Relatório de Estágio

A Prática Educativa Supervisionada representa, sem dúvida, a etapa mais aguardada pelos estudantes que se formam para serem professores, pois este é um momento recheado de expectativas e descobertas da profissionalidade docente. Por conseguinte, o presente relatório de estágio pretende espelhar o percurso evolutivo da mestranda ao longo dessa prática pedagógica. A passagem pelas escolas ficou marcada por uma postura crítica e reflexiva perante as opções pedagógicas tomadas, sendo que estas resultaram sempre de uma articulação entre os quadros teóricos e práticos de cada área disciplinar. A supervisão, processo crucial durante o estágio, é considerada pela professora estagiária como um momento de acompanhamento e orientação da ação educativa por parte dos supervisores institucionais. A par deste processo foi sempre visível um trabalho colaborativo com o par pedagógico e com os professores cooperantes, com o principal objetivo de atingir novos e melhores modos de agir, ancorando-se, assim, nos pilares da metodologia de investigação-ação. O trajeto construído pela formanda é o retrato de uma experiência de desenvolvimento pessoal e profissional, tendo, porém, a convicção de que, apesar de este relatório marcar o término de um ciclo de estudos inicial, há muito mais para aprender e construir.

Mechanisms underlying activation of neural stem cells in the adult central nervous system

À la fin du 19e siècle, Dr. Ramón y Cajal, un pionnier scientifique, a découvert les éléments cellulaires individuels, appelés neurones, composant le système nerveux. Il a également remarqué la complexité de ce système et a mentionné l’impossibilité de ces nouveaux neurones à être intégrés dans le système nerveux adulte. Une de ses citations reconnues : “Dans les centres adultes, les chemins nerveux sont fixes, terminés, immuables. Tout doit mourir, rien ne peut être régénérer” est représentative du dogme de l’époque (Ramón y Cajal 1928). D’importantes études effectuées dans les années 1960-1970 suggèrent un point de vue différent. Il a été démontré que les nouveaux neurones peuvent être générés à l’âge adulte, mais cette découverte a créé un scepticisme omniprésent au sein de la communauté scientifique. Il a fallu 30 ans pour que le concept de neurogenèse adulte soit largement accepté. Cette découverte, en plus de nombreuses avancées techniques, a ouvert la porte à de nouvelles cibles thérapeutiques potentielles pour les maladies neurodégénératives. Les cellules souches neurales (CSNs) adultes résident principalement dans deux niches du cerveau : la zone sous-ventriculaire des ventricules latéraux et le gyrus dentelé de l’hippocampe. En condition physiologique, le niveau de neurogenèse est relativement élevé dans la zone sous-ventriculaire contrairement à l’hippocampe où certaines étapes sont limitantes. En revanche, la moelle épinière est plutôt définie comme un environnement en quiescence. Une des principales questions qui a été soulevée suite à ces découvertes est : comment peut-on activer les CSNs adultes afin d’augmenter les niveaux de neurogenèse ? Dans l’hippocampe, la capacité de l’environnement enrichi (incluant la stimulation cognitive, l’exercice et les interactions sociales) à promouvoir la neurogenèse hippocampale a déjà été démontrée. La plasticité de cette région est importante, car elle peut jouer un rôle clé dans la récupération de déficits au niveau de la mémoire et l’apprentissage. Dans la moelle épinière, des études effectuées in vitro ont démontré que les cellules épendymaires situées autour du canal central ont des capacités d’auto-renouvellement et de multipotence (neurones, astrocytes, oligodendrocytes). Il est intéressant de noter qu’in vivo, suite à une lésion de la moelle épinière, les cellules épendymaires sont activées, peuvent s’auto-renouveller, mais peuvent seulement ii donner naissance à des cellules de type gliale (astrocytes et oligodendrocytes). Cette nouvelle fonction post-lésion démontre que la plasticité est encore possible dans un environnement en quiescence et peut être exploité afin de développer des stratégies de réparation endogènes dans la moelle épinière. Les CSNs adultes jouent un rôle important dans le maintien des fonctions physiologiques du cerveau sain et dans la réparation neuronale suite à une lésion. Cependant, il y a peu de données sur les mécanismes qui permettent l'activation des CSNs en quiescence permettant de maintenir ces fonctions. L'objectif général est d'élucider les mécanismes sous-jacents à l'activation des CSNs dans le système nerveux central adulte. Pour répondre à cet objectif, nous avons mis en place deux approches complémentaires chez les souris adultes : 1) L'activation des CSNs hippocampales par l'environnement enrichi (EE) et 2) l'activation des CSNs de la moelle épinière par la neuroinflammation suite à une lésion. De plus, 3) afin d’obtenir plus d’information sur les mécanismes moléculaires de ces modèles, nous utiliserons des approches transcriptomiques afin d’ouvrir de nouvelles perspectives. Le premier projet consiste à établir de nouveaux mécanismes cellulaires et moléculaires à travers lesquels l’environnement enrichi module la plasticité du cerveau adulte. Nous avons tout d’abord évalué la contribution de chacune des composantes de l’environnement enrichi à la neurogenèse hippocampale (Chapitre II). L’exercice volontaire promeut la neurogenèse, tandis que le contexte social augmente l’activation neuronale. Par la suite, nous avons déterminé l’effet de ces composantes sur les performances comportementales et sur le transcriptome à l’aide d’un labyrinthe radial à huit bras afin d’évaluer la mémoire spatiale et un test de reconnaissante d’objets nouveaux ainsi qu’un RNA-Seq, respectivement (Chapitre III). Les coureurs ont démontré une mémoire spatiale de rappel à court-terme plus forte, tandis que les souris exposées aux interactions sociales ont eu une plus grande flexibilité cognitive à abandonner leurs anciens souvenirs. Étonnamment, l’analyse du RNA-Seq a permis d’identifier des différences claires dans l’expression des transcripts entre les coureurs de courte et longue distance, en plus des souris sociales (dans l’environnement complexe). iii Le second projet consiste à découvrir comment les cellules épendymaires acquièrent les propriétés des CSNs in vitro ou la multipotence suite aux lésions in vivo (Chapitre IV). Une analyse du RNA-Seq a révélé que le transforming growth factor-β1 (TGF-β1) agit comme un régulateur, en amont des changements significatifs suite à une lésion de la moelle épinière. Nous avons alors confirmé la présence de cette cytokine suite à la lésion et caractérisé son rôle sur la prolifération, différentiation, et survie des cellules initiatrices de neurosphères de la moelle épinière. Nos résultats suggèrent que TGF-β1 régule l’acquisition et l’expression des propriétés de cellules souches sur les cellules épendymaires provenant de la moelle épinière.

