Knowledge of the dissociation constants of the ionizable protons of weak acids in aqueous media is of fundamental importance in many areas of chemistry and biochemistry. The pKa value, or equilibrium dissociation constant, of a molecule determines the relative concentration of its protonated and deprotonated forms at a specified pH and is therefore an important descriptor of its chemical reactivity. Considerable efforts have been devoted to the determination of pKa values by different experimental techniques. Although in most cases the determination of pKa values from experimental is straightforward, there are situations where interpretation is difficult and the results ambiguous. It is, therefore, not surprising that the capability to provide accurate estimates of the pKa value has been a central goal in theoretical chemistry and there has been a large effort in developing methodologies for predicting pKa values for a variety of chemical systems by differing quantum chemical techniques. A prediction accuracy within 0.5 pKa units of experiment is the desirable level of accuracy. This is a non-trivial exercise, for an error of 1 kcal/mol in estimates of the free energy value would result in an error of 0.74 pKa units. In this thesis ab initio Car-Parrinello molecular dynamics (CPMD) has been used for investigating the Brϕnsted acid-base chemistry of weak acids in aqueous solution. A key issue in any dissociation event is how the solvating water molecules arrange themselves spatially and dynamically around the neutral and dissociated acid molecule. Ab initio methods have the advantage that all solvent water molecules can, in principle, be con- sidered explicitly. One of the factors that has inhibited the widespread use of ab initio MD methods to study the dissociation reaction is that dissociation of weak acids are rare events that require extremely long simulation times before one is observed. The metady- namics formalism provides a solution to this conundrum by preventing the system from revisiting regions of configuration space where it has been in the past. The formalism allows the system to escape the free-energy minima by biasing the dynamics with a history dependent potential (or force) that acts on select degrees of freedom, referred to as collective variables. The bias potentials, modeled by repulsive inverted Gaussians that are dropped during propagation, drive the system out of any free-energy minima and allow it to explore the configurational space by a relatively quick and efficient sampling. The the- sis deals with a detailed investigation of the Brϕnsted acid-base chemistry of weak acids in aqueous solutions by the CPMD-metadynamics procedure. In Chapter 1, current approaches for the theoretical estimation of pKa values are summarized while in Chapter 2 the simulation methodology and the metadynamics sampling techniques used in this study are described. The potential of the CPMD-metadynamics procedure to provide estimates of the acid dissociation constant (pKa) is explored in Chapter 3, using acetic acid as a test sys- tem. Using the bond-distance dependent coordination number of protons bound to the dissociating carboxylic groups as the collective variable, the free-energy profile for the dissociation reaction of acetic acid in water was computed. Convergence of the free-energy profiles and barriers for the simulations parameters is demonstrated. The free-energy profiles exhibit two distinct minima corresponding to the dissociated and neutral states of the acid and the deterrence in their values provides the estimate for pKa. The estimated value of pKa for acetic acid from the simulations, 4.80, is in good agreement with the experiment at value of 4.76. It is shown that the good agreement with experiment is a consequence of the cancellation of errors, as the pKa values are computed as the divergence in the free energy values at the minima corresponding to the neutral and dissociated state. The chapter further explores the critical factors required for obtaining accurate estimates of the pKa values by the CPMD-metadynamics procedure. It is shown that having water molecules sufficient to complete three hydration shells as well as maintaining water density in the simulation cell as close to unity is important. In Chapter 4, the CPMD-metadynamics procedure described in Chapter-3 has been used to investigate the dissociation of a series of weak organic acids in aqueous solutions. The acids studied were chosen to highlight some of the major factors that influence the dissociation constant. These include the influence of the inductive effect, the stabilization of the dissociated anion by H-bonding as well as the presence of multiple ionizable groups. The acids investigated were aliphatic carboxylic acids, chlorine-substituted carboxylic acids, cis- and trans-butenedioic, the isomers of hydroxybenzoic acid and ophthalmic acids and its isomers. It was found that in each of these examples the CPMD-metadynamics procedure correctly estimates the pKa