Horizontal genetic transfer in asexual fungi

Four aspects of horizontal genetic transfer during heterokaryon formation were examined in the asexual pathogen Fusarium oxysporum f.sp. cubense (Foc): (1) variability based on method of heterokaryon formation; (2) differences in nuclear and mitochondrial inheritance; (3) the occurrence of recombination without nuclear fusion; (4) the occurrence of horizontal genetic transfer between distantly related isolates. The use of non-pathogenic strains of Fusarium oxysporum as biocontrol agents warrants a closer examination at the reproductive life cycle of this fungus, particularly if drug resistance or pathogenicity genes can be transmitted horizontally. Experiments were divided into three phases. Phase I looked at heterokaryon formation by hyphal anastomosis and protoplast fusion. Phase II was a time course of heterokaryon formation to look at patterns of nuclear and mitochondrial inheritance. Phase III examined the genetic relatedness of the different vegetative compatibility groups using a multilocus analysis approach. Heterokaryon formation was evident within and between vegetative compatibility groups. Observation of non-parental genotypes after heterokaryon formation confirmed that, although a rare event, horizontal genetic transfer occurred during heterokaryon formation. Uniparental mitochondria inheritance was observed in heterokaryons formed either by hyphal anastomosis or protoplast fusion. Drug resistance was expressed during heterokaryon formation, even across greater genetic distances than those distances imposed by vegetative compatibility. Phylogenies inferred from different molecular markers were incongruent at a significant level, challenging the clonal origins of Foc. Mating type genes were identified in this asexual pathogen Polymorphisms were detected within a Vegetative Compatibility Group (VCG) suggesting non-clonal inheritance and/or sexual recombination in Foc. This research was funded in part by a NIH-NIGMS (National Institutes of Health-National Institute of General Medical Sciences) Grant through the MBRS (Minority Biomedical Research Support), the Department of Biological Sciences and the Tropical Biology Program at FIU. ^

Pressão de sono e perfil acadêmico de estudante de medicina do 1º período da UFRN

Academic demands, new social context, new routines and decrease of the parental control, are factors that may influence the sleep pattern of freshman students at the University. Medical students from the Federal University of Rio Grande do Norte (UFRN) have a full-time course, subjects with high-level content, and, at the first semester, classes begin at 7 a.m. This group composed by young adults who still suffering with delayed sleep phase, common in adolescence, indicating that this class schedule can be inappropriate at this age. The reduction of nocturnal sleep during school days, and the attempt to recover sleep on free days – social jet lag (JLS), suggests that in the first semester, students suffer from high sleep pressure. High sleep pressure may reflect on cognitive tasks and performance. Therefore, the aim of this study was to investigate the relationship between sleep pressure and the academic profile of medical students from the first semester of UFRN, characterizing this population socio-demographically and investigating possible impacts on therestactivity rhytm and academic performance. A sample of 88 students, healthy men and women awswered the following questionnaires: Pittsburgh Sleep Quality (PSQI), Epworth Sleepiness Scale (ESS), Horne & Ostberg Chronotype (HO), Munich Chronotype (MCTQ) and “Health and Sleep” adapted. Actigraphy was used during 14 days to make actogramas and obtain non-parametric variables of the rest-activity rhythm and the grades of the morning schedule were used as academic performance. The JLS was used as a measure of sleep pressure. Statistics significance level was 95%. The population was sociodemographic homogeneous. Most students have healthy lifestyle, practice physical activity, use car to go to the university and take between 15 and 30 minutes for this route. Regarding CSV, most were classify as intermediate (38.6%) and evening (32%) chronotypes, needs to nap during the week, suffer daytime sleepiness and have poor sleep quality. 83% of the sample has at least 1h JLS, which led us to divide into two groups: Group <2h JLS (N = 44) and Group ≥ 2h JLS (N = 44). The groups have differences only in chronotype, showing that most evening individuals have more JLS, however, no differences were found in relation to sociodemographic aspect, rest-activity rhythm or academic performance. The homogeneity of the sample was limited to compare the groups, however, is alarming that students already present in the first half: JLG, poor sleep quality and excessive daytime sleepiness, which can be accentuated through the university years, with the emergence of night shifts and increased academic demand. Interventionsaddressingthe importance of good sleep habits and the change of the class start time are strategies aimed to improve student’s health.