A cidade e o rio: origem e evolução da frente ribeirinha de Lisboa

Em Lisboa, ao longo dos séculos, o homem foi conquistando as águas do Tejo. Hoje, após os diversos aterros, a frente ribeirinha da cidade é uma consolidada faixa de terreno, rematada por muros que, contra a «ondulação» do Tejo, definem uma expandida área que acolhe uma intensa actividade portuária. Foi nesta faixa junto do rio que se desenrolou parte importante da história de Lisboa, desde as ocupações romana e muçulmana, e também muito particularmente aquando do período dos Descobrimentos, da reconstrução pombalina pós-terramoto e do surto industrial do século XIX. Alguns destes momentos históricos encontram-se reflectidos nas inúmeras plantas, cartas e mapas disponíveis neste estudo, desde a Planta da Cidade de Lisboa : 1650, de João Nunes Tinoco, até ao Plano de Melhoramentos do Porto de Lisboa, de 1946. É com base nessas plantas, mas também em cartas manuscritas, relatos de época, gravuras e fotografias antigas – documentos em grande parte inéditos –, que este trabalho de investigação propõe cartografar este território, realizando desenhos originais que possibilitam um novo olhar sobre o seu processo de crescimento e consolidação. Assim, este estudo concilia todos estes elementos, constituindo uma análise completa que se debruça sobre a evolução da frente ribeirinha de Lisboa e que permite descobrir inúmeros aspectos até aqui desconhecidos, ajudando a responder à pergunta que hoje se coloca: perante o cenário que o porto actual atravessa, como melhor poderá Lisboa recuperar a relação com o rio?; THE CITY AND THE RIVER: ORIGIN AND EVOLUTION OF LISBON'S RIVERFRONT ABSTRACT: In Lisbon, over the centuries, man was conquering the waters of the Tagus. Today, after the various landfills, the city's riverfront is a consolidated strip of land, finished by walls that, against the "ripple" of the Tagus, define an expanded area that hosts an intense port activity. It was in this band along the river that unfolded important part of the history of Lisbon, from the Roman and Muslim occupations, and also very particularly during the period of the Discoveries, the post-earthquake reconstruction, and the industrial boom of the nineteenth century. Some of these historical moments are reflected in many plans, charts and maps available in this study, since the plan designated Planta da Cidade de Lisboa : 1650, made by João Nunes Tinoco, to the plan called Plano de Melhoramentos do Porto de Lisboa, drawn in the year of 1946. Based on these plans, but also in handwritten letters, time reports, antique prints and photographs – documents that are mostly unpublished – this research work proposes map this territory, performing original drawings that provide a new look at their growth process and consolidation. Thereby, this study combines all these elements, providing a complete analysis which focuses on the evolution of the Lisbon riverfront and that allows you to discover many aspects unknown until now, helping to answer the question that now arises: according to the present scenario that the harbour is going through, how can Lisbon recover the relationship with the river?