values, indicating that the formulism is capable of capturing these influences and equally importantly indicating that the cancellation of errors is indeed universal. Further, it is shown that the procedure can provide accurate estimates of the successive pKa values of polypro tic acids as well as the subtle difference in their values for different isomers of the acid molecule. Changes in protonation-deprotonation of amino acid residues in proteins play a key role in many biological processes and pathways. It is shown that CPMD simulations in conjunction with metadynamics calculations of the free energy profile of the protonation- deprotonation reaction can provide estimates of the multiple pKa values of the 20 canonical α-amino acids in aqueous solutions in good agreement with experiment (Chapter 5). The distance-dependent coordination number of the protons bound to the hydroxyl oxygen of the carboxylic and the amine groups is used as the collective variable to explore the free energy profiles of the Brϕnsted acid-base chemistry of amino acids in aqueous solutions. Water molecules, sufficient to complete three hydration shells surrounding the acid molecule were included explicitly in the computation procedure. The method works equally well for amino acids with neutral, acidic and basic side chains and provides estimates of the multiple pKa values with a mean relative error with respect to experimental results, of 0.2 pKa units. The tripeptide Glutathione (GSH) is one of the most abundant peptides and the major repository for non-protein sulfur in both animal and plant cells. It plays a critical role in intracellular oxidative stress management by the reversible formation of glutathione disulfide with the thioldisulfide pair acting as a redox buffer. The state of charge of the ionizable groups of GSH can influences the redox couple and hence the pKa value of the cysteine residue of GSH is critical to its functioning. In Chapter 6, it has been reported that ab initio Car-Parrinello Molecular Dynamics simulations of glutathione solvated by 200 water molecules, all of which are considered in the simulation. It is shown that the free-energy landscape for the protonation - deprotonation reaction of the cysteine residue of GSH computed using metadynamics sampling provides accurate estimates of the pKa and correctly predicts the shift in the dissociation constant values as compared to the isolated cysteine amino acid. The dissociation constants of weak acids are commonly determined from pH-titration curves. For simple acids the determination of the pKa from the titration curves using the Henderson-Hasselbalch equation is relatively straightforward. There are situations, however, especially in polyprotic acids with closely spaced dissociation constants, where titration curves do not exhibit clear inflexion and equivalence stages and consequently the estimation of multiple pKa values from a single titration curve is no longer straightfor- ward resulting in uncertainties in the determined pKa values. In Chapter 7, the multiple dissociation constant of the hexapeptide glutathione disulfide (GSSG) with six ionizable groups and six associated dissociation constants has been investigated. The six pKa values of GSSG were estimated using the CPMD-metadynamics procedure from the free-energy profiles for each dissociation reaction computed using the appropriate collective variable. The six pKa values of GSSG were estimated and the theoretical pH-titration curve was then compared with the experimentally measured pH-titration curve and found to be in excellent agreement. The object of the exercise was to establish whether interpretation of pH-titration curves of complex molecules with multiple ionizable groups could be facilitated using results of ab initio molecular dynamics simulations.

In 1990, Richard Jorgensen’s lab initiated a study to test if they could create a more vivid color petunia (Napoli et al. 1990). Their plan was to transform plants with the chalcone synthase transgene––the predicted rate limiting factor in the production of purple pigmentation. Much to their surprise, the transgenic plants, as well as their progeny, displayed a great reduction in pigmentation. This loss of endogenous function was termed “cosuppression” and it was thought that sequence-specific repression resulted from over-expression of the homologous transgene sequence. In 1998, Andrew Fire and Craig Mello described a phenomenon in which double stranded RNA (dsRNA) can trigger silencing of cognate sequences when injected into the nematode, Caenorhabditis elegans (Fire et al. 1998). This data explained observations seen years earlier by other worm researchers, and suggested that repression of pigmentation in plants was caused by a dsRNA-intermediate (Guo and Kemphues 1995; Napoli et al. 1990). The phenomenon––which soon after was coined RNA interference (RNAi)––was soon discovered to be a post-transcriptional surveillance system in plants and animals to remove foreign nucleic acids.

