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Excitotoxicity mediated by Ca2+-permeable GluR4-containing AMPA receptors involves the AP-1 transcription factor

Santos, A. E.; Duarte, C. B.; Iizuka, M.; Barsoumian, E. L.; Ham, J.; Lopes, M. C.; Carvalho, A. P.; Carvalho, A. L.
Fonte: Nature Publishing Group Publicador: Nature Publishing Group
Tipo: Artigo de Revista Científica
Português
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65.84%
Cells preferentially expressing GluR4-containing alpha-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA) receptors are particularly sensitive to excitotoxicity mediated through non-N-methyl-D-aspartate receptors. However, the excitotoxic signalling pathways associated with GluR4-containing AMPA receptors are not known. In this work, we investigated the downstream signals coupled to excitotoxicity mediated by Ca2+-permeable GluR4-containing AMPA receptors, using a HEK 293 cell line constitutively expressing the GluR4flip subunit of AMPA receptors (HEK-GluR4). Glutamate stimulation of GluR4-containing AMPA receptors decreased cell viability, in a calcium-dependent manner, when the receptor desensitisation was prevented with cyclothiazide. The excitotoxic stimulation mediated through GluR4-containing AMPA receptors increased activator protein-1 (AP-1) DNA-binding activity. Inhibition of the AP-1 activity by overexpression of a c-Jun dominant-negative form protected HEK-GluR4 cells against excitotoxic damage. Taken together, the results indicate that overactivation of Ca2+-permeable GluR4-containing AMPA receptors is coupled to a death pathway mediated, at least in part, by the AP-1 transcription factor

Cdx2, cytokeratin 20, thyroid transcription factor 1, and prostate-specific antigen expression in unusual subtypes of prostate cancer

LEITE, Katia Ramos Moreira; MITTELDORF, Cristina A. T. S.; Srougi, Miguel; DALL`OGLIO, Marcos F.; ANTUNES, Alberto A.; PONTES JR., Jose; CAMARA-LOPES, Lulz Heraldo
Fonte: ELSEVIER SCIENCE INC Publicador: ELSEVIER SCIENCE INC
Tipo: Artigo de Revista Científica
Português
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There are some unusual histologic variants of prostate carcinoma, including mucinous, signet-ring cells, and ductal carcinomas that can metastasize in a problematic way and simulate lung, colorectal, or bladder primaries. Currently, antibodies that are organ-specific have been used in the routine surgical pathology practice. Our aim is to study the profile of expression of Cdx2, thyroid transcription factor 1 (TTF1), and cytokeratin 20 (CK20) in prostate cancer with unusual histologic finding. Twenty-nine prostate adenocarcinomas with unusual histologic findings were submitted to immunohistochemistry with prostate-specific antigen (PSA), CK20, Cdx2, and TTF1 antibodies. There were 7 mucinous, 5 ductal, 2 signet-ring cells, and 15 usual acinar adenocarcinomas with focal mucinous differentiation. To compare the results with usual acinar adenocarcinomas, we studied 10 primary and their respective lymph node metastases in a tissue microarray, 2 unusual metastatic adenocarcinomas, and 6 usual acinar high-grade carcinomas. For tumors with special histologic finding, Cdx2 was expressed by 9 (31.0%) mucinous, signet-cell, or with focal mucinous differentiation. Thyroid transcription factor I was moderately positive in mucinous differentiation areas of 2 (6.9%) adenocarcinomas. Cytokeratin 20 was expressed by 9 (31.0%) tumors...

Toxicidade causada pela cocaína in vitro: participação da via dopaminérgica e do fator de transcrição NF-kB.; In vitro cocaine toxicity: participation of the dopaminergic pathway and the transcription factor NF-kB.