Statistical considerations in the kinetic analysis of PET-FDG brain tumour studies

Dynamic positron emission tomography (PET) imaging can be used to track the distribution of injected radio-labelled molecules over time in vivo. This is a powerful technique, which provides researchers and clinicians the opportunity to study the status of healthy and pathological tissue by examining how it processes substances of interest. Widely used tracers include 18F-uorodeoxyglucose, an analog of glucose, which is used as the radiotracer in over ninety percent of PET scans. This radiotracer provides a way of quantifying the distribution of glucose utilisation in vivo. The interpretation of PET time-course data is complicated because the measured signal is a combination of vascular delivery and tissue retention effects. If the arterial time-course is known, the tissue time-course can typically be expressed in terms of a linear convolution between the arterial time-course and the tissue residue function. As the residue represents the amount of tracer remaining in the tissue, this can be thought of as a survival function; these functions been examined in great detail by the statistics community. Kinetic analysis of PET data is concerned with estimation of the residue and associated functionals such as ow, ux and volume of distribution. This thesis presents a Markov chain formulation of blood tissue exchange and explores how this relates to established compartmental forms. A nonparametric approach to the estimation of the residue is examined and the improvement in this model relative to compartmental model is evaluated using simulations and cross-validation techniques. The reference distribution of the test statistics, generated in comparing the models, is also studied. We explore these models further with simulated studies and an FDG-PET dataset from subjects with gliomas, which has previously been analysed with compartmental modelling. We also consider the performance of a recently proposed mixture modelling technique in this study.

Le décours temporel de l'utilisation des fréquences spatiales dans les troubles du spectre autistique

Notre système visuel extrait d'ordinaire l'information en basses fréquences spatiales (FS) avant celles en hautes FS. L'information globale extraite tôt peut ainsi activer des hypothèses sur l'identité de l'objet et guider l'extraction d'information plus fine spécifique par la suite. Dans les troubles du spectre autistique (TSA), toutefois, la perception des FS est atypique. De plus, la perception des individus atteints de TSA semble être moins influencée par leurs a priori et connaissances antérieures. Dans l'étude décrite dans le corps de ce mémoire, nous avions pour but de vérifier si l'a priori de traiter l'information des basses aux hautes FS était présent chez les individus atteints de TSA. Nous avons comparé le décours temporel de l'utilisation des FS chez des sujets neurotypiques et atteints de TSA en échantillonnant aléatoirement et exhaustivement l'espace temps x FS. Les sujets neurotypiques extrayaient les basses FS avant les plus hautes: nous avons ainsi pu répliquer le résultat de plusieurs études antérieures, tout en le caractérisant avec plus de précision que jamais auparavant. Les sujets atteints de TSA, quant à eux, extrayaient toutes les FS utiles, basses et hautes, dès le début, indiquant qu'ils ne possédaient pas l'a priori présent chez les neurotypiques. Il semblerait ainsi que les individus atteints de TSA extraient les FS de manière purement ascendante, l'extraction n'étant pas guidée par l'activation d'hypothèses.

Seawater carbonate chemistry, mass, length and gene expression of Sepia officinalis during experiments, 2011

The specific transporters involved in maintenance of blood pH homeostasis in cephalopod molluscs have not been identified to date. Using in situ hybridization and immuno histochemical methods, we demonstrate that Na+/K+-ATPase (soNKA), a V-type H+-ATPase (soV-HA), and Na+/HCO3- cotransporter (soNBC) are co-localized in NKA-rich cells in the gills of Sepia officinalis. mRNA expression patterns of these transporters and selected metabolic genes were examined in response to moderately elevated seawater pCO2 (0.16 and 0.35 kPa) over a time-course of six weeks in different ontogenetic stages. The applied CO2 concentrations are relevant for ocean acidification scenarios projected for the coming decades. We determined strong expression changes in late stage embryos and hatchlings, with one to three log2-fold reductions in soNKA, soNBCe, socCAII and COX. In contrast, no hypercapnia induced changes in mRNA expression were observed in juveniles during both short- and long-term exposure. However a transiently increased demand of ion regulatory demand was evident during the initial acclimation reaction to elevated seawater pCO2. Gill Na+/K+-ATPase activity and protein concentration were increased by approximately 15% in during short (2-11 day), but not long term (42 day) exposure. Our findings support the hypothesis that the energy budget of adult cephalopods is not significantly compromised during long-term exposure to moderate environmental hypercapnia. However, the down regulation of ion-regulatory and metabolic genes in late stage embryos, taken together with a significant reduction in somatic growth, indicates that cephalopod early life stages are challenged by elevated seawater pCO2.

