Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of boundaries on swimming of Paramecium multimicronucleatum

Microorganisms swimming in their natural habitat interact with debris and boundaries, which can modify their swimming characteristics. However, the boundary effect on swimming microorganisms have not been completely understood yet, and is one of most active areas of research. Amongst microorganisms, unicellular ciliates are the fastest swimmers and also respond to a variety of external cues. We choose Paramecium multimicronucleatum as a model system to understand the locomotion of ciliates. First, we explore the effects of boundaries on swimming modes of Paramecium multimicronucleatum by introducing them in 2D films and 1D channels. The geometric confinements cause the Paramecia to transition between: a directed, a meandering and a self-bending behaviors. During the self-bending mode the cell body exerts forces on the walls; which is quantified by using a beam bending analogy and measuring the elasticity of the cell body. The first investigation reveals the complicated swimming patterns of Paramecium caused by boundaries. In the second study we investigate the directed swimming of Paramecium in cylindrical capillaries, which mimics the swimming of ciliates in the pores of soil. A finite-sized cell locomoting in extreme confinements creates a pressure gradient across its ends. By developing a modified envelop model incorporating the confinements and pressure gradient effects, we are able to predict the swimming speed of the organisms in confined channels. Finally we study how Paramecium can swim and feed efficiently by stirring the fluid around its body. We experimentally employ μ-Particle Image Velocimetry to characterize flows around the freely swimming Parameicum and numerically use Boundary Element Method to quantify the effect of body shapes on the swimming and feeding process. Results show that the body shape of Paramecium (slender anterior and bulky posterior) is hydrodynamically optimized to swim as well as feed efficiently. The dissertation makes significant advances in both experimentally characterizing and theoretically understanding the flow field and locomotion patterns of ciliates near solid boundaries.
Simulation of potato late blight in the Netherlands: Validation of the BLIGHTSPACE model reveals dichotomy in the epidemiological effects of resistance components

Summary Th e epidemiological model BLIGHTSPACE is a spatiotemporal integro-diff erence equation model of the potato late blight pathosystem. To test and scrutinize the validity of model predictions, simulations were made and compared to independent data, collected in fi eld trials on the spread of two genotypes of Phytophthora infestans in fi ve potato cultivars in the Netherlands. Cultivar-isolate specifi c interactions were characterized in the model using three quantitative components of resistance: infection effi ciency, lesion growth rate, and sporulation intensity. Th ese were measured on potato leafl ets in the laboratory. System and model were compared visually using disease progress curves, and numerically through a comparison of predicted and observed t 5 and t 50 points (time in days until 5 and 50 % disease severity is reached respectively). For 80 % of the epidemics, performance criteria for both the t 5 and t 50 points were met. Sensitivity analyses with the model revealed a dichotomy in the epidemiological eff ects of fi tness parameters of P. infestans, providing two useful reference curves with which to formulate hypotheses regarding diff erences between observed and predicted epidemics.
Elevated levels of reactive oxygen species in heart failure patients: role for increased mononuclear NADPH oxidase expression (1153.9)

Although heart failure (HF) patients exhibit elevated levels of ROS, the sources and mechanisms contributing to the increase in ROS remain unclear. Recent work has shown that peripheral blood mononuclear cells (PBMCs) are a major source of NADPH oxidase‐derived superoxide (O2●‐) production. Therefore, we measured systemic ROS, O2●‐, and expression of NADPH oxidase and its potential activators, angiotensin II type 1 receptors (AT1R) and Rho Kinase (ROCK) 1, in PBMCs from 6 HF (ejection fraction 22±4%) and 6 age‐matched healthy controls. Total ROS and O2●‐ levels were measured in blood using electron paramagnetic resonance spectroscopy. Protein expression of NADPH oxidase subunits (gp91phox, p22phox, p47phox and p67phox), AT1R and ROCK1 were assessed from PBMCs using western blot. Total ROS and O2●‐ levels were elevated in blood from HF patients compared to controls (P<0.05). HF patients showed augmented protein expression of all NADPH oxidase subunits (e.g. 4±1 fold increase in gp91phox; P<0.05 vs. control). ROCK1 protein expression was also greater in HF patients (3±1 fold; P<0.05 vs. control), whereas AT1R tended to be higher (2±1 fold; P=0.13 vs. control). These preliminary findings suggest that PBMC‐derived NADPH oxidase expression is up‐regulated in HF patients and may contribute to the elevated levels of ROS, including O2●‐, through a ROCK1 and/or AT1R dependent mechanism.
Analyse de la diversité génétique d’ Aegilops geniculata Roth en Bulgarie

