Software components expose Application Programming Interfaces (APIs) as a means to access their functionality, and facilitate reuse. Developers use APIs supplied by programming languages to access the core data structures and algorithms that are part of the language framework. They use the APIs of third-party libraries for specialized tasks. Thus, APIs play a central role in mediating a developer's interaction with software, and the interaction between different software components. However, APIs are often large, complex and hard to navigate. They may have hundreds of classes and methods, with incomplete or obsolete documentation. They may encapsulate concurrency behaviour that the developer is unaware of. Finding the right functionality in a large API, using APIs correctly, and maintaining software that uses a constantly evolving API are challenges that every developer runs into. In this thesis, we design automated techniques to address two problems pertaining to APIs (1) Concurrency analysis of APIs, and (2) API mining. Speci cally, we consider the concurrency analysis of asynchronous APIs, and mining of math APIs to infer the functional behaviour of API methods. The problem of concurrency bugs such as race conditions and deadlocks has been well studied for multi-threaded programs. However, developers have been eschewing a pure multi-threaded programming model in favour of asynchronous programming models supported by asynchronous APIs. Asynchronous programs and multi-threaded programs have different semantics, due to which existing techniques to analyze the latter cannot detect bugs present in programs that use asynchronous APIs. This thesis addresses the problem of concurrency analysis of programs that use asynchronous APIs in an end-to-end fashion. We give operational semantics for important classes of asynchronous and event-driven systems. The semantics are designed by carefully studying real software and serve to clarify subtleties in scheduling. We use the semantics to inform the design of novel algorithms to find races and deadlocks. We implement the algorithms in tools, and show their effectiveness by finding serious bugs in popular open-source software. To begin with, we consider APIs for asynchronous event-driven systems supporting pro-grammatic event loops. Here, event handlers can spin event loops programmatically in addition to the runtime's default event loop. This concurrency idiom is supported by important classes of APIs including GUI, web browser, and OS APIs. Programs that use these APIs are prone to interference between a handler that is spinning an event loop and another handler that runs inside the loop. We present the first happens-before based race detection technique for such programs. Next, we consider the asynchronous programming model of modern languages like C]. In spite of providing primitives for the disciplined use of asynchrony, C] programs can deadlock because of incorrect use of blocking APIs along with non-blocking (asynchronous) APIs. We present the rst deadlock detection technique for asynchronous C] programs. We formulate necessary conditions for deadlock using a novel program representation that represents procedures and continuations, control ow between them and the threads on which they may be scheduled. We design a static analysis to construct the pro-gram representation and use it to identify deadlocks. Our ideas have resulted in research tools with practical impact. Sparse Racer, our tool to detect races, found 13 previously unknown use-after-free bugs in KDE Linux applications. Dead Wait, our deadlock detector, found 43 previously unknown deadlocks in asynchronous C] libraries. Developers have fixed 43 of these races and deadlocks, indicating that our techniques are useful in practice to detect bugs that developers consider worth fixing. Using large APIs effectively entails finding the right functionality and calling the methods that implement it correctly, possibly composing many API elements. Automatically infer-ring the information required to do this is a challenge that has attracted the attention of the research community. In response, the community has introduced many techniques to mine APIs and produce information ranging from usage examples and patterns, to protocols governing the API method calling sequences. We show how to mine unit tests to match API methods to their functional behaviour, for the specific but important class of math APIs. Math APIs are at the heart of many application domains ranging from machine learning to scientific computations, and are supplied by many competing libraries. In contrast to obtaining usage examples or identifying correct call sequences, the challenge in this domain is to infer API methods required to perform a particular mathematical computation, and to compose them correctly. We let developers specify mathematical computations naturally, as a math expression in the notation of interpreted languages (such as Matlab). Our unit test mining technique maps subexpressions to math API methods such that the method's functional behaviour matches the subexpression's executable semantics, as defined by the interpreter. We apply our technique, called MathFinder, to math API discovery and migration, and validate it in a user study. Developers who used MathFinder nished their programming tasks twice as fast as their counterparts who used the usual techniques like web and code search, and IDE code completion. We also demonstrate the use of MathFinder to assist in the migration of Weka, a popular machine learning library, to a different linear algebra library.

