Sperm DNA: organization;protection and vulnerability: from basic science to clinical applications. a position rep

This paper reports the results of the most recent in a series of EHSRE workshops designed to synthesize the current state of the field in Andrology and provide recommendations for future work (ESHRE 1998; 1996). Its focus is on methods for detecting sperm DNA damage and potential application of new knowledge about sperm chromatin organization, vulnerability and repair to improve the diagnosis and treatment of clinical infertility associated with that damage. Equally important is the use and reliability of these tests to identify the extent to which environmental contaminants or pharmaceutical agents may contribute to the incidence of sperm DNA damage and male fertility problems. A working group# under the auspices of ESHRE met in May 2009 to assess the current knowledgebase and suggest future basic and clinical research directions. This document presents a synthesis of the working group’s understanding of the recent literature and collective discussions on the current state of knowledge of sperm chromatin structure and function during fertilization. It highlights the biological, assay and clinical uncertainties that require further research and ends with a series of recommendations.

Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets

Motivation: Recently, many univariate and several multivariate approaches have been suggested for testing differential expression of gene sets between different phenotypes. However, despite a wealth of literature studying their performance on simulated and real biological data, still there is a need to quantify their relative performance when they are testing different null hypotheses.

Results: In this article, we compare the performance of univariate and multivariate tests on both simulated and biological data. In the simulation study we demonstrate that high correlations equally affect the power of both, univariate as well as multivariate tests. In addition, for most of them the power is similarly affected by the dimensionality of the gene set and by the percentage of genes in the set, for which expression is changing between two phenotypes. The application of different test statistics to biological data reveals that three statistics (sum of squared t-tests, Hotelling's T2, N-statistic), testing different null hypotheses, find some common but also some complementing differentially expressed gene sets under specific settings. This demonstrates that due to complementing null hypotheses each test projects on different aspects of the data and for the analysis of biological data it is beneficial to use all three tests simultaneously instead of focusing exclusively on just one.

Identification of candidate small-molecule therapeutics to cancer by gene-signature perturbation in connectivity mapping.

Connectivity mapping is a recently developed technique for discovering the underlying connections between different biological states based on gene-expression similarities. The sscMap method has been shown to provide enhanced sensitivity in mapping meaningful connections leading to testable biological hypotheses and in identifying drug candidates with particular pharmacological and/or toxicological properties. Challenges remain, however, as to how to prioritise the large number of discovered connections in an unbiased manner such that the success rate of any following-up investigation can be maximised. We introduce a new concept, gene-signature perturbation, which aims to test whether an identified connection is stable enough against systematic minor changes (perturbation) to the gene-signature. We applied the perturbation method to three independent datasets obtained from the GEO database: acute myeloid leukemia (AML), cervical cancer, and breast cancer treated with letrozole. We demonstrate that the perturbation approach helps to identify meaningful biological connections which suggest the most relevant candidate drugs. In the case of AML, we found that the prevalent compounds were retinoic acids and PPAR activators. For cervical cancer, our results suggested that potential drugs are likely to involve the EGFR pathway; and with the breast cancer dataset, we identified candidates that are involved in prostaglandin inhibition. Thus the gene-signature perturbation approach added real values to the whole connectivity mapping process, allowing for increased specificity in the identification of possible therapeutic candidates.

Cold-formed steel sections with web openings subjected to web crippling under two-flange loading conditions - part I: Tests and finite element analysis

The results of 82 web crippling tests are presented, with 20 tests conducted on channel sections without web openings and 62 tests conducted on channel sections with web openings. The tests consider both end-two-flange and interior-two-flange loading conditions. In the case of the tests with web openings, the hole was located directly under the concentrated load. The concentrated load was applied through bearing plates; the effect of different bearing lengths is investigated. In addition, the cases of both flanges fastened and unfastened to the support is considered. A non-linear elasto-plastic finite element model is described, and the results compared against the laboratory test results; a good agreement was obtained in terms of both strength and failure modes.