Lepsch, Lucília Brochado
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 18/04/2008 Português
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A cocaína é uma droga amplamente utilizada, e seu abuso está associado a inúmeros problemas de ordem física, psiquiátrica e social. Anormalidades em recém-nascidos têm sido reportadas devido aos efeitos tóxicos da cocaína durante o desenvolvimento fetal. O mecanismo pelo qual a cocaína causa danos neurológicos é muito complexo e envolve interações da droga com diversos sistemas de neurotransmissão, como o aumento dos níveis extracelulares de dopamina e radicais livres e a modulação de fatores de transcrição. Neste estudo investigamos a toxicidade causada pela cocaína em culturas primárias de estriado e mesencéfalo e cultura de linhagem de células dopaminérgicas (PC 12). Observamos que a exposição à cocaína causou morte destas células. Na cultura primária de mesencéfalo, a morte celular foi revertida pelo prétratamento com superóxido dismutase (SOD). A exposição à cocaína também induziu a inibição do prolongamento dos neuritos nessas culturas primárias. Já na cultura de células PC 12, a cocaína ativou os fatores de transcrição NF-kB e CREB (após 6 horas), que regulam a transcrição de genes envolvidos na morte celular. O GBR 12909 (inibidor da recaptação de dopamina), a lidocaína (anestésico local) e a dopamina não ativaram o NF-kB de maneira semelhante à cocaína...

Estudo do fator de transcrição Max no hipocampo de camundongos adolescentes submetidos a um modelo de submissão social prolongada.; Study of the Max transcription factor in the adolescent mice hippocampus subjected to a model of prolonged social defeat.

Amaral, Camila Ematne do
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Dissertação de Mestrado Formato: application/pdf
Publicado em 22/10/2012 Português
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Transtornos depressivos afetam de 1-6% dos adolescentes a cada ano ao redor do mundo. Esse aparecimento precoce anuncia uma doença mais grave e persistente na vida adulta, sendo considerada a terceira principal causa de suicídio na faixa etária entre 14-29 anos. Os exatos mecanismos moleculares envolvidos na fisiopatologia da depressão ainda não são compreendidos, e muitos estudos destacam o processo de apoptose como um possível mecanismo de contribuição para a depressão relacionada ao estresse crônico. Desta forma, o objetivo deste trabalho foi avaliar os efeitos da submissão social em camundongos machos adolescentes, sobre comportamentos emocionais e sobre a localização celular hipocampal do fator de transcrição Max. Metodologia: Camundongos machos adolescentes, C57BL/6, foram submetidos durante 21 dias consecutivos a um modelo de submissão social e ambos os grupos, experimental (n=16) e controle (n=16) foram analisados nos aspectos comportamental, expressão gênica e localização da proteína Max. Resultados: Dados retidos devido à solicitação (publicação de dados, patentes ou diretos autorais).; Depressive disorders affect 1-6% of adolescents each year around the world. This early appearance heralds a more serious and persistent disease in adulthood...

Influencia do fator de transcrição MEF2C na hipertrofia miocardica induzida por sobrecarga pressorica em camundongos; Influence of the transcription factor MEF2 in cardiac hypertrophy induced by overload pressure in mice

Ana Helena Macedo Pereira
Fonte: Biblioteca Digital da Unicamp Publicador: Biblioteca Digital da Unicamp
Tipo: Dissertação de Mestrado Formato: application/pdf
Publicado em 05/08/2008 Português
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Doenças do coração são freqüentemente associadas à hipertrofia miocárdica. Estímulos mecânicos induzem o crescimento hipertrófico e contribuem para a degeneração e morte dos miócitos cardíacos. Dentre os fatores de transcrição envolvidos no processo de hipertrofia miocárdica, estão os da família MEF2 (Myocyte Enhancer Factor-2), que é composto por 4 membros, MEF2A, B, C e D. O MEF2C é descrito como o principal transcrito no miocárdio. Tanto a deleção quanto a hiperexpressão de seu gene causam efeitos deletérios na formação e na função do músculo cardíaco. Estudos anteriores do nosso laboratório demonstraram que o MEF2 é ativado por estiramento de cardiomiócitos e influencia a expressão de genes do programa hipertrófico. O presente estudo tem como objetivo avaliar os efeitos do silenciamento gênico do MEF2C nas alterações estruturais e funcionais do ventrículo esquerdo de camundongos submetidos à sobrecarga pressórica. Para isso, utilizamos a técnica de interferência por RNA para o MEF2C. A padronização constituiu de: 1) avaliação do silenciamento do MEF2C em cultura de células C2C12 e no ventrículo esquerdo de camundongos Swiss; 2) determinação da dose necessária de siRNA para o silenciamento da expressão protéica do MEF2C; 3) determinação do curso temporal do silenciamento; 4) avaliação dos efeitos do tratamento com molécula irrelevante de siRNA direcionada para a proteína exógena GFP; 5) avaliação da especificidade do silenciamento (off-targets) pela análise do RNAm para o MEF2A e das proteínas FAK...