Genes de plantas que codificam inibidores de enzimas digestivas de insetos têm sido introduzidos em plantas cultivadas visando o controle de pragas. Os inibidores de proteinases estão presentes nos tecidos vegetais, principalmente nas sementes, e atuam em resposta a ataques por herbívoros e patógenos. Inibidores de serino-proteinases (IPs) dos tipos Bowman-Birk e Kunitz isolados de sementes de soja foram inseridos em variedades de cana-de-açúcar para aumentar a resistência à broca Diatraea saccharalis (Fabr.), principal praga desta cultura. Para utilização de plantas geneticamente modificadas contendo inibidores de proteinases é necessário um conhecimento profundo de sua sustentabilidade e segurança ambiental, determinando a estabilidade da característica inserida e os seus efeitos nos organismos não-alvo. O objetivo desta pesquisa foi avaliar os efeitos diretos e indiretos de inibidores de proteinases de soja em organismos não-alvos: um parasitóide larval, Cotesia flavipes (Cam.) (Hymenoptera: Braconidae); um patógeno, Metarhizium anisopliae (Mestch.) Sorokin (Deuteromycotina: Hyphomycetes); um polinizador, Apis mellifera L. (Hymenoptera: Apidae) e um decompositor, Scheloribates praeincisus (Berlese) (Acari: Oribatida: Scheloribatidae); associados à cultura da cana-de-açúcar. O consumo de Kunitz e BBI não afetou a sobrevivência de S. praeincisus. Por outro lado, a ingestão dos inibidores semi-purificados e purificados do tipo Kunitz diminuiu a duração das fases imaturas de S. praeincisus. A ingestão de folhas de cana GM expressando inibidores de proteinases (Kunitz e BBI) não afetou o tempo de desenvolvimento e a sobrevivência dos imaturos deste oribatídeo quando comparada à ingestão de suas isolinhas. Os inibidores de proteinases semi-purificados e purificados não afetaram a duração dos períodos larval e pupal, o peso e número de pupas e percentual de emergência do parasitóide C. flavipes em D. saccharalis. Por outro lado, a proporção de fêmeas em relação a machos de C. flavipes foi maior no tratamento onde as lagartas foram alimentadas com dieta contendo 0,5% de inibidores semi-purificados comparado-se à testemunha. A proporção fêmea:macho foi significativamente maior também quando os parasitóides foram alimentados com o inibidor do tipo Kunitz em relação ao controle e aos parasitóides alimentados com BBI. A adição de 0,5% (p/v) de inibidores de proteinases semi-purificados e 0,05% (p/v) de inibidores purificados do tipo Kunitz nos meios de cultura MC e BDA resultaram em maiores crescimento vegetativo e produção de conídios de M. anisopliae. Os inibidores purificados do tipo BBI não alteraram a esporulação do fungo. Os resultados dos estudos com A. mellifera não foram conclusivos e novas investigações precisam ser conduzidas para esclarecer os potenciais efeitos de inibidores de proteinases em abelhas. De uma forma geral, observou-se que os inibidores de proteinases (Kunitz e BBI) não afetaram negativamente os organismos não-alvo testados. Por outro lado, a ingestão de inibidor do tipo Kunitz alterou positivamente alguns parâmetros biológicos de C. flavipes, M. anisopliae e S. praeincisus. / Genes of plants expressing insect proteinase inhibitors have been introduced into plants for pest control. Proteases inhibitors are present in plant tissues, mainly in seeds, and act in response to predators and pathogens. The Bowman-Birk type and Kunitz type of serine proteases inhibitors (PI) from soybean seeds are been used to increase resistance of sugarcane to Diatraea saccharalis (Fabr.), the most important pest of this crop. The sustainability and environmental safety of PI crops is still unknown. For these reasons, it is necessary to understand the stability and the non-target effects of this new trait. The objective of this study was to evaluate the direct and indirect effects of soybean PI on the following non-target