The use of biomarkers to diagnose the ecological impact of pollutants in Mediterranean rivers

Um assunto que requer atenção é a avaliação ecológica da qualidade da água de ecossistemas de água doce. Uma abordagem que surge como promissora é a biomonitorização baseada em biomarcadores, porque pode avaliar a saúde dos organismos e obter sinais de alerta precoce acerca dos riscos ambientais. Até agora, porém, o uso de biomarcadores em espécies de invertebrados, para diagnosticar danos ecológicos nos rios, é escasso. Por essa razão, existe uma necessidade urgente de desenvolver biomarcadores nas principais espécies de macroinvertebrados dos ecossistemas fluviais que são alvo de estudo. Esta tese tem como objectivo averiguar se as respostas in situ, aliadas aos biomarcadores, podem ser um método viável para avaliar os danos ecológicos de contaminantes em ecossistemas de água doce. Numa primeira fase, os biomarcadores foram usados para averiguar os mecanismos fisiológicos de adaptação genética de clones de Daphnia magna ao pesticida organofosforado fenitrothion. Numa segunda fase, os biomarcadores foram usados como ferramentas de diagnóstico de poluição em zonas ribeirinhas. Estes estudos foram realizados com três espécies-chave de macroinvertebrados: Daphnia magna, Corbicula fluminea e Hydropsyche exocellata, nos rios Besós e Llobregat e no Delta do rio Ebro (NE Espanha). Além disso, foram realizados com animais capturados nos rios, ou com ensaios de transplantes, e foram complementados com índices biológicos de macroinvertebrados e análises químicas da água e dos animais. Como os contaminantes químicos têm vários modos toxicológicos de acção e, portanto, afectam várias respostas bioquímicas dos organismos, foram analisados nas três espécies um conjunto de biomarcadores pertencentes a diferentes vias metabólicas. A abordagem experimental indica que o uso combinado de biomarcadores e outras medidas, tais como índices biológicos e testes in situ, contribui para diagnosticar os efeitos prejudiciais de contaminantes nas comunidades ribeirinhas.

Biological colonization on majolica glazed tiles: biodeterioration, bioreceptivity and mitigation strategies

The impact of microbial activity on the deterioration of cultural heritage is a well-recognized global problem. Glazed wall tiles constitute an important part of the worldwide cultural heritage. When exposed outdoors, biological colonization and consequently biodeterioration may occur. Few studies have dealt with this issue, as shown in the literature review on biodiversity, biodeterioration and bioreceptivity of architectural ceramic materials. Due to the lack of knowledge on the biodeteriogens affecting these assets, the characterization of microbial communities growing on Portuguese majolica glazed tiles, from Pena National Palace (Sintra, Portugal) and another from Casa da Pesca (Oeiras, Portugal) was carried out by culture and molecular biology techniques. Microbial communities were composed of microalgae, cyanobacteria, bacteria and fungi, including a new fungal species (Devriesia imbrexigena) described for the first time. Laboratory-based colonization experiments were performed to assess the biodeterioration patterns and bioreceptivity of glazed wall tiles produced in laboratory. Microorganisms previously identified on glazed tiles were inoculated on pristine and artificially aged tile models and incubated under laboratory conditions for 12 months. Phototrophic microorganisms were able to grow into glaze fissures and the tested fungus was able to form oxalates over the glaze. The bioreceptivity of artificially aged tiles was higher for phototrophic microorganisms than pristine tile models. A preliminary approach on mitigation strategies based on in situ application of commercial biocides and titanium dioxide (TiO2) nanoparticles on glazed tiles demonstrated that commercial biocides did not provide long term protection. In contrast, TiO2 treatment caused biofilm detachment. In addition, the use of TiO2 thin films on glazed wall tiles as a protective coating to prevent biological colonization was analysed under laboratorial conditions. Finally, conservation notes on tiles exposed to biological colonization were presented.

