O presente trabalho teve como objetivo: 1. Determinar o efeito de diferentes tamanhos de células de cria de operárias (favos novos construídos naturalmente por abelhas Africanizadas e européias e favos velhos) sobre o peso e variabilidade morfológica das abelhas operárias emergentes em colônias de abelhas (Apis mellifera); 2. Examinar a influência das células de operárias de menor tamanho do favo velho em relação às células novas construídas por abelhas Africanizadas e às células de operárias construídas por abelhas européias (italianas e cárnicas) sobre a infestação e reprodução do ácaro Varroa jacobsoni. O trabalho foi todo realizado no Departamento de Genética da FMRP-USP em Ribeirão Preto. Foram utilizadas colônias de abelhas africanizadas do próprio apiário experimental (N=8). Foram usados neste experimento quatro tipos de favos: favo africanizado novo (FAFn), favo italiano novo (FITn), favo cárnico novo (FCAn) e favo velho africanizado (FVE) com as paredes das células engrossadas por efeito de muitas gerações de abelhas emergidas. Um total de três medidas foram feitas nas células de operárias de cada favo: diâmetro da célula (DC), profundidade da célula (PC) e peso da abelha emergente (PA). O volume da célula (VC) foi calculado a partir do DC e da PC. As abelhas, uma vez pesadas, foram posteriormente preservadas em solução de álcool a 70%. As seguintes medidas morfométricas foram tomadas sobre cada abelha individual e sobre a asa anterior direita: Comprimento e Largura total da asa anterior direita. Investigamos os índices de infestação e as taxas de reprodução do ácaro nos quatro tipos de favos com diferentes células de crias de operárias, para verificar possíveis variações na infestação entre os favos estudados. Para as dimensões das células (DC, PC e VC), entre o favo FVE e os novos (FAFn, FITn e FCAn), observou-se de maneira geral que o DC e VC foram as medidas que apresentaram diferenças notáveis entre os diferentes favos. Comparando-se os diâmetros das células de cria entre os favos estudados, percebe-se uma média menor para as células do FVE (4.56 mm) e médias maiores para as células dos favos FITn (5.13 mm) e FCAn (5.27 mm); sendo diferentes estatisticamente (p< 0.001, One-Way ANOVA). Em relação à PC a situação foi inversa, percebe-se que a PC construída pelas operárias a partir da cera alveolada (FITn) foi de 11.62 mm e a PC em favos construídos por operárias cárnicas (FCAn) foi de 11.64 mm, sendo inferiores às do FVE (12.22 mm). As médias dos volumes dos diferentes tipos de alvéolos estudados mostram uma média menor para as células do FVE (220.12 mm3) e médias maiores para os FITn (264.82 mm3) e FCAn (279.59 mm3); sendo diferentes estatisticamente (p< 0.001, One-Way ANOVA). Os resultados indicaram que as abelhas compensaram a menor ou maior largura da célula ao produzir células com maior ou menor profundidade respectivamente. Das asas analisadas, as operárias do FVE apresentaram menor comprimento (9.10 mm), enquanto que esses comprimentos foram bem maiores nas operárias do favo FAFn, FITn e FCAn sendo 9.26 mm, 9.32 mm e 9.32 mm respectivamente. Em relação à largura da asa, encontramos também que as operárias do FVE apresentaram menor largura (3.31 mm), sendo essas medidas maiores nas operárias dos favos novos FAFn, FITn e FCAn (3.43 mm, 3.49 mm e 3.46 mm respectivamente). O comprimento e largura da asa anterior direita das abelhas emergentes diferiram estatisticamente entre os quatro tipos de favos estudados (p= 0.014 e p= 0.003 respectivamente, One-Way ANOVA). Comparando-se o peso médio das operárias ao nascer, entre os diferentes tipos de células de crias do FVE (88.12 mg), FAFn (92.67 mg), FITn (95.82 mg) e FCAn (96.89 mg) percebe-se que ocorre um acréscimo no peso à medida que o tamanho da célula é aumentado. A comparação do peso das operárias mostrou que ocorrem diferenças altamente significantes em nível de 5% de probabilidade entre os diferentes favos de cria (p<0.001, One-way ANOVA). Comparando-se o peso médio das abelhas operárias emergentes infestadas e não infestadas pela varroa, percebe-se que ocorre um forte decréscimo no peso da abelha infestada em 14.9% para o FVE e FAFn. Os índices de infestação da varroa verificados nos diferentes tamanhos de células de operárias diferiram estatisticamente entre os quatro tipos de favos (x2 = 41.122, p< 0.001). A infestação média do ácaro foi maior em células de cria do FVE que em células do favo FAFn que apresentou menor índice de infestação (20.6 ± 6.4% vs 10.4 ± 4.2% respectivamente). Esses índices médios diferiram estatisticamente (p< 0.001). Houve maior número de fêmeas adultas do ácaro em células do FVE, que apresentou menor diâmetro e menor volume da célula, comparado com as células dos favos novos de maiores tamanhos (FAFn, FITn e FCAn). Obtiveram-se taxas de reprodução total de 1.28, 0.98, 1.19 e 1.58 para os favos FVE, FAFn, FITn e FCAn respectivamente, quando