Comparative mitochondrial genomics toward understanding genetics and evolution of arbuscular mycorrhizal fungi

Les champignons mycorhiziens arbusculaires (CMA) sont très répandus dans le sol où ils forment des associations symbiotiques avec la majorité des plantes appelées mycorhizes arbusculaires. Le développement des CMA dépend fortement de la plante hôte, de telle sorte qu'ils ne peuvent vivre à l'état saprotrophique, par conséquent ils sont considérés comme des biotrophes obligatoires. Les CMA forment une lignée évolutive basale des champignons et ils appartiennent au phylum Glomeromycota. Leurs mycélia sont formés d’un réseau d’hyphes cénocytiques dans lesquelles les noyaux et les organites cellulaires peuvent se déplacer librement d’un compartiment à l’autre. Les CMA permettent à la plante hôte de bénéficier d'une meilleure nutrition minérale, grâce au réseau d'hyphes extraradiculaires, qui s'étend au-delà de la zone du sol explorée par les racines. Ces hyphes possèdent une grande capacité d'absorption d’éléments nutritifs qui vont être transportés par ceux-ci jusqu’aux racines. De ce fait, les CMA améliorent la croissance des plantes tout en les protégeant des stresses biotiques et abiotiques. Malgré l’importance des CMA, leurs génétique et évolution demeurent peu connues. Leurs études sont ardues à cause de leur mode de vie qui empêche leur culture en absence des plantes hôtes. En plus leur diversité génétique intra-isolat des génomes nucléaires, complique d’avantage ces études, en particulier le développement des marqueurs moléculaires pour des études biologiques, écologiques ainsi que les fonctions des CMA. C’est pour ces raisons que les génomes mitochondriaux offrent des opportunités et alternatives intéressantes pour étudier les CMA. En effet, les génomes mitochondriaux (mt) publiés à date, ne montrent pas de polymorphismes génétique intra-isolats. Cependant, des exceptions peuvent exister. Pour aller de l’avant avec la génomique mitochondriale, nous avons besoin de générer beaucoup de données de séquençages de l’ADN mitochondrial (ADNmt) afin d’étudier les méchanismes évolutifs, la génétique des population, l’écologie des communautés et la fonction des CMA. Dans ce contexte, l’objectif de mon projet de doctorat consiste à: 1) étudier l’évolution des génomes mt en utilisant l’approche de la génomique comparative au niveau des espèces proches, des isolats ainsi que des espèces phylogénétiquement éloignées chez les CMA; 2) étudier l’hérédité génétique des génomes mt au sein des isolats de l’espèce modèle Rhizophagus irregularis par le biais des anastomoses ; 3) étudier l’organisation des ADNmt et les gènes mt pour le développement des marqueurs moléculaires pour des études phylogénétiques. Nous avons utilisé l’approche dite ‘whole genome shotgun’ en pyroséquençage 454 et Illumina HiSeq pour séquencer plusieurs taxons de CMA sélectionnés selon leur importance et leur disponibilité. Les assemblages de novo, le séquençage conventionnel Sanger, l’annotation et la génomique comparative ont été réalisés pour caractériser des ADNmt complets. Nous avons découvert plusieurs mécanismes évolutifs intéressant chez l’espèce Gigaspora rosea dans laquelle le génome mt est complètement remanié en comparaison avec Rhizophagus irregularis isolat DAOM 197198. En plus nous avons mis en évidence que deux gènes cox1 et rns sont fragmentés en deux morceaux. Nous avons démontré que les ARN transcrits les deux fragments de cox1 se relient entre eux par épissage en trans ‘Trans-splicing’ à l’aide de l’ARN du gene nad5 I3 qui met ensemble les deux ARN cox1.1 et cox1.2 en formant un ARN complet et fonctionnel. Nous avons aussi trouvé une organisation de l’ADNmt très particulière chez l’espèce Rhizophagus sp. Isolat DAOM 213198 dont le génome mt est constitué par deux chromosomes circulaires. En plus nous avons trouvé une quantité considérable des séquences apparentées aux plasmides ‘plasmid-related sequences’ chez les Glomeraceae par rapport aux Gigasporaceae, contribuant ainsi à une évolution rapide des ADNmt chez les Glomeromycota. Nous avons aussi séquencé plusieurs isolats de l’espèces R. irregularis et Rhizophagus sp. pour décortiquer leur position phylogénéque et inférer des relations évolutives entre celles-ci. La comparaison génomique mt nous montré l’existence de plusieurs éléments mobiles comme : des cadres de lecture ‘open reading frames (mORFs)’, des séquences courtes inversées ‘short inverted repeats (SIRs)’, et des séquences apparentées aux plasimdes ‘plasmid-related sequences (dpo)’ qui impactent l’ordre des gènes mt et permettent le remaniement chromosomiques des ADNmt. Tous ces divers mécanismes évolutifs observés au niveau des isolats, nous permettent de développer des marqueurs moléculaires spécifiques à chaque isolat ou espèce de CMA. Les données générées dans mon projet de doctorat ont permis d’avancer les connaissances fondamentales des génomes mitochondriaux non seulement chez les Glomeromycètes, mais aussi de chez le règne des Fungi et les eucaryotes en général. Les trousses moléculaires développées dans ce projet peuvent servir à des études de la génétique des populations, des échanges génétiques et l’écologie des CMA ce qui va contribuer à la compréhension du rôle primorial des CMA en agriculture et environnement.

