Complex systems are those which exhibit one or more of the following inter-related behaviours: 1. Nonlinear behaviour: the component parts do not act in linear ways, that is the superposition of the actions of the parts is not the output of the system. 2. Emergent behaviour: the output of the system may be inexpressible in terms of the rules or equations of the component parts. 3. Self-organisation: order appears from the chaotic interactions of individuals and the rules they obey. 4. Layers of description: in which a rule may apply at some higher levels of description but not at lower layers. 5. Adaptation: in which the environment becomes encoded in the rules governing the structure and/or behaviour of the parts (in this case strictly agents) that undergo selection in which those that are by some measure better become more numerous than those that are not as “fit”. A single cell is a complex system: we cannot explain all of its behaviour as simply the sum of its parts. Similarly, DNA structures, social networks, cancers, the brain, and living beings are intricate complex systems. This thesis tackles all of these topics from a complex systems approach. I have skirted some of the philosophical issues of complex systems and mainly focussed on appropriate tools to analyse these systems, addressing important questions such as: • What is the best way to extract information from DNA? • How can we model and analyse mutations in DNA? • Can we determine the likely spread of both viruses and ideas in social networks? • How can we model the growth of cancer? • How can we model and analyse interactions between genes in such living systems as the fruit fly, cancers, and humans? • Can complex systems techniques give us some insight into the human brain? / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1290759 / Thesis (Ph.D.)-- School of Electrical and Electronic Engineering, 2007

Lymphomas are neoplasms of the human immune system and can be divided into two categories, Hodgkin’s lymphoma (HL) and non-Hodgkin lymphoma (NHL). Anaplastic large cell lymphoma (ALCL) is a form of NHL that shares a common distinctive feature with HL, the overexpression CD30. The expression of cytokine receptor CD30 is restricted to proliferating B and T lymphocytes in healthy individuals while its overexpression is associated with several lymphoproliferative diseases such as ALCL and HL. The activation of CD30 via ligand or antibodies triggers various cellular responses ranging from apoptosis to cell proliferation and it is thought that the variable cellular response to CD30 activation may be due to cell surface levels of CD30. The human CD30 gene is regulated at the transcriptional level and previous studies characterising its promoter have identified several factors that regulate the expression this gene. However none of these identified factors explain for the high levels of CD30 observed in HL and ALCL. Therefore this study focused on the identification and functional analysis of transcriptionally active regions located up or downstream of the CD30 promoter region. The first aim for this study was to identify and characterise regions within the human CD30 gene that are involved in its transcriptional regulation. Phylogenetic footprinting identified several regions downstream of the CD30 promoter that displayed high levels of sequence homology indicating potential functional significance. Validation of these regions through two in vivo approaches, DNase 1 hypersensitivity assay and chromatin accessibility studies localised potential transcriptionally active regions to intron 1 of the CD30 gene.

Thesis (Ph. D.)--University of Missouri--Columbia, 1997. / Typescript. Vita. Includes bibliographical references (leaves : 144-159). Also available on the Internet.

Thesis (M.S.)--Miami University, Dept. of Zoology, 2005. / Title from first page of PDF document. Document formatted into pages; contains [1], ix, 75 p. : ill. Includes bibliographical references (p. 69-75).

Thesis (M.S.)--University of Missouri--Columbia, 2004. / Typescript. Vita. Includes bibliographical references (leaves 70-75). Also issued on the Internet.