Estudos sugerem que a presença de células metastáticas ocultas em medula óssea pode ser fator prognóstico em câncer de mama. Além disso, é possível que um perfil gênico tumoral específico, caracterizado por repressão da expressão gênica, esteja associado à detecção de células tumorais na medula óssea. O silenciamento de genes é controlado pela desacetilação de histonas e metilação de DNA, esta última catalisada por enzimas DNA metil transferases. Outro alvo de metil-transferases são as histonas, e histona H3 quando sofre metilação em lisina 9, gera sítio de ligação a proteínas HP1 (Heterocromatin protein-1 ou cromobox). Membros da família HP1 (HP1Hsalfa, HP1Hsbeta e HP1HsY) participam da formação da heterocromatina e da regulação da expressão de genes. Logo, nosso objetivo foi determinar no tumor primário de mama, a expressão de HP1Hsalfa, HP1Hsbeta e HP1Hsy , que participam da repressão gênica, em relação à presença ou ausência de células metastáticas ocultas na medula óssea. Neste estudo foram incluídas 37 pacientes de forma prospectiva, atendidas no Instituto Brasileiro de Controle do Câncer (IBCC) no período de junho de 2004 a julho de 2005, com diagnóstico histopatológico de carcinoma invasivo de mama, estádio clínico (EC) I (16,2%), II (51,4%) ou III (32,4%), segundo a classificação patológica. A idade mediana das pacientes foi 63 anos (41 a 90) e 62.2% delas encontravam-se na pós-menopausa, sendo que 24.3% relatava história familiar para câncer de mama. O tipo histológico predominante foi carcinoma ductal invasivo (89.2% dos casos), sendo, o restante, representado por carcinoma lobular invasivo (10.8%). Foram coletadas amostras de tumor primário de mama e de aspirado de medula óssea de cada paciente. A presença de células metastáticas ocultas (CMO) na medula óssea (MO) foi detectada através da expressão de citoqueratina 19 (CK19) pelo método de nested RT-PCR. A expressão relativa dos genes HP1Hsalfa, HP1Hsbeta e HP1Hsy foi determinada no tumor primário, usando-se a técnica de RT-PCR em tempo real. Presença de CMO foi detectada na MO de 20 pacientes (54.1%). Não observamos diferença na expressão de HP1Hs? (1,93 ± 2,25 MO- vs 3,84 ± 5,53 MO+), HP1Hs? (6,74 ± 6,31 MO- vs 6,49 ± 5,86 MO+) e HP1Hs? (24,58 ± 11,14 MO- vs 24,91 ± 15,88 MO+) entre as amostras tumorais de pacientes com presença (MO+) ou ausência (MO-) de micrometástase medular. Também não observamos variação da expressão de genes HP1 em relação ao comprometimento linfonodal, dimensão e grau histológico do tumor, expressão tumoral de receptores de estrógeno e estado menopausal da paciente. A expressão de HP1Hsalfa em tumores de pacientes com câncer de mama ERBB2 negativos, entretanto, foi maior do que em tumores ERBB2 positivos. Nossos dados indicam que em tumores de mama, a expressão de HP1Hsalfa, HP1Hsbeta e HP1Hsy não parece se associar à presença de células ocultas em medula óssea / Studies suggest that the presence of occult metastatic cells (OMC) in the bone marrow (BM) may be a prognostic factor in breast cancer. Besides, it is possible that a specific tumor gene profile, characterized by repression of gene expression, may be associated to the presence of tumoral cells in the bone marrow. Gene silencing is controlled by histone deacetylation and DNA methylation, the last one catalized by enzymes DNA methyltransferases (DNMTs). Histones are another target of methyltransferases, and methylation of histone H3 on lysine-9 generate a binding site for HP1 proteins (Heterocromatin protein-1 or chromobox). Members of the HP1 family (HP1Hsalfa, HP1Hsbeta e HP1Hsy) take part in heterochromatin formation and gene expression regulation. Hence, our aim was to determine in the primary tumor of the breast, the expression of HP1Hsalfa, HP1Hsbeta e