Cotton fiber development is a fundamental biological phenomenon. In spite of its economical importance, a large proportion of cotton fiber initiation is unknown. A naked seed mutant (N1N1) was compared with its isogenic lines of cotton (Gossypium hirsutum, TM-1) using a 70-mer oligonucleotide microarray that contained 1,536 features designed from a subset of cotton fiber ESTs. Statistical analysis and quantitative RT-PCR identified 23 "fiber-associated" genes. The annotation suggested that the temporal regulation of genes involved in transcriptional and translational regulation, signal transduction, and cell differentiation during early stages of fiber development. To get a large view of fiber initiation, a new cotton oligonucleotide microarray was developed containing sequences from an ovule EST library from Gossypium hirsutum L. T̲M̲-1 immature o̲vules (GH_TMO), a set from Jonathan Wendel's lab at Iowa State University, and the pilot set of oligos used for previous study. Global gene expression studies were performed with microdissected fiber initials (or epidermis) and inner ovules to investigate fiber preferentially expressed genes. Laser capture microdissection and antisense RNA (aRNA) amplification allowed us to collect fiber initials (0 DPA and 2 DPA) or epidermal layers (-2 DPA) from whole ovule tissues. The gene expression profiles of fiber initials showed up-regulation of fiber proteins, myb transcription factors, and hormonal regulators as well as trichome related factors during fiber initiation. In each developmental stage, different sets of gene categories in molecular function or biological processes were over- or under-represented, suggesting temporal regulation of genes during fiber development. One of the possible "fiber associated genes" found in microarray analyses, RD22 like gene (GhRDL), was highly enriched in the epidermis of cotton ovules during fiber initiation. The function of GhRDL was studied with the Arabidopsis trichome system which shares many similarities with fiber development. Overexpression of 35S::GhRDL into Arabidopsis thaliana Columia-0 induced seed hairs (or seed trichomes) and pRDL:GUS was localized in Arabidopsis seeds. This suggests that GhRDL plays an important role in the seed trichome development and can be a key player in cell differentiation and fiber development. / text

As distrofias musculares formam um grupo amplo e heterogêneo de doenças genéticas, caracterizado basicamente pela degeneração e fraqueza muscular. Ao longo das últimas décadas muitos estudos vêm sendo realizados para a identificação dos genes causadores dessas doenças. Entretanto, apesar da identificação da mutação responsável pela grande maioria das formas descritas, os processos moleculares subjacentes ao defeito genético primário são muito complexos e ainda precisam ser melhor compreendidos. E a compreensão dos mecanismos de cada uma das formas é muito importante para o desenvolvimento adequado de terapias. A avaliação da expressão gênica global por microarranjos de DNA é uma ferramenta bastante poderosa, capaz de produzir uma grande quantidade de dados, delineando o panorama geral do estado do transcriptoma de um determinado tecido ou célula. Assim, os objetivos desse trabalho foram estudar os perfis de expressão do músculo de três linhagens de camundongos modelos de formas distintas de distrofia muscular (Dmdmdx, Largemyd-/- e Dmdmdx/Largemyd-/-) em diferentes fases da progressão da doença (21 dias, três meses e seis meses de idade), com o intuito de caracterizar o processo distrófico e como o perfil de expressão varia com a progressão da idade e a depender da mutação genética. Em cada um dos modelos e idades estudados identificamos um grande número de genes diferencialmente expressos (GDEs), refletindo a complexidade dessas doenças. A análise dos processos e vias biológicas nas quais esses genes estão envolvidos mostrou o forte envolvimento de componentes do sistema imunológico e inflamação, e também de genes relacionados com os processos de degeneração/regeneração e remodelamento da matriz extracelular. De modo geral, as funções biológicas alteradas são bem semelhantes entre as linhagens, sugerindo que apesar de as mutações serem em genes distintos, com funções diferentes, os processos moleculares que são afetados em decorrência dessas mutações são praticamente os mesmos. As maiores diferenças foram vistas na idade de 21 dias, especialmente na linhagem Dmdmdx que apresentou uma grande quantidade de GDEs, dos quais grande parte relacionada com a maior capacidade regenerativa dessa linhagem e, assim, são genes que podem explicar o porquê desses animais apresentarem um fenótipo benigno em relação aos pacientes humanos. A caracterização do modelo duplo-mutante Dmdmdx/Largemyd-/- mostrou que a junção das duas mutações não ocasiona alterações no transcriptoma distintas das obsevadas nas linhagens parentais, sendo que o perfil do duplo-mutante é mais próximo ao de seu parental Largemyd-/-, não apresentando a mesma capacidade regenerativa que o Dmdmdx / The muscular dystrophies form a large and heterogeneous group of genetic diseases, characterized mainly by progressive muscular degeneration and weakness. In the last decades, many studies have been carried on in order to identify the involved genes in these disorders. However, despite the identification of responsible mutations of the majority of the described forms, the underlying molecular processes to the primary mutation are very complex and