In the past fifteen years, ubiquitin has emerged as a central regulator of membrane protein trafficking. In this context, covalent attachment of this small protein to lysine residues of cargo proteins, a reversible modification termed ubiquitylation, provides a signal for their targeting to the vacuolar/lysosomal lumen where they are degraded, both in yeast and higher eukaryotes. Ubiquitylation is also used as a means of controlling the function of specific proteins in several trafficking machineries. The role of lipids - and in particular of membrane domains named lipid rafts - in controlling the intracellular trafficking of membrane proteins has also been the subject of intense investigation in recent years.<p>One of the membrane proteins of the yeast Saccharomyces cerevisiae whose intracellular trafficking has been extensively studied is the general amino acid permease Gap1. Yet some aspects of the function of ubiquitin in the nitrogen-dependent control of this protein remain controversial. Moreover, the potential role of lipid rafts in regulating the functional properties and traffic of the Gap1 permease had not been investigated before this thesis work. <p>The first part of our work readdresses the role of Gap1 ubiquitylation, and more precisely of the modification of the permease with polyubiquitin chains linked through the lysine 63 of ubiquitin, in controlling the fate of this protein in the secretory pathway. Our observations indicate that nitrogen-induced ubiquitylation of newly synthesised Gap1 occurs in the trans-Golgi complex. However, contrary to the generally accepted view, this modification is not necessary for the permease to exit this compartment en route to the endosome but only for its subsequent targeting to the vacuolar lumen via the multivesicular body (MVB) pathway. Our results also provide evidence that K63-linked polyubiquitylation is important mostly at the late endosomal level, for proper sorting of Gap1 into the MVB pathway, whether the permease comes from the cell surface by endocytosis or directly from the secretory pathway. <p>In the second part of this work, we present a set of data providing novel insights into the controversial question of the exact nature of lipid rafts in yeast. We first showed that the Gap1 permease is associated with detergent-resistant membranes (DRMs) - the proposed biochemical equivalent of lipid rafts - when it is located at the cell surface. Our data further suggest that this may be true for most if not all yeast plasma membrane proteins. Moreover, we found that Gap1 production must be coupled to de novo synthesis of sphingolipids (SLs), major constituents of rafts, in order for the newly synthesised permease to be correctly folded, active, associated with DRMs, and stable at the cell surface. We propose a model where Gap1 would associate with newly synthesised SLs during its biogenesis and/or secretion, this association shaping the permease into its native conformation and ensuring its incorporation and stabilisation in specific lipid domains at the plasma membrane. Failure of Gap1 to acquire this lipidic microenvironment in turns leads to its ubiquitin-dependent degradation by a quality-control mechanism. This model might be valid for many other plasma membrane proteins and might account for their lateral distribution between distinct membrane domains. <p> / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Studies on pancreatic cell physiology rely on the investigation of exocrine and endocrine cells in vitro. Particularly, in the case of the exocrine tissue these studies have suffered from a reduced functional viability of acinar cells in culture. As a result not only investigations on dispersed acinar cells and isolated acini were limited in their potential, but also prolonged studies on pancreatic exocrine and endocrine cells in an intact pancreatic tissue environment were unfeasible. To overcome these limitations, we aimed to establish a pancreas tissue slice culture platform to allow long-term studies on exocrine and endocrine cells in the intact pancreatic environment. Mouse pancreas tissue slice morphology was assessed to determine optimal long-term culture settings for intact pancreatic tissue. Utilizing optimized culture conditions, cell specificity and function of exocrine acinar cells and endocrine beta cells were characterized over a culture period of 7 days. We found pancreas tissue slices cultured under optimized conditions to have intact tissue specific morphology for the entire culture period. Amylase positive intact acini were present at all time points of culture and acinar cells displayed a typical strong cell polarity. Amylase release from pancreas tissue slices decreased during culture, but maintained the characteristic bell-shaped dose-response curve to increasing caerulein concentrations and a ca. 4-fold maximal over basal release. Additionally, endocrine beta cell viability and function was well preserved until the end of the observation period. Our results show that the tissue slice culture platform provides unprecedented maintenance of pancreatic tissue specific morphology and function over a culture period for at least 4 days and in part even up to 1 week. This analytical advancement now allows mid -to long-term studies on the cell biology of pancreatic disorder pathogenesis and therapy in an intact surrounding in situ.

