Miracle-dz/UniFAR-FTUs huggingface dataset:
Measurement of insertional mutagenesis by retroviral and lentiviral vectors.

Retroviral vectors have been successfully used in the clinic for the correction of inherited immunodeficiencies. However, in 2 recent gene therapy trials for X-linked Severe Combined Immunodeficiency, 5 patients developed leukaemia. This was associated with vector integration near cellular proto-oncogenes, leading to their activation a process known as insertional mutagenesis. This thesis describes the development of a cell line assay that allows us to quantify insertional mutagenesis by retroviral and lentiviral vectors and to analyse the mechanisms by which this occurs. The interleukin-3 (IL-3) dependent cell line BCL15 is derived from the mouse bone marrow cell line BAF3 and over- expresses human Bcl2. The frequency at which IL-3 independent mutants are obtained following vector transduction is measured. Lentiviral and retroviral vectors transform BCL15 cells at similar integrant frequencies of 4.3 x 108 and 1.2 x 107, respectively. However, they cause insertional mutagenesis in this assay by different mechanisms. The human immunodeficiency virus-1 (HIV-1)- derived lentiviral vector HV transforms BCL15 cells by insertional activation of the growth hormone receptor (Ghr) gene. An HIV-Ghr fusion transcript was detected. It originates from the HIV-1 5'-LTR it then splices from the HIV-1 major splice donor to the splice acceptor of Ghr exon 2. The mutants express GHR and grow in response to bovine growth hormone in the foetal calf serum of the culture medium. Deletion of the HIV-1 enhancer/promoter in a self-inactivating vector prevents this mechanism of transformation. Retroviral vector transformation of the BCL15 cell line does not occur via Ghr gene activation. Retroviral vectors up- regulate expression of the cytokine IL-3, either by insertion into the IL-3 gene or by insertion into other genes, which may act as upstream activators of IL-3 expression. This assay is a general method to quantitate insertional mutagenesis. It may inform the design of safer vectors and can be used in initial safety testing of (pre-) clinical vectors.
Assembly, annotation, and polymorphic characterization of the Erysiphe necator transcriptome

The objectives of this study were to develop a transcriptomic reference resource and to characterize polymorphism between isolates of Erysiphe necator (syn. Uncinula necator), grape powdery mildew. The wine and fresh fruit markets are economically vital to many countries worldwide, and E. necator infection can cause severe crop damage and subsequent financial loss. Most of the publicly available sequence data for Erysiphales are from research done on Blumeria graminis f. sp. hordei, barley powdery mildew, which occupies a distinct clade within the Erysiphales. We obtained 641,601 sequencing reads from a Roche 454-FLX next-generation sequencer (RNA-Seq) and performed multiple assemblies using the Mira assembly software. The best assembly was de novo and yielded 39,686 contiguous sequences. The reference was then ordered based on similarity to B. graminis genes and annotated based on sequence similarity to known proteins. 11,605 SNPs and 5,248 INDELs were called against the reference using RNASeq data from 55 additional geographically and phenotypically distinct isolates of E. necator. The reference transcriptome, annotations, and polymorphic characterization collections from this project represent a vast resource for E. necator and should allow for future research of this organism and other Erysiphales. Our results illustrate that RNA-Seq is a valid alternative to whole-genome sequencing for genetic characterization of non-model organisms.
Novel Molecular Interactions and Biological Functions of the Neurofibromatosis 2 Tumor Suppressor Protein, Merlin

Abstract : The project has studied the functions of the neurofibromatosis 2 tumor suppressor protein merlin and the related ERM protein ezrin. We identified novel binding partners and functions for both proteins. Merlin was shown to regulate both the microtubule and actin cytoskeleton. Two important kinases, protein kinase A (PKA) and AKT, were shown to phosphorylate merlin at S10. This phosphorylation affects actin dynamics, cell morphology and migration of mouse embryonic fibroblasts (MEF) and Schwann cells. Thus, merlin may serve as a regulator of PKA and AKT induced changes in actin cytoskeleton. We identified a link between merlin and cell cycle control by demonstrating a novel functional interaction between merlin and HEI10. In studies of the biological activities of ezrin we discovered that oncogenic tyrosine kinases Src and c-Met phosphorylate ezrin at Y477. Using reconstituted MEF cells from ezrin -/- mice we studied the biological importance of Y477 phosphorylation. Our results show that ezrin is a key regulator of Src induced malignant behavior in three dimensional culture conditions.
Estimation of Houbara Bustard, Chlamydotis macqueenii, population density in the central Iranian steppes