organisms associated to sugarcane: the larval parasitoid, Cotesia flavipes (Cam.) (Hymenoptera: Braconidae); the entomopathogen, Metarhizium anisopliae (Mestch.) Sorokin (Deuteromycotina: Hyphomycetes); the pollinator Apis mellifera L. (Hymenoptera: Apidae) and the soil mite involved in the process of recycling organic matter, Scheloribates praeincisus (Berlese) (Acari: Oribatida: Scheloribatidae). Kunitz and BBI did not affect S. praeincisus survival. On the other hand, Kunitz semi-purified and purified inhibitor ingestion reduced duration of the immature stages of S. praeincisus. Ingestion of GM senescent leaves did not have an effect on mite immatures development time and survival compared to ingestion of its isolines leaves. The semi-purified and purified proteinases inhibitors did not alter either the duration of larval and pupal stages of C. flavipes on D. saccharalis, or weight and number of pupae and parasitoid emergence. In other hand, the parasitism and proportion of female was higher on the treatment where caterpillars were fed with diet containing 0.5% of semi-purified inhibitors, comparing to control. The ratio female:male was significantly higher also when parasitoids were fed to the Kunitz type inhibitor compared to the control and BBI. The addition of 0.5 % (w/v) of semi- purified proteinase inhibitors and 0.05% (w/v) of Kunitz type purified inhibitors on two culture media (CM and PDA), resulted in increase of vegetative growth and production of conidia. BBI type purified inhibitors did not change the fungus sporulation. The results from the studies with A. mellifera were not conclusive and investigations are needed to clarify the potential impact of proteinase inhibitors on A. mellifera. Overall, proteinase inhibitors (Kunitz and BBI) did not negatively affect the non-target organisms tested. Conversely, ingestion of the Kunitz type of proteinase inhibitors altered positively some biological parameters of C. flavipes, M. anisopliae and S. praeincisus.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Organo-synthetic insecticides are widely used to control pests in crops and stored products. The indiscriminate use of these products are responsible for many economic and environmental problems, which has been generating a growing demand for alternative control methods. The essential oils of plants have been studied as a viable alternative to pest management. Recent jobs indicate that the essential oil of alecrim-de-tabuleiro Lippia gracilis presents great potential for biopospection insecticide compounds. Thus, the aim of the present work was study the essential oils of two chemotypes of L. gracilis and their major compounds thymol and carvacrol, evaluating: i) the toxicity of these compounds against Diaphania hyalinata and selectivity over non-target organisms Apis mellifera and Polybia micans ii) the toxicity and behavioral effects of these compounds over Cryptolestes ferrugineus. The essential oils of both chemotypes of L. gracilis were toxic to D. hyalinata. The carvacrol chemotype was 29% more toxic than thymol chemotype. The monoterpenes thymol and carvacrol when applied alone, were about two and five times more toxic than their respective chemotypes. Essential oils acted very quickly causing mortality in half the population of D. hyalinata in less than three hours. All treatments were not selective in favor of A. mellifera and P. micans. The essential oils and the major compounds were highly toxic by fumigation to adults of C. ferrugineus. The concentrations of the thymol and carvacrol chemotypes required to cause 50% mortality of C. ferrugineus were 20.7 and 25.1 μL L-1, respectively. The isolated thymol and carvacrol were 1.7 and 1.9 times more toxic to C. ferrugineus. Essential oils thymol and carvacrol chemotypes caused a mortality half the population of C. ferrugineus in 63.3 and 83.1 hours. All