Mécanismes psychophysiques et neuronaux de la compensation dynamique de multiples champs de force : facilitation et anticipation liée à des indices de couleur

Dans cette thèse, nous abordons le contrôle moteur du mouvement du coude à travers deux approches expérimentales : une première étude psychophysique a été effectuée chez les sujets humains, et une seconde implique des enregistrements neurophysiologiques chez le singe. Nous avons recensé plusieurs aspects non résolus jusqu’à présent dans l’apprentissage moteur, particulièrement concernant l’interférence survenant lors de l’adaptation à deux ou plusieurs champs de force anti-corrélés. Nous avons conçu un paradigme où des stimuli de couleur aident les sujets à prédire la nature du champ de force externe actuel avant qu’ils ne l’expérimentent physiquement durant des mouvements d’atteinte. Ces connaissances contextuelles faciliteraient l’adaptation à des champs de forces en diminuant l’interférence. Selon le modèle computationnel de l’apprentissage moteur MOSAIC (MOdular Selection And Identification model for Control), les stimuli de couleur aident les sujets à former « un modèle interne » de chaque champ de forces, à s’en rappeler et à faire la transition entre deux champs de force différents, sans interférence. Dans l’expérience psychophysique, quatre groupes de sujets humains ont exécuté des mouvements de flexion/extension du coude contre deux champs de forces. Chaque force visqueuse était associée à une couleur de l’écran de l’ordinateur et les deux forces étaient anti-corrélées : une force résistante (Vr) a été associée à la couleur rouge de l’écran et l’autre, assistante (Va), à la couleur verte de l’écran. Les deux premiers groupes de sujets étaient des groupes témoins : la couleur de l’écran changeait à chaque bloc de 4 essais, tandis que le champ de force ne changeait pas. Les sujets du groupe témoin Va ne rencontraient que la force assistante Va et les sujets du groupe témoin Vr performaient leurs mouvements uniquement contre une force résistante Vr. Ainsi, dans ces deux groupes témoins, les stimuli de couleur n’étaient pas pertinents pour adapter le mouvement et les sujets ne s’adaptaient qu’à une seule force (Va ou Vr). Dans les deux groupes expérimentaux, cependant, les sujets expérimentaient deux champs de forces différents dans les différents blocs d’essais (4 par bloc), associés à ces couleurs. Dans le premier groupe expérimental (groupe « indice certain », IC), la relation entre le champ de force et le stimulus (couleur de l’écran) était constante. La couleur rouge signalait toujours la force Vr tandis que la force Va était signalée par la couleur verte. L’adaptation aux deux forces anti-corrélées pour le groupe IC s’est avérée significative au cours des 10 jours d’entraînement et leurs mouvements étaient presque aussi bien ajustés que ceux des deux groupes témoins qui n’avaient expérimenté qu’une seule des deux forces. De plus, les sujets du groupe IC ont rapidement démontré des changements adaptatifs prédictifs dans leurs sorties motrices à chaque changement de couleur de l’écran, et ceci même durant leur première journée d’entraînement. Ceci démontre qu’ils pouvaient utiliser les stimuli de couleur afin de se rappeler de la commande motrice adéquate. Dans le deuxième groupe expérimental, la couleur de l’écran changeait régulièrement de vert à rouge à chaque transition de blocs d’essais, mais le changement des champs de forces était randomisé par rapport aux changements de couleur (groupe « indice-incertain », II). Ces sujets ont pris plus de temps à s’adapter aux champs de forces que les 3 autres groupes et ne pouvaient pas utiliser les stimuli de couleurs, qui n’étaient pas fiables puisque non systématiquement reliés aux champs de forces, pour faire des changements prédictifs dans leurs sorties motrices. Toutefois, tous les sujets de ce groupe ont développé une stratégie ingénieuse leur permettant d’émettre une réponse motrice « par défaut » afin de palper ou de sentir le type de la force qu’ils allaient rencontrer dans le premier essai de chaque bloc, à chaque changement de couleur. En effet, ils utilisaient la rétroaction proprioceptive liée à la nature du champ de force afin de prédire la sortie motrice appropriée pour les essais qui suivent, jusqu’au prochain changement de couleur d’écran qui signifiait la possibilité de changement de force. Cette stratégie était efficace puisque la force demeurait la même dans chaque bloc, pendant lequel la couleur de l’écran restait inchangée. Cette étude a démontré que les sujets du groupe II étaient capables d’utiliser les stimuli de couleur pour extraire des informations implicites et explicites nécessaires à la réalisation des mouvements, et qu’ils pouvaient utiliser ces informations pour diminuer l’interférence lors de l’adaptation aux forces anti-corrélées. Les résultats de cette première étude nous ont encouragés à étudier les mécanismes permettant aux sujets de se rappeler d’habiletés motrices multiples jumelées à des stimuli contextuels de couleur. Dans le cadre de notre deuxième étude, nos expériences ont été effectuées au niveau neuronal chez le singe. Notre but était alors d’élucider à quel point les neurones du cortex moteur primaire (M1) peuvent contribuer à la compensation d’un large éventail de différentes forces externes durant un mouvement de flexion/extension du coude. Par cette étude, nous avons testé l’hypothèse liée au modèle MOSAIC, selon laquelle il existe plusieurs modules contrôleurs dans le cervelet qui peuvent prédire chaque contexte et produire un signal de sortie motrice approprié pour un nombre restreint de conditions. Selon ce modèle, les neurones de M1 recevraient des entrées de la part de plusieurs contrôleurs cérébelleux spécialisés et montreraient ensuite une modulation appropriée de la réponse pour une large variété de conditions. Nous avons entraîné deux singes à adapter leurs mouvements de flexion/extension du coude dans le cadre de 5 champs de force différents : un champ nul ne présentant aucune perturbation, deux forces visqueuses anti-corrélées (assistante et résistante) qui dépendaient de la vitesse du mouvement et qui ressemblaient à celles utilisées dans notre étude psychophysique chez l’homme, une force élastique résistante qui dépendait de la position de l’articulation du coude et, finalement, un champ viscoélastique comportant une sommation linéaire de la force élastique et de la force visqueuse. Chaque champ de force était couplé à une couleur d’écran de l’ordinateur, donc nous avions un total de 5 couleurs différentes associées chacune à un champ de force (relation fixe). Les singes étaient bien adaptés aux 5 conditions de champs de forces et utilisaient les stimuli contextuels de couleur pour se rappeler de la sortie motrice appropriée au contexte de forces associé à chaque couleur, prédisant ainsi leur sortie motrice avant de sentir les effets du champ de force. Les enregistrements d’EMG ont permis d’éliminer la possibilité de co-contractions sous-tendant ces adaptations, étant donné que le patron des EMG était approprié pour compenser chaque condition de champ de force. En parallèle, les neurones de M1 ont montré des changements systématiques dans leurs activités, sur le plan unitaire et populationnel, dans chaque condition de champ de force, signalant les changements requis dans la direction, l’amplitude et le décours temporel de la sortie de force musculaire nécessaire pour compenser les 5 conditions de champs de force. Les changements dans le patron de réponse pour chaque champ de force étaient assez cohérents entre les divers neurones de M1, ce qui suggère que la plupart des neurones de M1 contribuent à la compensation de toutes les conditions de champs de force, conformément aux prédictions du modèle MOSAIC. Aussi, cette modulation de l’activité neuronale ne supporte pas l’hypothèse d’une organisation fortement modulaire de M1.