The dynamics of Brazilian protozoology over the past century

Brazilian scientists have been contributing to the protozoology field for more than 100 years with important discoveries of new species such as Trypanosoma cruzi and Leishmania spp. In this work, we used a Brazilian thesis database (Coordination for the Improvement of Higher Education Personnel) covering the period from 1987-2011 to identify researchers who contributed substantially to protozoology. We selected 248 advisors by filtering to obtain researchers who supervised at least 10 theses. Based on a computational analysis of the thesis databases, we found students who were supervised by these scientists. A computational procedure was developed to determine the advisors’ scientific ancestors using the Lattes Platform. These analyses provided a list of 1,997 researchers who were inspected through Lattes CV examination and allowed the identification of the pioneers of Brazilian protozoology. Moreover, we investigated the areas in which researchers who earned PhDs in protozoology are now working. We found that 68.4% of them are still in protozoology, while 16.7% have migrated to other fields. We observed that support for protozoology by national or international agencies is clearly correlated with the increase of scientists in the field. Finally, we described the academic genealogy of Brazilian protozoology by formalising the “forest” of Brazilian scientists involved in the study of protozoa and their vectors over the past century.

Curar a própria história : uma análise sociológica da terapêutica da depressão

Tese (doutorado)—Universidade de Brasília, Instituto de Ciências Sociais, Departamento de Sociologia, 2015.

A pesca do bacalhau durante o período do Estado Novo (1933-1974) : contributo para as relações interculturais

A presente dissertação tem como objeto de estudo a pesca do bacalhau feita por portugueses sob a bandeira de Portugal durante o período do Estado Novo (1933-1974). Investigou-se as razões para um investimento e um protecionismo tão forte à indústria da pesca do bacalhau. É indissociável do estudo da demanda portuguesa por este peixe, à época muito abundante no noroeste atlântico, as políticas autárcicas e de subsistência pilares da economia do Estado Novo, assim como a implantação e robustecimento da Instituição Corporativa. Subjacente a estas linhas de matriz económica mas paradigmáticas do novo regime, estava também a reconstrução da identidade portuguesa, a sacralização do trabalho e a heroicidade do pescador português do bacalhau. A existência da tentativa de revivificação da glória dos descobrimentos na pesca do bacalhau. A criação de um ambiente social, político e religioso que levaram à persecução destas políticas e consequentemente do engrandecimento da estrutura do Estado Novo, resultando até na sedimentação de apoio popular. O desenvolvimento da frota de pesca longínqua foi quase uma única janela de oportunidades para o conhecimento de novos mundos. A montante e a jusante da atividade piscatória também se desenvolveram indústrias e comércio internacional. A participação em organizações internacionais de regulação das pescas proporcionou contatos Institucionais com outras nações, não raro utilizados para quebrar isolamentos e propagandear o Estado Novo e as suas manifestações culturais e identitárias que suscitaram relacionamentos interculturais. Para além destes contatos mais formais, também se desenvolveram contatos informais, que se repercutiram na criação e manifestação de conhecimento mútuo e claro de condições para a gestação da interculturidade. Estes desenvolvimentos de relações informais, de contatos profissionais também geraram relações culturais que se manifestaram em projetos individuais de vida associados às migrações.