treatments caused repellency and irritability in adult C. ferrugineus. Thus, our results show the great potential of essential oils of L. gracilis and their major compounds for the development of new products to be used in the pest control field and in stored products. / Inseticidas organossintéticos são amplamente utilizados no controle de pragas em lavouras e em produtos armazenados. O uso abusivo destes produtos é responsável por diversos problemas econômicos e ambientais, o que tem gerado uma demanda crescente por métodos alternativos de controle. Os óleos essenciais de plantas têm sido estudados como uma alternativa viável ao manejo de pragas. Trabalhos recentes apontam que o óleo essencial do alecrim-de-tabuleiro Lippia gracilis apresenta grande potencial para bioprospecção de compostos inseticidas. Desta forma, objetivou-se neste trabalho estudar os óleos essenciais de dois quimiotipos de L. gracilis e seus compostos majoritários timol e carvacrol, avaliando: i) a toxicidade destes compostos sobre Diaphania hyalinata e a seletividade sobre os organismos não-alvos Apis mellifera e Polybia micans; e ii) a toxicidade e os efeitos comportamentais destes compostos sobre Cryptolestes ferrugineus. Os óleos essenciais de ambos quimiotipos de L. gracilis se mostraram tóxicos a D. hyalinata, sendo o quimiotipo carvacrol 29% mais tóxico do que o quimiotipo timol. Os monoterpenos timol e carvacrol quando aplicados isoladamente foram cerca de duas e cinco vezes mais tóxicos que seus quimiotipos, respectivamente. Os óleos essenciais atuaram de forma rápida causando mortalidade na metade da população de D. hyalinata em menos de três horas. Todos os tratamentos não foram seletivos à A. mellífera e P. micans. Os óleos essenciais e os compostos majoritários foram altamente tóxicos por fumigação aos adultos de C. ferrugineus. As concentrações dos óleos essenciais dos quimiotipos timol e carvacrol necessárias para causar 50% de mortalidade a C. ferrugineus foram 20,7 e 25,1 μL L-1, respectivamante. O timol e o carvacrol isolados foram 1,7 e 1,9 vezes mais tóxicos a C. ferrugineus. Os óleos essenciais dos quimiotipos timol e carvacrol causaram mortalidade em metade da população de C. ferrugineus em 63,3 e 83,1 horas. Todos os tratamentos causaram repelência e irritabilidade em adultos de C. ferrugineus. Assim, nossos resultados mostram o grande potencial dos óleos essenciais de L. gracilis e seus compostos majoritários para o desenvolvimento de novos produtos a serem utilizados no controle de pragas em campo e nos produtos armazenados.

European honey bee (Apis mellifera) is major pollinator for agriculture and vital for food production. Large number of viruses infecting A. mellifera have been discovered over the years, but it isn't yet known if they are pathogenic for their host. However, presence of non-viral pathogens like Varroa destructor can greatly increase their virulence and have fatal consequences for the colony. The aim of this study was to test and verify robustness of the method for virome detection on healthy honey bees from the Czech Republic. Last but not least we aimed to detect non-viral parasites and correlate their presence with detected viruses. We have successfully identified large number of viral sequences from different viral families. Viral composition was found to be influenced mainly by colony from where the honey bees were collected. That was mainly given by a large amount of bacteriophages in the samples. However, analysis of individual viruses, known to infect honey bee, indicated that viral prevalence and viral loads of specific viruses is quite different among individual honey bees from the same colony. Interestingly we were able to find highly diverse Lake Sinai viruses. We were able to observe correlations either between individual viruses or viral other non-viral pathogens. Further analysis is...