computadas todas as varroas adultas originais. Essas taxas de reprodução total do ácaro não apresentaram diferenças significativas entre si (p= 0.074, One-Way ANOVA). As células do FVE atraíram mais varroa em relação às células dos favos novos, apesar de que as células do FVE tiveram um diâmetro menor. Embora o tamanho da célula seja importante, característica inerente à larva, ao favo ou ao alimento nas células de crias do FVE poderiam ter uma importante influência de atração ao ácaro varroa. / The purposes of the present work were: 1. To determine the effect of different sizes of worker brood cells in new and old combs built naturally by Africanized and European bees on the weight and morphology of emerging worker honey bees in africanized honey bee colonies (Apis mellifera). 2. To examine the influence of the smaller worker cells of the old comb in relation to new cells built by Africanized bees and larger new cells built by European races on the infestation and reproduction rates of the mite Varroa jacobsoni. We used eight Africanized honey bee colonies. Four types (sizes) of brood combs were placed in each colony: new Africanized comb (NAC), new Italian comb (NIC), new Carniolan comb (NCC) and old Africanized brood comb (OC), that had thickened brood cell walls and relatively small comb cells. Three measurements were made for 80-100 worker brood cells in each comb: Cell width (CW), cell depth (CD), and emerging bee weight (BW). Cell volume (CV) was calculated from CW and CD. The bees were weighed and then preserved in a 70% ethanol. The length and width of the right fore wing were measured for each individual bee. We studied the infestation and the reproduction rates of the mite in four types of combs with different kinds of worker brood cells, to verify possible variations in the infestation by varroa. The comb cell measurements CW and CV differed significantly among the various types of combs. We found that the OC cells (4.56 mm) had a significantly (p <0.001, One-Way ANOVA) smaller diameter than the NIC cells (5.13 mm) and NCC cells (5.27 mm). An opposite trend was found for cell depth, which was significantly smaller in NIC (11.62 mm) and NCC (11.64 mm) than OC (12.22 mm). For the different types of brood combs, the cell depth increased as the cell diameter decreased, in other words, the bees compensated the reduced cell width by producing deeper cells to accommodate the developing bee. The OC cells had a significantly smaller volume (220.12 mm3) than the NIC cells (264.82 mm3) and NCC cells (279.59 mm3) (p< 0.001, One-Way ANOVA). The worker bees reared in OC had a significantly shorter fore wing (9.10 mm) than in the new worker combs NAC (9.26 mm), NIC (9.32 mm) and NCC (9.32 mm). Fore wing width, was also significantly smaller for workers from OC combs (3.31 mm), than from NAC, NIC and NCC combs (3.43 mm, 3.49 mm and 3.46 mm, respectively). The right fore wing length and width of the emerging workers bees differed significantly among the four types of combs (p = 0.014 and p = 0.003 respectively, One-Way ANOVA). In summary, the wing size of the emerging worker bees increased with increasing volume and diameter of the comb cell. The bees from the OC comb had significantly smaller fore wings (both length and width) than those from NAC comb (p< 0.05, Tukey Test). The same was true for workers from NIC and NCC combs. The mean weights of the worker bees among the different types of brood combs were: 88.12 mg, 92.67 mg, 95.82 mg and 96.89 mg for OC, NAC, NIC and NCC respectively. There was an increment in bee weight as the diameter of the cell increased. Bee weights from the different types of combs were significantly different (p< 0.001, One-way ANOVA). Bees infested during the brood phase with the mite Varroa jacobsoni weighed on average 14.9% less than uninfested bees. The varroa infestation rates differed significantly among the four types of combs (x2= 41.122, p< 0.001). The varroa infestation was significantly (p< 0.001) higher in OC cells (20.6±6.4%) than in NAC cells (10.4±4.2%) and NIC cells (14.7%, p= 0.003). The mean infestation rate in NIC cells did not differ significantly (p= 0.094) from the infestation rate in NCC cells (19.2%). The infestation rate in OC cells was not significantly different from that of NCC cells (p= 0.347). Within each colony the OC comb was generally twice as infested with varroa as NAC. The total varroa reproduction rate (TRR) was 1.28, 0.98, 1.19 and 1.58 for the OC, NAC, NIC and NCC combs respectively, when we included all the original adult females (p= 0.074, One-way ANOVA). The OC cells attracted more varroa than new comb cells, even though the OC cells had a smaller diameter. Though cell size is important, characteristics inherent to the larvae, to the comb or the food in the OC worker cells apparently have an overriding influence on attractiveness to the varroa mite.