Cinemática de partículas em fluidos de viscosidade variável com o tempo e sua aplicação na construção de poços de petróleo: avaliação durante paradas operacionais

The new oil reservoirs discoveries in onshore and ultra deep water offshore fields and complex trajectories require the optimization of procedures to reduce the stops operation during the well drilling, especially because the platforms and equipment high cost, and risks which are inherent to the operation. Among the most important aspects stands out the drilling fluids project and their behavior against different situations that may occur during the process. By means of sedimentation experiments, a correlation has been validated to determe the sedimentation particles velocity in variable viscosity fluids over time, applying the correction due to effective viscosity that is a shear rate and time function. The viscosity evolution over time was obtained by carrying out rheologic tests using a fixed shear rate, small enough to not interfere in the fluid gelling process. With the sedimentation particles velocity and the fluid viscosity over time equations an iterative procedure was proposed to determine the particles displacement over time. These equations were implemented in a case study to simulate the cuttings sedimentation generated in the oil well drilling during stops operation, especially in the connections and tripping, allowing the drilling fluid project in order to maintain the cuttings in suspension, avoiding risks, such as stuck pipe and in more drastic conditions, the loss of the well

¿Qué mil años... no son nada? : vuelos, guerras y sueños

Fondo Margaritainés Restrepo

Milenio 2001 - 3000, a punto de milagros, navegantes y amigos de la no violencia

Fondo Margaritainés Restrepo

Aplicação de termogravimetria acoplada à espectrometria de massas para caracterização de petróleo e determinação da curva de evolução de gás sulfídrico

With the new discoveries of oil and gas, the exploration of fields in various geological basins, imports of other oils and the development of alternative fuels, more and more research labs have evaluated and characterized new types of petroleum and derivatives. Therefore the investment in new techniques and equipment in the samples analysis to determine their physical and chemical properties, their composition, possible contaminants, especification of products, among others, have multiplied in last years, so development of techniques for rapid and efficient characterization is extremely important for a better economic recovery of oil. Based on this context, this work has two main objectives. The first one is to characterize the oil by thermogravimetry coupled with mass spectrometry (TG-MS), and correlate these results with from other types of characterizations data previously informed. The second is to use the technique to develop a methodology to obtain the curve of evaluation of hydrogen sulfide gas in oil. Thus, four samples were analyzed by TG-MS, and X-ray fluorescence spectrometry (XRF). TG results can be used to indicate the nature of oil, its tendency in coke formation, temperatures of distillation and cracking, and other features. It was observed in MS evaluations the behavior of oil main compounds with temperature, the points where the volatilized certain fractions and the evaluation gas analysis of sulfide hydrogen that is compared with the evaluation curve obtained by Petrobras with another methodology

Two roads to planet detection

One of the most exciting discoveries in astrophysics of the last last decade is of the sheer diversity of planetary systems. These include "hot Jupiters", giant planets so close to their host stars that they orbit once every few days; "Super-Earths", planets with sizes intermediate to those of Earth and Neptune, of which no analogs exist in our own solar system; multi-planet systems with planets smaller than Mars to larger than Jupiter; planets orbiting binary stars; free-floating planets flying through the emptiness of space without any star; even planets orbiting pulsars. Despite these remarkable discoveries, the field is still young, and there are many areas about which precious little is known. In particular, we don't know the planets orbiting Sun-like stars nearest to our own solar system, and we know very little about the compositions of extrasolar planets. This thesis provides developments in those directions, through two instrumentation projects.

The first chapter of this thesis concerns detecting planets in the Solar neighborhood using precision stellar radial velocities, also known as the Doppler technique. We present an analysis determining the most efficient way to detect planets considering factors such as spectral type, wavelengths of observation, spectrograph resolution, observing time, and instrumental sensitivity. We show that G and K dwarfs observed at 400-600 nm are the best targets for surveys complete down to a given planet mass and out to a specified orbital period. Overall we find that M dwarfs observed at 700-800 nm are the best targets for habitable-zone planets, particularly when including the effects of systematic noise floors caused by instrumental imperfections. Somewhat surprisingly, we demonstrate that a modestly sized observatory, with a dedicated observing program, is up to the task of discovering such planets.

We present just such an observatory in the second chapter, called the "MINiature Exoplanet Radial Velocity Array," or MINERVA. We describe the design, which uses a novel multi-aperture approach to increase stability and performance through lower system etendue, as well as keeping costs and time to deployment down. We present calculations of the expected planet yield, and data showing the system performance from our testing and development of the system at Caltech's campus. We also present the motivation, design, and performance of a fiber coupling system for the array, critical for efficiently and reliably bringing light from the telescopes to the spectrograph. We finish by presenting the current status of MINERVA, operational at Mt. Hopkins observatory in Arizona.