Apis mellifera Linnaeus (1758) è un insetto eusociale conosciuto in tutto il mondo sia per la produzione di miele sia per il suo ruolo di impollinatore, uno dei servizi ecosistemici fondamentali per la biodiversità del pianeta. Durante la sua attività di foraggiamento, l’ape è esposta agli inquinanti ambientali tra cui il particolato atmosferico aerodisperso (PM). Il particolato atmosferico può depositarsi sul corpo dell’insetto e infine contaminare anche i prodotti apistici come polline e miele. Il PM può avere diverse dimensioni (es. PM10, PM2.5, PM0.1), composizione chimica, morfologia e fonti di emissione (naturale o antropica). Nel presente elaborato di tesi, tecniche di microscopia elettronica a scansione (SEM-EDX) sono state utilizzate per caratterizzare la contaminazione da PM di origine antropica del corpo dell’ape e dei suoi prodotti (Capitolo 2 e Capitolo 3) e analisi molecolari per studiare gli eventuali effetti sub-letali sul microbiota intestinale di api esposte ai PM per via orale (Capitolo 4). / Apis mellifera Linnaeus (1758) order Hymenoptera family Apidae, is a eusocial insect widely known for its role in pollination, a fundamental ecosystem service for plant biodiversity and ultimately for the planet. During flight and foraging activity, the honey bee can collect airborne particulate matter (PM) on their own body, especially on the forewings, and can also contaminate bee products as pollen and honey. Particulate matter can originate from natural or anthropic sources, and is characterised by size (e.g., PM10, PM2.5, PM0.1), chemical composition, and morphology. In this thesis, honey bee, pollen and honey were used as bioindicator of PM – from coarse to ultrafine – in industrial areas of the Po Valley, Italy (Chapter 2 and Chapter 3). The (sub-lethal) effects of Titanium dioxide – a widespread airborne PM1 pollutant – on the honey bee through oral exposure was then investigated (Chapter 4). The technique used to analyse the PM contaminating bees and bee products is the scanning electron microscopy (SEM) coupled with X-ray spectrometer (EDX). EDX spectra allowed us to obtain chemical information from specimens, while backscattered-electron (BSE) imaging and elemental mapping provided both compositional and topographic information of PM.

Paenibacillus larvae is a gram-positive spore-forming bacterium that affects and kills the larvae of the honey bee (Apis mellifera) and causes the American foulbrood disease. Adults bees do not become infected, but they transmit tenacious spores within the hive and between hives and can infect larvae while caring for them. It is not allowed by law to treat bees in the Czech Republic, but the recommended preventive method for reducing the amount of spores in the hive is the shook swarm method (bees are moved to a new clean hive and the old hive is destroyed with all brood and supplies). The aim of this work was to detect and quantify P. larvae in bee workers using the quantitative real-time polymerase chain reaction (qPCR). In the first experiment, the two set of samples were taken - bees before and after the shook swarm method, but the expected decrease in spores in the samples taken after shook swarm was not confirmed, and conversely, non-specific products were amplified. In the second experiment, the presence of P. larvae spores in samples from heavily infected hives (with clinical symptoms of American foulbrood) and from hives with almost no findings of P. larvae spores, both originating from the same habitat, were compared. In this case, the differences were clearly visible. There were not...

Classical experiments on honey bee time-memory showed that foragers trained to collect food at a fixed time of day return the following day with a remarkable degree of time-accuracy. A series of field experiments revealed that not all foragers return to a food source on unrewarded test days. Rather, there exist two subgroups: "persistent" foragers reconnoiter the source; "reticent" foragers wait in the hive for confirmation of source availability. A forager's probability of being persistent is dependent both on the amount of experience it has had at the source and the environmental conditions present, but the probability is surprisingly high (0.4-0.9). Agent-based simulation of foraging behavior indicated these high levels of persistence represent an energetically optimal strategy, which is likely a compromise solution to an ever-changing environment. Time-memory, with its accompanying anticipation, enables foragers to improve time-accuracy, quickly reactivating the foraging group to more efficiently exploit a food source.

