Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of Vav proteins in macrophage morphology and migration.

The Rho family GTPases are key signalling components that regulate the cytoskeleton and adhesion during cell migration. The Vav family of proteins act as guanine nucleotide exchange factors for several Rho GTPases. There are three isoforms of Vav expressed in mammalian cells: Vav1, the expression of which is largely restricted to haematopoietic cells, Vav2 and Vav3. In this study the role of Vav proteins in macrophage migration has been investigated using macrophages derived from mice lacking one or all three Vav isoforms. Cell migration and morphology were not significantly affected when single isoforms of Vav were absent from macrophages. However macrophages lacking all three isoforms adopted an elongated morphology in culture, which resulted in more persistent cell migration. Vav proteins were not required for chemotaxis to the macrophage chemo-attractant, colony-stimulating factor-1 (CSF-1). Vav proteins were also not required for CSF-1-stimulated Rac1 activation or Rac-mediated cytoskeletal reorganization in response to CSF-1. However, in response to CSF-1 stimulation Vav1 and Vav3 were phosphorylated on tyrosine residues, which has previously been shown to regulate their GEF catalytic activity. Macrophages lacking all three Vav proteins were defective in spreading upon adhesion to both glass and plastic. The defect correlated with reduced activation of Rac1 and RhoA, and a reduction in the activation of Erk1/2 and phosphorylation of paxillin in response to adhesion. Vav proteins are therefore not required for directed macrophage migration to the chemo-attractant CSF-1, but have an important role in adhesion-dependent signalling and are needed to maintain normal macrophage migration and morphology.
Untersuchungen zur antiangiogenen Aktivität des matrizellulären Proteins Thrombospondin-2

The formation of new tumor vessels (tumorangiogenesis) is an important mechanism for the growth and progression of tumors. Tumorangiogenesis depends on a complex interplay between pro-and antiangiogenic factors. Thrombospondin-2 (TSP-2) belongs to the endogenous antiangiogenic factors. TSP-2 inhibits tumor growth through inhibition of angiogenesis, which is necessary for the progression of tumors. Compared to TSP-1, which has similar structures, the exact antiangiogenic mechanisms of TSP-2 remain unclear. To elucidate the biologic functions and antiangiogenic mechanisms of TSP-2 an 80 kDa N-terminal fragment of human TSP-2 (NTF-TSP-2), which is bound as a fusion protein to IgG2-Fc, was recombinantly produced. The treatment of microvascular endothelial cells (HDMEC) with NTF-TSP-2 led to a significant inhibition of VEGF-stimulated tube-like structures. Tumor growth and angiogenesis of xenotransplanted breast carcinomas were significantly reduced by systemic delivery of NTF-TSP-2. The treatment with NTF-TSP-2 resulted in a considerable inhibition of metastasis both in lymph nodes and lungs. After intraperitoneal injection the fusion protein NTF-TSP-2 is detectable in the blood using an inhibition-ELISA as well as in the tumor tissue using immunoprecipitation. It is shown with different in vitro assays that the CD36 mediated induction of apoptosis of microvascular endothelial cells is an important mechanism for the inhibition of angiogenesis.
Clonal propagation of cacti through axillary buds in vitro

SummaryThe technique is based on hormonal stimulation of growth and development of quiescent meristems in vitro and consists in cultivating sterilized shoot fragments, including axillary buds, on agar nutrient media with the addition of low concentrations (0.5-5 mg l-1) of auxins (IAA or NAA) and cytokinins (kinetin or BAP). In these conditions the production of new entire shoots occurs directly from the sites of axillary meristems. The method was successfully applied in Mammillaria carmenae, M. prolifera (cultivated mammillae with adjacent meristems), Astrophytum myriostigma and Trichocereus spachianus (explanted areoles). The method promises higher genetic stability and uniformity of cloned plants than earlier methods.
Cas de coccidiose cæcale chez des poules pondeuses après diverses manipulations