Interferons are known cytokines that display antiviral, anti-proliferative and immuno-modulatory functions in the host. Interferon-gamma (Ifnγ) is the only type II family interferon that binds to the heterodimeric receptor consisting of two subunits, IfnγR1 and IfnγR2. This specific interaction between Ifnγ and its receptor triggers the activation of Janus Kinase (Jak) – Signal Transducer and Activator of Transcription (Stat) pathway. This triggers a cascade of events leading to modulation of a wide variety of genes resulting in a plethora of responses including antimicrobial activities, induction of Major Histocompatibility Complex encoded molecules etc. The impact of Ifnγ in regulating host defense is observed in patients who lack functional IFNγ or its receptor as they succumb to less virulent strains of intracellular bacteria such as Mycobacterium and Salmonella. Also, mice lacking important downstream signaling components such as Stat1 and Interferon Regulated Factor 1 (Irf1) are known to be highly susceptible to a variety of bacterial and viral infections. Consequently, studies on uncharacterized signaling and regulatory molecules downstream to Ifnγ are of great interest. The modulatory functions of Ifnγ have been attributed to its ability to regulate the expression of a vast number of genes in a Stat1 and Irf1 dependent manner. Also, gene regulation in response to Ifnγ in a target cell such as mouse hepatoma cell line, H6, can be categorized broadly into two subsets: Reactive Oxygen Species (ROS) - Reactive Nitrogen Intermediates (RNI) dependent (e.g. Nos2, Catalase, Id2 etc.) as well as ROS – RNI independent (e.g. Tap1, Lmp2 etc.). However, the effect of Ifnγ induced ROS and RNI in the regulation of the expression of genes at the level of transcriptome and how these could impact cellular and host responses are not well characterized. To investigate these questions, we standardized an in vitro Ifnγ responsive primary cell culture system using mouse adherent peritoneal macrophages (PMs). It needs to be highlighted that this study has, primarily, utilized unstimulated resident PMs. The adherent cells from the peritoneal cavity were positive for macrophage markers such as F4/80 and CD11b, but negative for granulocyte marker Gr1. Also, PMs were resistant to Ifnγ induced cell death, unlike cell lines such as the mouse fibroblast cell line L929, for the time points studied. There are three distinct parts to this study involving the system of PMs: I. To understand the contribution of Nitric Oxide (NO) in regulating the expression of novel Ifnγ responsive genes, PMs from C57BL/6 mice and mice lacking nitric oxide synthase 2 (Nos2-/-), the enzyme isoform responsible for the generation of NO in PMs, were stimulated with Ifnγ for 8 h and microarray analysis was performed. Detailed analysis led to identification of several annotated genes that were uniquely regulated in C57BL/6 and Nos2-/- PMs. Further analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database identified several differentially regulated pathways. Interestingly, a large number of metabolism related pathways, Butirosin and neomycin, Galactose, Phenylalanine and glyoxylate and dicarboxylate, were specifically up-regulated in the C57BL/6 PMs treated with Ifnγ. Similarly, other metabolism related pathways were differentially regulated by Ifnγ in PMs from C57BL/6 and Nos2-/- mice. One of the pathways that was up regulated in a Nos2 dependent manner in the C57BL/6 PMs upon Ifnγ treatment was that of circadian rhythm, which consisted of genes Per1, Bhlhb2 and Bhlhb3. All three are known circadian rhythm regulators, with Bhlhb2 and Bhlhb3 being transcriptional repressors that bind to E-box consensus sequence (CANNTG) as heterodimers, using the basic helix-loop-helix (bHLH) domains, along with other transcriptional regulators. Both Bhlhb2 and Bhlhb3 were up regulated at RNA and protein levels in a kinetic manner upon Ifnγ treatment in L929 cells. Studies with inhibitors to ROS