HP1Hsy, which participate in gene repression, in the presence or absence of occult metastatic cells in the bone marrow. In this study, 37 patients treated at Instituto Brasileiro de Controle do Câncer, from June 2004 to July 2005, with invasive breast cancer histopathologically confirmed, pathological clinical stages I (16,2%), II (51,4%) or III (32,4), were included. The median age of the patients was 63 years (41 to 90), 62.2% were post-menopausal and 24.3% reported family history of breast cancer. Invasive ductal carcinoma was diagnosed in most patients (89.2%), and invasive lobular carcinoma was detected in the other patients (10.8%). Tumor samples and bone marrow aspirates were obtained from each patient. The presence of CMO in BM was detected by keratin-19 (CK19) expression by nested RT-PCR. The relative expression of the genes HP1Hsalfa, HP1Hsbeta e HP1Hsy was determined by real-time RT-PCR. Occult metastatic cells (OMC) in BM were detected in 20 patients (54.1%). No differences were observed in the expression of HP1Hs? (1,93 ± 2,25 BM- vs 3,84 ± 5,53 BM+), HP1Hsalfa (6,74 ± 6,31 BM- vs 6,49 ± 5,86 BM+) and HP1Hsbeta (24,58 ± 11,14 BM- vs 24,91 ± 15,88 BM+) between tumor samples of BM+ patients and BM- patients. Variations of HP1 gene expression were neither observed according to lymph node involvement, tumor size, histological grade, estrogen receptor status and menopausal status. However, HP1Hsbeta expression in ERBB2-negative tumors was higher than in ERBB2-positive tumors. Our data indicate that in breast cancer tumors, expression of HP1Hsalfa, HP1Hsbeta e HP1Hsy does not seem to be associated with the presence of occult metastatic cells in the bone marrow

Parmi les rétrovirus tumorigènes, les rétrovirus appelés « complexes » dont font partie HTLV-1 chez l’homme et BLV chez le mouton, sont responsables de leucémies lymphoïdes chroniques caractérisées par des pathogenèses similaires. Bien que la contribution essentielle de la protéine Tax dans la leucémogenèse soit bien établie pour ces deux virus, il existe toujours une contreverse quant à l’expression des protéines virales -dont l’oncoprotéine Tax- dans les cellules transformées. Dans le cas de HTLV-1 et BLV, le virus est latent. Une hypothèse attrayante suggère que l’extinction complète du provirus accompagnée du blocage transcriptionnel de l’expression de Tax dans la cellule leucémique serait un élément indispensable au développement de la tumeur en réduisant son immunogénicité. Le silencing viral permettrait à la cellule infectée d’échapper à la reconnaissance par le système immunitaire de l’hôte. <p>Dans la première partie de notre travail, nous avons pu montrer, grâce à l’observation et le suivi de deux moutons infectés par BLV, que l’extinction virale était associée au développement tumoral. Alors que la phase asymptomatique est caractérisée par l’existence de différents clones cellulaires infectés et exprimant le virus, la phase tumorale est caractérisée par l’existence d’un seul clone cellulaire dans lequel l’expression virale est éteinte. Dans le cas du mouton S2531, nous avons mis en évidence que le silencing observé dans la phase tumorale est d’origine génétique. L’extinction de l’expression virale et la domination du clone muté au niveau de la protéine Tax (K303) sont associées à l’émergence de la leucémie et constituent une caractéristique de la phase tumorale. Le deuxième mouton étudié, S267, est caractérisé par la présence de cellules infectées non transformées et transformées au même moment. Par ailleurs, le mouton S267 est caractérisé par une absence de mutations ou délétions au niveau du provirus intégré dans les cellules tumorales. Dans la deuxième partie de notre travail, nous avons pu, grâce à l’établissement de la lignée L267 