Indiana University-Purdue University Indianapolis (IUPUI) / Non-alcoholic steatohepatitis (NASH), which is characterized by the induction of hepatocellular death and inflammation, is associated with the activation of cellular stress pathways such as the Unfolded Protein Response (UPR), an adaptive response to disruptions in endoplasmic reticulum (ER) homeostasis. Because the role of the UPR in the progression of liver disease is not well understood, we established an in vitro model to evaluate the role of the UPR in NASH and translated results to clarify disease progression in human liver biopsy samples. Treating HepG2 cells and primary human hepatocytes with saturated, but not unsaturated free fatty acids (FFAs), at physiologic concentrations induced hepatotoxicity by inhibiting autophagic flux. Saturated FFA treatment activated the UPR, including the transcription factors CHOP (GADD153/DDIT3) and NF-κB, leading to increased expression and secretion of cytokines such as TNFα and IL-8 that contributed to hepatic cell death and inflammation. Depletion of either CHOP or the RELA subunit of NF-κB in hepatocytes alleviated autophagy and cytokine secretion, resulting in enhanced cell viability and lowered inflammatory responses during exposure to saturated FFAs. We carried out next generation sequencing on cells deleted for either CHOP or RELA and identified IBTKα as a novel UPR member directly regulated by CHOP and NF-κB. In response to saturated FFAs, loss of IBTKα increased cell survival through lowered phagophore formation and reduced cytokine secretion. We also identified binding partners of IBTKα by immunoprecipitation and LC/MS, indicating that that IBTKα is part of a protein complex which functions at ER exit sites to facilitate initiation of autophagy and protein secretion. Furthermore, we discovered that CHOP and RELA coordinately regulate proteasome activity through NRF2 as an adaptive response to an inhibition of autophagic flux following palmitate exposure. To validate our model, we utilized human liver biopsy samples and demonstrated up-regulation of the UPR coincident with accumulation of autophagy markers, as well as secretion of cytokines IL 8 and TNFα in serum of NASH patients. Our study provides a mechanistic understanding of the roles of the UPR and autophagy in regulating saturated FFA induced hepatotoxicity at the cellular level.

Indiana University-Purdue University Indianapolis (IUPUI) / Polycystic kidney diseases (PKD) are genetic disorders characterized by fluid filled cysts in the kidney tubules and liver bile ducts. There are two forms of PKD, autosomal dominant polycystic kidney disease (ADPKD) and autosomal recessive polycystic kidney disease (ARPKD). The focus of the studies in this thesis has been on ADPKD. The disease progresses slowly and the fluid-filled cysts grow in size due to increased rates of cell proliferation and fluid secretion into the cyst lumen. The expanding cysts compromise the normal kidney function and result in a decrease of renal function to the point of end-stage renal failure in midlife. Cyst enlargement is due, at least in part, to chloride secretion via the cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel. Currently therapy is limited to renal cyst aspiration, dialysis, and eventually renal transplantation after organ failure, thus it has critical to determine possible drug therapies for the treatment of PKD. Previous studies showed that cyst fluid caused a secretory response in cells lining the cysts. We hypothesized that once the cyst have expanded and become so large that they burst or leak, which could also occur due to renal injury or aging, the cyst fluid may stimulate additional cyst growth. Lysophosphatidic Acid (LPA) was determined to be the active component of human cyst fluid, and we investigated the LPA stimulated signaling pathway. Our data suggest that the LPA stimulates chloride and fluid secretion by a combination of CFTR and Calcium-Activated chloride channels (CaCC) and that the two channels may functionally be linked to each other. The secretion is not occurring through a cAMP stimulated pathway, and it is possible that TMEM16A, a CaCC, plays a larger role than previously expected. Previous studies demonstrated that PPARγ agonists, insulin sensitizing drugs used to treat diabetes, inhibit chloride secretion by the collecting duct principal cells by decreasing CFTR synthesis. It was logical therefore to considered PPARγ agonists as long-term treatment for PKD. The first preclinical studied showed that high (20 mg/kg BW) dose pioglitazone, a PPARγ agonist, inhibited cyst growth in the PCK rat model, a slow progressing model, of PKD. To continue to look at the effects of the PPARγ agonists another preclinical study was completed, which tested if there was a class action of PPARγ agonists and if a lower dose was effective in treating the cystic burden. Using the PCK rat model, and another PPARγ agonist, rosiglitazone, a 24 week study was completed using 3 doses (4, 0.4, and 0.04 mg/kg BW). 4 mg/kg BW rosiglitazone is analogous to 20 mg/kg BW pioglitazone. The data indicated that the rosiglitazone is effective in lowering the cystic burden, and importantly the low dose proved to be effective. An additional rat model, the W-WPK rapidly progressing model was used to determine efficacy across multiple models, and to determine if there was a way to track the progress of the disease in a manner analogous to that used in human patients. The animals were treated with pioglitazone using 2 doses (2 and 20 mg/kg BW), and were imaged using CT scans to track the progress of the disease. The data suggest that pioglitazone was not as effective in the W-WPK rat model as it was the PCK rat model. There was a trend however, that low dose PPARγ agonist was as effective ad high dose. Even more important, the CT scans proved to be an effective way to track the progress of the disease in animal models.