and RNI revealed that up regulation of Bhlhb2 and Bhlhb3 was RNI, but not ROS, dependent in response to Ifnγ. Interestingly, the RNI inhibitor, NG-Methyl-L-Arginine (LNMA) rescued Ifnγ induced ROS. On the other hand, ROS inhibitors, e.g. Apocyanin and polyethylene glycol Catalase (PEG-Catalase), did not affect the nitrite amounts in the supernatant. These experiments suggested that RNI was upstream to ROS in L929 cells and both contributed to Ifnγ induced cell death. The knockdown of Bhlhb3 using specific siRNAs in the untreated L929 cells increased Bhlhb2 amounts, but not vice versa. This observation is consistent with the fact that Bhlhb3 is a known repressor of Bhlhb2. However, this repression of Bhlhb2 by Bhlhb3 was not detected upon Ifnγ treatment in L929 cells possibly because of heterodimerization of Bhlhb3 with other Ifnγ induced transcriptional modulators. Finally, knockdown of either of the proteins did not affect induced nitrite but decreased ROS amounts resulting in significant rescue of Ifnγ induced cell death of L929 cells. Thus, Bhlhb2 and Bhlhb3 are novel Ifnγ induced proteins that are NO dependent and contribute to Ifnγ induced cell death. Ifnγ and Nos2 are known to elicit antibacterial defense in the host. Interestingly, recent studies have implicated circadian rhythm to regulate bacterial infection in mice. Therefore, regulation of both Bhlhb2 and Bhlhb3 upon Ifnγ treatment and during Salmonella enterica Serovar Typhimurium (S. typhimurium) infection in the bone marrow derived macrophages (BMDMs) was performed. Both Bhlhb2 and Bhlhb3 were induced in a Nos2 dependent manner upon Ifnγ addition in BMDMs. Similar to L929 cells, Bhlhb3 repressed Bhlhb2 in the untreated BMDMs. Also, infection of BMDMs with S. typhimurium increased the protein amounts of Bhlhb2, while repressing Bhlhb3. Importantly, knockdown of Bhlhb2 resulted in higher colony forming units (CFU), whereas knockdown of Bhlhb3 reduced CFU in BMDMs 18 h post infection with S. typhimurium. Thus, Bhlhb2 induced whereas Bhlhb3 repressed antibacterial defense in BMDMs. The exact mechanism downstream to these two proteins and their inter-relationship in regulating S. typhimurium infection is of considerable interest and will be studied in future. II. Macrophages are known to produce a large number of different cytokines and chemokines upon activation. To identify novel cytokines and chemokines that may be differentially regulated in response to Ifnγ, a protein array was performed using the supernatants of C57BL/6 PMs treated with and without Ifnγ. Chemokine Ccl3 was found to be repressed by Ifnγ in the supernatant of PMs. Further analysis using Enzyme Linked Immuno-Sorbent Assay (ELISA) revealed that both Ccl3 and Ccl4, highly homologous proteins that chemo-attract almost all types of leukocytes, were repressed upon Ifnγ treatment. This response was ligand and cell specific as Lip polysaccharide (LPS) stimulation of PMs and Ifnγ stimulation of thioglycollate elicited PMs did not result in repression of Ccl3 and Ccl4. Also, studies with fludarabine, an inhibitor to Stat1, revealed that the repression of Ccl3 and Ccl4 as well as induction of Cxcl10 in response to Ifnγ was Stat1 dependent. Importantly, the use of LNMA as well as PMs from Nos2-/- mice established the role of Nos2 in the repression of Ccl3 and Ccl4, but not Cxcl10 induction, in response to Ifnγ. Furthermore, activation of p38 Mapk, but not Jnk, was downstream to Nos2 activation and contributed functionally to the repression of Ccl3 and Ccl4 in response to Ifnγ. Finally, the transcriptional repressor, Activating Transcription Factor 3 (Atf3), was induced in a Stat1-Nos2-p38 Mapk dependent manner and knockdown of Atf3 using siRNAs established the functional role of the same in the repression of Ccl3 and Ccl4 in response to Ifnγ. Further, to understand the regulation of Ccl3 and Ccl4, their modulation upon S. typhimuirum infection of BMDMs was performed. Apart from regulating the CFU in BMDMs, Ifnγ and