Les coccidies sont des protozoaires difficiles à éviter en élevage industriel, sévissant principalement sur de jeunes sujets et souvent lors d’altération de l’environnement. Toutefois, elles peuvent affecter des sujets adultes lorsque les conditions de leur développement dans l’organisme sont favorisées (1, 2, 4, 7). Ce sont probablement ces conditions qui ont permis aux coccidies d’affecter les poules pondeuses, objets de cette communication.
Investigating tumour evolution through graph theoretical analysis of gene regulatory networks

The main aim of this work was to develop methods to aid biologists and clinicians investigate the progression and evolution of tumours through the analysis of microarray data, concentrating on the inference and analysis of Gene Regulatory Networks (GRNs) representing different evolutionary and clinical stages of cancer microarray data. Three main areas of work were carried out. The first was the development and implementation of a network inference method designed to infer GRNs at differently defined classes from a single microarray dataset. The second was the investigation of appropriate graph theory metrics to quantitatively analyse the different defined stages of disease. Genes identified by the various metrics were scored for the particular disease of interest, allowing the graph theory metrics to be ranked against each other for the various GRNs. The third was the comparison of GRNs inferred for different disease stages across datasets for the same disease, neuroblastoma, from two different studies. This work has shown that analysis of GRNs inferred using a method designed to infer multiple GRNs from a single microarray dataset has identified genes involved in different stages of disease, thereby having the potential to aid in the investigation of the progression and evolution of tumours.
Coccidiostats in poultry manure - a potential threat to beneficial soil invertebrates.

Monensin and lasalocid are polyether ionophore antibiotics used in veterinary medicine for prevention and treatment of coccidiosis in poultry. They are extensively used in the poultry industry throughout Europe. Both substances are excreted with the faeces mostly in their active form. The use of manure from treated animals on agricultural soil results in contamination that could pose a threat to soil organisms and thereby reduce the production potential of farmlands. Their degradation rates in manure and soil, as well as their effects on non-target soil organisms are mostly unknown. We conducted several studies to measure the degradation of lasalocid and monensin in broiler manure and after application to soil. Ecotoxicological studies were also performed to obtain concentrations at which these coccidiostats are harmful to soil invertebrates, namely earthworms and woodlice. Degradation rates in manure and compost depend mostly on moisture levels and temperature. Half-lives in compost are significantly shorter than if manure is aged in a pile with no treatment. Avoidance of the test animals was the most sensitive endpoint in the ecotoxicity tests. On the basis of our results, we recommend that poultry manure from treated animals be stored for at least one month before application to soil.
A procedure using Rotylenchulus reniformis nucleotide sequences to quantitatively measure plant-parasitic nematode infestation levels using metagenomic DNA isolated directly from soil

Molecular diagnostic tests have been developed and utilized to diagnose and to confirm diagnoses of many plant-parasitic nematodes. We evaluate the potential of a qPCR assay to detect and quantify Rotylenchulus reniformis in Mississippi directly from soil. A novel pipeline utilizing multiple databases containing nematode DNA and EST sequences was developed to aid in the selection of R. reniformis primers used in a PCR and qPCR assays. In vitro testing showed that the primers and probes developed from the novel pipeline for the qPCR assays could accurately detect the presence of R. reniformis. Subsequent testing resulted in a trend of increasing observed number of R. reniformis resulting in increasing estimates by qPCR
A stoichiometric model of Escherichia coli's macromolecular synthesis machinery and its integration with metabolism