Sleep in vitro : Erk pathway regulates sleep duration and sleep related genes

To date, for most biological and physiological phenomena, the scientific community has reach a consensus on their related function, except for sleep, which has an undetermined, albeit mystery, function. To further our understanding of sleep function(s), we first focused on the level of complexity at which sleep-like phenomenon can be observed. This lead to the development of an in vitro model. The second approach was to understand the molecular and cellular pathways regulating sleep and wakefulness, using both our in vitro and in vivo models. The third approach (ongoing) is to look across evolution when sleep or wakefulness appears. (1) To address the question as to whether sleep is a cellular property and how this is linked to the entire brain functioning, we developed a model of sleep in vitro by using dissociated primary cortical cultures. We aimed at simulating the major characteristics of sleep and wakefulness in vitro. We have shown that mature cortical cultures display a spontaneous electrical activity similar to sleep. When these cultures are stimulated by waking neurotransmitters, they show a tonic firing activity, similar to wakefulness, but return spontaneously to the "sleep-like" state 24h after stimulation. We have also shown that transcriptional, electrophysiological, and metabolic correlates of sleep and wakefulness can be reliably detected in dissociated cortical cultures. (2) To further understand at which molecular and cellular levels changes between sleep and wakefulness occur, we have used a pharmacological and systematic gene transcription approach in vitro and discovered a major role played by the Erk pathway. Indeed, pharmacological inhibition of this pathway in living animals decreased sleep by 2 hours per day and consolidated both sleep and wakefulness by reducing their fragmentation. (3) Finally, we tried to evaluate the presence of sleep in one of the most primitive species with a neural network. We set up Hydra as a model organism. We hypothesized that sleep as a cellular (neuronal) property may occur with the appearance of the most primitive nervous system. We were able to show that Hydra have periodic rest phases amounting to up to 5 hours per day. In conclusion, our work established an in vitro model to study sleep, discovered one of the major signaling pathways regulating vigilance states, and strongly suggests that sleep is a cellular property highly conserved at the molecular level during evolution. -- Jusqu'à ce jour, la communauté scientifique s'est mise d'accord sur la fonction d'une majorité des processus physiologiques, excepté pour le sommeil. En effet, la fonction du sommeil reste un mystère, et aucun consensus n'est atteint le concernant. Pour mieux comprendre la ou les fonctions du sommeil, (1) nous nous sommes d'abord concentré sur le niveau de complexité auquel un état ressemblant au sommeil peut être observé. Nous avons ainsi développé un modèle du sommeil in vitro, (2) nous avons disséqué les mécanismes moléculaires et cellulaires qui pourraient réguler le sommeil, (3) nous avons cherché à savoir si un état de sommeil peut être trouvé dans l'hydre, l'animal le plus primitif avec un système nerveux. (1) Pour répondre à la question de savoir à quel niveau de complexité apparaît un état de sommeil ou d'éveil, nous avons développé un modèle du sommeil, en utilisant des cellules dissociées de cortex. Nous avons essayé de reproduire les corrélats du sommeil et de l'éveil in vitro. Pour ce faire, nous avons développé des cultures qui montrent les signes électrophysiologiques du sommeil, puis quand stimulées chimiquement passent à un état proche de l'éveil et retournent dans un état de sommeil 24 heures après la stimulation. Notre modèle n'est pas parfait, mais nous avons montré que nous pouvions obtenir les corrélats électrophysiologiques, transcriptionnels et métaboliques du sommeil dans des cellules corticales dissociées. (2) Pour mieux comprendre ce qui se passe au niveau moléculaire et cellulaire durant les différents états de vigilance, nous avons utilisé ce modèle in vitro pour disséquer les différentes voies de signalisation moléculaire. Nous avons donc bloqué pharmacologiquement les voies majeures. Nous avons mis en évidence la voie Erkl/2 qui joue un rôle majeur dans la régulation du sommeil et dans la transcription des gènes qui corrèlent avec le cycle veille-sommeil. En effet, l'inhibition pharmacologique de cette voie chez la souris diminue de 2 heures la quantité du sommeil journalier et consolide l'éveil et le sommeil en diminuant leur fragmentation. (3) Finalement, nous avons cherché la présence du sommeil chez l'Hydre. Pour cela, nous avons étudié le comportement de l'Hydre pendant 24-48h et montrons que des périodes d'inactivité, semblable au sommeil, sont présentes dans cette espèce primitive. L'ensemble de ces travaux indique que le sommeil est une propriété cellulaire, présent chez tout animal avec un système nerveux et régulé par une voie de signalisation phylogénétiquement conservée.