Nos2 functionally repressed Ccl3 and Ccl4 upon S. typhimurium infection. Oral infection of mice with S. typhimurium was performed and mice lacking Ifnγ and Nos2 were found to have greater CFU in their organs as well as more leukocytes in the infected liver sections in comparison to the infected C57BL/6 mice. Importanly, absence of Ifnγ as well as Nos2 increased the amounts of Ccl3 and Ccl4 in the sera upon S. typhimurium infection in comparison to the C57BL/6 infected mice. Overall, this part of the study identified Ifnγ and Nos2 to repress chemokines Ccl3 and Ccl4 in macrophages and in mice upon S. typhimurium infection. III. While working on the above mentioned studies, it was noticed that addition of Ifnγ to PMs induced in a dose and time dependent manner aggregation of cells. Experiments with LPS, TG PECs and BMDMs established that Ifnγ induced aggregation of PMs was ligand and cell type specific. A panel of cell surface integrins and selectins were screened for regulation upon Ifnγ addition, namely Icam1, Lfa1, CD11b, P-selectin and E-selectin. Most of the cell surface integrins were repressed by Ifnγ in a kinetic manner. Interestingly, CD11b as well as E-Selectin co-localized to the sites of interactions between the PMs upon Ifnγ treatment. Studies with Reopro, a purified F(ab’)2 to glycoprotein GPIIb that is also known to functionally block CD11b, revealed the functional contribution of CD11b during Ifn induced aggregation of PMs. Further, studies with specific inhibitors identified RNI, but not ROS, to contribute to Ifnγ induced PM aggregation. Also, lack of Nos2 in PMs upon Ifnγ treatment resulted in minimal aggregation together with morphological changes, e.g. flattening of cells. Since differences in the morphology of PMs was observed in the absence of Nos2 upon Ifnγ treatment, the regulation and roles of cytoskeleton proteins, Actin and tubulin, during Ifnγ induced aggregation of PMs was studied. Upon Ifnγ stimuli, actin and tubulin get stabilized. On the other hand, the absence of Nos2 leads to depolymerization of actin, while tubulin failed to stabilize to the membrane, in response to Ifnγ. Further, addition of actin and tubulin depolymerizing agents, Cytochalasin D and Colcemid respectively, decreased Ifnγ induced aggregation of PMs. Live cell imaging studies revealed that PMs needed actin, but not tubulin or CD11b, for mobility. Upon Ifnγ treatment, PMs from C57BL/6 mice exhibited reduced mobility and aggregated with each other. The Nos2-/- PMs exhibited lower mobility compared to C57BL/6 PMs and, upon Ifnγ treatment, underwent morphological changes with time, e.g. flattening. On the other hand, Nos2 is important for endogenous mobility and maintaining the cellular morphology in response to Ifnγ. To understand the physiological relevance of our observations, oral infection of C57BL/6 and Nos2-/- mice with S. typhimurium was performed. Four days post infection, no significant differences in the number of peritoneal cells were found. Importantly, PMs from infected Nos2-/- mice had higher CFU in comparison to C57BL/6 mice. However, the amounts of cytokines such as Ifnγ, Tnfα, Il6 and Il1β in the peritoneal lavage were not significantly different between the two infected strains. Interestingly, PMs isolated from infected Nos2-/- mice displayed distinct morphology, e.g. flattening. In comparison, infected C57BL/6 PMs aggregated when cultured for 24 h in vitro. In the future, it will be interesting to address the functional roles of aggregates of macrophages during physiologically relevant responses such as combating intracellular bacterial infection. This part of the study adds a new dimension to the ability of Ifnγ in the regulation of macrophage-macrophage interactions and their roles during intracellular bacterial infections. Overall, the present study has elucidated hitherto uncharacterized roles of Nos2 and mechanisms involved in regulation of novel functional responses of PMs to Ifnγ and during S. typhimurium infection.