Abstract Iran hosts both resident and migratory populations of the vulnerable Houbara Bustard, Chlamydotis macqueenii, especially in the region of Yazd where resident birds occur. For investigation of its density and abundance, 8000 ha of the Harat area in Yazd province were studied from February to March 2006. The distance sampling method (line transect) in different plant communities, with a completely randomized sampling design, was used. In total, 766 km of transects were surveyed and 147 individuals were counted. Based on distance sampling analysis we found that the Houbara Bustard density is 0.87 individual per km2. The highest density was recorded in Seidlitzia rosmarinus and Artemisia sieberi plant communities.
dynStruct An automatic reverse engineering tool for structure recovery and memory use analysis

In computer security, reverse engineering is understanding how a program work. It can be used for multiple purposes, like malware analysis or security audit of a program. Reverse engineering is possible even without the source of the program. In this case, knowing what data structures are used by the program is a considerable help. But recovering these structures is di cult and time consuming. Also, at the time of writing, no tool doing this recovery has been publicly released. This paper introduces dynStruct, an open source structure recovery tool. dynStruct recovers structures in two steps. First a data gatherer executes the program and monitors it. The list of all memory accesses made by the program is written to a Json file. Afterwards a script analyzes this Json file to recover the structures. dynStruct also provides a powerful web interface. This interface, in addition to displaying e ciently the structures and raw data from the data gatherer, links the raw data and the recovered structures to allow a quick and powerful exploitation of all this information. The tests shows that dynStruct can analyze complex program like emacs or xterm. The tests also show that the recovered structures are similar to the original ones. This ensures dynStruct can provide quick and useful information to help reverse engineers in their task. Number of words: 12530
Structure and molecular recognition in riboswitches

Riboswitches are cis-acting gene regulatory RNAs, which function without involvement of proteins. They have been implicated as drug targets and are attractive systems for the study of RNA-ligand binding and RNA folding. The purine riboswitch was used as a model system for RNA-ligand docking. Published binding data was successfully reproduced in silico and compounds predicted to bind the riboswitch in a virtual screening were tested experimentally. Structural data confirming the predicted binding mode for several cases was obtained. The problems encountered were not specific to RNA-ligand docking but known from the far more explored field of protein-ligand docking. The SAM-I riboswitch was also subjected to virtual ligand screening. This receptor is a system of greater complexity than the purine riboswitch and consequently posed a harder challenge to the docking protocol. After initial validation of the docking setup based on previously published data, a set of compounds selected from the in-house database of commercially available compounds was screened. One compound identified in silico was confirmed to bind experimentally. The k-turn motif found in the SAM-I riboswitch was investigated with respect to its folding. The k-turn motif was found to be foldable in context of the SAMI riboswitch as well as in isolation as was expected. Furthermore, mutations disrupting key interactions within the k-turn motif were found to be prohibitive of k-turn folding in isolation as well as in context of the riboswitch, leading to a loss of ligand binding. Interestingly, two sequences were identified which fold in context of the riboswitch but do not fold in isolation. This confirms the contribution of tertiary interactions to k-turn folding. This conclusion was backed up with structural data.
Microcirculation and inflammation in a numerical simulation approach

