Detection of JC virus DNA sequence and expression of the viral oncoprotein, tumor antigen, in brain of immunocompetent patient with oligoastrocytoma.

We describe molecular and clinical findings in an immunocompetent patient with an oligoastrocytoma and the concomitant presence of the human papovavirus, JC virus (JCV), which is the etiologic agent of the subacute, debilitating demyelinating disease, progressive multifocal leukoencephalopathy. Histologic review revealed a glial neoplasm consisting primarily of a moderately cellular oligodendroglioma with distinct areas of a fibrillary astrocytoma. Immunohistochemical analysis revealed nuclear staining of tumor cells with antibodies against the viral oncoprotein [tumor antigen (T antigen)], the proliferation marker (Ki67), and the cellular proliferation regulator (p53). Using primers specific to the JCV control region, PCR yielded amplified DNA that was identical to the control region of the Mad-4 strain of the virus. PCR analysis demonstrated the presence of the genome for the viral oncoprotein, T antigen, and results from primer extension studies revealed synthesis of the viral early RNA for T antigen in the tumor tissues. The presence of viral T antigen in the tumor tissue was further demonstrated by immunoblot assay. To our knowledge, this is the first report of the presence of JCV DNA, RNA, and T antigen in tissue in which viral T antigen is localized to tumor cell nuclei and suggests the possible association of JCV with some glial neoplasms.

The site of action of neuronal acidic fibroblast growth factor is the organ of Corti of the rat cochlea.

Here we show that the mature cochlear neurons are a rich source of acidic fibroblast growth factor (aFGF), which is expressed in the neuronal circuitry consisting of afferent and efferent innervation. The site of action of neuronal aFGF is likely to reside in the organ of Corti, where one of the four known FGF receptor (FGFR) tyrosine kinases--namely, FGFR-3 mRNA--is expressed. Following acoustic overstimulation, known to cause damage to the organ of Corti, a rapid up-regulation of FGFR-3 is evident in this sensory epithelium, at both mRNA and protein levels. The present results provide in vivo evidence for aFGF being a sensory neuron-derived, anterogradely transported factor that may exert trophic effects on a peripheral target tissue. In this sensory system, aFGF, rather than being a neurotrophic factor, seems to promote maintenance of the integrity of the organ of Corti. In addition, aFGF, released from the traumatized nerve endings, may be one of the first signals initiating protective recovery and repair processes following damaging auditory stimuli.

A synthetic inhibitor of the mitogen-activated protein kinase cascade.

Treatment of cells with a variety of growth factors triggers a phosphorylation cascade that leads to activation of mitogen-activated protein kinases (MAPKs, also called extracellular signal-regulated kinases, or ERKs). We have identified a synthetic inhibitor of the MAPK pathway. PD 098059 [2-(2'-amino-3'-methoxyphenyl)-oxanaphthalen-4-one] selectively inhibited the MAPK-activating enzyme, MAPK/ERK kinase (MEK), without significant inhibitory activity of MAPK itself. Inhibition of MEK by PD 098059 prevented activation of MAPK and subsequent phosphorylation of MAPK substrates both in vitro and in intact cells. Moreover, PD 098059 inhibited stimulation of cell growth and reversed the phenotype of ras-transformed BALB 3T3 mouse fibroblasts and rat kidney cells. These results indicate that the MAPK pathway is essential for growth and maintenance of the ras-transformed phenotype. Further, PD 098059 is an invaluable tool that will help elucidate the role of the MAPK cascade in a variety of biological settings.

Role Expectations and State Socialization: Germany's Rediscovery of the Use of Force 1990-1995