Cell replication and division are central to the proliferation of life, and have implications for normal growth and development as well as disease state. Assembly of a complete picture of the systems which control this process requires identification of individual genetic components, but the identity and complete sequence of events that trigger initiation of cell division, at a point called START in yeast, remain unknown. Here, we evaluated panels of non-essential single gene deletion strains and tested the effects of FDA-approved drugs on cell-cycle progression, using flow cytometry to detect altered DNA content. Previous studies relied mainly on cell size changes to systematically identify genes required for the timely completion of START. This analysis revealed that most gene deletions that altered cell-cycle progression did not change cell size. Our results highlight a strong requirement for ribosomal biogenesis and protein synthesis for initiation of cell division. We also identified numerous factors that have not been previously implicated in cell-cycle control mechanisms. We found that cystathionine-beta-synthase (CBS) advances START in two ways: by promoting cell growth, which requires CBS's catalytic activity, and by a separate function which does not require that activity. CBS defects cause disease in humans, and in animals CBS has vital, non-catalytic, unknown roles. Hence, our results may be relevant for human biology. Screening chemical libraries to identify compounds that affect overall cell proliferation is common. However, it is generally not known whether the compounds tested alter the timing of particular cell-cycle transitions. Our approach revealed strong cell-cycle effects of several commonly used pharmaceuticals. We show that the antilipemic gemfibrozil delays initiation of DNA replication, while cells treated with the antidepressant fluoxetine severely delay progression through mitosis. We discovered a strong suppressive interaction between gemfibrozil and fluoxetine. The novel interaction between gemfibrozil and fluoxetine suggests that identifying and combining drugs that show cell-cycle effects might streamline identification of drug combinations with a pronounced impact on cell proliferation. Our studies not only transform our view of START, but also expand the repertoire of genetic and chemical means to modulate the eukaryotic cell cycle.

The coordination between cell growth and division is a highly regulated process that is intimately linked to the cell cycle. Efforts to identify an independent mechanism that measures cell size have been unsuccessful. Instead, we propose that size control is an intrinsic function of the basic cell cycle machinery. My work shows that in the fission yeast Schizosaccharomyces pombe Cdc25 accumulates in a size dependent manner. This accumulation of Cdc25 occurs over a large range of cell sizes. Additionally, experiments with short pulses of cycloheximide have shown that Cdc25 is an inherently unstable protein that quickly returns to a size dependent equilibrium in the cell suggesting that Cdc25 concentration is dependent on size and not time. Thus, Cdc25 can act as a sizer for the cell. However, cells are still viable when Cdc25 is constitutively expressed suggesting that there is another sizer in the case that Cdc25 expression is compromised. Cdc13 is a likely candidate due to the similar characteristics to Cdc25 and the ability to activate Cdc2. Cdc13 accumulates during the cell cycle in a manner similar to Cdc25. I show that in the absence of Cdc2 tyrosine phosphorylation, the cell size is sensitive to Cdc13 activity showing that Cdc13 accumulation can determine when cells enter mitosis. These results suggest a two sizer model where Cdc25 is the main sizer with Cdc13 acting as a backup sizer in the event of Cdc25 expression is compromised. Additionally, in the absence of Cdc2 phosphorylation by the kinases Wee1 and Mik1, mitotic entry is regulated by the activity of Cdc2. In the absence of Cdc2 phosphorylation, this activity is regulated by binding of cyclins to Cdc2. Under these circumstances, the activity of Cdc13 can regulate mitotic entry provide further evidence that Cdc13 could be a sizer of the cell in the case where Cdc25 expression is compromised. The results I present in this dissertation provide the groundwork for understanding how cells regulate size and how this size regulation affects cell cycle control in S. pombe . The results show how the intrinsic cell cycle machinery can act as a sizer for the G2/M transition in S. pombe . Interestingly, this mitotic commitment pathway is well conserved suggesting a general solution for size control in eukaryotes at the G2/M transition. Understanding the mechanism of how protein concentration is regulated in a size dependent manner will give much needed insight into how cells control size. Elucidating the mechanism for size control will capitalize on decades of research and deepen our understanding of basic cell biology.