dans laquelle le silencing viral n’est pas lié à une défection dans la structure génomique du provirus, élucider les mécanismes épigénétiques responsables du silencing. Nous montrons que ce provirus silencieux peut être réactivé in vitro 1) lorsque la protéine Tax sauvage est introduite par transfert rétroviral, 2) après traitement des cellules par la trichostatine A (TSA), un inhibiteur des histones désacétylases, 3) par traitement des cellules à la 5’azacytidine, un agent inhibiteur de DNA méthyltransférases. La réactivation du provirus silencieux lui confère la capacité d’infecter des moutons sains, suggérant que le provirus est complet et exempt de mutation qui pourrait altérer son fonctionnement. Les complexes de désacétylation des histones msin3A et HDAC-1 jouent un rôle important dans l’établissement du silencing viral via la condensation de la chromatine, et ce changement de la structure chromatinienne est lié a un ensemble de modifications ciblant les acides aminés des queues N-terminales des histones H3 et H4 établissant ainsi un code histone pour l’extinction et l’expression du provirus. Enfin, l’étude comparative des profils d’expression génique de cellules B tumorales dans lesquelles le provirus BLV est soit silencieux, soit ré-activé suite à l’expression exogène de Tax a montré que les mécanismes épigénétiques de silencing se superposent même dans le modèle génétique de silencing. De plus le rétablissement de l’expression virale par Tax est associé à une élimination des complexes de désacétylation des histones au niveau du promoteur viral.<p>Nos résultats ouvrent le champ vers l’utilisation de modèle de leucémie ovine dans des essais thérapeutiques basés sur la combinaison du traitement par des inhibiteurs des HDACs et des DNMTs et une immunothérapie ciblant des antigènes tumoraux d’origine virale ou cellulaire. De telles expériences in vivo constitueront un modèle utile pour le traitement l’ATLL et de pathologies prolifératives touchant les cellules B chez l’homme.<p><p> / Doctorat en sciences biomédicales / info:eu-repo/semantics/nonPublished

Plant invertases are a class of proteins that have enzymatic function in cleaving sucrose to fructose and glucose. Cell wall invertase, located on the exterior of the cell wall of plant cells, plays a key role in the unloading of sucrose from the apoplast to the sink tissues. Cell wall invertase interacts with an inhibitor, cell wall invertase inhibitor, post-transcriptionally to regulate its activity. The inhibitor is constitutively expressed in pollen development, early developing seeds, and senescing leaves: indicative of sucrose allocation being a limiting factor at these stages of development. We introduced algal bicarbonate transporters LCIA/CCP1 to Camelina sativa for the purpose of increasing photosynthetic capacity. The bicarbonate transporters concentrate CO2 at RuBisCO by pumping CO2 in the form of bicarbonate through the membrane, then converting it back to CO2 at RuBisCO, increasing CO2 concentration. Results from these plants have shown an increase in seed number, but not seed mass, along with a faster rate of maturity and senescence. This is indicative of acclimation to high CO2 conditions, resulting from insertion of the bicarbonate transporters. RNA sequencing was performed and a putative invertase inhibitor was recognized as being expressed in the transgenic C. sativa but not in the wild type. Our strategy is to knock out two invertase inhibitors using induced RNA silencing, dramatically altering sucrose allocation into developing seeds and resulting in an increase in seed biomass. It is the aim of this research to increase the biomass of C. sativa seeds in order to increase its effectiveness as an agent to create sustainable biofuels.