Background: Glucose homeostasis is tightly regulated by hormones secreted within the pancreatic islets of Langerhans. The most important are insulin and glucagon produced by beta and alpha cells respectively. Changes in beta cell mass and/or their functional deficit can lead to hyperglycemia, a major hallmark of both type 1 (T1D) and type 2 (T2D). Moreover, a dysregulation in glucagon secretion is thought to also play a major role in patients with diabetes, suggesting a failure in the counterregulatory mechanisms of glucose homeostasis in disease pathogenesis. Dysfunction at the alpha cell level in T1D manifests are blunt glucagon response to low glucose levels, which can cause severe hypoglycemic events in patients with T1D. Furthermore, exaggerated glucagon responses to glucose or amino acid intake significantly contributes to dysglycemia in both T1D and T2D patients. Most of our knowledge about glucagon and alpha cell physiology in the human setting was generated using in vivo systemic assessments or in vitro investigations of isolated human islets or dispersed single cells. Despite the increasing knowledge regarding alpha cells and glucagon biology, the underlying mechanisms of alpha cell dysfunction are still uncertain. Studies on alpha cell physiology were hindered by limited human tissue accessibility, technical methodologies and translational value of findings from rodents to humans. To fill the gap between the currently available in vivo and in vitro approaches and a more precise understanding of mechanisms of diabetes pathogenesis detailed investigation of islet cells within their native environment is needed. Aim The overall objective of this thesis was characterize alpha cell function in diabetes pathogenesis. To this end, the human pancreas slice preparation would to be adapted and advanced for the study of alpha cell physiology. These adjustments would be then used to investigate changes in alpha cell mass and function in T1D and T2D. Methods: Pancreas tissue slices were prepared from donor organs with and without T1D and from tissue donors after pancreatectomy at different stages of T2D. Immunofluorescent staining with subsequent 3D morphometry was used to quantify alpha cell volumes from 120μm thick tissue slices. Furthermore, human tissue slices were subjected to dynamic slice perifusion for the assessment of glucagon and insulin secretion kinetics in response to specific stimuli. Finally, functional and morphometrical analysis was performed on the same tissue slices to enable direct correlation of glucagon secretion and alpha cell volume in a subset of cases in the context of T1D. Results: Here we developed a semi-automatic 3D approach to quantify total endocrine cell volumes within a given volume of pancreas tissue. In addition, we established an in situ method for dynamic insulin release measurements from islets preserved in their native environment. We successfully modified this protocol to allow the measurement of glucagon release in slices from organ donors. After further optimizations, we were additionally able to also measure alpha cell function from surgical specimens after pancreatectomy. To gain insight into alpha cell pathophysiology in T1D we investigated alpha cell volume in donor organs with different disease duration and age at onset. Alpha cell volumes in slices of individuals with T1D did not show a dramatic change (neither increase nor decrease) in comparison to slices generated from non-diabetic (ND) pancreata. Furthermore, functional assessment of glucagon release using a specific stimulation protocol for alpha cells suggests preserved stimulatory capacity of these cells in slices from autoantibody positive donors. Interestingly, this is also the case in the so far studied slices from donors with different durations of diabetes. Nevertheless, normalization of secreted glucagon to the total alpha cell mass within the slice indicated reduced glucagon release in the here investigated two cases of T1D. In the context of T2D, 3D morphometrical analysis revealed that overall endocrine cell volume, including alpha cell volume, is maintained in our cohort of IGT and T2D individuals. Glucagon release can also be measured in tissue procured from patients undergoing pancreatectomy, given the presence of amino acids in the perifusion media and increased trypsin inhibitors. While we provided proof of concept using tissue from ND individuals, we are confident that the approach will give valuable insight in different states of diabetes. Conclusion: These results demonstrate that human pancreas tissue slices represent a complementary platform to study alpha cell pathophysiology in both major types of diabetes. We provide evidence that this approach can be used to study alpha cell pathophysiology in T1D and T2D. Our preliminary data indicates no defect in the stimulatory capacity in slices from Aab+ and T1D donors, however more cases need to be investigated given the heterogeneous nature of the disease. We anticipate that the here proposed protocol for measurement of glucagon release from tissue slices will help us to gain insight in the role of alpha cells in diabetes pathophysiology. / Hintergrund: Die Aufrechterhaltung der Glukosehomöostase