A complex network of genes and proteins governs the robust progression through cell cycles in the presence of inevitable noise. Stochastic modeling is viewed as a key paradigm to study the effects of intrinsic and extrinsic noise on the dynamics of biochemical networks. A detailed quantitative description of such complex and multiscale networks via stochastic modeling poses several challenges. First, stochastic models generally require extensive computations, particularly when applied to large networks. Second, the accuracy of stochastic models is highly dependent on the quality of the parameter estimation based on experimental observations. The goal of this dissertation is to address these problems by developing new efficient methods for modeling and simulation of stochastic effects in biochemical systems. Particularly, a hybrid stochastic model is developed to represent a detailed molecular mechanism of cell cycle control in budding yeast cells. In a single multiscale model, the proposed hybrid approach combines the advantages of two regimes: 1) the computational efficiency of a deterministic approach, and 2) the accuracy of stochastic simulations. The results show that this hybrid stochastic model achieves high computational efficiency while generating simulation results that match very well with published experimental measurements. Furthermore, a new hierarchical deep classification (HDC) algorithm is developed to address the parameter estimation problem in a monomolecular system. The HDC algorithm adopts a neural network that, via multiple hierarchical search steps, finds reasonably accurate ranges for the model parameters. To train the neural network in the presence of experimental data scarcity, the proposed method leverages the domain knowledge from stochastic simulations to generate labeled training data. The results show that the proposed HDC algorithm yields accurate ranges for the model parameters and highlight the potentials of model-free learning for parameter estimation in stochastic modeling of complex biochemical networks. / Doctor of Philosophy / Cell cycle is a process in which a growing cell replicates its DNA and divides into two cells. Progression through the cell cycle is regulated by complex interactions between networks of genes, transcripts, and proteins. These interactions inside the confined volume of a cell are subject to inherent noise. To provide a quantitative description of the cell cycle, several deterministic and stochastic models have been developed. However, deterministic models cannot capture the intrinsic noise. In addition, stochastic modeling poses the following challenges. First, stochastic models generally require extensive computations, particularly when applied to large networks. Second, the accuracy of stochastic models is highly dependent on the accuracy of the estimated model parameters. The goal of this dissertation is to address these challenges by developing new efficient methods for modeling and simulation of stochastic effects in biochemical networks. The results show that the proposed hybrid model that combines stochastic and deterministic modeling approaches can achieve high computational efficiency while generating accurate simulation results. Moreover, a new machine learning-based method is developed to address the parameter estimation problem in biochemical systems. The results show that the proposed method yields accurate ranges for the model parameters and highlight the potentials of model-free learning for parameter estimation in stochastic modeling of complex biochemical networks.