This dissertation engages the question of why German political elites accepted the use of force during the 1990s and started to commit the country's armed forces to multilateral peacekeeping missions. Previous governments of the Federal Republic had opposed foreign deployment of the military and Germany was characterized by a unique strategic culture in which the efficacy of military force was widely regarded as negative. The rediscovery of the use of force constituted a significant reorientation of German security policy with potentially profound implications for international relations. I use social role theory to explain Germany's security policy reorientation. I argue that political elites shared a national role conception of their country as a dependable and reliable ally. Role expectations of the international security environment changed as a result of a general shift to multilateral intervention as means to address emerging security problems after the Cold War. Germany's resistance to the use of force was viewed as inappropriate conduct for a power possessing the economic and military wherewithal of the Federal Republic. Elites from allied countries exerted social pressure to have Germany contribute commensurate with capabilities. German political elites adapted role behavior in response to external expectations in an effort to preserve the national role conception of a dependable and reliable ally. Security policy reorientation to maintain Germany's national role conception was pursued by conservative elites who acted as 'role entrepreneurs'. CDU/CSU politicians initiated a process of role adaptation to include the use of force for non-defensive missions. They persuaded Social Democrats and Alliance 90/Green party politicians that the maintenance of the country's role conception necessitated a reorientation in security policy to accommodate the changes in the security environment.

Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida

Petunia hybrida is a popular bedding plant that has a long history as a genetic model system. We report the whole-genome sequencing and assembly of inbred derivatives of its two wild parents, P. axillaris N and P. inflata S6. The assemblies include 91.3% and 90.2% coverage of their diploid genomes (1.4 Gb; 2n = 14) containing 32,928 and 36,697 protein-coding genes, respectively. The genomes reveal that the Petunia lineage has experienced at least two rounds of hexaploidization: the older gamma event, which is shared with most Eudicots, and a more recent Solanaceae event that is shared with tomato and other solanaceous species. Transcription factors involved in the shift from bee to moth pollination reside in particularly dynamic regions of the genome, which may have been key to the remarkable diversity of floral colour patterns and pollination systems. The high-quality genome sequences will enhance the value of Petunia as a model system for research on unique biological phenomena such as small RNAs, symbiosis, self-incompatibility and circadian rhythms.

Conservation of the oligomeric state of native VDAC1 in detergent micelles.

The voltage-dependent anion-selective channel (VDAC) is an intrinsic β-barrel membrane protein located within the mitochondrial outer membrane where it serves as a pore, connecting the mitochondria to the cytosol. The high-resolution structures of both the human and murine VDACs have been resolved by X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) in 2008. However, the structural data are not completely in line with the findings that were obtained after decades of research on biochemical and functional analysis of VDAC. This discrepancy may be related to the fact that structural biology studies of membrane proteins reveal specific static conformations that may not necessarily represent the physiological state. For example, overexpression of membrane proteins in bacterial inclusion bodies or simply the extraction from the native lipid environment using harsh purification methods (i.e. chaotropic agents) can disturb the physiological conformations and the supramolecular assemblies. To address these potential issues, we have developed a method, allowing rapid one step purification of endogenous VDAC expressed in the native mitochondrial membrane without overexpression of recombinant protein or usage of harsh chaotropic extraction procedures. Using the Saccharomyces cerevisiae isoform 1 of VDAC as a model, this method yields efficient purification, preserving VDAC in a more physiological, native state following extraction from mitochondria. Single particle analysis using transmission electron microscopy (TEM) demonstrated conservation of oligomeric assembly after purification. Maintenance of the native state was evaluated using functional assessment that involves an ATP-binding assay by micro-scale thermophoresis (MST). Using this approach, we were able to determine for the first time the apparent KD for ATP of 1.2 mM.

A display of the religious principles of the Associate Synod of North America.

"Contains all the printed papers which display the religious principles of the Associate Presbytery of Pennsylvania." -- Pref. signed: William Marshall.

Optimal preventive maintenance of leased equipment with corrective minimal repairs

For leased equipment, the lessor carries out the maintenance of the equipment. Usually, the contract of lease specifies the penalty for equipment failures and for repairs not being carried out within specified time limits. This implies that optimal preventive maintenance policies must take these penalty costs into account and properly traded against the cost of preventive maintenance actions. The costs associated with failures are high as unplanned corrective maintenance actions are costly and the resulting penalties due to lease contract terms being violated. The paper develops a model to determine the optimal parameters of a preventive maintenance policy that takes into account all these costs to minimize the total expected cost to the lessor for new item lease. The parameters of the policy are (i) the number of preventive maintenance actions to be carried out over the lease period, (ii) the time instants for such actions, and (iii) the level of action. (c) 2005 Elsevier B.V. All rights reserved.