are not fully understood. And to understand the mechanisms of each form is of major importance to the development of therapies. Global gene expression profiling by DNA microarrays is a powerful tool, able to yield a huge quantity of data, outlining the general landscape of the transcriptome of a given tissue or cell. In this sense, the objectives of this work were to study the expression profile of the muscles from three mice lineages, models for different forms of muscular dystrophy (Dmdmdx, Largemyd-/- and Dmdmdx/Largemyd-/-) in different phases of disease progression (21-day-old, three-month-old and six-month-old), in order to characterize the dystrophic process and how the expression profile changes according to aging and depending on the genetic mutation. In each model and age studied we identified a substantial number of differentially expressed genes (DEGs), reflecting the diseases\' complexity. The analysis of the biological processes and pathways in which these genes are implicated showed a strong involvement of immune system and inflammation components, and also genes related to degeneration/regeneration and extracellular matrix remodeling processes. Altogether, the altered biologic functions are very similar in lineages, suggesting that although mutations are in different genes, with diverse functions, the affected molecular processes due to these mutations are basically the same. The most notable differences were seen on 21-day-old, especially on Dmdmdx lineage that showed a great quantity of DEGs, many of which are related to the better regenerative capacity this lineage exhibits and, thus, they are genes that could explain why these animals manifest a mild phenotype in comparison to human patients. The characterization of the double mutant Dmdmdx/Largemyd-/- showed that the union of both mutations does not bring on alterations on the transcriptome different from those seen in the parental lineages, with the double mutant profile closer to its parental Largemyd-/-, not bearing the same regenerative capacity that Dmdmdx

As distrofias musculares formam um grupo amplo e heterogêneo de doenças genéticas, caracterizado basicamente pela degeneração e fraqueza muscular. Ao longo das últimas décadas muitos estudos vêm sendo realizados para a identificação dos genes causadores dessas doenças. Entretanto, apesar da identificação da mutação responsável pela grande maioria das formas descritas, os processos moleculares subjacentes ao defeito genético primário são muito complexos e ainda precisam ser melhor compreendidos. E a compreensão dos mecanismos de cada uma das formas é muito importante para o desenvolvimento adequado de terapias. A avaliação da expressão gênica global por microarranjos de DNA é uma ferramenta bastante poderosa, capaz de produzir uma grande quantidade de dados, delineando o panorama geral do estado do transcriptoma de um determinado tecido ou célula. Assim, os objetivos desse trabalho foram estudar os perfis de expressão do músculo de três linhagens de camundongos modelos de formas distintas de distrofia muscular (Dmdmdx, Largemyd-/- e Dmdmdx/Largemyd-/-) em diferentes fases da progressão da doença (21 dias, três meses e seis meses de idade), com o intuito de caracterizar o processo distrófico e como o perfil de expressão varia com a progressão da idade e a depender da mutação genética. Em cada um dos modelos e idades estudados identificamos um grande número de genes diferencialmente expressos (GDEs), refletindo a complexidade dessas doenças. A análise dos processos e vias biológicas nas quais esses genes estão envolvidos mostrou o forte envolvimento de componentes do sistema imunológico e inflamação, e também de genes relacionados com os processos de degeneração/regeneração e remodelamento da matriz extracelular. De modo geral, as funções biológicas alteradas são bem semelhantes entre as linhagens, sugerindo que apesar de as mutações serem em genes distintos, com funções diferentes, os processos moleculares que são afetados em decorrência dessas mutações são praticamente os mesmos. As maiores diferenças foram vistas na idade de 21 dias, especialmente na linhagem Dmdmdx que apresentou uma grande quantidade de GDEs, dos quais grande parte relacionada com a maior capacidade regenerativa dessa linhagem e, assim, são genes que podem explicar o porquê desses animais apresentarem um fenótipo benigno em relação aos pacientes humanos. A caracterização do modelo duplo-mutante Dmdmdx/Largemyd-/- mostrou que a junção das duas mutações não ocasiona alterações no transcriptoma distintas das obsevadas nas linhagens parentais, sendo que o perfil do duplo-mutante é mais próximo ao de seu parental Largemyd-/-, não apresentando a mesma capacidade regenerativa que o Dmdmdx / The muscular dystrophies form a large and heterogeneous group of genetic diseases, characterized mainly by progressive muscular degeneration and weakness. In the last decades, many studies have been carried on in order to identify the involved genes in these disorders. However, despite the identification of responsible mutations of the majority of the described forms, the underlying molecular processes to the primary mutation are very complex and are not fully understood. And to understand the mechanisms of each form is of major importance to the development of therapies. Global gene expression profiling by DNA microarrays is a powerful tool, able to yield a huge quantity of data, outlining the general landscape of the transcriptome