L’obésité abdominale est associée à de nombreuses complications métaboliques, telles que la résistance à l’insuline, le diabète de type 2 et les maladies cardiovasculaires. Récemment, il a été suggéré que ces anomalies métaboliques sont étroitement associées à la taille des adipocytes, cellules constitutives du tissu adipeux. En effet, plusieurs travaux suggèrent que plus les adipocytes sont gros, plus ils produisent des adipokines pro-inflammatoires, responsables de l’inflammation chronique associée à l’obésité. Dans ce contexte, le but de ce travail de thèse était, dans un premier temps, d’établir les répartitions en fréquences de tailles des adipocytes dans différentes situations physiologiques et physiopathologiques et dans différents dépôts adipeux à l’aide du Multisizer IV Coulter counter et dans un second temps de corréler la taille des adipocytes à leurs fonctions physiologiques. D’une part, nous avons montré que quels que soient les dépôts adipeux, les répartitions en fréquences de tailles des adipocytes ont toutes le même profil, elles sont bimodales avec une population de petits adipocytes (diamètre < nadir) et une population de gros adipocytes (diamètre > nadir). La privation en insuline (diabète de type I) entraînant une diminution de 60% de la masse du tissu adipeux, altére profondément la répartition bimodale en fréquences de tailles des adipocytes. La supplémentation en insuline de ces animaux diabétiques restaure la cellularité du tissu adipeux et la répartition en fréquences de tailles des adipocytes, suggérant un rôle régulateur majeur de l’insuline sur ces paramètres. La restriction calorique partielle, nous a permis de mettre en évidence un phénomène d’hystérésis dans certains tissus adipeux. De plus, à partir des données de restriction calorique prolongée il a été possible d’établir un modèle prédisant la cinétique des changements de tailles des adipocytes et de la répartition en fréquences de tailles. D’autre part, après avoir séparé les adipocytes en deux populations : les gros (diamètre > 50 µm) et les petits adipocytes (diamètre < 50 µm) nous avons montré que les petits adipocytes sont plus sensibles à l’insuline que les gros. Nous avons aussi constaté que les gros adipocytes sont plus lipolytiques que les petits adipocytes. Ces données sont en accord avec le modèle établi montrant que les échanges avec le micro-environnement tissulaire sont surtout dépendants de la surface des membranes cellulaires. Ainsi, nos résultats mettent en évidence que si la quantité de tissu adipeux est importante, sa qualité, dont la répartition en fréquences de tailles des adipocytes, est également importante et pourrait servir de paramètre prédictif du développement des désordres métaboliques. / Abdominal obesity is associated with several metabolic complications such as insulin resistance, type 2 diabetes and cardiovascular diseases. Recently, it has been suggested that these metabolic abnormalities are closely related to the size of adipocytes, cells constituting adipose tissue. Indeed, numerous studies suggested that the more adipocytes are larger, the more they produce pro-inflammatory adipokines which are responsible for obesity-associated chronic inflammation. In this context, the aim of this work was, in the first time, to establish the size frequency distributions of adipocytes in different physiological and pathological situations and in different fat depots using the Coulter counter Multisizer IV, and in the second time to correlate the size of the adipocytes to their physiological functions. On the one hand, we have shown that, all adipocyte size frequency distributions have the same profile regardless of fat depots, they are bimodal with both the population of small adipocytes (diameter < nadir) and the population of large adipocytes (diameter > nadir). Deprivation of insulin (type I diabetes) resulting in a decrease of 60% of adipose tissue mass, profoundly alters the bimodal distribution of adipocyte size frequency. Insulin supplementation of these diabetic animals restores cellularity of adipose tissue and the size-frequency distribution of adipocytes, suggesting a major regulatory role of insulin on these parameters. Partial caloric restriction has allowed us to a hysteresis phenomenon in some adipose tissues. In addition, following data from extended caloric restriction it has been possible to develop a model predicting the kinetic of changes concerning both the size of adipocytes and the frequency distribution. On the other hand, after separating the adipocytes in two populations: large (diameter > 50 microns) and small adipocytes (diameter < 50 microns), we have shown that small adipocytes are more insulin-sensitive than large ones. We also observed that larger adipocytes are more lipolytic than smaller ones. These data are in agreement with the established model showing that the interactions with the tissue microenvironment are mainly dependent on the surface of cell membranes. Thus, our results show that if the amount of adipose tissue is important, the quality which noticed by the adipocyte size frequency distributions is also important and could be used as a marker to predict the development of metabolic disorders.