Neuronal Assembly Detection and Cell Membership Specification by Principal Component Analysis

LOPES-DOS-SANTOS, V. , CONDE-OCAZIONEZ, S. ; NICOLELIS, M. A. L. , RIBEIRO, S. T. , TORT, A. B. L. . Neuronal assembly detection and cell membership specification by principal component analysis. Plos One, v. 6, p. e20996, 2011.

Theta-associated high-frequency oscillations (110–160 Hz) in the hippocampus and neocortex

TORT, A. B. L. ; SCHEFFER-TEIXEIRA, R ; Souza, B.C. ; DRAGUHN, A. ; BRANKACK, J. . Theta-associated high-frequency oscillations (110-160 Hz) in the hippocampus and neocortex. Progress in Neurobiology , v. 100, p. 1-14, 2013.

Local Field Potentials in the Gustatory Cortex Carry Taste Information

It has been recently shownthat localfield potentials (LFPs)fromthe auditory and visual cortices carry information about sensory stimuli, but whether this is a universal property of sensory cortices remains to be determined. Moreover, little is known about the temporal dynamics of sensory information contained in LFPs following stimulus onset. Here we investigated the time course of the amount of stimulus information in LFPs and spikes from the gustatory cortex of awake rats subjected to tastants and water delivery on the tongue. We found that the phase and amplitude of multiple LFP frequencies carry information about stimuli, which have specific time courses after stimulus delivery. The information carried by LFP phase and amplitude was independent within frequency bands, since the joint information exhibited neither synergy nor redundancy. Tastant information in LFPs was also independent and had a different time course from the information carried by spikes. These findings support the hypothesis that the brain uses different frequency channels to dynamically code for multiple features of a stimulus.