L’expression des gènes chez les organismes eucaryotes est un processus hautement régulé dans l’espace et dans le temps. Les ARN messagers, premièrement décrits comme simples intermédiaires entre l’ADN et les protéines, s’avèrent être des éléments centraux de la régulation de l’expression génique :les régulations post-transcriptionnelles vont influencer la stabilité, la traductibilité et la localisation des ARN messagers (ARNm). Le contrôle de la dégradation des ARNm est un moyen efficace d’adapter rapidement la production des protéines en fonction des besoins de la cellule. La dégradation des ARNm est un processus actif qui nécessite soit l’élimination de la coiffe en 5’ ou de la queue polyA en 3’, soit un clivage endonucléolytique. Dans la plupart des cas, le messager est premièrement déadénylé, puis décoiffé avant d’être dégradé dans le sens 5’-3’ ou dans le sens 3’-5’. De plus, les ARNm en cours de dégradation sont relocalisés dans des granules cytoplasmiques appelés Processing Bodies où les facteurs de la dégradation sont concentrés. On trouve dans les messagers codant pour des protéines dont la production doit être finement régulée, une variété importante d’éléments régulateurs (éléments cis) le plus souvent au sein de leur région 3’ non traduite. La régulation de la stabilité d’ARNm porteurs d’éléments riches en adénine et uridine (ARE) dans leur région 3’ non traduite (3’UTR) par les protéines capables de reconnaitre et lier ces éléments (ARE-BP) constitue un des exemples les plus documentés de régulations post-transcriptionnelles de l’expression des gène, mais le mécanisme moléculaire de cette régulation est encore mal compris.<p>Nous avons utilisé le messager codant pour le peptide antimicrobien CécropineA1 lié par l’ARE-BP dTIS11 comme modèle pour étudier les régulations post-transcriptionnelles dépendantes des ARE chez la drosophile. Au cours de ce travail, nous avons démontré que le messager CecA1 subit une déadénylation biphasique. En effet, une déadénylation initiale racourcie la queue polyA sans diminuer la quantité de messager, puis une seconde déadénylation, prise en charge par le complexe de déadénylation CCR-NOT nécessite la présence de la protéine dTIS11 et conduit à la dégradation totale du transcrit. L’observation des intermédiaires de la dégradation nous montre que, après sa déadénylation totale, le messager est décoiffé, puis dégradé dans les deux directions: 3’-5’ et 5’-3’. Contrairement à ce qui a été montré pour ces homologues mammifères, la protéine dTIS11 n’induit pas l’accumulation du messager CecA1 dans les Processing Bodies mais favorise la deuxième phase de déadénylation alors que le messager CecA1 est associé à la machinerie de traduction afin d’induire une dégradation rapide et efficace du transcrit.<p> / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

L'ADN mitochondrial des plantes est dynamique et son expression est complexe. Par la voie naturelle d'import d'ARN de transfert codés par le noyau, nous avons adressé dans les mitochondries d'Arabidopsis l'ARN orf77 caractéristique de la S-CMS du maïs et nous avons analysé les effets sur le transcriptome mitochondrial. Celui-ci s'est avéré strictement régulé durant le développement et fortement tamponné aux stades précoces. L'adressage mitochondrial de l'orf77 a aussi promu un cross-talk avec le noyau. D'autre part, la réplication et la réparation de l'ADN dans les mitochondries de plante impliquent une recombinaison active contrôlée par des facteurs codés par le noyau. Nous avons identifié l'exonucléase 5'-3' potentiellement responsable de la résection des extrémités de l'ADN dans la réparation par recombinaison des cassures double-brin. Nos résultats ouvrent des perspectives pour la génération de diversité génétique mitochondriale et la création de lignées CMS d'intérêt agronomique. / The mitochondrial DNA of plants is dynamic and its expression is complex. Using a strategy based on the natural import of nuclear-encoded transfer RNAs from the cytosol, we targeted to mitochondria in Arabidopsis thaliana the orf77 RNA characteristic for S-CMS in maize and we analyzed the effects on the transcriptome. The results showed that the mitochondrial transcriptome is tighly regulated during plant development and is strongly buffered at early stages. Mitochondrial targeting of orf77 also triggered a cross-talk with the nucleus. On the other hand, DNA replication and repair in plant mitochondria involve active recombination controled by nuclear-encoded factors. We identified a new member of this set of factors, the 5'-3' exonuclease potentially responsible for the resection of DNA ends in recombination-mediated repair of double-strand breaks. As a whole, the results open prospects for generating mitochondrial genetic diversity and creating CMS lines with agronomical interest.