Complexity quantification of dense array EEG using sample entropy analysis

n this paper, a time series complexity analysis of dense array electroencephalogram signals is carried out using the recently introduced Sample Entropy (SampEn) measure. This statistic quantifies the regularity in signals recorded from systems that can vary from the purely deterministic to purely stochastic realm. The present analysis is conducted with an objective of gaining insight into complexity variations related to changing brain dynamics for EEG recorded from the three cases of passive, eyes closed condition, a mental arithmetic task and the same mental task carried out after a physical exertion task. It is observed that the statistic is a robust quantifier of complexity suited for short physiological signals such as the EEG and it points to the specific brain regions that exhibit lowered complexity during the mental task state as compared to a passive, relaxed state. In the case of mental tasks carried out before and after the performance of a physical exercise, the statistic can detect the variations brought in by the intermediate fatigue inducing exercise period. This enhances its utility in detecting subtle changes in the brain state that can find wider scope for applications in EEG based brain studies.

Permutation Entropy Based Analysis of Complex Signals for Characterising Change in System Dynamics

Timely detection of sudden change in dynamics that adversely affect the performance of systems and quality of products has great scientific relevance. This work focuses on effective detection of dynamical changes of real time signals from mechanical as well as biological systems using a fast and robust technique of permutation entropy (PE). The results are used in detecting chatter onset in machine turning and identifying vocal disorders from speech signal.Permutation Entropy is a nonlinear complexity measure which can efficiently distinguish regular and complex nature of any signal and extract information about the change in dynamics of the process by indicating sudden change in its value. Here we propose the use of permutation entropy (PE), to detect the dynamical changes in two non linear processes, turning under mechanical system and speech under biological system.Effectiveness of PE in detecting the change in dynamics in turning process from the time series generated with samples of audio and current signals is studied. Experiments are carried out on a lathe machine for sudden increase in depth of cut and continuous increase in depth of cut on mild steel work pieces keeping the speed and feed rate constant. The results are applied to detect chatter onset in machining. These results are verified using frequency spectra of the signals and the non linear measure, normalized coarse-grained information rate (NCIR).PE analysis is carried out to investigate the variation in surface texture caused by chatter on the machined work piece. Statistical parameter from the optical grey level intensity histogram of laser speckle pattern recorded using a charge coupled device (CCD) camera is used to generate the time series required for PE analysis. Standard optical roughness parameter is used to confirm the results.Application of PE in identifying the vocal disorders is studied from speech signal recorded using microphone. Here analysis is carried out using speech signals of subjects with different pathological conditions and normal subjects, and the results are used for identifying vocal disorders. Standard linear technique of FFT is used to substantiate thc results.The results of PE analysis in all three cases clearly indicate that this complexity measure is sensitive to change in regularity of a signal and hence can suitably be used for detection of dynamical changes in real world systems. This work establishes the application of the simple, inexpensive and fast algorithm of PE for the benefit of advanced manufacturing process as well as clinical diagnosis in vocal disorders.