The role of government research establishments : a study of the concept of public patronage for applied research and development

This thesis follows the argument that, to fully understand the current position of national research laboratories in Great Britain one needs to study the historical development of the government research establishment as a specific social institution. A particular model is outlined in which it is argued that institutional characteristics evolve through the continual interplay between internal development and environmental factors within a changing political and economic context, and that the continuous development of an institution depends on its ability to adapt to changes in its operational environment. Within this framework important historical precedents for formal government institutional support for applied research are identified. and the transition from private to public patronage documented. The emergence and consolidation of government research laboratories in Britain is described in detail. The subsequent relative decline of public laboratories is interpreted in terms of the undermining of a traditional role resulting in legitimation crisis. It is concluded that it is no longer feasible to consider the public research laboratory as a coherent institutional form, and that the future of each individual laboratory can only be considered in relation to the institutional needs of its own sphere of operation. Nevertheless the laboratories have been forced into decline in an essentially unplanned way which may have serious consequences for the maintenance of the scientific and technical infrastructures, necessary for material progress in the national context.

The impact of the New University Code on the physical education curriculum of four-year colleges and universities in Taiwan, Republic of China

With the establishment of The New University Code in 1994, Taiwan's colleges and universities were mandated to shift physical education from a required course to an elective. The four-year colleges and universities are now responsible for either developing new physical education programs or removing existing programs from their curriculum. Planned change and curriculum leadership are considered in light of policy changes regarding required physical education programs enacted by the Ministry of Education. ^ This study compared the organizational structure and the curriculum of physical education at accredited colleges and universities in Taiwan. Chairpersons of physical education departments from 60 four-year colleges and universities were surveyed using a modified version of the Hensley's Basic Instruction Program (BIP) Questionnaire. Results were analyzed using analysis of variance (ANOVA) and crosstabs. The findings confirmed that physical education programs were effected by declining enrollment and administrative decisions to eliminate them. However, at the same time, chairpersons expressed strong support for the maintenance of the traditional physical education curriculum. ^

Adventures and Misfortunes in Macondo: Rehabilitation of the Cienaga Grande

We describe trajectories of selected ecological indicators used as performance measures to evaluate the success of a mangrove rehabilitation project in the Ciénaga Grande de Santa Marta (CGSM) Delta-Lagoon complex, Colombia, as result of freshwater diversions initiated in 1995. There is a significant reduction in soil and water column salinity in all sampling stations following the hydraulic reconnection of the Clarín and Aguas Negras channels to the Magdalena River. Soil intersticial water salinity (depth: 0.5 m) (7 stations) and water column salinity (0.5 m) (10 stations) values declined significantly (soil <30 g kg-1; water <10 g kg-1) from 1994 to 2000. During 1994 soil interstitial water salinity ranged from 40 g kg-1 (Rinconada) to 100 g kg-1 (KM 13), while water column salinity fluctuated between 25-35 g kg-1 for most of the sampling stations. This salinity reduction increased mangrove forest regeneration promoting a net gain of 99 km2 from 1995 to 1999. The high precipitation recorded in 1995 and 1999 caused by El Niño-La Niña (ENSO), coinciding with the channels rehabilitation, influenced rapid mangrove regeneration. The lack of economic investment in the maintenance of the diversion structures from 2001 to 2004 caused a salinity increase affecting negatively already restored vegetation. A sustainable effort from the international community and the Colombian government is needed to maintain the strategic social and economic benefits reached until 2000 in the CGSM region.

Characterization of the effect of nitrogen deficiency on above-ground plant phenotypes in relation to root complexity in maize