Plant reproductive development begins when vegetative shoot apical meristems change their fate to inflorescence meristems which develop floral meristems on the flanks. This process of meristem fate change and organ development involves regulated activation and/or repression of many cell fate determining factors that execute down-stream gene expression cascades. Flowers are formed when floral organs are specified on the floral meristem in four concentric whorls. In the model dicot plant Arabidopsis, the identity and pattern of floral organs is determined by combined actions of MADS-domain containing transcription factors of the classes A, B, C, D and E. Rice florets are produced on a compact higher order branch of the inflorescence and have morphologically distinct non-reproductive organs that are positioned peripheral to the male and female reproductive organs. These unique outer organs are the lemma and palea that create a closed floret internal to which are a pair of lodicules that are asymmetrically positioned fleshy and reduced petal-like organs. The unique morphology of these rice floret organs pose intriguing questions on how evolutionary conserved floral meristem specifying and organ fate determining factors bring about their distinct developmental functions in rice. We have studied the functions for two rice MADS-box proteins, OsMADS2 and OsMADS1, to understand their role as master regulators of gene expression during rice floret meristem specification and organ development. OsMADS2; a transcriptional regulator of genes expression required for lodicule development Arabidopsis B-function genes AP3 and PI are stably expressed in the whorl 2 and 3 organ primordia and they together with other MADS-factors (Class A+E or C+E) regulate the differentiation of petals and stamens (Jack et al, 1992; Goto and Meyerowitz, 1994). Rice has a single AP3 ortholog, SPW1 (OsMADS16) but has duplicated PI-like genes, OsMADS2 and OsMADS4. Prior studies in our lab on one of these rice PI-like genes OsMADS2 showed that it is needed for lodicule development but is dispensable for stamen specification (Kang et al., 1998; Prasad and Vijayraghavan, 2003). Functional divergence between OsMADS2 and OsMADS4 may arise from protein divergence or from differences in their expression patterns within lodicule and stamen whorls. In this study, we have examined the dynamic expression pattern of both rice PI-like genes and have examined the likelihood of their functional redundancy for lodicule development. We show OsMADS2 transcripts occur at high levels in developing lodicules and transcripts are at reduced levels in stamens. In fully differentiated lodicules, OsMADS2 transcripts are more abundant in the distal and peripheral regions of lodicules, which are the tissues that are severely affected in OsMADS2 knock-down florets (Prasad and Vijayraghavan, 2003). The onset of OsMADS4 expression is in very young floret meristems before organ primordia emergence and this is expressed before OsMADS2. In florets undergoing organogenesis, high level OsMADS4 expression occurs in stamens and carpels and transcripts are at low level in lodicules (Yadav, Prasad and Vijayraghvan, 2007). Thus, we show that these paralogous genes differ in the onset of their activation and their stable transcript distribution within lodicules and stamens that are the conserved expression domains for PI-like genes. Since the expression of OsMADS4 in OsMADS2 knock-down florets is normal, our results show OsMADS2 has unique functions in lodicule development. Thus our data show subfunctionalization of these paralogous rice PI-like genes. To identify target genes regulated by OsMADS2 that could contribute to lodicule differentiation, we have adopted whole genome transcript analysis of wild-type and dsRNAiOsMADS2 panicles with developing florets. This analysis has identified potential down-stream targets of OsMADS2 many of which encode transcription factors, components of cell division cycle and signalling factors whose activities likely control lodicule differentiation. The expression levels of few candidate targets of OsMADS2 were examined in various floret organs. Further, the spatial expression pattern for four of these down-stream targets of OsMADS2 was analysed and we find overlap with OsMADS2 expression domains (Yadav, Prasad and Vijayraghvan, 2007). The predicted functions of these OsMADS2 target genes can explain the regulation of growth and unique vascular differentiation of this short fleshy modified petal analog. OsMADS1, a rice E-class gene, is a master regulator of other transcription factors and auxin and cytokinin signalling pathways In Arabidopsis four redundant SEPALLATA factors (E-class) are co-activators of other floral organ fate