The bacteria in host-associated microbial communities influence host health through various mechanisms, such as immune stimulation or the release of metabolites. However, viruses that target bacteria, called bacteriophages (phages), may also shape the animal microbiome. Most phage lifecycles can be classified as either lytic or temperate. Lytic phages infect and directly kill bacterial hosts and can directly regulate bacterial population size. Temperate phages, in contrast, have the potential to undergo either a lytic cycle or integrate into the bacterial genome as a prophage. As a prophage, the phage may alter bacterial host phenotypes by carrying novel genes associated with auxiliary metabolic functions, virulence-enhancing toxins, or resistance to other phage infections. Lytic phages may also carry certain auxiliary metabolic genes, which are instead used to takeover bacterial host functions to better accommodate the lytic lifecycle. In either case, the ability to alter bacterial phenotypes may have important ramifications on host-associated communities. This dissertation focused on the genetic contributions that phages, and particularly prophages, provide to the bacterial members of two separate host-associated communities: the honey bee (Apis mellifera) gut microbiome and the amphibian skin microbiome. My second chapter surveyed publicly available whole genome sequences of common honey bee gut bacterial species for prophages. It revealed that prophage distribution varied by bacterial host, and that the most common auxiliary metabolic genes were associated with carbohydrate metabolism. In chapter three, this bioinformatic pipeline was applied to the amphibian skin microbiome. Prophages were identified in whole genome bacterial sequences of bacteria isolated from the skin of American bullfrogs (Lithobates catesbeianus), eastern newts (Notophthalmus viridescens), Spring peepers (Pseudacris crucifer) and American toads (Anaxyrus americanus). Prophages were additionally identified in publicly available genomes of non-amphibian isolates of Janthinobacterium lividum, a bacteria found both on amphibian skin and broadly in the environment. In addition to a diverse set of predicted prophages across amphibian bacterial isolates, several Janthinobacterium lividum prophages from both amphibian and environmental isolates appear to encode a chitinase-like gene undergoing strong purifying selection within the bacterial host. While identifying the specific function of this gene would require in vitro isolation and testing, its high homology to chitinase and endolysins suggest it may be involved in the breakdown of either fungal or bacterial cellular wall components. Finally, my fourth chapter revisits the honey bee gut system by investigating the role of geographic distance in bacteriophage community similarity. A total of 12 apiaries across a transect of the United States, from Virginia to Washington, were sampled and honey bee viromes were sequenced, focusing on the lytic and actively lysing temperate community of phages. Although each apiary possessed many unique bacteriophages, apiaries that were closer together did have more similar communities. Each bacteriophage community also carried auxiliary carbohydrate genes, especially those associated with sucrose degradation, and antimicrobial resistance genes. Combined, the results of these three studies suggest that bacteriophages, and particularly prophages, may be contributing to the genetic diversity of the bacterial community through nuanced relationships with their bacterial hosts. / Doctor of Philosophy / The microbial communities of animals, called "microbiomes", play important roles in the health of animals. The bacteria in these microbiomes can help strengthen the immune system, provide resistance to dangerous pathogens, and break down nutrients. However, bacteria are not alone in the microbiome; viruses are also present. Surprisingly, the vast majority of the world's viruses, even those living inside animals, infect bacteria. These viruses, called "bacteriophages" or "phages", can impact the bacterial communities in a microbiome. Phages can be grouped in to two broad categories based on lifecycle. Lytic phages kill the bacterial host directly after infection. Temperate phages, on the other hand, can either immediately kill the host like lytic phages or alternatively, become a part of the bacterial genome and live as prophages. Phages with both lifecycles can sometimes carry genes that, although not essential to the phage, may change the traits of the bacteria during infection. For example, some phages carry toxin genes, which bacteria use to cause disease in animals. Other phages might carry genes that provide antibiotic resistance or alter the metabolism of the infected bacteria. If a phage gene benefits the infected bacteria, the bacteria may begin interacting with its environment in a new way or may even become more abundant. Alternatively, phages that directly kill infected bacteria may have a negative effect on bacterial population sizes. To begin unraveling how phages influence bacterial species in microbiomes, I investigated two different animal systems: the Western honey bee (Apis mellifera) gut microbiome and the amphibian skin microbiome. I first identified prophages of several common bacterial species that reside in the honey bee gut (Chapter 2). Prophages were more common in certain bacterial species than others, and some possessed genes associated with the breakdown of sugars or pollen, suggesting they help honey bees process their food. Using similar techniques, I then identified prophages in bacteria isolated from the skin microbiomes of several amphibian species common in the eastern United States (American bullfrogs, Eastern newts, Spring peepers, and American toads) (Chapter 3). Most notably, the bacteria Janthinobacterium lividum may benefit from prophages that carry genes for potentially antifungal chitinase enzymes that destroy the fungal cell wall. Finally, I returned to the honey bee gut microbiome system by investigating how honey bee bacteriophage communities change over large geographic distances (Chapter 4). This study, which examined honey bees from 12 apiaries sampled from the east to west coast of the United States, looks primarily at lytic phage and temperate phage that are not integrated as prophage, but are instead seeking a bacterial host to infect. I found that nearby apiaries tended to have more similar communities of bacteriophages, compared to apiaries far away. Additionally, most bacteriophage communities carry genes associated with the breakdown of sugars like sucrose. Overall, these three studies show that phages, and especially prophages, contribute to the genetic landscape of the microbiome by broadly providing bacterial hosts with access to a diverse set of genes.