Systems biology is a rapidly growing discipline. It is widely believed to have a broad transformative potential on both basic and applied studies in the life sciences. In particular, biochemical network reconstructions are playing a key role as they provide a framework for investigation of the mechanisms underlying the genotype- phenotype relationship. In this thesis, the procedure to reconstruct metabolic networks is illustrated and extended to other cellular processes. In particular, the constraint -based reconstruction and analysis approach was applied to reconstruct the transcriptional and translational (tr/tr) machinery of Escherichia coli. This reconstruction, denoted 'Expression-matrix'/ (E-matrix), represents stoichiometrically all known proteins and RNA species involved in the macromolecular synthesis machinery. It accounts for all biochemical transformations to produce active, functional proteins, tRNAs, and rRNAs known to be involved in macromolecular synthesis in E. coli. An initial study investigated basic properties of the E- matrix, including its capability to produce ribosomes, which was found to be in good agreement with experimental data from literature. Furthermore, quantitative gene expression data could be integrated with, and analyzed in the context of, the resulting constraint-based model. Adding mathematically derived constraints to couple certain reactions in the model allowed the quantitative representation of the size of steady state protein and RNA pools. Furthermore, the E-matrix was integrated with the genome-scale E. coli metabolic model and extended the transcriptional and translational reactions to encompass genes encoding all the respective metabolic enzymes. The resulting Metabolite-Expression-matrix (MExv matrix), has exceeds the predictive capacity of the metabolic model and it can, for example, be used to predict the biomass yield since it represents the production of almost 2,000 proteins. E. coli 's ME-matrix is the first of its kind and represents a milestone in systems biology as demonstrates how to quantitatively integrate 'omics'- datasets into a network context, and thus, to study the mechanistic principles underlying the genotype-phenotype relationship. Possible applications are just beginning to become apparent and may include protein engineering, interpretation of adaptive evolution, and minimal genome design. An integration of the ME-matrix with remaining cellular processes, such as regulation, signaling, and replication, will be a next step to complete the first whole-cell model.
Fitting the gene lineage into its species lineage

activating regulator mutations. Analysis of amino acid sequence data from the alpha and beta hemoglobins and myoglobins suggests that the gene lineages deviate relatively little from established species relationships, and that most contemporary gene pairs in this phylogenetic system may be regarded as orthologous (split at the time of speciation) rather than paralogous (split prior to speciation). It also appears that as the statistical sample of orthologous sequence sites becomes greatly enlarged by tandem alignment of enough different types of protein chains, the parsimony reconstruction based strictly on minimal nucleotide replacement length will itself reveal the correct cladogram for the set of contemporary species. [Phylogeny reconstruction; parsimony methods; globin sequences; gene phylogeny; species phylogeny. ]
Modelling the Economics of Controlling Nodding Broomrape (Orobanche cernua) in Sunflower (Helianthus annuus)

Field studies were conducted at nine locations in southern Spain during 2 yr to develop models of nodding broomrape competition with sunflower and to establish economic thresholds. At each location, 30 to 35 small plots, each consisting of three sunflower plants, were chosen at random. The infection severity (BIS, no. of emerged broomrapes per sunflower plant) varied from 0 to 35. Plots were harvested at maturity to assess several sunflower and broomrape population variables. The percent sunflower yield reduction averaged over locations due to broomrape was estimated by the equation: % SYR = 1.7 x BIS (r2 = 0.92). Crop yield loss per BIS unit increased with the expected yield and was estimated to be about 25, 50, and 75 kg ha−1 for yields of 1000, 2000, and 3000 kg ha−1, respectively. A consistent relationship could be established between broomrape-infected sunflower yield, crop and broomrape biomass, and BIS parameters: SSYI = 0.2259 x PoBio/(1 + 0.0687 x BIS) (r2 = 0.7820). The BIS economic threshold was about 1.5 and 3.5 for control treatment cost of $ 40 ha−1 and potential yields of 2000 and 1000 kg ha−1, respectively.
Replicator Regions of the Yeast Mitochondrial DNA Active In Vivo and in Yeast Transformants

The replication of the mtDNA in Saccharomyces cerevisiae is independent from that of the nuclear DNA. It is continuous throughout the cell cycle (Williamson and Moustacchi 1971; Sena et al. 1975), it is active in the cdc mutants deficient for the initiation of nuclear DNA synthesis (Cottrell et al. 1973; Wintersberger et al. 1974; Newlon and Fangman 1975), and it is catalyzed by a specific mtDNA polymerase (Wintersberger and Blutsch 1976). Furthermore, in most density-labeling experiments, gradual shifts in mtDNA densities are observed (Sena et al. 1975Sena et al. 1976; Williamson and Fennell 1974). This apparent dispersive mode of replication of the mtDNA probably results from the high rate of genetic recombination between the different nonsynchronous mtDNA molecules of each yeast cell, each molecule undergoing a semiconservative replication. But the exact mechanisms of the initiation and control of yeast mtDNA replication remain poorly understood. This situation is at contrast with the precise descriptions of the process of mtDNA replication now available for some other organisms, such as the vertebrates (in this case, a distinctive D-loop mechanism with specific origins for the replication of the H and L strands has been described [Arnberg et al. 1971; Berk and Clayton 1974, 1976; Kasamatsu and Vinograd 1974; Crews et al. 1979; Martens and Clayton 1979; Nass 1980; Sekiya et al. 1980]) and the insects (in this case, the replication is initiated within the A + T-rich segment [Goddard and Wolstenholme 1980]). In the case of yeast, the difficulty in isolating intact mtDNA molecules from the.
Improving the detection of donations within the RHD negative blood donor panel which weakly express the RHD antigen