determining MADS-domain factors (classes ABCD) and thus contribute to floral meristem and floral organ development (Krizek and Fletcher, 2005). Among the grass-specific sub-clade of SEP-like genes, rice OsMADS1 is the best characterized. Prior studies in our lab showed that OsMADS1 is expressed early throughout the floret meristem before organ primordia emergence and later is restricted to the developing lemma and palea primordia with weak expression in carpel (Prasad et al, 2001). Stable expression continues in these floret organs. OsMADS1 plays critical non-redundant functions to specify a determinate floret meristem and also regulates floret organ identities (Jeon et al., 2000; Prasad et al, 2001; 2005; Agarwal et al., 2005; Chen et al., 2006). In the present study, we have adopted two different functional genomic approaches to identify genes down-stream of OsMADS1 in order to understand its mechanism of action during floret development. We have studied global transcript profiles in WT and dsRNAiOsMADS1 panicles and find OsMADS1 is a master regulator of a significant fraction of the genome’s transcription factors and also a number of genes involved in hormone-dependent cell signalling. We have validated few representative genes for transcription factors as targets regulated by OsMADS1. In a complementary approach, we have determined the consequences of induced-ectopic over-expression of a OsMADS1:ΔGR fusion protein in shoot apical meristems of transgenic plants. Transcript levels for candidate target genes were assessed in induced tissues and compared to mock-treated meristems and also with meristems induced for OsMADS1:ΔGR but blocked for new protein synthesis. These analyses show that OsMADS55 expression is directly regulated by OsMADS1. Importantly, OsMADS55 is related to SVP that plays an important role in floral transition and floral meristem identity in Arabidopsis. OsHB3 and OsHB4, homeodomain transcription factors, with a probable role in meristem function, are also directly regulated by OsMADS1. The regulation of such genes by OsMADS1 can explain its role in floret meristem specification. In addition to regulating other transcription factors, OsMADS1 knock-down affects expression of genes encoding proteins in various steps of auxin and cytokinin signalling pathways. Our differential expression profiling showed OsMADS1 positively regulates the auxin signalling pathway and negatively regulates cytokinin mediated signalling events. Through our induced ectopic expression studies of OsMADS1:ΔGR, we show OsMADS1 directly regulates the expression of OsETTIN2, an auxin response transcription factor, during floret development. Overall, we demonstrate that OsMADS1 modulates hormonal pathways to execute its functions during floret development on the spikelet meristems. Functional studies of OsMGH3; an auxin-responsive indirect target of OsMADS1 To better understand the contribution of auxin signalling during floret development, we have functionally characterized OsMGH3, a down-stream indirect target of OsMADS1, which is a member of the auxin-responsive GH3 family. The members of this family are direct targets of auxin response factors (ARF) class of transcription factors. GH3-proteins inactivate cellular auxin by conjugating them with amino acids and thus regulate auxin homeostasis in Arabidopsis (Staswick et al., 2005). OsMGH3 expression in rice florets overlaps with that of OsMADS1 (Prasad et al, 2005). In this study, we have demonstrated the consequences of OsMGH3 over-expression and knock-down. The over-expression of OsMGH3 during vegetative development causes auxin-deficient phenotypes such as dwarfism and loss of apical dominance. Its over-expression in developing panicles that was obtained by driving its expression from tissue-specific promoters created short panicles with reduced branching. The latter is a phenotype similar to that observed upon over-expression of OsMADS1. In contrast, the down-regulation of endogenous OsMGH3 through RNA-interference produced auxin over-production phenotypes such as ectopic rooting from aerial nodes. Knock-down of OsMGH3 expression in florets affected carpel development and pollen viability both of which affect floret fertility. Taken together, this study provides evidence for the importance of auxin homeostasis and its transcriptional regulation during rice panicle branching and floret organ development. Our analysis of various conserved transcription factors during rice floret development suggest that factors like OsMADS2, OsMADS4 and OsMADS1 are master regulators of gene expression during floret meristem specification and organ development. The target genes regulated by these factors contribute to development of morphologically distinct rice florets.