Effect of rural transportation system on agricultural productivity in Oyo State, Nigeria

Food farming in Oyo North, Nigeria is characterised by an increasing use of Intermediary Mode of Transportation (IMT) to ease inputs and outputs mobility and farm access. To assess the influence on food farmer’s productivity, a random sample of 230 respondents was selected and data collected on their socio-economic and farm specific characteristics. Descriptive statistics, Herfindhal Index and Technical Efficiency Approach were used to analyse the data. The results indicate that majority of food farmers were in their middle age with mean age of 50 years and most of them used one plot at a location between 5 and 10km to their village of residence. They acquired land by inheritance and practiced intensive crop diversification as risk management strategy. The transportation modes used in addition to walking include bicycle, motorcycle, and car with increasing trend in the use of motorcycle. The mean Technical Efficiency (TE) of food farmers was 0.82 with significant inefficiency effects. The inefficiency analysis indicates positive effect of distance, crop diversification and un-tarred type of road on farmer’s productivity, while poor level of education among farmers, use of bicycle; trekking and weekly working time negatively affect farmer’s efficiency. The negative effect of trekking and use of bicycle and the excess working time suggest the adoption of more IMT of motorized type to optimize farming time and increase farmer’s productivity.

Time Discretization of the SST-generalized Navier-Stokes Equations: Positive and Negative Results

In the theory of the Navier-Stokes equations, the proofs of some basic known results, like for example the uniqueness of solutions to the stationary Navier-Stokes equations under smallness assumptions on the data or the stability of certain time discretization schemes, actually only use a small range of properties and are therefore valid in a more general context. This observation leads us to introduce the concept of SST spaces, a generalization of the functional setting for the Navier-Stokes equations. It allows us to prove (by means of counterexamples) that several uniqueness and stability conjectures that are still open in the case of the Navier-Stokes equations have a negative answer in the larger class of SST spaces, thereby showing that proof strategies used for a number of classical results are not sufficient to affirmatively answer these open questions. More precisely, in the larger class of SST spaces, non-uniqueness phenomena can be observed for the implicit Euler scheme, for two nonlinear versions of the Crank-Nicolson scheme, for the fractional step theta scheme, and for the SST-generalized stationary Navier-Stokes equations. As far as stability is concerned, a linear version of the Euler scheme, a nonlinear version of the Crank-Nicolson scheme, and the fractional step theta scheme turn out to be non-stable in the class of SST spaces. The positive results established in this thesis include the generalization of classical uniqueness and stability results to SST spaces, the uniqueness of solutions (under smallness assumptions) to two nonlinear versions of the Euler scheme, two nonlinear versions of the Crank-Nicolson scheme, and the fractional step theta scheme for general SST spaces, the second order convergence of a version of the Crank-Nicolson scheme, and a new proof of the first order convergence of the implicit Euler scheme for the Navier-Stokes equations. For each convergence result, we provide conditions on the data that guarantee the existence of nonstationary solutions satisfying the regularity assumptions needed for the corresponding convergence theorem. In the case of the Crank-Nicolson scheme, this involves a compatibility condition at the corner of the space-time cylinder, which can be satisfied via a suitable prescription of the initial acceleration.

Computer Analysis of Visual Properties of Curved Objects

A method is presented for the visual analysis of objects by computer. It is particularly well suited for opaque objects with smoothly curved surfaces. The method extracts information about the object's surface properties, including measures of its specularity, texture, and regularity. It also aids in determining the object's shape. The application of this method to a simple recognition task ??e recognition of fruit ?? discussed. The results on a more complex smoothly curved object, a human face, are also considered.

Representation and Detection of Shapes in Images

We present a set of techniques that can be used to represent and detect shapes in images. Our methods revolve around a particular shape representation based on the description of objects using triangulated polygons. This representation is similar to the medial axis transform and has important properties from a computational perspective. The first problem we consider is the detection of non-rigid objects in images using deformable models. We present an efficient algorithm to solve this problem in a wide range of situations, and show examples in both natural and medical images. We also consider the problem of learning an accurate non-rigid shape model for a class of objects from examples. We show how to learn good models while constraining them to the form required by the detection algorithm. Finally, we consider the problem of low-level image segmentation and grouping. We describe a stochastic grammar that generates arbitrary triangulated polygons while capturing Gestalt principles of shape regularity. This grammar is used as a prior model over random shapes in a low level algorithm that detects objects in images.