wird durch die Hormonsekretion der Langerhans’schen Inseln im Pankreas reguliert. Die wichtigste Rolle hierbei spielen die Insulin-produzierenden Betazellen und die Glukagon-produzierenden Alphazellen. Der Verlust der Betazellmasse und/oder der Funktion kann zur Entwicklung einer Hyperglykämie führen, die ein Hauptmerkmal des Typ 1 (T1D) und Typ 2 (T2D) Diabetes ist. Darüber hinaus wird vermutet, dass auch der Mechanismus der Gegenregulierung durch die Sekretion von Glukagon eine wichtige Rolle in der Pathogenese des Diabetes spielt. Während eine fehlende Glukagonsekretion zu schweren hypoglykämischen Phasen bei Typ 1 Diabetikern führen kann, geht man zusätzlich davon aus, dass eine erhöhte Reaktivität von Alphazellen sowohl auf Glukose als auch Aminosäuren ebenfalls zum Verlust der Glukosehomöostase im T1D und T2D beitragen kann. Trotz der stetig wachsenden Erkenntnisse über die Physiologie der Alphazellen, die vor allem durch systemische Untersuchungen in vivo oder an isolierten Langerhans’schen Inseln und Einzelzellen in vitro durchgeführt wurden, sind die zugrundeliegenden Mechanismen für deren Fehlfunktion beim Menschen noch nicht eindeutig aufgeklärt. Dies beruht hauptsächlich auf nur bedingt vorhandenem humanem Gewebe, technischen Schwierigkeiten bei der Isolation der Zellen, sowie der nur bedingten Vergleichbarkeit zu Studien in Nagern. Um diese Wissenslücken zwischen in vivo und in vitro Studien schließen zu können, ist es notwendig detaillierte Untersuchungen der Zellen unter nahezu physiologischen Bedingungen und in der nativen Umgebung der Pankreas in situ durchzuführen, um Alphazell-spezifische Mechanismen in der Diabetespathogenese genauer beleuchten zu können. Ziele: Ziel dieser Dissertation war es, durch Anpassung und Weiterentwicklung der Technik zur Gewinnung von Gewebeschnitten des humanen Pankreas, die Funktion der Alphazellen sowohl unter physiologischen Bedingungen als auch in der Entwicklung des T1D und T2D genauer zu charakterisieren. Methoden: Zur Untersuchungen von Alphazellen in Gewebeschnitten in situ wurden Gewebestücke sowohl von Organspendern mit und ohne T1D, sowie von metabolisch charakterisierter Patienten in verschiedenen Stadien der T2D Pathogenese nach einer Pankreatektomie verwendet. Die aus dem Gewebe gewonnenen 120 μm dicken Schnitte wurden zum einen für immunhistochemischer Färbungen verwendet, die eine 3-dimensionale morphometrische Analyse der Alphazellmasse ermöglichen. Ferner wurden Schnitte zur Ermittlung der Kinetik von Glukagon- und Insulinsekretion nach Stimulation mittels Perifusion benutzt. Schließlich wurden sowohl die morphologischen als auch funktionellen Analysen auf denselben Gewebeschnitten durchgeführt, um die Funktion der Alphazellen mit deren Masse besser korrelieren zu können. Ergebnisse: Zusätzlich zur Mitentwicklung eines halbautomatisierten Verfahrens zur 3D Analyse von endokrinen Zellvolumina in Gewebeschnitten des Pankreas wurde die bereits vorhandene Methode zur Messung der Insulinsekretionskinetik weiterentwickelt. Außerdem erfolgte die Etablierung adäquater Protokolle zur Messung der Glukagonsekretion in humanen Gewebeschnitten, die im Kontext beider Diabetestypen verwendet wurden. Um einen besseren Einblick in die T1D Pathogenese zu erhalten, wurde das Alphazellvolumen- und die Funktion in Gewebeschnitten von Organspendern mit unterschiedlichem Diabetes Verlauf (Alter bei Diagnose, Dauer seit Diagnose) mit nicht-diabetischen, aber Autoantikörper-positiven Spendern und nicht-diabetische Kontrollen verglichen. In Bezug auf das Alphazellvolumen waren zwischen den einzelnen Gruppen keine Unterschiede zu erkennen, die auf Veränderungen in der Entwicklung und Manifestation des T1D hinweisen. Darüber hinaus ergab die funktionelle Analyse, dass die Glukagonsekretion in nicht-diabetischen, Autoantikörper-positiven Spendern erhalten bleibt. Dies konnte zusätzlich auch in den bisher untersuchten Geweben von Typ 1 Diabetikern nachgewiesen werden, obwohl die Volumen-normalisierte Sekretion auf eine geringere Glukagonausschüttung hindeutet. Im Hinblick auf die T2D Pathogenese konnte bei der 3D Morphometrie von Nichtdiabetikern, Patienten mit beeinträchtigter Glukosetoleranz und Typ 2 Diabetikern keinerlei Unterschiede in den endokrinen Zellvolumina festgestellt werden. Durch die Anpassung der Konditionen für die Perifusion von reseziertem Gewebe konnte bei Nichtdiabetikern die erfolgreiche Messung der Glukagonsekretion gezeigt werden und ermöglicht zukünftig auch die Untersuchung einer möglichen Alphazelldysfunktion in der Entwicklung eines T2D. Schlussfolgerung: Die Ergebnisse dieser Arbeit zeigen, dass die etablierte Plattform zur morphologischen und funktionellen Analyse humaner Pankreasgewebeschnitte in situ eine wichtige Rolle in der Untersuchung der Alphazellen in der Diabetes-Pathogenese spielt. Die bisher erhobenen Daten zur Untersuchung des T1D haben gezeigt, dass die Kapazität der Glukagonsekretion nicht signifikant verändert ist. Aufgrund des heterogenen Krankheitsverlaufs beider Diabetesformen ist es jedoch notwendig Gewebe von einer größeren Anzahl an Spendern/Patienten zu untersuchen, um einen besseren Einblick in die Rolle der Alphazellen in der Entstehung des Diabetes zu erhalten.