The second part of this thesis concerns a very different method of planet detection, direct imaging, which involves discovery and characterization of planets by collecting and analyzing their light. Directly analyzing planetary light is the most promising way to study their atmospheres, formation histories, and compositions. Direct imaging is extremely challenging, as it requires a high performance adaptive optics system to unblur the point-spread function of the parent star through the atmosphere, a coronagraph to suppress stellar diffraction, and image post-processing to remove non-common path "speckle" aberrations that can overwhelm any planetary companions.

To this end, we present the "Stellar Double Coronagraph," or SDC, a flexible coronagraphic platform for use with the 200" Hale telescope. It has two focal and pupil planes, allowing for a number of different observing modes, including multiple vortex phase masks in series for improved contrast and inner working angle behind the obscured aperture of the telescope. We present the motivation, design, performance, and data reduction pipeline of the instrument. In the following chapter, we present some early science results, including the first image of a companion to the star delta Andromeda, which had been previously hypothesized but never seen.

A further chapter presents a wavefront control code developed for the instrument, using the technique of "speckle nulling," which can remove optical aberrations from the system using the deformable mirror of the adaptive optics system. This code allows for improved contrast and inner working angles, and was written in a modular style so as to be portable to other high contrast imaging platforms. We present its performance on optical, near-infrared, and thermal infrared instruments on the Palomar and Keck telescopes, showing how it can improve contrasts by a factor of a few in less than ten iterations.

One of the large challenges in direct imaging is sensing and correcting the electric field in the focal plane to remove scattered light that can be much brighter than any planets. In the last chapter, we present a new method of focal-plane wavefront sensing, combining a coronagraph with a simple phase-shifting interferometer. We present its design and implementation on the Stellar Double Coronagraph, demonstrating its ability to create regions of high contrast by measuring and correcting for optical aberrations in the focal plane. Finally, we derive how it is possible to use the same hardware to distinguish companions from speckle errors using the principles of optical coherence. We present results observing the brown dwarf HD 49197b, demonstrating the ability to detect it despite it being buried in the speckle noise floor. We believe this is the first detection of a substellar companion using the coherence properties of light.

Earth-Abundant Zinc-IV-Nitride Semiconductors

This investigation is motivated by the need for new visible frequency direct bandgap semiconductor materials that are abundant and low-cost to meet the increasing demand for optoelectronic devices in applications such as solid state lighting and solar energy conversion. Proposed here is the utilization of zinc-IV-nitride materials, where group IV elements include silicon, germanium, and tin, as earth-abundant alternatives to the more common III-nitrides in optoelectronic devices. These compound semiconductors were synthesized under optimized conditions using reactive radio frequency magnetron sputter deposition. Single phase ZnSnN₂, having limited experimental accounts in literature, is validated by identification of the wurtzite-derived crystalline structure predicted by theory through X-ray and electron diffraction studies. With the addition of germanium, bandgap tunability of ZnSn_xGe_1-xN₂ alloys is demonstrated without observation of phase separation, giving these materials a distinct advantage over In_xGa_1-xN alloys. The accessible bandgaps range from 1.8 to 3.1 eV, which spans the majority of the visible spectrum. Electron densities, measured using the Hall effect, were found to be as high as 10²² cm⁻³ and indicate that the compounds are unintentionally degenerately doped. Given these high carrier concentrations, a Burstein-Moss shift is likely affecting the optical bandgap measurements. The discoveries made in this thesis suggest that with some improvements in material quality, zinc-IV-nitrides have the potential to enable cost-effective and scalable optoelectronic devices.

Análise paramétrica do método de injeção alternada de água e CO2(WAG) em reservatórios de petróleo