This project improved the detection and classification of very weakly expressed RhD variants in the Australian blood donor panel and contributed to the knowledge of anti-D reactivity patterns of RHD alleles that are undescribed. As such, the management of donations possessing these RHD alleles can be improved upon and the overall safety of transfusion medicine pertaining to the Rh blood group system will be increased. Future projects at ARCBS will be able to utilise the procedures developed in this project, thereby decreasing throughput time. The specificity of current testing will be improved and the need for outsourced RHD testing diminished.
Characterization of the TMV replicase proteins: localization and interactions with Rab GDI proteins

Title of Document: CHARACTERIZATION OF THE TMV REPLICASE PROTEINS: LOCALIZATION AND INTERACTIONS WITH RAB GDI PROTEINS Sabrina Renée Kramer Doctor of Philosophy 2008 Directed By: Dr. James Culver, Associate Professor Center for Biosystems Research University of Maryland Biotechnology Institute Tobacco mosaic virus (TMV) is a model positive-strand RNA virus. TMV encodes two replicase proteins, both of which contain methyltransferase and helicase domains; the 183 kDa protein contains an additional RNA-dependent RNA polymerase domain. Using this virus, virus-host interactions important in the initial establishment of infection and formation of replicase complexes were investigated. Specifically, on the virus side, replicase proteins were examined for regions that may contribute to its localization to the endoplasmic reticulum (ER) during TMV infection. An ER localization domain was identified in a region between amino acids 599 and 701. Alanine substitutions were introduced into this region and examined for their effects on the virus. Several possible hypotheses are discussed as to how this domain may function during infection. Concerning the host, an interaction with a host protein, a Rab GDP Dissociation Inhibitor (Rab GDI), was examined. This interaction occurred with tomato and tobacco Rab GDIs as well as with the originally identified Arabidopsis thaliana Rab GDI (AtGDI2). Silencing of Rab GDI transcripts enhanced the number of infection sites in TMV:GFP-infected plants, but did not alter viral movement or overall accumulation, indicating a possible role in initial establishment of infection. Rab GDI-silenced Nicotiana benthamiana plants showed cellular morphologies similar to those of TMV-infected cells. Moreover, TMV infection results in Rab GDI proteins localizing to structures associated with viral replication. Taken together these data indicate a role for Rab GDI proteins in the initial establishment of infection. Two models of how Rab GDI proteins may contribute to TMV infection are discussed. These studies examine parts of the viral life cycle that are not very well understood, in particular the initiation and establishment of infection. Although vesicle trafficking has been shown to be important for several different pathogens, this is the first time that a Rab GDI protein has been identified as participating in viral replication. Understanding initiation of infection and susceptibility of a host to a pathogen are vital to elucidating pathogen-host interactions and developing disease resistance strategies. CHARACTERIZATION OF THE TMV REPLICASE PROTEINS: LOCALIZATION AND INTERACTIONS WITH RAB GDI PROTEINS
Testing for frost tolerance in wheat (Triticum aestivum L.) transformed with a gene for antifreeze protein