Aegilops geniculata Roth (Ae. ovata. L.) est une espece tetraploide (genome UM) apparentee au ble, largement repandue dans le bassin mediterraneen. En Bulgarie, pays presentant une large gamme de conditions pedo-climatiques, 42 populations ont ete collectees dans differentes regions floristiques. Une etude de diversite genetique a ete conduite sur 18 d’entre elles sur la base de caracteres morphologiques et phenologiques. Ces populations ont egalement ete etudiees pour le polymorphisme de l’ADN, revele par des marqueurs RAPD (Random Amplified Polymorphic DNA, amplification d’ADN polymorphe par des amorces aleatoires). Une structuration des populations, liee a des criteres ecogeographiques, a pu etre mise en evidence : les populations de Bulgarie sud-centrale se distinguent nettement de celles de Bulgarie orientale (littoral de la mer Noire). L’analyse de la diversite a l’interieur de chacun de ces deux groupes fournit des hypotheses concernant l’evolution et la diffusion de l’espece en Bulgarie, qui sont presentees et discutees.
Life history information from tracks of domestic dogs (Canis familiaris) in ceramic building materials from a Roman bath-house at Vindolanda, Northumberland, England

Este estudio analiza las pisadas de perros (Canis familiaris) conservadas en ladrillos y tejas usadas en la construcción de una terma romana de Vindolanda (Northumberland, Inglaterra) durante el primer siglo de nuestra era. Se describen los tamaños y características de las huellas caninas, así como los senderos que éstas definieron y los tipos de marcha a los que remiten. Las medidas indican la presencia de entre tres y cinco tipos diferentes de perros. No resulta posible predecir el tamaño del perro a partir del tamaño de una huella. Las improntas del pelaje detectadas en determinadas huellas se han comparado con otras registradas en perros y gatos actuales. La colección de huellas de animales domésticos de Vindolanda es la mayor jamás documentada en yacimientos británicos de época Romana y una de las mayores conocidas en el mundo hasta la fecha. A la vista de la valiosa información que aportan las huellas animales sobre la biología de las especies, el trabajo concluye animando al abordaje de nuevos trabajos en el área de la icnoarqueología.
Growth Studies of Colletotrichum gloeosporioides (Penz.) Sacc. - a Taxol Producing Endophytic Fungus from Plumeria acutifolia

Plumeria acutifolia Poiret (Apocynaceae) is grown as an ornamental plant in India, Indonesia, Philippines and South Africa. Various species of this plant are used as medicine to cure many diseases and also as antipsychotic, diuretic, or antitumour agent. Some iridoids and triterpenoids obtained from this plant are reported to have algicidal, antibacterial and cytotoxic activity. Some species of Plumeria are also used for the cure of rheumatism, diarrhoea, blennorhea, venereal disease and leprosy. This study investigates the taxol production by Colletotrichum gloeosporioides , an endophytic fungus of Plumeria acutifolia . The presence of Taxol was confirmed through TLC, UV and IR spectroscopic methods. The amount of taxol was quantified through HPLC analysis. This is the first report that a coelomyceteous fungus producing taxol from this plant.
Omics analysis in Caenorhabditis elegans : pattern inference and interpretation

High-throughput molecular technologies have greatly enhanced our understanding of biological processes by characterizing expression changes of genes (microarray and RNA-Seq data) and proteins (proteomics data), or transcription factor targets and epigenetics states (ChIP-chip and ChIP-Seq data). Among them, transcriptome studies based on microarrays or RNA-Seq have the ability to identify genes involved in the response to environmental change or specific stressors, thereby helping us to infer the underlying biological processes. During my PhD, I mainly focused on transcriptomic data analysis, using in most cases the nematode Caenorhabditis elegans as a model taxon. In particular, I have addressed seven specific projects: i) development of ABSSeq, an improved detection approach of differential gene expression for RNA-Seq data; ii) development of aFold, a method to fully moderate fold-change of RNA-Seq data and to improve gene ranking and visualization; iii) development of WormExp, a knowledge-based approach for interpreting gene sets in C. elegans; iv) exploration of the regulation of the C. elegans immune system using curated data sets from WormExp; v) characterization of putative major effectors (GATA transcription factors) in the C. elegans innate immune system; vi) comparison of the immune response of C. elegans at protein and transcript level. In general, our work facilitates high-throughput data analysis via improving pattern inference and interpretation, which in practice provides new insights into the immune system of C. elegans.
A S-nitrosação do mTORC1 reduz a proliferação de linhagens tumorais humanas