La cellule est l’élément fondamental de la vie. Plus d’une vingtaine de trillions de cellules forment les organes et tissus de notre corps. Ces cellules sont de taille spécifique puisqu’elles ont des fonctions précises au sein de leur tissu respectif. Dans la plupart des cas, les cellules doivent proliférer en se divisant pour se renouveler et ainsi assurer le bon fonctionnement d’un organisme. La dernière étape de la division cellulaire, la cytokinèse, est exécutée par la contraction d’un anneau contractile d’actomyosine, nécessaire pour effectuer la séparation physique de la cellule en deux cellules filles. La première partie des travaux décrits dans cet ouvrage portent sur la caractérisation de la cytokinèse en utilisant, comme modèle in vivo, les cellules précurseur de la vulve (VPCs) du nématode C. elegans. Notre étude révèle que plusieurs aspects de l’anneau d’actomyosine s’ajustent en fonction de la taille de la cellule. Entre autres, la largeur de l’anneau contractile, juste avant sa constriction, s’ajuste en fonction de la longueur des VPCs. De plus, la rapidité avec laquelle l’anneau se contracte dépend de la circonférence de la cellule. Ces découvertes nous ont amené à nous demander comment la cellule régule sa taille? Les cellules en prolifération maintiennent leur taille en homéostasie en équilibrant leur taux de croissance et de division cellulaire. Afin d’interroger les gènes impliqués dans le maintien de la taille cellulaire du mammifère, nous avons utilisé la technologie CRISPR/Cas9, afin d’éliminer par délétion tous les gènes humains, à raison d’un par cellule, pour identifier ceux qui causent une augmentation ou une diminution de la taille cellulaire. Cette étude nous a permis d’identifier plusieurs gènes déjà connus régulant la croissance cellulaire. De plus, nous avons identifié un groupe de gènes, incluant TLE4 un corépresseur de la transcription que nous avons caractérisé, n’ayant jamais été associé avec une fonction de contrôle de la taille cellulaire chez les mammifères. En somme, nos travaux ont contribué à l’approfondissement des connaissances sur la division cellulaire, plus précisément la cytokinèse, et des gènes impliqués dans le maintien de la taille cellulaire. Une meilleure connaissance du fonctionnement de ces deux évènements cellulaires est essentielle puisque leur dérégulation peut entrainer plusieurs pathologies, incluant le cancer. / Cells are the fundamental building blocks of life. The human body contains over twenty trillion cells that make up the different tissues and organs of our bodies. Cells within organs are of specific sizes to perform their specialized functions. In most cases, these cells must divide to proliferate and replenish the population of cells essential for proper organism function. The final stage of cellular division, termed cytokinesis, entails the assembly and constriction of a contractile ring that drives the dramatic cell shape changes required to physically partition the cell into two daughter cells. The first part of the work presented in this thesis addresses the characterization of cytokinesis in the epithelial vulval precursor cells (VPCs) of the nematode worm C. elegans. This study principally revealed that several aspects of cytokinesis scale with cell size. For instance, I observed that the breadth of the actomyosin ring scaled with VPC length. In addition, the speed of contractile ring constriction scaled with the circumference of VPCs. These scaling events raised the more general question as to how cells regulate their size. Proliferating cells attain cell size homeostasis by balancing cell growth and cell division. In order to define the molecular regulators of size in human cells a genome-wide approach was taken. Recently developed CRISPR/Cas9 technology was used to perform the first pooled knockout screens for human cell size regulators in the NALM-6 pre-B lymphocytic cell line. These screens revealed many genes that affect the size of NALM-6 cells, a number of which were previously known to be involved in growth regulation. In addition, these screens revealed the identity of many genes with no previously established functions associated with cell size regulation. Amongst the previously unknown regulators, I characterized the function of a co-repressor of transcription, TLE4, which I showed functions as a regulator of the B-cell lineage. This work contributes to the knowledge of the mechanics of cytokinesis in C. elegans epithelial cells and of the genes that coordinate cell size in humans. These results provide insights into cell growth and division in normal cells and how these processes may be perturbed in cancer and other diseases.

This thesis deals with biodiversity-productivity relationship in desmid communities. Biodiversity is found to be changing globally. The biodiversity-productivity relationship is therefore an important research topic. Three aspects of biodiversity are thought to play an important role: species richness, functional diversity and phylogenetic diversity. It is known that in general, productivity is positively correlated with diversity. Interactions between different metrics of biodiversity are known less. Existing studies have shown that these interactions might be present. In general, biodiversity-productivity studies were mostly focused on plants. Less is known about other organisms, including algae. In this work I explore the relationship between overyielding and functional or phylogenetic diversity on a species richness gradient of desmid communities. I conducted an artificial biodiversity- ecosystem functioning experiment using combinations of two to 12 desmid species. Communities differed in the diversity aspects. I had measured the biomass growth. For the analysis, I have used the overyielding index, which is based on a comparison of a polyculture production with the production expected based on monoculture yields. The relationship of overyielding on functional diversity depended on species...