Vessels constructed in electrically conductive materials give rise to frequency-dependent, induced magnetic fields when waves of water cause them to roll in the Earth's magnetic field. These fields, typically referred to as roll-induced magnetic vortex fields, are a component of the ship's overall signature, where signature refers to measurable quantities which can reveal or identify objects. It is crucial for military platforms to keep the signature low and thereby increase the possibilities of operation. For magnetic signatures, this is done through strategic design and construction of the platform or by using magnetic silencing systems. The signature is then decreased to minimize the risk of detection from naval mines and marine detection systems.  This report covers the initial research on the subject of an inverse source model for roll induced magnetic fields. By limiting the analysis to two basic objects and applying a time variant magnetic field to them, we induce a magnetic field which we then model. The inverse modeling is done using magnetic dipoles as sources which are placed around the area of the object. The parameters of the model are then found by applying a least squares algorithm coupled with Tikhonov regularization. The focus of this report is the configuration of this setup in terms of measurements and sources, as well as finding a proper regularization parameter. Since the applied magnetic field is dependent on the roll frequency, also the inverse model depends on a frequency parameter in addition to the geometry and material of the object. The objects here studied are of two simple geometries, a rectangular block and a hollow cylinder. Both objects are constructed in an aluminum alloy with well known material parameters. Measurement data is gathered using a numerical solver utilizing the finite element method for solving the partial differential equations. The numerical measurement data is compared to physical measurements as well. The physical measurement data is gathered by placing the objects in a Helmholtz-cage which is used to apply a homogeneous time variant magnetic field upon them. The project was carried out at the Swedish Defence Research Agency (FOI) at the department of underwater research.

DRM is a conserved transcription factor complex that includes E2F/DP and pRB family proteins and plays important roles in the cell cycle and cancer. Recent work has unveiled a new aspect of DRM function in regulating genes involved in development and differentiation. These studies, however, were performed with cultured cells and a genome-wide study involving intact organisms undergoing active proliferation and differentiation was lacking. Our goal was to extend the knowledge of the role of DRM in gene regulation through development and in multiple tissues. To accomplish this, we employed genomic approaches to determine genome-wide targets of DRM using the nematode Caenorhabditis elegans as a model system. In this dissertation, I focus on the DRM component LIN-54 since it was proposed to exhibit DNA-binding activity. First, we confirmed the DNA-binding activity of C.elegans LIN-54 in vivo, and showed it is essential to recruit the DRM complex to its target genes. Next, chromatin immunoprecipitation and gene expression profiling revealed that LIN-54 controls transcription of genes implicated in cell division, development and reproduction. This work identified an interesting contrast in DRM function in soma vs. germline: DRM promotes transcription of germline-specific genes in the germline, but prevents their ectopic expression in the soma. Furthermore, we discovered a novel characteristic of DRM, sex chromosome-biased binding and function. We demonstrated that C. elegans DRM preferentially binds autosomes, yet regulates X-chromosome silencing by counteracting the H3K36 histone methyltransferase MES-4. By using genomics, cytology, and genetics, we defined DRM as an important player in the regulation of germline X-chromosome gene expression, and addressed molecular mechanisms vii behind the antagonistic interactions between DRM and MES-4. I present a model to explain the interplay of DRM and MES-4, and propose a novel function of DRM and MES-4 in maintaining proper chromosome gene expression dosage. This work extends our knowledge of the conserved roles of DRM in development, and provides a new view of differing DRM functions in soma versus germline. Furthermore, we defined a novel chromosome-specific aspect of DRM-mediated regulation.