23 matory response. The identification of a region of maximum shear stress is consistent with the molecular mechanisms that govern leukocyte rolling because it may actually correspond to the area that supports the interaction with the endothelium. On the other hand, the relatively lower shear stress regions may correlate with leukocyte surface areas where binding to the endothelium is not occurring at the moment, thus enabling the rolling of the cell along the endothelium. It was also observed that the shear stress at the endothelium gets higher as a cluster of leukocytes moves in the main stream. This suggests that the presence of a cluster of leukocytes may potentiate leukocyte rolling, as the increase in the shear stress promoted by the recruited leukocytes may support the migration and recruitment of additional cells. Despite closely simulating leukocyte recruitment, our initial numerical simulation considered the simple case of leukocytes as rigid spheres. However, while circulating leukocytes maintain an approximately spherical shape, rolling leukocytes are known to deform. In order to account for the leukocyte deformability changes that occur during its recruitment in inflammation, we needed to assess the deformability profile of the leukocytes under flow and therefore, to “directly” observe them regardless of the other blood cells. For such, intravital microscopy was performed in the mouse cremaster of a transgenic mice strain (Lys-EGFP-ki) in which fluorescent neutrophils can be individually tracked. By using PAF as an inflammatory agent, the analysis of the leukocyte-endothelial cell interactions showed a continuous increase in the number of rolling and adherent neutrophils up to 4 hours after the introduction of the inflammatory stimuli, thus confirming the development of an inflammatory response. As the properties of the red blood cells modulate blood flow properties, erythrocyte deformability was also addressed in this model. A continuous decrease of this parameter was observed throughout time. The decrease in the erythrocyte deformability will most probably lead to an increase in the blood viscosity and to the decrease of the blood flow velocity. These conditions should facilitate the migration of leukocytes from the mainstream to the endothelial wall and promote leukocyte slow rolling and adhesion during the inflammatory response. Importantly, in the intravital microcopy images obtained with this latter model, we clearly observed the deformation of neutrophils along the endothelial wall during rolling, as well
Quorum Sensing Inhibitory Activities of Various Folk-Medicinal Plants and the Thyme-tetracycline Effect.

Pseudomonas aeruginosa is an opportunistic, nosocomial pathogen for which antibiotic resistance and biofilm development is common. Quorum sensing communication is known to be a major controlling factor in virulence gene expression, biofilm development, antibiotic resistance factors, and specifically MexAB-OprM multi-drug efflux pump expression in P.aeruginosa. MexAB-OprM efflux pumps contribute to antibiotic resistance of tetracycline and other antibiotics in pseudomonads and other organisms. P.aeruginosa infections are problematic in cystic fibrosis and burn patients; it is also the number one causative agent of respiratory infections for intensive care unit patients. Present day antibiotics are losing the battle against these infections. In theory, quorum sensing inhibitors (QSI) reduce pathogencity of the organism; making it less virulent, thus allowing either the host immune system to clear the infection or use of a QSI in combination with an antibiotic to clear more persistent pathogens. For these reasons two alternative modes of treatment were explored in this study: quorum sensing inhibition by folk-medicinal plant extracts and an example of combination drug therapy, the ―thymetetracycline effect‖. Fifty folk-medicinal plant extracts were screened for potential anti-quorum sensing activity using two quorum sensing inhibition (QSI) reporter strains, Pseudomonas aeruginosa QSIS2 and Chromobacterium violaceum 12725. These were used to test specifically for C4-C6 and C12 HSL quorum sensing inhibition. Of the fifty plants tested, thirty plant families were represented. Eleven plant extracts (basil, chaparral, clove, cranberry, oregano, pomegranate, rosemary, sage, sassafras, thyme and witch hazel) showed C4 HSL quorum sensing inhibition as determined by both assays. Interestingly, five of the plants were from the Lamiaceae family. Thymus vulgaris (thyme), also from the Lamiaceae family, was chosen for further assessment. Previous research has shown that thyme extract can synergistically augment tetracycline activity against tetracycline-resistant Pseudomonas aeruginosa, creating the ―thyme-tetracycline effect. ‖ Disc diffusion assay, thin layer chromatography (TLC), and TLC bioassay techniques were used to show that thymol is the active component in the thyme extract that augments tetracycline activity against resistant Pseudomonas. This study also showed that thymol is a potent C4 HSL quorum sensing inhibitor. The collective data suggests a potential mode of action for the thyme-tetracycline effect: thymol appears to prevent MexAB-OprM efflux pump gene expression. By blocking MexAB-OprM expression, tetracycline antibiotic accumulation can occur within the cell, thus allowing cellular damage. INDEX WORDS: Thymus vulgaris, Quorum sensing inhibition, Medicinal plants, Pseudomonas aeruginosa QUORUM SENSING INHIBITORY ACTIVITIES OF VARIOUS FOLK MEDICINAL PLANTS AND THE ELUCIDATION OF THE THYME-TETRACYCLINE EFFECT
Polyploidy induction and identification in Lilium formosanum × Lilium longiflorum var. scabrum.