Modulation of the expression of the transcription factor Max in rat retinal ganglion cells by a recombinant adeno-associated viral vector

Petrs-Silva,H.; Chiodo,V.; Chiarini,L.B.; Hauswirth,W.W.; Linden,R.
Fonte: Associação Brasileira de Divulgação Científica Publicador: Associação Brasileira de Divulgação Científica
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/03/2005 Português
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Exclusion of the transcription factor Max from the nucleus of retinal ganglion cells is an early, caspase-independent event of programmed cell death following damage to the optic axons. To test whether the loss of nuclear Max leads to a reduction in neuroprotection, we developed a procedure to overexpress Max protein in rat retinal tissue in vivo. A recombinant adeno-associated viral vector (rAAV) containing the max gene was constructed, and its efficiency was confirmed by transduction of HEK-293 cells. Retinal ganglion cells were accessed in vivo through intravitreal injections of the vector in rats. Overexpression of Max in ganglion cells was detected by immunohistochemistry at 2 weeks following rAAV injection. In retinal explants, the preparation of which causes damage to the optic axons, Max immunoreactivity was increased after 30 h in vitro, and correlated with the preservation of a healthy morphology in ganglion cells. The data show that the rAAV vector efficiently expresses Max in mammalian retinal ganglion cells, and support the hypothesis that the Max protein plays a protective role for retinal neurons.

Molecular characterization of the Jatropha curcas JcR1MYB1 gene encoding a putative R1-MYB transcription factor

Li,Hui-Liang; Guo,Dong; Peng,Shi-Qing
Fonte: Sociedade Brasileira de Genética Publicador: Sociedade Brasileira de Genética
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/09/2014 Português
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The cDNA encoding the R1-MYB transcription factor, designated as JcR1MYB1, was isolated from Jatropha curcas using rapid amplification of cDNA ends. JcR1MYB1 contains a 951 bp open reading frame that encodes 316 amino acids. The deduced JcR1MYB1 protein was predicted to possess the conserved, 56-amino acid-long DNA-binding domain, which consists of a single helix-turn-helix module and usually occurs in R1-MYBs. JcR1MYB1 is a member of the R1-MYB transcription factor subfamily. A subcellular localization study confirmed the nuclear localization of JcR1MYB1. Expression analysis showed that JcR1MYB1 transcripts accumulated in various examined tissues, with high expression levels in the root and low levels in the stem. JcR1MYB1 transcription was up-regulated by polyethylene glycol, NaCl, and cold treatments, as well as by abscisic acid, jasmonic acid, and ethylene treatment. Analysis of transgenic tobacco plants over-expressing JcR1MYB1 indicates an inportant function for this gene in salt stress.

Transcription Factor Networks in Drosophila melanogaster

Rhee, David Young
Fonte: Harvard University Publicador: Harvard University
Tipo: Thesis or Dissertation
Português
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Differential gene expression is an essential component of the programs that give rise to specific cellular fates and functions. This differential regulation occurs primarily at the transcriptional level and is controlled by complex regulatory networks governed by the action of transcription factors at specific DNA regulatory elements. Transcription factors rarely act alone, often functioning through combinatorial interactions with other transcription factors, co-factors and chromatin-remodeling proteins. Defining these protein-protein interactions is an essential component to understanding transcription factor function and consequently, the cell as an integrated network.