A S-nitrosacao e uma modificacao pos-traducional dinâmica e reversivel de proteinas que controla importantes funcoes celulares atraves da alteracao de residuos tiois de cisteinas pelo oxido nitrico (NO). Assim como a fosforilacao, a S-nitrosacao e capaz de alterar a conformacao, a atividade e a funcao de proteinas e contribui em grande parte para a influencia ubiqua do NO nas vias de transducao de sinal celulares. Inumeras evidencias apontam para um papel crucial da S-nitrosacao nao apenas na fisiologia dos organismos, mas tambem em inumeras doencas humanas, entre elas o câncer. Entretanto, trata-se de um mecanismo ainda pouco explorado de modulacao de proteinas envolvidas com a progressao tumoral, como as presentes na via do mTOR. Assim, o objetivo do trabalho e analisar os mecanismos pelos quais o NO afeta a funcao do mTOR. A analise da S-nitrosacao do mTOR foi realizada atraves do Biotin Switch Method e demonstra que o doador exogeno de NO, GSNO, aumenta os niveis de mTOR S-nitrosada. Alem disso, a GSNO reduz a fosforilacao das proteinas mTOR, p70S6K e 4EBP-1 de forma tempo- e dose-dependente. A fosforilacao da proteina p70S6K, reduzida pela exposicao ao NO, e restaurada pela adicao do agente redutor e denitrosante DTT. Entretanto, o pre-tratamento das linhagens celulares PC-3, DU145 e MCF-7 com o inibidor da guanilil ciclase, ODQ, ou com o sequestrador de NO livre, PTIO, nao reverte o efeito da GSNO na fosforilacao das proteinas mTOR, p70S6K e 4EBP-1, corroborando a hipotese de que o mTORC1 e modulado por S-nitrosacao. A viabilidade das linhagens tumorais humanas PC3, DU145, MDA-MB-468, MCF-7, HT-29, CACO-2 e A549 tambem diminui apos exposicao aos doadores de NO, sendo observada reducao da proliferacao e aumento da morte celular. As linhagens PC-3, MCF-7 e MDA-MB-468, que apresentam mutacoes ativadoras na cascada de sinalizacao PI3K-mTOR, sao mais sensiveis a presenca do NO. Assim, a S-nitrosacao do mTORC1 e uma importante modificacao pos-traducional capaz de modular a atividade quinase da proteina mTOR e reduzir a proliferacao de celulas tumorais humanas, apresentando potenciais implicacoes terapeuticas. Abstract
The role of wild-type SOD1 in SOD1 mouse models of ALS

Amyotrophic lateral sclerosis (ALS) is the most common form of adult onset motor neuron disease. It is primarily sporadic, however a proportion of cases are inherited and of these ~10% are caused by mutations in the gene SOD1. Recent research points to a possible role for wild-type (WT) SOD1 in ALS. This thesis addresses questions about the role of WT-SOD1 in ALS in the context of mouse models of ALS. The first set of experiments address whether pathogenically misfolded SOD1 can act in a “prion-like” way, recruiting WT-SOD1 into a pathogenic conformation in vivo. SOD1 transgenic mice were intracerebrally inoculated with homogenates prepared from central nervous system tissue from mouse or human which contains pathogenic SOD1. Pathology was assessed at a number of post-inoculation time-points to determine whether misfolding of transgenically expressed SOD1G93A was increased, or misfolding of transgenically expressed WT-SOD1 was induced. The project described above used transgenic mice bred onto an endogenous Sod1 null background because evidence from the prion field suggests that the endogenous protein could interfere with transmission of human misfolded SOD1. The effect of endogenous SOD1 on the disease phenotype of SOD1G93A transgenic mice was not known, therefore mice of 4 genotypes were examined: WT, Sod1-/-, Tg SOD1G93A and Sod1-/-;Tg SOD1G93A. Grip-strength and survival was measured. Muscle and spinal cord pathology were also examined at two time-points. Finally, a project to create a new mouse model of SOD1-fALS is described; a genomically humanised mouse with an inducible LoxP-Cre mutant/WT allele. Cloning of the targeting constructs was carried out using a combination of traditional restriction endonuclease cloning and recombineering. Finalising the constructs and embryonic stem cell targeting is underway. This work aims to increase our understanding of how WT-SOD1 may be involved in both familial and sporadic ALS and provide more accurate models SOD1-fALS.
Probing the Structural Topology of HIV-1 Virion Infectivity Factor (VIF): A Dissertation