Spring frosts in wheat growing areas of Australia can result in significant damage during the heading stage, resulting in losses millions of dollars each year due to decreased yields. To address this issue, wheat has been co-transformed via micro-projectile bombardment with an antifreeze protein (AFP) gene targeted to the apoplast or endoplasmic reticulum. T0 transgenic plants expressed AFP and showed the potential for frost tolerance in in vitro tests on plant extracts (Khanna and Daggard 2005). Additional transgenic wheat plants carrying the AFP gene targeted to both apoplast and ER have subsequently been produced. DNA extracted from plants surviving selection on phosphinothricin revealed 63.8% were PCR positive for presence of the AFP gene, indicating a wheat transformation frequency of 3.97%. Co-transformation of AFP and bar genes occurred in 53% of samples tested. PCR and gene expression analysis (via RT-PCR) have been carried out on plants that were subsequently tested in a controlled frost environment at the Australian Genome Research Facility (AGRF Adelaide). Analysis of frost induced sterility (FIS) showed that frosted control plants were significantly higher in FIS compared to unfrosted controls, and that FIS of plants transformed with one of the constructs was not significantly different to that of the unfrosted controls. This result suggests that the introduced AFP may protect the transgenic wheat plants against frost.
Comparative study of seminal plasma proteins in dromedary camels

Semen ejaculates (30) were obtained from 5 Jaisalmeri camels. Fresh semen samples were centrifuged at 6,000 rpm for 30 min and clear supernatant of seminal plasma was separated and stored at –20°C until used. Total protein from the seminal plasma was estimated and the molecular weight was analysed. The total protein concentration was between 2.28–2.59 g/dl in the seminal plasma. In the seminal plasma of 4 camels, 11 protein bands were observed ranging from 11.7–104.0 kDa, whereas, 9 protein bands were observed in the seminal plasma of 1 camel. The present study showed similar seminal plasma protein profile in Jaisalmeri camels except 2 protein fractions of 40kDa and 12.9kDa were expressed in 4 camels and not in 1 camel. It can be concluded that at least 9 protein fractions were in common between these camels.
Limb Savlage Surgery with Custom Made Prosthesis for Proximal Tibial Osteosarcomas.

Introduction: “Walking is man’s best medicine” - Hippocrates Bony sarcomas arising from the proximal end of the tibia constitute the second most common site of occurrenceafter the distal end of the femur. However this area is a difficult site to perform a safe limb sparing resection in which function is preserved due to anatomical constraints and also surgical technique. Historically amputation had been the treatment for bony sarcomas. The use of effective chemotherapeutic regimen, modern imaging technology and advances in surgical techniques has broadened the horizon and scope of limb salvage surgery in this site. The primary difficulty in doing a limb salvage surgery for sarcoma of the proximal tibia is due to the local anatomy. A difficult surgical approach, intimate relationship to the neurovascular structures, inadequate soft tissue coverage are few of the challenges surgeons face during procedures at this site. Another important factor is the need to reconstruct the extensor mechanism of the knee joint. Many surgical techniques and reconstruction mechanisms have been described for the tumours at this site and have provided satisfactory survival and functional outcomes. AIMS OF THE STUDY : 1. To study the survival outcomes of the patients undergoing limb salvage surgery in proximal tibial tumours with custom made megaprosthesis. 2. To compare the quality of life assessment between groups undergoing extensor mechanism reconstruction with or without a prolene mesh. 3. To study the early and late complications. 4. To study the prosthesis survival time and the factors affecting prosthesis survival.
CD28 costimulation in T cells : requirements, outcomes and regulation

The costimulatory receptor CD28 and its inhibitory counterpart CTLA-4 share the same ligands and comprise a crucial checkpoint in T cell activation. CTLA-4 removes its ligands from antigen presenting cells by trans-endocytosis, which reduces the availability of costimulatory ligands for CD28 engagement to regulate T cell activation. This project examined the functional implications of reducing the availability of costimulatory molecules for CD4 T cell responses, and investigated the use of trans-endocytosis by other T cell receptors. Surprisingly, it was revealed that PD-1 and OX40 can also internalise their ligands, although perhaps not via the same mechanism as CTLA-4 trans-endocytosis. It was also shown that altering the availability of CD28 ligands affects the extent of T cell proliferation, suggesting that CTLA-4 trans-endocytosis can finely tune the T cell response. Furthermore, it was observed that CD28 costimulation is not always required for T cell activation and proliferation, but CD28 engagement is required for the optimal upregulation of a number of effector proteins and for TH2 cytokine production. Interestingly, T cells activated in the absence of CD28 signalling were not classically anergic. Strikingly, it was also found that memory T cells are dependent on CD28 costimulation.