The Inner Meaning of Outer Space: Human Nature and the Celestial Realm

Kant argued that humans possess a priori knowledge of space; although his argument focused on a physics of bodies, it also has implications for a psychology of beings. Many human cultures organize stars in the night sky into constellations (i.e., impose structure); attribute properties, behaviors, and abilities to objects in the celestial realm (i.e., impose meaning); and use perceived regularity in the celestial realms in development of calendars, long-range navigation, agriculture, and astrology (i.e., seek predictability and control). The physical inaccessibility of the celestial realm allows a potent source of metaphor, and also allows projection of myths regarding origin and ascension, places of power, and dwelling places of gods, immortals, and other souls. Developments in astronomy and cosmology influenced views of human nature and the place of humanity in the universe, and these changes parallel declines in egocentrism with human development. Views regarding alleged beings (e.g., angels, extraterrestrials) from the celestial realm (and to how communicate with such beings) are anthropocentric and ignore evolutionary factors in physical and cognitive development. It is suggested that in considering views and uses of the celestial realm, we learn not just about the universe, but also about ourselves. 

Eye movements of beginning and more skilled readers

The present study aimed to analyze and compare the eye movements of beginning (2nd grade) and more skilled (4th grade) readers, during reading words and pseudo-words aloud, that differ in frequency (just for words), regularity and length. In this way, one intends to analyze the process of visual information extraction, by both groups, and detect experience and practice-related changes in the ocular behavior. The eye movements of 34 children were monitored, while these were reading words/pseudo-words lists, and this was accomplished using eye-tracking technology. The results show statistically significant differences between the two groups, in mean and total fixations duration for high-frequency words, in mean fixation duration for regular words and in the mean saccade amplitude in irregular pseudo-words. However, no significant differences were found between the groups on the study of the other variables. Nevertheless, the results suggest that skilled readers tend to show more effective eye movements, what determined a lesser effect of words’ frequency, regularity and length on this group. Moreover, the pseudo-words processing was more difficult than that of words, in both groups.

Museums and quality, from the concept of the museum that carries out functions to the museum that provides services

Quality management Self-evaluation of the organisation Citizens/customers satisfaction Impact on society evaluation Key performance evaluation Good practices comparison (Benchmarking) Continuous improvement In professional environments, when quality assessment of museums is discussed, one immediately thinks of the honourableness of the directors and curators, the erudition and specialisation of knowledge, the diversity of the gathered material and study of the collections, the collections conservation methods and environmental control, the regularity and notoriety of the exhibitions and artists, the building’s architecture and site, the recreation of environments, the museographic equipment design. We admit that the roles and attributes listed above can contribute to the definition of a specificity of museological good practice within a hierarchised functional perspective (the museum functions) and for the classification of museums according to a scale, validated between peers, based on “installed” appreciation criteria, enforced from above downwards, according to the “prestige” of the products and of those who conceive them, but that say nothing about the effective satisfaction of the citizen/customers and the real impact on society. There is a lack of evaluation instruments that would give us a return of all that the museum is and represents in contemporary society, focused on being and on the relation with the other, in detriment of the ostentatious possession and of the doing in order to meet one’s duties. But it is only possible to evaluate something by measurement and comparison, on the basis of well defined criteria, from a common grid, implicating all of the actors in the self-evaluation, in the definition of the aims to fulfil and in the obtaining of results.

A orientação homossexual e as investigações acerca da existência de componentes biológicos e genéticos determinantes; The homosexual orientation and investigations about the existence of components biological and genetics determinants

The male and female homosexual orientation has substantial prevalence in humans and can be explained by determinants of various levels: biological, genetic, psychological, social and cultural. However, the biological and genetic evidence have been the main hypotheses tested in scientific research in the world. This article aims to review research studies about the existence of genetic and biological evidence that determine homosexual orientation. Was conducted a review of the literature, using the database MedLine/PubMed and Google scholar. The papers and books were searched in Portuguese and English, using the following keywords: sexual orientation, sexual behavior, homosexuality, developmental Biology and genetics. Was selected papers of the last 22 years. Were found five main theories about the biological components: (1) fraternal birth order, (2) brain androgenization and 2D:4D ratio; (3) brain activation by pheromones; and (4) epigenetic inheritance; and four theories about the genetic components: (1) genetic polymorphism; (2) pattern of X-linked inheritance; (3) monozygotic twins; and (4) sexual antagonistic selection. Concluded that there were many scientific evidence found over time to explain some of biological and genetic components of homosexuality, especially in males. However, today, there is no definitive explanation about what are the determinants of homosexual orientation components.