The role of molecular, clinical and socioeconomic factors in the long-term survival of axillary node negative breast cancer patients

The overall objective of this study was to investigate factors associated with long-term survival in axillary node negative (ANN) breast cancer patients. Clinical and biological factors included stage, histopathologic grade, p53 mutation, Her-2/neu amplification, estrogen receptor status (ER), progesterone receptor status (PR) and vascular invasion. Census derived socioeconomic (SES) indicators included median individual and household income, proportions of university educated individuals, housing type, "incidence" of low income and an indicator of living in an affluent neighbourhood. The effects of these measures on breast cancer-specific survival and competing cause survival were investigated. A cohort study examining survival among axillary node negative (ANN) breast cancer patients in the greater Toronto area commenced in 1 989. Patients were followed up until death, lost-to-follow up or study termination in 2004. Data were collected from several sources measuring patient demographics, clinical factors, treatment, recurrence of disease and survival. Census level SES data were collected using census geo-coding of patient addresses' at the time of diagnosis. Additional survival data were acquired from the Ontario Cancer Registry to enhance and extend the observation period of the study. Survival patterns were examined using KaplanMeier and life table procedures. Associations were examined using log-rank and Wilcoxon tests of univariate significance. Multivariate survival analyses were perfonned using Cox proportional hazards models. Analyses were stratified into less than and greater than 5 year survival periods to observe whether known markers of short-tenn survival were also associated with reductions in long-tenn survival among breast cancer patients. The 15 year survival probabilities in this cohort were: for breast cancerspecific survival 0.88, competing causes survival 0.89 and for overall survival 0.78. Estrogen receptor (ER) and progesterone receptor (PR) status (Hazard Ratio (HR) ERIPR- versus ER+/PR+, 8.15,95% CI, 4.74, 14.00), p53 mutation (HR, 3.88, 95% CI, 2.00, 7.53) and Her-2 amplification (HR, 2.66, 95% CI, 1.36, 5.19) were associated with significant reductions in short-tenn breast cancer-specific survival «5 years following diagnosis), however, not with long-term survival in univariate analyses. Stage, histopathologic grade and ERiPR status were the clinicallbiologieal factors that were associated with short-term breast cancer specific survival in multivariate results. Living in an affluent neighbourhood (top quintile of median household income compared to the rest of the population) was associated with the largest significant increase in long-tenn breast cancer-specific survival after adjustment for stage, histopathologic grade and treatment (HR, 0.36, 95% CI, 0.12, 0.89).

Isolation and partial characterization of host cell wall surface glycoproteins: their involvement in agglutination, attachment and appressorium formation by piptocephalis virginiana