Human Immunodeficiency Virus Type 1 (HIV-1), the virus that causes Acquired Immunodeficiency Syndrome (AIDS), attacks the immune system leaving patients susceptible to opportunistic infections that eventually cause death. Highly Active Antiretroviral Therapy, HAART, is the current drug strategy used to combat HIV. It is a combination therapy that includes HIV-1 Reverse Transcriptase and HIV-1 Protease inhibitors. Drug resistant strains arise that evade current HAART treatments; therefore novel drugs are needed. HIV-1 regulatory proteins such as Tat, Rev, Nef, Vpr, Vpu, and Vif are attractive new drug targets. Of particular interest is the HIV-1 Vif protein and its cellular binding partner APOBEC3G. In the absence of HIV-1 Vif, APOBEC3G, a cytidine deaminase, is able to mutate the viral cDNA and render the virus noninfectious. HIV-1 Vif binds to APOBEC3G and targets it for proteosomal degradation through an interaction with a CullinRING ligase complex. Blocking the HIV-1 Vif APOBEC3G interaction would allow APOBEC3G to perform its antiviral function. An attractive strategy to target the HIV-1 Vif APOBEC3G interaction would be a structure-based one. To apply structure-based drug design approaches to HIV-1 Vif and APOBEC3G, I attempted to collect high resolution structural data on HIV-1 Vif and APOBEC3G. My attempts were unsuccessful because the milligram quantities of soluble protein required were not obtained. Therefore, in Chapter III I used chemical cross-linking and mass spectrometry to probe the structural topology of HIV-1 Vif obtaining low resolution structural data.
Control of spot blotch in barley plants with fungicide and Bauhinia variegata Linn. leaf extract.

In barley plants (BRS-195), the disease detected as spot blotch is caused by Bipolaris sorokiniana, and is the most deleterious disease for the producers and the beer industry. For fungicides mediated control of this disease can cause risks to environment and human health. To eliminate these drawbacks, one of the methods considered is the use natural products. The purpose of the present study was to investigate the use of extract of leaves from Bauhinia variegata Link. and Opera® fungicide (active ingredient: pyraclostrobin) for controlling Bipolaris sorokiniana in barley plants. In Brazil there are two species of Bauhinia are seen, namely Bauhinia forficata and B. variegate. Extracts from B. variegata didn't show fungitoxic action but B. forficata the action exist. The barley plant showed protection of 92 to 100% in local and systemic action. The chemical TLC assays showed the presence of phenols (rutin, coumaric acid, kaempferol) that can be related to a signal for activation of the defense responses against pathogen or mechanism of salicylic acid. Treatment with fungicide Opera® gave another mechanism and have only 60% of protection.
A New and Improved Automated Technology for Early Sex Determination of Ginkgo biloba

Random amplified polymorphic DNA (RAPD) technique with male associated decamer primer S1478 was used to amplify DNA from 72 leaf samples collected from Ginkgo biloba trees with known sexual determinism in the canton of Geneva, Switzerland. This marker was found to be male-specific and was lacking in all female plants. Automated random polymorphic DNA analysis (ARPA), a new automated technology developed in the frame of this work, proved highly effective in distinguishing males and females with 100% efficiency and successful in male and female discrimination from a collection of young seedlings derived from a sexual cross. Our findings provide unambiguous evidence that ARPA combined with the male-associated decamer primer S1478 could be considered an efficient, rapid, and easy method to make an early sex determination in the dioecious tree Ginkgo biloba.
The metabolism and molecular physiology of Saccharomyces cerevisiae