Nitrogen (N) is an essential plant nutrient in maize production, and if considering only natural sources, is often the limiting factor world-wide in terms of a plant’s grain yield. For this reason, many farmers around the world supplement available soil N with synthetic man-made forms. Years of over-application of N fertilizer have led to increased N in groundwater and streams due to leaching and run-off from agricultural sites. In the Midwest Corn Belt much of this excess N eventually makes its way to the Gulf of Mexico leading to eutrophication (increase of phytoplankton) and a hypoxic (reduced oxygen) dead zone. Growing concerns about these types of problems and desire for greater input use efficiency have led to demand for crops with improved N use efficiency (NUE) to allow reduced N fertilizer application rates and subsequently lower N pollution. It is well known that roots are responsible for N uptake by plants, but it is relatively unknown how root architecture affects this ability. This research was conducted to better understand the influence of root complexity (RC) in maize on a plant’s response to N stress as well as the influence of RC on other above-ground plant traits. Thirty-one above-ground plant traits were measured for 64 recombinant inbred lines (RILs) from the intermated B73 & Mo17 (IBM) population and their backcrosses (BCs) to either parent, B73 and Mo17, under normal (182 kg N ha-1) and N deficient (0 kg N ha-1) conditions. The RILs were selected based on results from an earlier experiment by Novais et al. (2011) which screened 232 RILs from the IBM to obtain their root complexity measurements. The 64 selected RILs were comprised of 31 of the lowest complexity RILs (RC1) and 33 of the highest complexity RILs (RC2) in terms of root architecture (characterized as fractal dimensions). The use of the parental BCs classifies the experiment as Design III, an experimental design developed by Comstock and Robinson (1952) which allows for estimation of dominance significance and level. Of the 31 traits measured, 12 were whole plant traits chosen due to their documented response to N stress. The other 19 traits were ear traits commonly measured for their influence on yield. Results showed that genotypes from RC1 and RC2 significantly differ for several above-ground phenotypes. We also observed a difference in the number and magnitude of N treatment responses between the two RC classes. Differences in phenotypic trait correlations and their change in response to N were also observed between the RC classes. RC did not seem to have a strong correlation with calculated NUE (ΔYield/ΔN). Quantitative genetic analysis utilizing the Design III experimental design revealed significant dominance effects acting on several traits as well as changes in significance and dominance level between N treatments. Several QTL were mapped for 26 of the 31 traits and significant N effects were observed across the majority of the genome for some N stress indicative traits (e.g. stay-green). This research and related projects are essential to a better understanding of plant N uptake and metabolism. Understanding these processes is a necessary step in the progress towards the goal of breeding for better NUE crops.

Filling in gaps of Drosophila melanogaster urate degradation metabolic pathway using metabolomics approaches: towards the core metabolome of the fruit fly

The primary goal of systems biology is to integrate complex omics data, and data obtained from traditional experimental studies in order to provide a holistic understanding of organismal function. One way of achieving this aim is to generate genome-scale metabolic models (GEMs), which contain information on all metabolites, enzyme-coding genes, and biochemical reactions in a biological system. Drosophila melanogaster GEM has not been reconstructed to date. Constraint-free genome-wide metabolic model of the fruit fly has been reconstructed in our lab, identifying gaps, where no enzyme was identified and metabolites were either only produced or consume. The main focus of the work presented in this thesis was to develop a pipeline for efficient gap filling using metabolomics approaches combined with standard reverse genetics methods, using 5-hydroxyisourate hydrolase (5-HIUH) as an example. 5-HIUH plays a role in urate degradation pathway. Inability to degrade urate can lead to inborn errors of metabolism (IEMs) in humans, including hyperuricemia. Based on sequence analysis Drosophila CG30016 gene was hypothesised to encode 5- HIUH. CG30016 knockout flies were examined to identify Malpighian tubules phenotype, and shortened lifespan might reflect kidney disorders in hyperuricemia in humans. Moreover, LC-MS analysis of mutant tubules revealed that CG30016 is involved in purine metabolism, and specifically urate degradation pathway. However, the exact role of the gene has not been identified, and the complete method for gap filling has not been developed. Nevertheless, thanks to the work presented here, we are a step closer towards the development of a gap-filling pipeline in Drosophila melanogaster GEM. Importantly, the areas that require further optimisation were identified and are the focus of future research. Moreover, LC-MS analysis confirmed that tubules rather than the whole fly were more suitable for metabolomics analysis of purine metabolism. Previously, Dow/Davies lab has generated the most complete tissue-specific transcriptomic atlas for Drosophila – FlyAtlas.org, which provides data on gene expression across multiple tissues of adult fly and larva. FlyAtlas revealed that transcripts of many genes are enriched in specific Drosophila tissues, and that it is possible to deduce the functions of individual tissues within the fly. Based on FlyAtlas data, it has become clear that the fly (like other metazoan species) must be considered as a set of tissues, each 2 with its own distinct transcriptional and functional profile. Moreover, it revealed that for about 30% of the genome, reverse genetic methods (i.e. mutation in an unknown gene followed by observation of phenotype) are only useful if specific tissues are investigated. Based on the FlyAtlas findings, we aimed to build a primary tissue-specific metabolome of the fruit fly, in order to establish whether different Drosophila tissues have different metabolomes and if they correspond to tissue-specific transcriptome of the fruit fly (FlyAtlas.org). Different fly tissues have been dissected and their metabolome elucidated using LC-MS. The results confirmed that tissue metabolomes differ significantly from each other and from the whole fly, and that some of these differences can be correlated to the tissue function. The results illustrate the need to study individual tissues as well as the whole organism. It is clear that some metabolites that play an important role in a given tissue might not be detected in the whole fly sample because their abundance is much lower in comparison to other metabolites present in all tissues, which prevent the detection of the tissue-specific compound.