Changes in the perceived color of very bright stimuli

When very intense stimuli in the long-wavelength region of the visual spectrum are viewed continuously, they change in hue from red, through yellow, to green. The relation of the time course of these changes to the intensity of the stimulus is reported.

Neuronal Assembly Detection and Cell Membership Specification by Principal Component Analysis

LOPES-DOS-SANTOS, V. , CONDE-OCAZIONEZ, S. ; NICOLELIS, M. A. L. , RIBEIRO, S. T. , TORT, A. B. L. . Neuronal assembly detection and cell membership specification by principal component analysis. Plos One, v. 6, p. e20996, 2011.

Theta-associated high-frequency oscillations (110–160 Hz) in the hippocampus and neocortex

TORT, A. B. L. ; SCHEFFER-TEIXEIRA, R ; Souza, B.C. ; DRAGUHN, A. ; BRANKACK, J. . Theta-associated high-frequency oscillations (110-160 Hz) in the hippocampus and neocortex. Progress in Neurobiology , v. 100, p. 1-14, 2013.

Whole Genome Analysis of Gene Expression Reveals Coordinated Activation of Signaling and Metabolic Pathways during Pollen-Pistil Interactions in Arabidopsis

Plant reproduction depends on the concerted activation of many genes to ensure correct communication between pollen and pistil. Here, we queried the whole transcriptome of Arabidopsis (Arabidopsis thaliana) in order to identify genes with specific reproductive functions. We used the Affymetrix ATH1 whole genome array to profile wild-type unpollinated pistils and unfertilized ovules. By comparing the expression profile of pistils at 0.5, 3.5, and 8.0 h after pollination and applying a number of statistical and bioinformatics criteria, we found 1,373 genes differentially regulated during pollen-pistil interactions. Robust clustering analysis grouped these genes in 16 time-course clusters representing distinct patterns of regulation. Coregulation within each cluster suggests the presence of distinct genetic pathways, which might be under the control of specific transcriptional regulators. A total of 78% of the regulated genes were expressed initially in unpollinated pistil and/or ovules, 15% were initially detected in the pollen data sets as enriched or preferentially expressed, and 7% were induced upon pollination. Among those, we found a particular enrichment for unknown transcripts predicted to encode secreted proteins or representing signaling and cell wall-related proteins, which may function by remodeling the extracellular matrix or as extracellular signaling molecules. A strict regulatory control in various metabolic pathways suggests that fine-tuning of the biochemical and physiological cellular environment is crucial for reproductive success. Our study provides a unique and detailed temporal and spatial gene expression profile of in vivo pollen-pistil interactions, providing a framework to better understand the basis of the molecular mechanisms operating during the reproductive process in higher plants.

Calcium oscillations

Changes in cellular calcium concentration control a wide range of physiological processes, from the subsecond release of synaptic neurotransmitters, to the regulation of gene expression over months or years. Calcium can also trigger cell death through both apoptosis and necrosis, and so the regulation of cellular calcium concentration must be tightly controlled through the concerted action of pumps, channels and buffers that transport calcium into and out of the cell cytoplasm. A hallmark of cellular calcium signalling is its spatiotemporal complexity: stimulation of cells by a hormone or neurotransmitter leads to oscillations in cytoplasmic calcium concentration that can vary markedly in time course, amplitude, frequency, and spatial range. In this chapter we review some of the biological roles of calcium, the experimental characterisation of complex dynamic changes in calcium concentration, and attempts to explain this complexity using computational models. We consider the "toolkit" of cellular proteins which influence calcium concentration, describe mechanistic models of key elements of the toolkit, and fit these into the framework of whole cell models of calcium oscillations and waves. Finally, we will touch on recent efforts to use stochastic modelling to elucidate elementary calcium signal events, and how these may evolve into global signals.

Local Field Potentials in the Gustatory Cortex Carry Taste Information

It has been recently shownthat localfield potentials (LFPs)fromthe auditory and visual cortices carry information about sensory stimuli, but whether this is a universal property of sensory cortices remains to be determined. Moreover, little is known about the temporal dynamics of sensory information contained in LFPs following stimulus onset. Here we investigated the time course of the amount of stimulus information in LFPs and spikes from the gustatory cortex of awake rats subjected to tastants and water delivery on the tongue. We found that the phase and amplitude of multiple LFP frequencies carry information about stimuli, which have specific time courses after stimulus delivery. The information carried by LFP phase and amplitude was independent within frequency bands, since the joint information exhibited neither synergy nor redundancy. Tastant information in LFPs was also independent and had a different time course from the information carried by spikes. These findings support the hypothesis that the brain uses different frequency channels to dynamically code for multiple features of a stimulus.