Cell surface proteins obtained by alkaline extraction from isolated cell walls of Mortierella pusilla and M. candelabrum, host and nonhost, respectively, to the mycoparasite, Piptocephalis virginiana, were tested for their ability to agglutinate mycoparasite spores. The host cell wall protein extract had a high agglutinating activity (788 a.u. mg- t ) as compared with the nonhost extract (21 a.li. mg- t ). SDS-polyacrylamide gel electrophoresis of the cell wall proteins revealed four protein bands, a, b, c, and d (Mr 117, 100, 85 and 64 kd, respectively) at the host surface, but not at the nonhost surface, except for the faint band c. Deletion of proteins b or c from the host cell wall protein extract significantly reduced its agglutinating activity. Proteins band c, obtained as purified preparations by a series of procedures, were shown to be two glycoproteins. Carbohydrate analysis by gas chromatography demonstrated that glucose and Nacetylglucosamine were the major carbohydrate components of the glycoproteins. It was further shown that the agglutinating activity of the pure preparation containing both band c was 500-850 times that of the single glycoproteins, suggesting the involvement of both glycoproteins in agglutination. The results suggest that the glycoproteins band c are the two subunits of agglutinin present at the host cell surface. The two glycoproteins band c purified from the host cell wall protein extract were further examined after various treatments for their possible role in agglutination, attachment and appressorium formation by the mycoparasite. Results obtained by agglutination and attachment tests showed: (1) the two glycoprotein-s are not only an agglutinin responsible for the mycoparasite spore agglutination, but may also serve as a receptor for the specific recognition, attachment and appressorium formation by the mycoparasite; (2) treatment of the rnycoparasite spores with various sugars revealed that arabinose, glucose and N-acetylglucosamine inhibited the agglutination and attachment activity of the glycoproteins, however, the relative percentage of appressorium formation was not affected by the above sugars; (3) the two glycoproteins are relatively stable with respect to their agglutinin and receptor functions. The present results suggest that the agglutination and attachment may be mediated directly by certain sugars present at the host and mycoparasite cell surfaces while the appressorlum formation may be the response of complementary combinations of both sugar and protein, the two parts of the glycoproteins at the interacting surfaces of two fungi.

Exact Skewness-Kurtosis Tests for Multivariate Normality and Goodness-of-fit in Multivariate Regressions with Application to Asset Pricing Models

We study the problem of testing the error distribution in a multivariate linear regression (MLR) model. The tests are functions of appropriately standardized multivariate least squares residuals whose distribution is invariant to the unknown cross-equation error covariance matrix. Empirical multivariate skewness and kurtosis criteria are then compared to simulation-based estimate of their expected value under the hypothesized distribution. Special cases considered include testing multivariate normal, Student t; normal mixtures and stable error models. In the Gaussian case, finite-sample versions of the standard multivariate skewness and kurtosis tests are derived. To do this, we exploit simple, double and multi-stage Monte Carlo test methods. For non-Gaussian distribution families involving nuisance parameters, confidence sets are derived for the the nuisance parameters and the error distribution. The procedures considered are evaluated in a small simulation experi-ment. Finally, the tests are applied to an asset pricing model with observable risk-free rates, using monthly returns on New York Stock Exchange (NYSE) portfolios over five-year subperiods from 1926-1995.

Le meilleur intérêt de l'enfant, les tests de paternité et le droit civil québécois

"Mémoire présenté à la Faculté des études supérieures en vue de l'obtention du grade de maîtrise en Droit option Droit, Biotechnologies et Société"

Ligation properties of N4-phenylsemicarbazones towards transition metals: Synthesis and spectral studies

Semicarbazones and their transition metal complexes have been receiving considerable attention because of their biological relevance and applications in the field of analysis and in the field of organic NLO materials. Their structural diversity also attracted inorganic chemists. A good deal of work has been reported on the synthesis and structural investigation of semicarbazones and their complexes. This is due partially to their capability of acting as multidentate, NO, NNO, ONO and ONNO donors with the formation of either mono or bi or polynuclear complexes. Their chemistry and pharmacological applications have been extensively investigated. Appreciable biological applications as well as diverse stereochemistry of their metal complexes prompted us to synthesize two new tridentate ONO donor N4-phenyl semicarbazones derived from 2-hydroxy-4-methoxyacetophenone and 2-hydroxy-4-methoxybenzophenone and their transition metal complexes. These ketones were selected since they can provide a further binding site from phenolic–OH and can thus increase the denticity. Introduction of heterocyclic bases like 1,10-phenanthroline, 2,2′-bipyridine, 4,4′-dimethyl- 2,2′-bipyridine and 4-picoline and some pseudohalides like azide and thiocyanate ion can result in mixed ligand metal chelates with different geometries in coordination compounds In the present study, oxovanadium(IV), manganese(II), cobalt (II/III), nickel(II), copper(II) and zinc(II) complexes of 2-hydroxy-4- methoxyacetophenone-N4-phenylsemicarbazone (H2ASC) and 2-hydroxy-4- methoxybenzophenone-N4-phenylsemicarbazone (H2BSC) were synthesized and characterized.