Representing El Niño in coupled ocean–atmosphere GCMs: the dominant role of the atmospheric component

A systematic modular approach to investigate the respective roles of the ocean and atmosphere in setting El Niño characteristics in coupled general circulation models is presented. Several state-of-the-art coupled models sharing either the same atmosphere or the same ocean are compared. Major results include 1) the dominant role of the atmosphere model in setting El Niño characteristics (periodicity and base amplitude) and errors (regularity) and 2) the considerable improvement of simulated El Niño power spectra—toward lower frequency—when the atmosphere resolution is significantly increased. Likely reasons for such behavior are briefly discussed. It is argued that this new modular strategy represents a generic approach to identifying the source of both coupled mechanisms and model error and will provide a methodology for guiding model improvement.

A high efficiency technique for the generation of transgenic sugar beets from stomatal guard cells

An optimized protocol has been developed for the efficient and rapid genetic modification of sugar beet (Beta vulgaris L.). A polyethylene glycol-mediated DNA transformation technique could be applied to protoplast populations enriched specifically for a single totipotent cell type derived from stomatal guard cells, to achieve high transformation frequencies. Bialaphos resistance, conferred by the pat gene, produced a highly efficient selection system. The majority of plants were obtained within 8 to 9 weeks and were appropriate for plant breeding purposes. All were resistant to glufosinate-ammonium-based herbicides. Detailed genomic characterization has verified transgene integration, and progeny analysis showed Mendelian inheritance.

Towards a feminization of agricultural labour in northwest Syria

Smallholdings in the rural areas of northwest Syria are a result of land fragmentation that is due to inheritance. Because of rapid population growth combined with land fragmentation, these smallholdings are increasing and cannot sustain the rural households whose sizes and needs are also increasing rapidly. This situation has led to increasing numbers of mates migrating to urban areas in Syria and to neighbouring countries looking for work opportunities. In addition, recent agricultural intensification trends seem to have led to the emergence of a waged labour force which, in the absence of male workers owing to significant rates of migration, is now predominantly female. Agricultural labour use depends upon household characteristics and resources (type of labour used, gender of labour waged/exchanged/familial). The article attempts to present a comprehensive analysis of household labour use in distinctive farming systems in one region of Syria that has undergone great change in recent decades, and examines the changes in the composition of the agricultural labour force. Secondary information, rapid rural appraisals and formal farm surveys were used to gather information on the households in a study area where different farming systems coexist. The results show that the decrease in landholding size, the resulting male migration, and land intensification have resulted in the expansion of female labour in agricultural production, which has been termed in this research a 'feminization of agricultural labour'. This suggests that agricultural research and extension services will have to work more with women farmers and farm workers, seek their wisdom and involve them in technology and tran, fer This is not easy in conservative societies but requires research and extension institutions to take this reality into consideration in their programmes.

Effect of restricted suckling of calves on the productivity of crossbred dairy cattle

An experiment on restricted suckling of crossbred dairy cows was conducted at the Livestock Research Centre, Tanga in north-east Tanzania. The objective of the experiment was to evaluate the comparative productivity of Bos taurus x Bos indicus cows of medium and high levels of Bos taurus inheritance, whose calves were either bucket-reared or suckled residual milk. Lactation milk yield, length and persistency were 1563 L, 289 days, and 1.0, respectively, for the bucket-reared and 1592 L, 289 days and 1.4, respectively, for the suckling group. Days to observed oestrus, first insemination and conception for cows whose calves were bucket-reared were 47, 74 and 115 days, respectively, and 57, 81 and 126 days, respectively, for the suckling cows. The calf weights were similar at 1 year of age. The productivity of the cows, measured as the annual milk offtake, was not significantly higher for those that suckled their calves than for those whose calves were bucket-reared.