Small interfering RNAs (siRNAs), microRNAs (miRNAs), and piRNAs (piRNA) are conserved classes of small single-stranded ~21-30 nucleotide (nt) RNA guides that repress eukaryotic gene expression using distinct RNA Induced Silencing Complexes (RISCs). At its core, RISC is composed of a single-stranded small RNA guide bound to a member of the Argonaute protein family, which together bind and repress complementary target RNA. miRNAs target protein coding mRNAs—a function essential for normal development and broadly involved in pathways of human disease; small interfering RNAs (siRNA) defend against viruses, but can also be engineered to direct experimental or therapeutic gene silencing; piwi associated RNAs (piRNAs) protect germline genomes from expansion of parasitic nucleic acids such as transposons. Using the fruit fly, Drosophila melanogaster, as a model organism we seek to understand how small silencing RNAs are made and how they function. In Drosophila, miRNAs and siRNAs are proposed to have parallel, but separate biogenesis and effector machinery. miRNA duplexes are excised from imperfectly paired hairpin precursors by Dicer1 and loaded into Ago1; siRNA duplexes are hewn from perfectly paired long dsRNA by Dicer2 and loaded into Ago2. Contrary to this model we found one miRNA, miR-277, is made by Dicer1, but partitions between Ago1 and Ago2 RISCs. These two RISCs are functionally distinct—Ago2 could silence a perfectly paired target, but not a centrally bulged target; Ago1 could silence a bulged target, but not a perfect target. This was surprising since both Ago1 and Ago2 have endonucleolytic cleavage activity necessary for perfect target cleavage in vitro. Our detailed kinetic studies suggested why—Ago2 is a robust multiple turnover enzyme, but Ago1 is not. Along with a complementary in vitro study our data supports a duplex sorting mechanism in which Diced duplexes are released, and rebind to Ago1 or Ago2 loading machinery, regardless of which Dicer produced them. This allows structural information embedded in small RNA duplexes to direct small RNA loading into Ago1 and/or Ago2, resulting in distinct regulatory outputs. Small RNA sorting also has chemical consequences for the small RNA guide. Although siRNAs were presumed to have the signature 2′, 3′ hydroxyl ends left by Dicer, we found that small RNAs loaded into Ago2 or Piwi proteins, but not Ago1, are modified at their 3´ ends by the RNA 2´-O-methyltransferase DmHen1. In plants Hen1 modifies the 3´ ends all small RNAs duplexs, protecting and stabilizing them. Implying a similar function in flies, piRNAs are smaller, less abundant, and their function is perturbed in hen1 mutants. But unlike plants, small RNAs are modified as single-strands in RISC rather than as duplexes. This nicely explains why the dsRNA binding domain in plant Hen1 was discarded in animals, and why both dsRNA derived siRNAs and ssRNA derived piRNAs are modified. The recent discovery that both piRNAs and siRNAs target transposons links terminal modification and transposon silencing, suggesting that it is specialized for this purpose.

In the preceding chapters, I have discussed my doctoral research on studying the siRNA loading pathway in Drosophila using both biochemical and genetic approaches. We established a gel shift system to identify the intermediate complexes formed during siRNA loading. We detected at least three complexes, named complex B, RISC loading complex (RLC) and RISC. Using kinetic modeling, we determined that the siRNA enters complex B and RLC early during assembly when it remains double-stranded, and then matures in RISC to generate Argonaute bearing only the single-stranded guide. We further characterized the three complexes. We showed that complex B comprises Dcr-1 and Loqs, while both RLC and RISC contain Dcr-2 and R2D2. Our study suggests that the Dcr-2/R2D2 heterodimer plays a central role in RISC assembly. We observed that Dcr-1/Loqs, which function together to process pre-miRNA into mature miRNA, were also involved in siRNA loading. This was surprising, because it has been proposed that the RNAi pathway and miRNA pathway are separate and parallel, with each using a unique set of proteins to produce small RNAs, to assemble functional RNA-guided enzyme complexes, and to regulate target mRNAs. We further examined the molecular function of Dcr-1/Loqs in RNAi pathway. Our data suggest that, in vivo and in vitro, the Dcr-1/Loqs complex binds to siRNA. In vitro, the binding of the Dcr-1/Loqs complex to siRNA is the earliest detectable step in siRNA-triggered Ago2-RISC assembly. Futhermore, the binding of Dcr-1/Loqs to siRNA appears to facilitate dsRNA dicing by Dcr-2/R2D2, because the dicing activity is much lower in loqslysate than in wild type. Long inverted repeat (IR) triggered white silencing in fly eyes is an example of endogenous RNAi. Consistent with our finding that Dcr-1/Loqs function to load siRNA, less white siRNA accumulates in loqs mutant eyes compared to wild type. As a result, loqs mutants are partially defective in IR trigged whitesilencing. Our data suggest considerable functional and genetic overlap between the miRNA and siRNA pathways, with the two sharing key components previously thought to be confined to just one of the two pathways. Based on our study on siRNA loading pathway, we also elucidated the molecular function of Armitage (Armi) protein in RNAi. We showed that armi is required for RNAi. Lysates from armi mutant ovaries are defective for RNAi in vitro. Native gel analysis of protein-siRNA complexes suggests that armi mutants support early steps in the RNAi pathway, i.e., the formation of complex B and RLC, but are defective in the production of the RISC.