Spermathecae of the mangrove crab Ucides cordatus: a histological and histochemical view

Ucides cordatus is the most commercially, important mangrove crab in Brazil. In spite of its economic importance, there are few studies of its reproduction, in particular the female reproductive system. The present study describes the histology and histochemistry of the spermathecae of U. cordatus. Adult females were can lit monthly from July 2004 through June 2005, at Iguape, State of São Paulo. The crabs were anaesthetized, and their spermathecae removed and fixed in Davidson's fluid, following the histological routine for paraffin. The slides were stained with HE, xylidine Ponceau, PAS, alcian blue (pH 1.0 and 2.5), Sudan black B and picrosirius-haematoxylin. Histologically, the spermathecae possesses a capsule of conjunctive tissue, rich in collalgen fibres, which surrounds the secretory columnar epithelium. In the lumen, individual sperm packets are not observed; the spermatophores are intermixed with the seminal fluid and secretions of the spermathecae itself. A large proportion of the free spermatozoids and spermatophores are arranged in homogeneous masses in the proximal part of the spermathecae. The secretion produced by the columnar epithelium appears to promote the movement of the gametes to the fertilization chamber, in a ventral position, allowing fertilization of the oocytes. Histochemically, the secretion produced by the columnar epithelium was strongly positive for neutral polysaccharides, positive for acid polysaccharides, and weakly positive for proteins and lipids. Tills secretion forms a glycoprotein matrix which is associated with maintenance of the spermatophores, which can remain stored for long periods.

Probiotics for the prevention/treatment of human diseases and ecological study of the intestinal microbiota

The interest in human intestinal microbiota has increased in the last 20 years and significant advances have been achieved with regard to its composition and functions. The gut microbiota contributes to the maintenance of the host health status and, since alterations in the gut microbiota have been involved in the pathogenesis/progression of some diseases, several studies have focused on the manipulation of its composition. Probiotics are a strategy to maintain/restore the correct balance of gut microbial population and to prevent/treat diseases. The aim of this thesis was to explore the possibility of probiotic supplementation for the prevention/treatment of human diseases and the related study of the intestinal microbial environment. After reviewing studies concerning the use of Bifidobacterium breve as probiotic in paediatric diseases, the effectiveness of a probiotic formulation consisting of two strains of B. breve was assessed in paediatric subjects for the prevention or alleviation of gastrointestinal disorders, including coeliac disease and paediatric obesity. As the emerging role of gut microbiota in neurological diseases, the intestinal microbial environment in amyotrophic lateral sclerosis patients compared to healthy controls and the effects of a probiotic administration were examined. Considering the role of viruses in shaping gut microbiota, gut bacteriophages and bacterial community of preterm infants were investigated. The results evidenced differences in gut microbial composition of healthy controls and diseased subjects in coeliac and amyotrophic lateral sclerosis patients. The probiotic approach was effective in restoring the microbial composition in the former, whereas, in the latter, the influence was focused only on some microbial groups. The probiotic intervention was effective in improving the glyco-insulinemic profile in obese children and in preventing gastrointestinal disorders in healthy newborns. The study of the bacterial and phage composition in preterm infants suggested a transkingdom interplay between bacteria and viruses with a reciprocal influence on their composition.