An object-oriented framework is presented for developing and simulating individual-based models of cell populations. The framework supplies classes to define objects called simulation channels that encapsulate the algorithms that make up a simulation model. These may govern state-updating events at the individual level, perform global state changes, or trigger cell division. Simulation engines control the scheduling and execution of collections of simulation channels, while a simulation manager coordinates the engines according to one of two scheduling protocols. When the ensemble of cells being simulated reaches a specified maximum size, a procedure is introduced whereby random cells are ejected from the simulation and replaced by newborn cells to keep the sample population size constant but representative in composition. The framework permits recording of population snapshot data and/or cell lineage histories. Use of the framework is demonstrated through validation benchmarks and two case studies based on experiments from the literature.

An object-oriented framework is presented for developing and simulating individual-based models of cell populations. The framework supplies classes to define objects called simulation channels that encapsulate the algorithms that make up a simulation model. These may govern state-updating events at the individual level, perform global state changes, or trigger cell division. Simulation engines control the scheduling and execution of collections of simulation channels, while a simulation manager coordinates the engines according to one of two scheduling protocols. When the ensemble of cells being simulated reaches a specified maximum size, a procedure is introduced whereby random cells are ejected from the simulation and replaced by newborn cells to keep the sample population size constant but representative in composition. The framework permits recording of population snapshot data and/or cell lineage histories. Use of the framework is demonstrated through validation benchmarks and two case studies based on experiments from the literature.

An injured vascular system has a substantial impact on an individuals overall health, and an understanding of the mechanisms that underlie blood vessel pathophysiology is required for the development of rational and effective treatment strategies. The phenotypic modulation of smooth muscle cells (SMC) during vascular injury, characterized by altered adhesion, migration and synthetic behavior, plays an important role in the eventual outcome. Specifically, the ability of SMCs to adhere to and remodel their extracellular environment via regulation of the syndecan class of cell adhesion molecules dictates the response of the vascular wall to local injury. The effect of in vitro syndecan-4 regulation on SMC adhesion was investigated through the use of a glass microsphere centrifugation assay, and an antisense-mediated reduction in gene expression was found to correlate with decreased adhesive strength. Regulation of syndecan-1, syndecan-2, and syndecan-4 gene expression was observed experimentally by mechanical strain of SMCs. Using real-time polymerase chain reaction (PCR), the kinetics of both static and cyclic mechanical strain were found to modify the gene expression in a time and strain magnitude-dependent manner unique to each syndecan. In particular, the responses of syndecan-4 were acute, but transient, while the evolution of syndecan-1 and syndecan-2 regulation was delayed by comparison. Mechanical strain also modulated syndecan-4 protein expression and ectodomain shedding, as measured by Western immunoblotting, and this effect was found, through selective inhibition, to be at least in part dependent on mitogen-activated protein (MAP) kinase signaling. In particular, intact extracellular signal-regulated MAP kinase (ERK) 1/2 and c-Jun NH2-terminal kinase / stress-activated protein kinase (JNK/SAPK) signaling pathways were found to be required for the observed strain-induced shedding. These findings offer a better understanding of syndecan function in response to mechanical strain and suggest potential new mechanisms by which physical forces may modulate vascular SMC behavior and regulation during normal physiology, pathologic conditions, and engineered arterial substitute development.