Glicose e oxigênio são moléculas essenciais para a maioria dos organismos vivos. Além de sua importância nos processos de produção de energia - glicose como fonte de carbono e energia e oxigênio como aceptor dos elétrons doados por NADH e FADH2 - estes dois compostos funcionam como efetuadores, modulando vários processos metabólicos e fisiológicos nas células. Visto que a mitocôndria é um dos alvos afetados pelas disponibilidades destas duas moléculas, nós isolamos e seqüenciamos o genoma mitocondrial de Trichoderma reesei, um fungo multicelular empregado neste trabalho como sistema modelo. Foi estudado o efeito da variação de concentração de glicose e oxigênio sobre a expressão de transcritos do genoma mitocondrial, bem como sua implicação no metabolismo de glicose. São apresentadas análises da expressão gênica de aproximadamente 2000 transcritos de T. reesei submetido a concentrações limitantes de oxigênio dissolvido, realizadas com o emprego da técnica de microarrays de cDNA. Pelo menos 330 transcritos foram diferencialmente expressos em função da disponibilidade de oxigênio. Aqueles envolvidos nos processos de síntese protéica e divisão celular foram regulados negativamente, enquanto transcritos relacionados com funções de defesa celular e síntese de RNA foram positivamente regulados. Uma fração substancial de outros genes afetados pela baixa disponibilidade de oxigênio não possui, atualmente, funções celulares conhecidas. Esta observação deve contribuir para a posterior anotação funcional do genoma de T. reesei. Também foram identificados reguladores transcricionais diferencialmente expressos em baixas tensões de oxigênio. O perfil de expressão destes reguladores aponta-os como potenciais candidatos ao envolvimento com a expressão de genes afetados pela disponibilidade de oxigênio. / Glucose and oxygen are essential molecules in most of living organisms. In addition to their importance in production of energy - glucose as a carbon and energy source and oxygen as an acceptor of electrons donated by NADH and FADH2 - both molecules function as effectors modulating various metabolic and physiological processes in the cell. Because one of the targets affected by both molecules is the mitochondrion, we isolated and sequenced the mitochondrial genome of Trichoderma reesei, a multicellular fungus that is used in this study as a model system. The effect of varying the concentration of glucose and oxygen on the expression of the transcripts of the mitochondrial genome, and its implication on the metabolism of glucose, was studied. Gene-wide expression analyses of nearly 2000 transcripts of T. reesei under limited concentration of dissolved oxygen, using cDNA microarry technique, are presented. At least 330 transcripts were differentially expressed with respect to oxygen availability. Those involved in protein synthesis and cell division processes were downregulated, while transcripts involved in cell defense and RNA synthesis were upregulated. A substantive fraction of other anaerobically affected genes have currently unknown cellular roles, and these results should therefore contribute to further functional annotation of the genome. ln addition, we have identified transcriptional regulators that are differentially expressed at a low oxygen tensions. The expression profile of these regulators points them out as potential candidates involved in the expression of genes affected by oxygen availability.