Les cellules sont la plus petite forme de vie individuelle qui forme un organisme. La structure et la santé de tous les organismes est essentiellement définie par le nombre, le type et la taille de leurs cellules. Composé d'environ 30 trillions de cellules, l'homme possède des cellules aux fonctions et aux tailles remarquablement variées, allant d'un neurone pouvant atteindre un mètre à une cellule lymphoïde d'environ 16 µm de diamètre. Il est connu que la taille est fondamentalement l'équilibre entre la croissance cellulaire et la division cellulaire. Néanmoins, les questions sur les réseaux moléculaires qui contrôlent et déterminent le maintien de la taille optimale des cellules restent à déchiffrer. D'innombrables travaux ont caractérisé mTORC1 comme une voie régulatrice majeure de la croissance cellulaire jouant un rôle central, intégrant des stimuli intra et extracellulaires. Ce travail porte sur l'investigation et la caractérisation des acteurs moléculaires et des processus qui orchestrent la taille des cellules humaine déterminées par l'épistase chimique. J'ai entrepris une bibliothèque CRISPR / Cas9 à inactivation prolongée (EKO) dans NALM-6 (lignée cellulaire de lymphome pré-B), suivie d'un fractionnement de la taille des cellules par élutriation à contre-courant en présence de rapamycine (inhibiteur de mTOR), et comparé aux données non publiées données du laboratoire utilisant les mêmes méthodes sans rapamycine. Cette analyse de l'étude indique que dans le contexte amont de mTOR, la perte de gènes liés à la détection des nutriments entraîne une perte de taille en présence d'inhibition de mTOR. En outre, plusieurs knockouts géniques dans la biogenèse des ribosomes et l'homéostasie du calcium ont conduit à une perte ou un gain de taille, montrant un rôle pivot possible de ces processus dans le contrôle de la taille des cellules d'une manière dépendante de mTOR. Ce travail a fourni des informations sur les gènes et réseaux connus et inconnus qui peuvent réguler la taille des cellules d'une manière dépendante de mTOR. Ces résultats doivent être validés et approfondis. / All organisms are essentially structured and fitness defined by cell number, type and size. Composed of around 30 trillion cells, humans have cells with remarkably varied functions and size, ranging from a neuron that can reach one meter in length to a lymphoid cell that is around 16 μm in diameter. At a fundamental level, size is determined by the balance between cell growth and cell division. The molecular networks that control and maintain optimal cell size are yet to be deciphered. The mTORC1 pathway is a major regulator of cell growth that plays a central role in integrating intra- and extra-cellular stimuli. This study addresses the investigation and characterization of the molecular players and processes that orchestrate cell size in human cells, as determined by chemical-genetic size screens and epistasis analysis. I undertook a CRISPR/Cas9 extended-knockout (EKO) genome-wide library screen in the NALM-6 pre-B lymphoma cell line, followed by cell size fractionation by counter flow elutriation in the presence of the mTOR inhibitor rapamycin, and compared the screen data to a similar screen performed in the absence of rapamycin. The analysis indicates that upstream of mTOR, the loss of genes that are related to nutrient sensing, results in size changes in the presence of mTOR inhibition. Also, several gene knockouts in ribosome biogenesis and calcium homeostasis led to size alterations, suggesting a possible a pivotal role of these processes in cell size control in a mTOR-dependent fashion. This study provides insights into the genetic networks that regulate cell size in a mTOR-dependent fashion and establishes new hypotheses for future experimental tests.

An artificial neural network (ANN) is used to model nonlinear, large deformation plastic behavior of a material. This ANN model establishes a relationship between flow stress and dislocation structure content. The density of geometrically necessary dislocations (GNDs) was calculated based on analysis of local lattice curvature evolution. The model includes essential statistical measures extracted from the distributions of dislocation microstructures, including substructure cell size, wall thickness, and GND density as the input variables to the ANN model. The model was able to successfully predict the flow stress of aluminum alloy 6022 as a function of its dislocation structure content. Furthermore, a sensitivity analysis was performed to identify the significance of individual dislocation parameters on the flow stress. The results show that an ANN model can be used to calibrate and predict inelastic material properties that are often cumbersome to model with rigorous dislocation-based plasticity models.

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