After the decline of production from natural energy of the reservoir, the methods of enhanced oil recovery, which methods result from the application of special processes such as chemical injection, miscible gases, thermal and others can be applied. The advanced recovery method with alternating - CO2 injection WAG uses the injection of water and gas, normally miscible that will come in contact with the stock oil. In Brazil with the discovery of pre-salt layer that gas gained prominence. The amount of CO2 present in the oil produced in the pre-salt layer, as well as some reservoirs is one of the challenges to be overcome in relation to sustainable production once this gas needs to be processed in some way. Many targets for CO2 are proposed by researchers to describe some alternatives to the use of CO2 gas produced such as enhanced recovery, storage depleted fields, salt caverns storage and marketing of CO2 even in plants. The largest oil discoveries in Brazil have recently been made by Petrobras in the pre -salt layer located between the states of Santa Catarina and Espírito Santo, where he met large volumes of light oil with a density of approximately 28 ° API, low acidity and low sulfur content. This oil that has a large amount of dissolved CO2 and thus a pioneering solution for the fate of this gas comes with an advanced recovery. The objective of this research is to analyze which parameters had the greatest influence on the enhanced recovery process. The simulations were performed using the "GEM" module of the Computer Modelling Group, with the aim of studying the advanced recovery method in question. For this work, semi - synthetic models were used with reservoir and fluid data that can be extrapolated to practical situations in the Brazilian Northeast. The results showed the influence of the alternating injection of water and gas on the recovery factor and flow rate of oil production process, when compared to primary recovery and continuous water injection or continuous gas injection

La multifuncionalidad de los SIALES en zonas rurales de países en desarrollo. El caso de la agroindustria panelera Colombiana.

La multifuncionalidad (MF) de la agricultura tradicionalmente ha sido abordada desde la perspectiva de países desarrollados y muy pocas veces se ha analizado en el contexto de países en desarrollo. El presente estudio, mediante un trabajo de campo que consulta a varios actores sociales, identifica la presencia de múltiples funciones sociales, económicas y ambientales relevantes que van mas allá de la función productiva en el caso de la agroindustria de la panela (Azúcar no centrifugado) en Colombia y establece características diferenciales en la relevancia y ámbito de estas funciones en tres sistemas agroalimentarios locales (SIAL) de la panela. Finalmente, a partir de estos hallazgos plantea nuevos retos de investigación para la mediación de la MF y para el diseño de políticas basadas en la MF que permitan activar y fortalecer los SIAL de países en desarrollo.   ABSTRACT The multifunctionality (MF) of the agriculture traditionally has been approached from the perspective of developed countries and very few times it has been analyzed in the context of countries in development. The present study, by means of a field work that consults several social actor, identifies the presence of multiple social, economic and environmental functions that they go beyond the productive function in the case of the agroindustry of the panela (not centrifuged sugar) in Colombia and it establishes differential characteristics  in the relevance and environment of these function in three local agrifood systems (LAS) of the panela. Finally, starting from these discoveries it outlines new research challenges to measure the MF and for the design of policies based on the MF that allow to activate and strengthen LAS of undeveloped countries.

Arrangement of gene pairs, retrotransposon insertions, and regulation of gene expression in plants

Plant genomes are extremely complex. Myriad factors contribute to their evolution and organization, as well as to the expression and regulation of individual genes. Here we present investigations into several such factors and their influence on genome structure and gene expression: the arrangement of pairs of physically adjacent genes, retrotransposons closely associated with genes, and the effect of retrotransposons on gene pair evolution. All sequenced plant genomes contain a significant fraction of retrotransposons, including that of rice. We investigated the effects of retrotransposons within rice genes and within a 1 kb putative promoter region upstream of each gene. We found that approximately one-sixth of all rice genes are closely associated with retrotransposons. Insertions within a gene’s promoter region tend to block gene expression, while retrotransposons within genes promote the existence of alternative splicing forms. We also identified several other trends in retrotransposon insertion and its effects on gene expression. Several studies have previously noted a connection among genes between physical proximity and correlated expression profiles. To determine the degree to which this correlation depends on an exact physical arrangement, we studied the expression and interspecies conservation of convergent and divergent gene pairs in rice, Arabidopsis, and Populus trichocarpa. Correlated expression among gene pairs was quite common in all three species, yet conserved arrangement was rare. However, conservation of gene pair arrangement was significantly more common among pairs with strongly correlated expression levels. In order to uncover additional properties of gene pair conservation and rearrangement, we performed a comparative analysis of convergent, divergent, and tandem gene pairs in rice, sorghum, maize, and Brachypodium. We noted considerable differences between gene pair types and species. We also constructed a putative evolutionary history for each pair, which led to several interesting discoveries. To further elucidate the causes of gene pair conservation and rearrangement, we identified retrotransposon insertions in and near rice gene pairs. Retrotransposon-associated pairs are less likely to be conserved, although there are significant differences in the possible effect of different types and locations of retrotransposon insertions. The three types of gene pair also varied in their susceptibility to retrotransposon-associated evolutionary changes.