Seoimentology And Geochemistiiy Of Some Selected Mangrove Ecosystems Of Kerala, Southwest Coast Of India

As a result of the issues of care and conservation and sustainable utilisation, the proper management of mangrove forests have become more pressing than ever. Much recent ecological and toxicological debate has been centered around the question of validity of making predictions about the future of mangrove ecosystemas a result of the newly evolved environmental policy. Though muchinformation exist on the biodiversity, floristic composition and characteristics, geographical distribution and uses of mangroves, systematic documentation of the various sedimentological and geochemical phenomena in relation to the mangrove flora are scarce. Hazardous, persistent, man-made chemicals and waste produces are entering the mangrove ecosystem at from the adjacent watersheds which strengthened alarming rates the indispensible need for further researches on the environmental behaviours, fate and the effect of such products. Studies on the effect of heavy metals, pesticides and the other toxic signals through bioassay and toxicity tests on mangrove species as well as in sediments definitely will furnish ample clues to establish the actual operative mechanisms of these environments. A thorough review of literature made in this angle reveals that some attempts have already been initiated the world over the record the physico-chemical characteristics of major abiotic components such as sediments and water of many mangrove ecosystem, however, adequate information is lacking in the Indian Environmental Science scenario. The present investigation is an attempt to record the sedimentological, mineralogical and geochemical characteristics of sediments as well as the heavy metal enrichment in the various species ofmangrove flora of three important mangrove ecosystems of Kerala, located at Veli (SouthKerala), Kochi (Central Kerala) and Kannur (North Kerala). The results of the above investigation have been analysed statistically, discussed based on the available literature and presented in this thesis under seven chapters

BioJADE: A Design and Simulation Tool for Synthetic Biological Systems

The next generations of both biological engineering and computer engineering demand that control be exerted at the molecular level. Creating, characterizing and controlling synthetic biological systems may provide us with the ability to build cells that are capable of a plethora of activities, from computation to synthesizing nanostructures. To develop these systems, we must have a set of tools not only for synthesizing systems, but also designing and simulating them. The BioJADE project provides a comprehensive, extensible design and simulation platform for synthetic biology. BioJADE is a graphical design tool built in Java, utilizing a database back end, and supports a range of simulations using an XML communication protocol. BioJADE currently supports a library of over 100 parts with which it can compile designs into actual DNA, and then generate synthesis instructions to build the physical parts. The BioJADE project contributes several tools to Synthetic Biology. BioJADE in itself is a powerful tool for synthetic biology designers. Additionally, we developed and now make use of a centralized BioBricks repository, which enables the sharing of BioBrick components between researchers, and vastly reduces the barriers to entry for aspiring Synthetic Biologists.

A comparison of the variability of biological nutrients against depth and potential density.

The main biogeochemical nutrient distributions, along with ambient ocean temperature and the light field, control ocean biological productivity. Observations of nutrients are much sparser than physical observations of temperature and salinity, yet it is critical to validate biogeochemical models against these sparse observations if we are to successfully model biological variability and trends. Here we use data from the Bermuda Atlantic Time-series Study and the World Ocean Database 2005 to demonstrate quantitatively that over the entire globe a significant fraction of the temporal variability of phosphate, silicate and nitrate within the oceans is correlated with water density. The temporal variability of these nutrients as a function of depth is almost always greater than as a function of potential density, with he largest reductions in variability found within the main pycnocline. The greater nutrient variability as a function of depth occurs when dynamical processes vertically displace nutrient and density fields together on shorter timescales than biological adjustments. These results show that dynamical processes can have a significant impact on the instantaneous nutrient distributions. These processes must therefore be considered when modeling biogeochemical systems, when comparing such models with observations, or when assimilating data into such models.