La colonie d’abeille (Apis mellifera L.) est une société complexe où les individus interagissent entre eux, notamment par le biais de phéromones. L’étude de cette communication chimique est indispensable à la compréhension des régulations sociales mises en place dans la colonie. Chez l’abeille, plus de 50 substances chimiques avec des effets incitateurs ou modificateurs sur la colonie ont été identifiées. Malgré ces découvertes, de nombreux travaux sont à accomplir pour mieux comprendre ce système de communication particulier.La problématique de cette thèse vise à caractériser l’histoire de vie d’une phéromone majeure l’Oléate d’Ethyle (EO), qui permet d’optimiser l’équilibre nourrices / butineuses dans la colonie. Parallèlement, d’autres recherches ont été entreprises, notamment l’étude de la communication chimique de la reine et du couvain, chez qui seulement deux phéromones ont été identifiées avec des effets pléiotropiques dans la colonie.Nos résultats ont mis en évidence une production variable d’EO par les ouvrières, en fonction de l’environnement de la colonie. La production de cette molécule chimique dans la colonie peut également être modifiée par un stress : des abeilles parasitées par du Nosema spp. ont une production anormalement élevée d’EO. En outre, cette molécule phéromonale est transmise des butineuses vers les nourrices par contact cuticulaire et par le pollen.Pour la compréhension de la communication entre la reine et les ouvrières, nos résultats montrent que la reine utilise d’autres composés phéromonaux puissant en redondance de la QMP pour orienter la construction de cire, le phénomène de cour et l’inhibition des ovaires des ouvrières.Chez le couvain, nous avons identifié un composé phéromonal volatil, le E-ß-ocimène, produit majoritairement par les jeunes larves, inhibant le développement des ovaires des ouvrières et accélérant leur maturation comportementale.Ces études nous ont permis d’avoir une connaissance plus précise de la communication chimique au sein de la colonie. Ainsi nous expliquons par deux théories le rôle de la complexité et de la redondance phéromonale de la colonie d’abeilles / In the honeybee colony (Apis mellifera L.) studies of the chemical communication are essential to understand social regulations. In the honey bee colony more than 50 chemical substances with releaser and primer effects have been identified. Despite years of research on this type of communication, significant work remains to be done.In this thesis, the aim is to characterize the dynamics of a major pheromone: ethyl oleate (EO), which optimizes the balance between nurses and foragers in the colony. In addition, we initiated research on the queen and brood chemical communication in which only two pheromones have been identified in the colony.We have demonstrated that EO production by workers varies under different colony environment. EO production can also be modified by stress; honey bees parasitized by the Nosema spp. have abnormally high EO production. In addition, we identified that EO is transmitted from foragers to nurses by contact (cuticle and pollen).For the queen, our results indicate that the queen uses multiple redundant pheromones (QMP and other unknown compounds), that affect wax construction, retinue behaviour and worker ovary inhibition.For the brood we have identified a volatile pheromone E-ß-ocimene produced mostly by the young larvae to inhibit the development of workers ovaries and accelerate workers’behavioural maturation.With these studies we clarify some aspects of what is known about chemical communication in the honey bee colony. Then we try to explain the role of complexity and redundancy of pheromones in the honey bee colony by two theories

Les insectes contribuent à la pollinisation de 70% des espèces cultivées aujourd’hui à travers le monde. Avec l’intensification de l’agriculture au début du XXème siècle, les agriculteurs se sont mis à introduire des colonies d’abeilles mellifères dans leurs cultures entomophiles pour assurer le service de pollinisation. Avec la reconnaissance croissante du rôle majeur joué par les insectes sauvages dans la pollinisation des cultures, le concept de pollinisation intégrée des cultures a récemment vu le jour, encourageant à combiner insectes pollinisateurs introduits et sauvages en adaptant les pratiques agricoles pour assurer une pollinisation durable des cultures. Mais