LIFE CYCLE AND MORPHOGENESIS J. Richard Dickinson MOTHER CELL-SPECIFIC AGEING Michael Breitenbach, Peter Laun, Gino Heeren, Stefanie Jarolim, and Alena Pichova CARBON METABOLISM Arthur Kruckeberg and J. Richard Dickinson NITROGEN METABOLISM J. Richard Dickinson MOLECULAR ORGANIZATION AND BIOGENESIS OF THE CELL WALL Frans M. Klis, Piet de Groot, Stanley Brul and Klaas J. Hellingwerf LIPIDS AND MEMBRANES Michael Schweizer PROTEIN TRAFFICKING Jeremy D.Brown PROTEIN PHOSPHORYLATION AND DEPHOSPHORYLATION Michael J.R. Stark STRESS RESPONSES Ian W. Dawes short toc
Survival of Fall Armyworm, Spodoptera Frugiperda, (Lepidoptera: Noctuidae) Exposed to Cold Temperatures

All life stages of seasonally acclimatized fall armyworms, Spodoptera frugiperda (J. E. Smith), were subjected to temperatures of 0, -2.5, -5, -7.5, and -10@*C for 3 h in a temperature cabinet. The adult stage was most susceptible to cold temperatures, with only 26% of the moths surviving at -5@*C and no survival at the colder temperatures. The egg was the most tolerant stage, with 30% survival at -10@*C. Fall armyworm pheromone traps located near Belle Glade, Fla. were checked weekly during the winters of 1985-86 and 1986-87. Seven nights of subfreezing temperatures during those two winters resulted in little or no adult mortality. Our study, which included lethal temperature data, microclimate data, and field population data, shows that extreme low temperatures are not important mortality factors on fall armyworm populations in southern Florida.
Cryptic Lineages of Nigerian Agama (Squamata: Agamidae) within the West African Radiation

The genus Agama is diverse and found commonly in Africa. The dearth of herpetological studies in Nigeria has limited knowledge on the genetic diversity and distribution of Agama and the matrilineal affinities within the West African (WA) radiation. This limits an understanding of the biogeography of West Africa. Thus, we collected 112 specimens of Agama across Nigeria. Analyses of mitochondrial DNA (16S rRNA sequences) infer the matrilineal relationships of all the currently recognized Nigerian species of Agama within the WA radiation. The result of our genealogical analysis adds a new matrilineal lineage from north-eastern Nigeria to the WA radiation. Further, our result shows that Nigerian Agama has closest relationship with Cameroon and Niger. This indicates that the Guinean forest may be a biogeographic corridor for dispersal and diversification. Our collections from Nigeria also first document the presence of A. parafricana from the montane savannah region of Gashaka Gumti National Park, eastern Nigeria. Accordingly, we describe its external features.
Callus Induction and Plant Regeneration from Mature Embryos of Oat (Avena sativa L.)

The aim of this study, which was conducted in Ankara University, Faculty of Agriculture, Department of Field Crops, biotechnology laboratory in 1998-1999, was to determine the callus induction and plant regeneration capacity of oat (Avena sativa L.). The mature embryos of 10 oat genotypes were utilised for callus induction. The statistical analysis of the results revealed that callus induction and plant regeneration capacity were dependent on the oat genotype. However, a significant relationship was not established between callus induction and regeneration capacity and, furthermore, the number of regenerated plants was determined to be directly related to the callus production capacity.
Susceptibility of the freshwater pulmonate snail Lymnea luteola L. to copper oxide nanoparticle

Copper oxide nanoparticles (CuONP) are among the most widely used engineered nanoparticles and thus likely to permate the environment predominantly in sediments. The present study was designed to examine the adverse effects of CuONP in freshwater snail Lymnea luteola L. (L. luteola) exposed for 5 days. Induction of oxidative stress in digestive gland was evidenced by a decrease in reduced glutathione (GSH) levels, and activities of glutathione peroxidase (GPx) and glutathione-S-transferase (GST) whereas lipid peroxidation levels were increased at CuONP 7 or 21 µg/L. Superoxide dismutase activity was numerically higher at lower concentration of CuONP at 1 day but significantly decreased at 5 days. Catalase activity was reduced at 2 days but elevated at lower concentration of CuONP at 5 days. DNA impairment was noted in L. luteola based upon comet assay findings and expressed in terms of % tail DNA and olive tail moment. Results indicate that interaction of CuONP with snail produces toxicity, which is mediated by oxidative stress.