In the paper,we reported the results on polyploidy induction by colchicines treatments and cytological in Lilium formosanum×Lilium longiflorum var.scabrum. It was treated with colchicines at different concentration and time duration in vitro,and also was treated with admixture of colchicines and 2% Dimethyl Sulfoxide(DMSO). The results indicated that the highest induction frequency(86%)was achieved in the treatment of immersing the shoot tips in colchicines solution at 0.05% for 36h with the 0.2% DMSO;in mixed culture,the highest mutation rate(54%)was achieved when the explants were cultured in a medium containing colchicines at 0.05% for 10d with the 0.2% DMSO.The rate of polyploidy induction by colchicines treatments with DMSO was higher than without it.There were the differences of leaf stoma density and guard cell size(length and width)between diploids and tetraploids,based on the cytological identifications by microscopic watching.
A causal model to understand the impact of blue infrastructures on health and well-being

The model proposed leads to a new representation of the " Water component " in the city. It takes into account the diversity of waters (rain water, storm water, wastewater, urban river …), the dynamics of water in the city (related to the water cycles) and the heterogeneity of territories in terms of water management. This model helps to understand the impacts (benefits/risks) of blue infrastructures and blue space on health and well-being. Backgrounds and relevance.
Partial Characterization of Spiroplasma citri Isolates Associated with Necrotic Yellows Disease of Safflower in Iran

Spiroplasma citri was associated with a disease of safflower characterized by stunting, yellowing, phloem discoloration and local or general necrosis in the Fars province of Iran. It was identified by ELISA using a locally produced polyclonal antiserum, by PCR with specific primers and isolation in culture medium. The 16S rDNA restriction fragment length polymorphism patterns of safflower isolates were identical with those of the other S. citri isolates. A known isolate of S. citri from periwinkle induced stunting, yellowing, phloem discoloration and wilting in safflower seedlings when transmitted by dodder under greenhouse conditions. A primer pair designed on the basis of S. citri plasmid was more sensitive than those based on spiralin gene or 16S rDNA for the detection of S. citri. Based on the sequence of the spiralin gene, S. citri isolates from safflower as well as other Iranian isolates were variable and grouped into two genetic clusters with 91.9–92.9% identity between groups. This is the first report of association of S. citri with a safflower disease.
Suitability of sweet cherry cultivars for organic production in eastern Austria.

The intention of the trial was to find out the suitability of old and new early ripening cherry cultivars in organic production. In autumn 2003, 13 cultivars were planted in the research orchard of the Institute in the East of Vienna. All cultivars were grafted on Gisela5 rootstock and cultivated organically. Between 2004 and 2009 yield and growth characteristics, as well as susceptibility to plant diseases and pests (especially fruit damages by the cherry fruit fly Rhagoletis cerasi L.) were evaluated. Based on the statistically analysed data originating from 5 years of research in total, recommendations for growers can be given.
Can foraging behaviour reveal the eco-evolutionary dynamics of habitat selection?