An object-oriented framework is presented for developing and simulating individual-based models of cell populations. The framework supplies classes to define objects called simulation channels that encapsulate the algorithms that make up a simulation model. These may govern state-updating events at the individual level, perform global state changes, or trigger cell division. Simulation engines control the scheduling and execution of collections of simulation channels, while a simulation manager coordinates the engines according to one of two scheduling protocols. When the ensemble of cells being simulated reaches a specified maximum size, a procedure is introduced whereby random cells are ejected from the simulation and replaced by newborn cells to keep the sample population size constant but representative in composition. The framework permits recording of population snapshot data and/or cell lineage histories. Use of the framework is demonstrated through validation benchmarks and two case studies based on experiments from the literature.

Poaceae (or Gramineae) belong to the grass family and is one of the largest families among flowering plants on land. They include some of the most important cereal crops such as rice (Oryza sativa), barley (Hordeum vulgare), wheat (Triticum aestivum), maize (Zea mays), and sorghum (Sorghum bicolor). The characteristic bushy appearance of grass plants, including cereal crops, is formed by the activities of axillary meristems (AMs) generated in the leaf axil. These give rise to tillers from the basal nodes which recapitulate secondary growth axis and AMs are formed during vegetative development. On transition to flowering the apical meristem transforming to an inflorescence meristem (IM) which produces branches from axillary meristem. These IM gives rise to branches that ultimately bear florets. Vegetative branching/tillering determines plant biomass and influences the number of inflorescences per plant. While inflorescence branching determines the number of florets and hence seeds. Thus the overall activity of axillary meristems plays a key role in determining plant architecture during both vegetative and reproductive stages. In Arabidopsis, research on the plant specific transcription factor LEAFY (LFY) has pioneered our understanding of its regulatory functions during transition from vegetative to reproductive development and its role in specifying a floral meristem (FM) identity to the newly arising lateral meristems. In the FM LFY activates other FM genes and genes for floral organ patterning transcription factors. LFY is strongly expressed throughout the young floral meristems from the earliest stages of specification but is completely absent from the IM (Weigel et al., 1992). LFY expression can also be detected at low levels in the newly emerging leaf primordia during the vegetative phase, and these levels gradually increase until the floral transition (Blazquez et al., 1997; Hempel et al., 1997). In rice, the LFY ortholog-RFL/APO2 is expressed predominantly in very young branching panicles/ inflorescence meristems (Kyozuka et al., 1998; Prasad et al., 2003) while in the vegetative phase RFL is expressed at axils of leaves (Rao et al., 2008). In rice FMs expression is restricted to primordia of lodicules, stamens, carpels and ovules (Ikeda-Kawakatsu et al., 2012). Knockdown of RFL activity or loss of function mutants show delayed flowering and poor panicle branching with reduced number of florets and lower fertility (Rao et al., 2008, Ikeda-Kawakatsu et al., 2012). In some genotypes reduced vegetative axillary branching is also compromised (Rao et al., 2008). On the other hand RFL overexpression leads to the early flowering, attributing a role as an activator for the transition of vegetative meristems to inflorescence meristems (Rao et al., 2008). Thus, RFL shows a distinct developmental expression profile, has unique mutant phenotypes as compared to Arabidopsis LFY thus indicating a divergence in functions. We have used various functional genomics approaches to investigate regulatory networks controlledby RFL in the vegetative axillary meristems and in branching panicles with florets. These regulatory effects influence tillering and panicle branching, thus contributing to rice plant architecture. RFL functions in axillary meristem Vegetative AMs are secondary shoot meristems whose outgrowth determines plant architecture. In rice, AMs form tillers from basal nodes and mutants with altered tillering reveal that an interplay between transcription factors and the phytohormones - auxin, strigolactone underpins this process. We probed the relationship between RFL and other factors that control AM development. Our findings indicate that the derangements in AM development that occur on RFL knockdown arise from its early effects during specification of these meristems and also later effects during their outgrowth of AM as a tiller. Overall, the derailments of both steps of AM development lead to reduced tillering in plants with reduced RFL activity. Our studies on the gene expression status for key transcription factor genes, genes for strigolactone pathway and for auxin transporters gave an insight on the interplay between RFL, LAX1 and strigolactone signalling. Expression levels of LAX1 and CUC genes, that encode transcription factors with AM specification functions, were modulated upon RFL knockdown and on induction of RFL:ΔGR fusion protein. Thus our findings imply a likely, direct