Systemic glucose regulation is essential for human survival as low or chronically high glucose levels can be detrimental to the health of an individual. Glucose levels are highly regulated via inter-organ communication networks that alter metabolic function to maintain euglycemia. For example, when nutrient levels are low, pancreatic α-cells secrete glucagon, which signals to the liver to promote glycogen breakdown and glucose production. In times of excess nutrient intake, pancreatic β-cells release insulin. Insulin signals to the liver to suppress hepatic glucose production, and signals to the adipose tissue and the skeletal muscle to take up excess glucose via insulin-regulated glucose transporters. Defects in this inter-organ communication network including insulin resistance can result in glucose deregulation and ultimately the onset of type-2 diabetes (T2D). To identify novel regulators of insulin-mediated glucose transport, our laboratory performed an siRNA-mediated gene-silencing screen in cultured adipocytes and measured insulin-mediated glucose transport. Gene silencing of Mitogen-activated protein kinase kinase kinase kinase 4 (Map4k4), a Sterile-20-related serine/threonine protein kinase, enhanced insulin-stimulated glucose transport, suggesting Map4k4 inhibits insulin action and glucose transport. Thus, for the first part of my thesis, I explore the role of Map4k4 in cultured adipose cells and show that Map4k4 also represses lipid synthesis independent of its effects on glucose transport. Map4k4 inhibits lipid synthesis in a Mechanistic target of rapamycin complex 1 (mTORC1)- and Sterol regulatory element-binding transcription factor 1 (Srebp-1)-dependent mechanism and not via a c-Jun NH2-terminal kinase (Jnk)-dependent mechanism. For the second part of my thesis, I explore the metabolic function of Map4k4 in vivo. Using mice with loxP sites flanking the Map4k4 allele and a ubiquitously expressed tamoxifen-activated Cre, we inducibly ablated Map4k4 expression in adult mice and found significant improvements in metabolic health indicated by improved fasting glucose and whole-body insulin action. To assess the role of Map4k4 in specific metabolic tissues responsible for systemic glucose regulation, we employed tissue-specific knockout mice to deplete Map4k4 in adipose tissue using an adiponectin-cre transgene, liver using an albumin-cre transgene, and skeletal muscle using a Myf5-cre transgene. Ablation of Map4k4 expression in adipose tissue or liver had no impact on whole body glucose homeostasis or insulin resistance. However, we surprisingly found that Map4k4 depletion in Myf5-positive tissues, which include skeletal muscles, largely recapitulates the metabolic phenotypes observed in systemic Map4k4 knockout mice, restoring obesity-induced glucose intolerance and insulin resistance. Furthermore these metabolic changes were associated with enhanced insulin signaling to Akt in the visceral adipose tissue, a tissue that is nearly devoid of Myf5-positive cells and does not display changes in Map4k4 expression. Thus, these results indicate that Map4k4 in Myf5-positive cells, most likely skeletal muscle cells, inhibits whole-body insulin action and these effects may be mediated via an indirect effect on the visceral adipose tissue. The results presented here provide evidence for Map4k4 as a potential therapeutic target for the treatment of insulin resistance and T2D.