of a given tissue or cell. In this sense, the objectives of this work were to study the expression profile of the muscles from three mice lineages, models for different forms of muscular dystrophy (Dmdmdx, Largemyd-/- and Dmdmdx/Largemyd-/-) in different phases of disease progression (21-day-old, three-month-old and six-month-old), in order to characterize the dystrophic process and how the expression profile changes according to aging and depending on the genetic mutation. In each model and age studied we identified a substantial number of differentially expressed genes (DEGs), reflecting the diseases\' complexity. The analysis of the biological processes and pathways in which these genes are implicated showed a strong involvement of immune system and inflammation components, and also genes related to degeneration/regeneration and extracellular matrix remodeling processes. Altogether, the altered biologic functions are very similar in lineages, suggesting that although mutations are in different genes, with diverse functions, the affected molecular processes due to these mutations are basically the same. The most notable differences were seen on 21-day-old, especially on Dmdmdx lineage that showed a great quantity of DEGs, many of which are related to the better regenerative capacity this lineage exhibits and, thus, they are genes that could explain why these animals manifest a mild phenotype in comparison to human patients. The characterization of the double mutant Dmdmdx/Largemyd-/- showed that the union of both mutations does not bring on alterations on the transcriptome different from those seen in the parental lineages, with the double mutant profile closer to its parental Largemyd-/-, not bearing the same regenerative capacity that Dmdmdx

The formation of blood, hematopoiesis, is a dynamic process originating from a small number of hematopoietic stem cells (HSCs). To sustain hematopoiesis throughout life HSCs have the unique capacity to differentiate into all mature hematopoietic lineages as well as generating more HSCs by a mechanism referred to as self-renewal. However, the regulation of these processes is largely unknown. During embryonic development HSCs expand in the fetal liver, indicating that this environment supports HSC self-renewal. The LIM-homeobox gene Lhx2 is expressed in the fetal liver during this period and Lhx2 null mutant mice die in utero due to severe anemia caused by an environmental defect in the fetal liver. Embryonic stem cells differentiate in vitro, forming embryoid bodies (EBs) containing various tissues including hematopoietic progenitor cells. Introduction of Lhx2 into this system by retroviral transfer led to the generation of cytokine dependent HSC-like cell lines that were multipotent and expressed surface markers similar to embryonic HSCs. However, the specificity and efficiency of this event could not be elucidated. To further evaluate the function of Lhx2 expression during hematopoietic development, Lhx2 was introduced into an ES cell system where expression could be efficiently turned on. This approach revealed that Lhx2 induce self-renewal of distinct multipotent hematopoietic progenitor/stem cells present in the EB, with the ability to form HSC-like cell lines. The Lhx2 induced self-renewal is growth factor specific since stem cell factor and interleukin-6 are necessary and sufficient for this process. However, Lhx2 expression blocked erythroid differentiation and interfered with early ES cell commitment, indicating that the effect of Lhx2 is cell type specific. Since HSCs of early embryonic origin are inefficient in engrafting adult recipients upon transplantation, we wanted to address whether we could generate cell lines retaining this capacity by expression of Lhx2 in hematopoietic cells from adult bone marrow. This led to the generation of clonal and cytokine dependent HSC-like cell lines capable of generating erythroid, myeloid and lymphoid cells upon transplantation into lethally irradiated recipients. When transplanted into stem cell-deficient mice, they contributed to circulating erythrocytes for at least 18 months, revealing a remarkable potential for self-renewal and differentiation in vivo. However, expression of Lhx2 was maintained in vivo and most engrafted mice developed a transplantable myeloproliferative disorder resembling human chronic myeloid leukemia. Thus, elucidation of the mechanism for Lhx2 function in HSC-like cell lines would give insights into both normal and pathological regulation of HSCs. Down-regulation of Lhx2 expression in HSC-like cell lines with inducible Lhx2 expression led to rapid loss of stem cell characteristics and differentiation into various hematopoietic cell types. Thus, global gene expression analysis comparing Lhx2+ HSC-like cell lines to their Lhx2- progeny would give insights into the molecular basis for Lhx2 function in stem cells. A number of differentially expressed genes overlapped with previously reported HSC enriched genes, further emphasizing the resemblance between HSCs and the HSC-like cell lines also at the molecular level. Moreover, a number of genes were identified with functions or expression patterns related to Lhx2 in other organs. Collectively, these data suggest that these HSC-like cell lines represent a relevant model system for normal HSCs on the molecular and the functional level as well as for evaluating Lhx2 function in the development of various tissues in the embryo as well as in disease.