Rationale: Adaptive behaviours, particularly those related to resource harvest and the time available for fitness-enhancing activities, may serve as suitable surrogates for fitness. Methods: I explore this potential link between behaviour and eco-evolutionary dynamics with controlled field experiments. The experiments manipulated densities of meadow voles foraging in large replicated enclosures. I used the lock-step connection between resource harvest and fitness to generate three fitness surrogates: giving-up densities from artificial resource patches, quitting-harvest rates, and time available for non-foraging behaviours that enhance fitness. Results: Per capita consumption from food trays did not change with population size. Time allocated to foraging increased with population density. Quitting-harvest rates in both safe and risky patches declined linearly with population density. The total amount of time necessary for a new individual to acquire sufficient energy for maintenance increased hyperbolically. Invasion landscapes based on the three fitness surrogates yielded the same behaviourally and evolutionarily stable strategy (ESS) of habitat selection. But the fitness benefits, subsequent convergence towards the ESS, and potential variation about the ESS, varied. Conclusions: Adaptive foraging behaviour is a reliable and rapid metric for assessing the evolutionary stability of habitat selection. This proof of concept suggests that behavioural metrics may play a prominent role in assessments of other strategies. We may even be able to use behavioural metrics to forecast ecological and evolutionary futures associated with ecological change.
ANEURETUS SIMONI EMERY OCCURRENCE AND THE ANT COMMUNITY OBSERVED BY MULTIPLE METHODS AND REPEATED SAMPLING IN "POMPEKELLE", SRI LANKA

The ant community of “Pompekelle” is of special interest due to the presence of island-endemic Aneuretus simoni Emery among them. Frequency of occurrence and proportional abundance of A. simoni workers and, species richness and composition of ant community were investigated using several sampling methods simultaneously on six visits to the forest from February to November 2004. Day time sampling of ants was carried out along ten, 100 m transects by mini-Winkler extraction, soil sifting, pitfall trapping, honey and canned fish baiting, leaf litter sifting, timed hand collection and beating tray method. Honey baits at 1 m height on trees and honey-baited pitfall traps on the ground were also set overnight. Aneuretus simoni workers were detected on all occasions. Honey baiting and litter sifting in day time caught the workers more often than canned fish baits, soil sifting, day time pitfall traps and night pitfall traps. Detectability of A. simoni was irregular in the ten transects but the frequency of occurrence ranged from 30-80 percent and the species comprised 1-6 percent of workers collected on each of the six occasions. It was a permanent minor component in the forest despite its absence in the area of transect 8. Fifty species of 36 genera in 11 subfamilies including the resident species, A. simoni , Anochetus sp. , Anoplolepis gracilipes , Camponotus sp. , Hypoponera sp. 2, Lophomyrmex quadrispinosus , Myrmicaria brunnea , Odontomachus simillimus , Pheidole sp. 7, Pheidologeton sp. , Prenolepis sp. , Solenopsis sp. and Technomyrmex albipes and other occasional ant species can be considered the first preliminary ant inventory of the forest.
Effect of Low Vegetation on the Recruitment of Plants in Successional Habitat Types 1

I assessed the role of low vegetation (plants ca 1 yr old and ≤50 cm tall) as a biotic facilitator or barrier in the recruitment of different growth forms and species in primary forests, secondary forests, and old‐fields (abandoned pastures) in southeastern Mexico. I removed by hand all plants (≤100 cm tall, including roots) and litter from 20, 0.25 m2 plots in each habitat. For 1 yr, I counted the number of plant species (5–50 cm tall) recruited, grouped them into different growth forms, and compared them to undisturbed control plots. Prior to manipulation, the standing density of trees and lianas was highest in primary and secondary forests. Shrubs were more abundant in secondary forests, whereas herbs, epiphytes, and hemi‐epiphytes were more abundant in old‐fields. Herbaceous plants appeared as important components of the community in all habitats. The removal of low vegetation increased total plant recruitment in all habitats. Considering each growth form, the absence of vegetation increased recruitment in primary forests for herbs, in secondary forests for epiphytes and hemi‐epiphytes, in old‐fields for trees, and for lianas in primary forests and old‐fields. In vegetation removal plots, recruitment of species was greater in pastures, lower in secondary forest, and similar in primary forest with respect to control plots. Depending on habitat type, species, and growth form, the presence of low vegetation may act as a recruitment barrier or facilitator for different species, affecting plant community structure, diversity, and composition in different habitats.