l’introduction d’insectes pollinisateurs d’élevage est une pratique encore très empirique qui manque de références techniques pour pouvoir être mise en œuvre avec précision. L’objectif général de cette thèse était de fournir des éléments pour mettre au point une méthode objective pour définir la charge en unités opérationnelles d’abeilles mellifères à introduire par unité de surface de culture cible pour complémenter la faune pollinisatrice sauvage pour que la pollinisation ne soit pas un facteur de production limitant.Nous avons travaillé sur une lignée mâle fertile et une lignée mâle stérile de colza (Brassica napus L.), les productions de semence hybride dépendant entièrement des insectes pour la pollinisation chez cette espèce. Nous avons pu déterminer (i) le nombre minimum de grains de pollen viables devant être déposés par stigmate pour que la grenaison puisse être complète en fonction de la température, (ii) la durée après anthèse pendant laquelle le pollen doit être déposé sur le stigmate pour que la grenaison puisse être complète en fonction de la température, (iii) la durée pendant laquelle une fleur sécrète du nectar en fonction de la température pour chacune des deux lignées, et (iv) la vitesse de cette sécrétion nectarifère en fonction de la température pour chacune des deux lignées. Nous avons également validé une méthode d’évaluation rapide de la taille des cheptels d’abeilles mellifères introduits dans les cultures entomophiles, couramment utilisée dans certains pays, en tenant compte de la température.A partir de ces éléments, nous avons proposé d’introduire les concepts d’offre et de demande en pollinisation d’une culture cible, afin de quantifier les déficits de pollinisation et le nombre d’insectes pollinisateurs à introduire pour compléter ces déficits. Ces premiers éléments fournissent une base pour construire un modèle mécaniste de gestion intégrée de la pollinisation, pour prédire le nombre d’insectes pollinisateurs à introduire dans une culture étant donné son contexte climatique, paysager et variétal. / Insects contribute to the pollination of 70% of the species cultivated today around the world. With the agriculture intensification in the early twentieth century, farmers began to introduce honey bees colonies into their entomophilous crops to provide pollination service. With the growing recognition of the major role played by wild insects in crop pollination, the concept of integrated crop pollination recently emerged, encouraging the combination of introduced and wild pollinating insects by adapting agricultural practices to ensure sustainable pollination of crops. But the introduction of managed pollinating insects is still an empirical practice that lacks technical references to be implemented with precision. The general objective of this thesis was to provide elements to develop an objective method to define the operational unit load of honey bees to be introduced per unit area of target crop to complement wild pollinating fauna so that pollination is not a limiting factor for production.We worked on a male fertile and a male sterile oilseed rape (Brassica napus L.) lines, hybrid seed productions being entirely dependent on insects for pollination in this species. We were able to determine (i) the minimum number of viable pollen grains to be deposited on stigma so that seed set was complete depending on the temperature, (ii) the duration after anthesis during which the pollen must be deposited on the stigma so that seed set was complete depending on the temperature, (iii) the length of time a flower secretes nectar as a function of temperature for each of the two lines, and (iv) the rate of this nectar secretion as a function of temperature for each of the two lines. We also validated a method for rapid assessment of the size of honey bee stocking rate introduced into entomophilous crops, commonly used in some countries, taking into account temperature.From these elements, we proposed to introduce the concepts of supply and demand in pollination of a target crop, in order to quantify the pollination deficits and the number of pollinating insects to introduce to complete these deficits. These first elements provide a basis for constructing a mechanistic model of integrated pollination management, to predict the number of pollinating insects to be introduced into a crop given its climatic, landscape and varietal context.