benih Holtikultura (KBH) Kecamatan Salaman, Magelang. Penelitian dilaksanakan selama enam minggu, dimulai Maret-April 2014. Penelitian menggunakan Rancangan Acak Lengkap (RAL) dengan 4 perlakuan dan 4 kali ulangan yaitu perlakuan 1 (BP1) menggunakan 0 ppm IAA, pelakuan 2 (BP2) menggunakan 0,1 ppm IAA, perlakuan 3 (BP3) menggunakan 0,3 ppm IAA, dan perlakuan 4 (BP4) menggunakan 0,6 ppm. Data yang diperoleh dianalisis dengan menggunakan Uji Jarak Ganda Duncan (UJGD). Hasil Analisis Varians menunjukkan konsentrasi paling optimal untuk meningkatkan jumlah anakan tunas 0,3 ppm IAA dan 0,6 ppm untuk meningkatkan jumlah akar, panjang daun, serta panjang batang semu. Kesimpulan dari penelitian ini yaitu variasi konsentrasi Indole Acetic Acid (IAA) secara umum tidak berpengaruh nyata terhadap pertumbuhan pisang Barangan (Musa acuminata L. triploid AAA), meskipun terdapat satu parameter yang berpengaruh nyata, yaitu jumlah anakan tunas pisang Barangan. Kata kunci : Indole Acetic acid (IAA), kultur in vitro, pisang Barangan.
DYSREGULATION OF ENDOGENOUS NITRIC OXIDE EXPRESSION AS RELATED TO AIR POLLUTION AS A RISK FACTOR FOR AUTISM

The arginine-nitric oxide pathway is likely to be involved in the neuropathophysiology of autism through dysregulation of nitric oxide (NO) expression during fetal development. This in turn would lead to a cascade of cell signaling effects that impact early brain development and nervous system connectivity, leading to an autism phenotype. Chemical pathways involving nitric oxide expression are influenced by other cell signaling mechanisms, such as the MET tyrosine kinase receptor-ligand system, which is associated with a robust genetic finding of over- transmission of the MET "C" allele in multiplex families having more than one child with autism spectrum disorder (ASD). Dysregulation of nitric oxide expression, it is proposed, will be found in children with autism who have inherited the MET "C" allele based on downstream under- activation of Nitric Oxide Synthase (NOS). This will likely be reflected in significantly different levels of nitric oxide metabolites (NOx or nitrites + nitrates) in the blood and the airways of autistic individuals with the MET "C" allele. Since the Nitric Oxide Synthase (NOS) enzymes that produce nitric oxide are potentially sensitive to allosteric feedback, it is further suggested that nitric oxide air pollution may be a potential envi- ronmental risk factor for autism in the genetically susceptible fetus.
Kittiwake eggs viewed by conspecifics and predators: implications for colour signal evolution

Colour traits evolve under the antagonistic selective pressures of increasing detectability to intended receivers (e.g. conspecifics) while minimizing detectability to unintended receivers (e.g. predators). Primarily selected for camouflage, avian egg coloration has also been suggested to have intraspecific signalling functions. A first step in assessing the relative importance of camouflage/communication requires quantifying detectability for different visual systems, which is rarely done. Here, we compared brightness and colour contrasts of black-legged kittiwake (Rissa tridactyla) speckled and soiled eggs as seen from a distance by conspecifics and their main avian predator, the common raven (Corvus corax). We also examined how egg speckling and soiling deposition on incubated eggs affected egg detectability and egg coloration variability. We found that eggs were detectable by both species, but were more conspicuous to conspecifics than to predators. Egg speckling reduced brightness contrast and increased colour contrast, contributing to reducing detectability by predators while maintaining potential for intraspecific communication, respectively. Soiling reduced egg detectability for both perceivers, but soiled eggs remained more conspicuous to conspecifics than predators. Moreover, soiling did not homogenize the clutch signature of egg colour and speckling, thus allowing intraspecific exploitation of information on female quality that egg coloration may convey or individual clutch recognition. We suggest that further studies of egg colour adaptive functions and evolution should consider all perceivers as well as soiling deposition, an overlooked mechanism that may be favoured by selection against predation.
Antiproliferative and pro-apoptotic effects of Andean berry juice (Vaccinium meridionale Swartz) on human colon adenocarcinoma SW480 cells