activating role for RFL in AM development that acts in part, through attaining appropriate LAX1 expression levels. Our data place meristem specification transcription factors LAX1 and CUC downstream to RFL. Arabidopsis LFY has a predominant role in conferring floral meristem (FM) identity (Weigel et al., 1992; Wagner, 2009; Irish, 2010; Moyroud et al., 2010). Its functions in axillary meristems were not known until recently. The latter functions were uncovered with the new LFYHARA allele with only partial defects in floral meristem identity (Chahtane et al., 2013). This mutant allele showed LFY can promote growth of vegetative AMs through its direct target REGULATOR OF AXILLARY MERISTEMS1 (RAX1), a R2R3 myb domain factor (Chahtane et al., 2013). These functions for Arabidopsis LFY and RAX1 in AMs development are parallel to and redundant with the pathway regulated by LATERAL SUPPRESSOR (LAS) and REGULATOR OF AXILLARY MERISTEM FORMATION1 (ROX1) (Yang et al., 2012; Greb et al., 2003). Interestingly, ROX1 is orthologous to rice LAX1 and our data show LAX1 expression levels in rice panicles and in culms with vegetative AMs is dependent on the expression status of RFL. Thus, we speculate that as compared to Arabidopsis AM development, in rice the LFY-dependent and LFY-independent regulatory pathways for AMs development are closely linked. In Arabidopsis, CUC2 and CUC3 genes in addition to their role in shoot meristem formation and organ separation play a role in AM development possibly by defining a boundary for the emerging AM. These functions for the Arabidopsis CUC genes are routed through their effects on LAS and also by mechanisms independent of LAS (Hibara et al., 2006; Raman et al., 2008). These data show modulation in RFL activity using the inducible RFL:∆GR protein leads to corresponding expression changes in CUC1/CUC2 and CUC3 genes expression in culm tissues. Thus, during rice AM development the meristem functions of RFL and CUC genes are related. Consequent to specification of AM the buds are kept dormant. Bud outgrowth is influenced by auxin and strigolactone signalling pathways. We investigated the transcript levels, in rice culms of genes involved in strigolactone biosynthesis and perception and found the strigolactone biosynthesis gene D10 and hormone perception gene are significantly upregulated in RFL knockdown plants. Further, bioassays were done for strigolactone levels, where we used arbuscular mycorrhiza colonization assay as an indicator for strigolactone levels in wild type plants and in RFL knockdown plants. These data validate higher strigolactone signalling in RFL knockdown plants. To probe the relationship between RFL and the strigolactone pathway we created plants knocked down for both RFL and D3. For comparison of the tillering phenotype of these double knockdown plants we created plants with D3 knockdown alone. We observed reduced tillering in plants with knockdown of both RFL and D3 as compared to the tiller number in plants with knockdown of D3 alone. These data suggest that RFL acts upstream to D3 of control bud outgrowth. As effects of strigolactones are influenced by auxin transport we studied expression of OsPIN1 and OsPIN3 in RFL knockdown plants. Their reduced expression was correlated with auxin deficiency phenotypes of the roots in RFL knockdown plants. These data in conjunction with observations on OsPIN3 the gene expression modulation by the induction of RFL:∆GR allow us to speculate on a relationship between RFL, auxin transport and strigolactones with regard to bud outgrowth. We propose that the low tillering phenotype of RFL knockdown plants arises from weakened PATS, consequent to low levels of PIN1 and PIN3, coupled with moderate increase in strigolactones. Taken together, our findings suggest functions for RFL during AM specification and tiller bud outgrowth. RFL functions in panicle branching Prior studies on phenotypes of RFL knockdown or loss of function mutants suggested roles for RFL in transition to flowering, inflorescence meristem development, emergence of lateral organs and floral organ development (Rao et al., 2008; Ikeda-Kawakatsu et al., 2012). It has been speculated that RFL acts to suppress the transition from inflorescence meristem to floral meristem through its interaction with APO1 (Ikeda-Kawakatsu et al., 2012). The downstream genes regulated by RFL in these processes have not yet been elucidated. To identify direct targets of RFL in developing panicles we adopted ChIP-seq coupled with studies on gene expression modulation on induction of RFL. For the former we raised polyclonal anti-sera and chromatin from branching panicles with few florets. For gene expression modulation studies, we created transgenics with a T-DNA construct where an artificial miRNA against 3’UTR specifically knocked endogenous RFL and the same T-DNA had a second expression cassette for generation of a chemically inducible RFL-ΔGR protein that is not targeted by amiR RFL. Our preliminary ChIP-seq data in the wild type panicle tissues hints that RFL binds to hundreds of loci across the genome thus providing first glimpse of direct targets of RFL in these tissues. These data, while preliminary, were manually curated to identify likely targets that function in flowering, we summarize here some key findings. Our study indicates a role of RFL in flowering transition by activating genes like OsSPL14 and OsPRMT6a. Recent studies indicate that OsSPL14 directly binds to the promoter of OsMADS56 or FTL1, the rice homologs of SOC1 and FT to promote flowering (Lu et al., 2013). As RFL knockdown plants show highly reduced expression of OsMADS50/SOC1 and for RFT1 (Rao et al., 2008), and we show here RFL can bind and induce OsSPL14 expression we suggest the RFL¬OsSPL14 module can contribute to the transition of the SAM to flowering. Further, OsSPL14 in the young panicles directly activates DENSE AND ERECT PANICLE1 (DEP1) to control panicle length (Lu et al., 2013). Thus RFL-OsSPL14-DEP1 module could explain the role of RFL in controlling panicle architecture (Rao et al., 2008; Ikeda-Kawakatsu et al., 2012). Thus RFL plays a role in floral transition and this function is conserved across several LFY homologs. Our data ChIP-seq in the wild type tissue and gene expression modulation studies in transgenics also give molecular evidences for the role of RFL in suppression of floral fate. The direct binding of RFL to OsMADS17, OsYABBY3, OsMADS58 and HD-ZIP-IV loci and the changes in their transcript levels on induction of RFL support this hypothesis. Once the transition from SAM to FM takes place, we speculate RFL represses the conversion of inflorescence branch meristems to floral fate by negatively regulating OsYABBY3, HD-ZIP class IV and OsMADS17 that can promote differentiation. These hypotheses indicate a diverged function for RFL in floral fate repression. Arabidopsis LFY is known to activate the expression of AGAMOUS (AG), whose orthologs in rice are OsMADS3 and OsMADS58. Our studies confirm conservation with regard to RFL binding to cis elements at OsMADS58 locus that is homologous to Arabidopsis AG. But importantly we show altered consequences of this binding on gene expression. We find RFL can suppress the expression of OsMADS58 which we speculate can promote a meristematic fate. Further, we also present the abnormal upregulation of floral organ fate genes on RFL downregulation. These data too indicate functions of RFL, are in part, distinct from the role of Arabidopsis LFY where it works in promoting floral meristem specification and development. These inferences are supported by our data that rice gene homologs for AP1, AP3 and SEP3 are not directly regulated by RFL, unlike their direct regulation by Arabidopsis LFY during flower development. We also report the expression levels of LAX1, FZP, OsIDS1 and OsMADS34 genes involved in meristem phase change and IM branching are RFL dependent. This is consistent with its role in the suppression of determinacy, thereby extending the IM activity for branch formation. But as yet we do not know if these effects are direct. Together, our data report direct targets of RFL that contribute to its functions in meristem regulation, flowering transition, and suppression of floral organ development. Overall, our preliminary data on RFL chromatin occupancy combined with our detailed studies on the modulation of gene expression provides evidence for targets and pathways unique to the rice RFL during inflorescence development. Comparative analysis of genes downstream to RFL in vegetative tillers Vs panicles Tillers and panicle branches arise from the axillary meristems at vegetative and reproductive stages, respectively, of a rice plant and overall contribute to the plant architecture. Some regulatory factors control branching in both these tissues - for example, MOC1 and LAX1. Mutants at these loci affect tillers and panicle branch development thus indicating common mechanisms control lateral branch primordia development (Li et al., 2003; Komatsu et al., 2003; Oikawa and Kyozuka, 2009). Knockdown of RFL activity or loss-of-function mutants cause significantly reduced panicle branching and in few instances, reduction in vegetative axillary branching (Rao et al., 2008; Ikeda- Kawakatsu et al., 2012). We took up the global expression profiling of RFL knockdown plants compared to wild type plants in the axillary meristem and branching panicle tissue. These data provide a useful list of potential targets of RFL in axillary meristem and branching panicle tissue. The comparative analysis of the genes affected in the two tissues indicates only a subset of genes is affected by RFL in both the vegetative axillary meristems and branching panicle. These genes include transcription factors (OsSPL14, Zn finger domain protein, and bHLH domain protein), hormone signalling molecules (GA2 ox9) and cell signalling (LRR protein) as a set of genes activated by RFL in both tissues. On the other hand, these comparative expression profiling studies also show distinct set of genes deregulated by RFL knockdown in these two tissues therefore implicating RFL functions have a tissue-specific context. The genes deregulated only in axillary meristem tissue only include D3- involved in the perception of strigolactone, OsMADS34 speculated to have a role in floral transition and RCN1 involved in transition to flowering. On the other hand, the genes – CUC1, OsMADS3, OsMADS58 involved in organ development and floral meristem determination were found to be deregulated only in panicle tissues of RFL knockdown plants. These data point towards presence of distinct mechanisms for the development of AMs as tillers versus the development of panicle axillary as rachis branches. Overall, these data implicate genes involved in transition to flowering, axillary meristem development and floral meristem development are controlled by RFL in different meristems to thereby control plant architecture and transition to flowering.