Vaccium meridionale Swartz, commonly Andean Berry, has a high content of several phytochemicals, such as anthocyanins, phenolic acids, and other flavonoids. However, in spite of its antioxidant capacity, there is little information about its anticarcinogenic properties. This study evaluated the antiproliferative and pro-apoptotic activity of Andean Berry Juice (ABJ) on human colon adenocarcinoma SW480 cells. The antiproliferative activity of ABJ was evaluated on SW480 cells using the Sulphorodamine B assay.The effect on cell viability, cytotoxicity and activation of caspase-3 was analyzed using The ApoTox-Glo™ Triplex Assay. Specific apoptotic biomarkers cleaved PARP, total Bcl-2-associated death promote (BAD), phosphorylated BAD, total p53, and phosphorylated p53 were also analyzed. To determine the intracellular redox-state, the Glutathione Assay Kit and 2′-7′-Dichlorodihydrofluorescein diacetate (DCFH-DA) were used, respectively. The antiproliferative assay showed a IC50 value of 8% v/v ABJ, the caspase 3 activity was increased in time-dependent manner in SW480 treated cells, the proapoptotic proteins (cleaved caspase 3, cleaved PARP, P53 and total BAD) were increased by 1.6 to 2.0 fold. In addition, the ABJ-treated SW480 cells increased significantly the production of intracellular reactive oxygen species (ROS), parallel with reduction in the intracellular content of glutathione (GSH) and consequently a decrease of GSH/ oxidized glutathione (GSSG) ratio. In conclusion, the ABJ was able to inhibit SW480 cells proliferation involving apoptotic mechanisms through the perturbation of intracellular oxidative state. Key words: Vaccinum, colon cancer, anthocyanins, apoptosis, oxidative stress.
Predicting HIV virulence evolution in response to widespread treatment

A recommendation of: Herbeck JT, Mittler JE, Gottlieb GS, Goodreau SM, Murphy JT, Cori A, Pickles M, Fraser C Evolution of HIV virulence in response to widespread scale up of antiretroviral therapy: a modeling study 10.1093/ve/vew028
Feeding a Diet with Precise Lysine Level improved Laying Performance and Feed Efficiency of Broiler Breeder Hens at the Early Laying Stage

A dose-response experiment was conducted to determine the lysine requirement for broiler breeder hens during pre-peak production. Totally, one hundred and twenty-six flock 23-week-old Ross 308 broiler breeder hens with similar body weight were selected (2,188±32 g) for a 6-week experiment. Hens were fed with a basal diet of corn-wheat-soybean meal formulated to achieve the Ross 308 breeder nutrient specifications (2016), except for lysine. The 7 graded, daily lysine intake levels used in this experiment were 732, 785, 838, 891, 944, 997, and 1,050 mg, and hens were restricted to 133 g of feed throughout this experiment. Pen based egg production were recorded once a day and all eggs were weighed daily. Age at sexual maturity was determined when the hens attained age at 25% production. Body weight at 23∼29 weeks of age was not affected (P>0.05) by lysine levels. By fitting a linear-plateau model, the daily lysine requirements for feed conversion ratio, total produced egg weight, and age at sexual maturity at 23∼29 weeks of age were estimated as 865, 907, and 891 mg, respectively. Using a quadratic-plateau model, the daily lysine requirement at 23∼29 weeks of age were estimated as 974, 964, and 950 mg for feed conversion ratio, total produced egg weight, and age at sexual maturity, respectively. These results suggested that the daily lysine requirement for modern broiler breeder hens according to the National Research Council (1994) are insufficient for higher total produced egg weight, sexual maturity, and feed efficiency, and 120% of the NRC recommendation level would improve hen productivity when data are fitted under linearand quadratic-plateau models. (
Bovine CD4 T cell memory subsets and immunological markers in Mycobacterium bovis infection and vaccination

Effector and memory T cells are generated through developmental programing of naïve cells following antigen recognition. If the infection is controlled up to 95 % of the T cells generated during the expansion phase are eliminated (i.e., contraction phase) and memory T cells remain, sometimes for a lifetime. In humans, two functionally distinct subsets of memory T cells have been described based on the expression of lymph node homing receptors. Central memory T cells express C-C chemokine receptor 7 and CD45RO and are mainly located in Tcell areas of secondary lymphoid organs. Effector memory T cells express CD45RO, lack CCR7 and display receptors associated with lymphocyte homing to peripheral or inflamed tissues. Effector T cells do not express either CCR7 or CD45RO but upon encounter with antigen produce effector cytokines, such as interferon-γ. Interferon-γ release assays are used for the diagnosis of bovine and human tuberculosis and detect primarily effector and effector memory T cell responses. Central memory T cell responses by CD4+ T cells to vaccination, on the other hand, may be used to predict vaccine efficacy, as demonstrated with simian immunodeficiency virus infection of non-human primates, tuberculosis in mice, and malaria in humans. Several studies with mice and humans as well as unpublished data on cattle, have demonstrated that interferon-γ ELISPOT assays measure central memory T cell responses. With this assay, peripheral blood mononuclear cells are cultured in decreasing concentration of antigen for 10 to 14 days (long-term culture), allowing effector responses to peak and wane; facilitating central memory T cells to differentiate and expand within the culture.