Regulation of MAPK activation, AP-1 transcription factor expression and keratinocyte differentiation in wounded fetal skin

Gangnuss, S.; Cowin, A.; Daehn, I.; Hatzirodos, N.; Rothnagel, J.; Varelias, A.; Rayner, T.
Fonte: Blackwell Publishing Inc Publicador: Blackwell Publishing Inc
Tipo: Artigo de Revista Científica
Publicado em //2004 Português
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Fetal epithelium retains the ability to re-epithelialize a wound in organotypic culture in a manner not dependent on the presence of underlying dermal substrata. This capacity is lost late in the third trimester of gestation or after embryonic day 17 (E(17)) in the rat such that embryonic day 19 (E(19)) wounds do not re-epithelialize. Moreover, wounds created in E(17) fetuses in utero heal in a regenerative, scar-free fashion. To investigate the molecular events regulating re-epithelialization in fetal skin, the wound-induced expression profile and tissue localization of activator protein 1 (AP-1) transcription factors c-Fos and c-Jun was characterised in E(17) and E(19) skin using organotypic fetal cultures. The involvement of mitogen-activated protein kinase (MAPK) signaling in mediating wound-induced transcription factor expression and wound re-epithelialization was assessed, with the effect of wounding on the expression of keratinocyte differentiation markers determined. Our results show that expression of AP-1 transcription factors was induced immediately by wounding and localized predominantly to the epidermis in E(17) and E(19) skin. c-fos and c-jun induction was transient in E(17) skin with MAPK-dependent c-fos expression necessary for the re-epithelialization of an excisional wound in organotypic culture. In E(19) skin...

Functional characterization of GATA3 mutations causing the hypoparathyroidism-deafness-renal (HDR) dysplasia syndrome: insight into mechanisms of DNA binding by the GATA3 transcription factor

Ali, A.; Christie, P.; Grigorieva, I.; Harding, B.; Van Esch, H.; Ahmed, S.; Bitner-Glindzicz, M.; Blind, E.; Bloch, C.; Christin, P.; Clayton, P.; Gecz, J.; Gilbert-Dussardier, B.; Guillen-Navarro, E.; Hackett, A.; Halac, I.; Hendy, G.; Lalloo, F.; Mache
Fonte: Oxford Univ Press Publicador: Oxford Univ Press
Tipo: Artigo de Revista Científica
Publicado em //2007 Português
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The hypoparathyroidism-deafness-renal (HDR) dysplasia syndrome is an autosomal dominant disorder caused by mutations of the dual zinc finger transcription factor, GATA3. We investigated 21 HDR probands and 14 patients with isolated hypoparathyroidism for GATA3 abnormalities. Thirteen different heterozygous germline mutations were identified in patients with HDR. These consisted of three nonsense mutations, six frameshifting deletions, two frameshifting insertions, one missense (Leu348Arg) mutation and one acceptor splice site mutation. The splice site mutation was demonstrated to cause a pre-mRNA processing abnormality leading to the use of an alternative acceptor site 8 bp downstream of the normal site, resulting in a frameshift and prematurely terminated protein. Electrophoretic mobility shift assays (EMSAs) revealed three classes of GATA3 mutations: those that lead to a loss of DNA binding which represent over 90% of all mutations, and involved a loss of the carboxy-terminal zinc finger; those that resulted in a reduced DNA-binding affinity; and those (e.g. Leu348Arg) that did not alter DNA binding or the affinity but likely altered the conformational change that occurs during binding in the DNA major groove as predicted by a three-dimensional modeling. These results elucidate further the molecular mechanisms underlying the altered functions of mutants of this zinc finger transcription factor and their role in causing this developmental anomaly. No mutations were identified in patients with isolated hypoparathyroidism...

Predicting distinct organization of transcription factor binding sites on the promoter regions: a new genome-based approach to expand human embryonic stem cell regulatory network

Hosseinpour, B.; Bakhtiarizadeh, M.; Khosravi, P.; Ebrahimie, E.
Fonte: Elsevier Science BV Publicador: Elsevier Science BV
Tipo: Artigo de Revista Científica
Publicado em //2013 Português
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Self-proliferation and differentiation into distinct cell types have been made stem cell as a promising target for regenerative medicine. Several key genes can regulate self-renewal and pluripotency of embryonic stem cells (hESCs). They work together and build a transcriptional hierarchy. Coexpression and coregulation of genes control by common regulatory elements on the promoter regions. Consequently, distinct organization and combination of transcription factor binding sites (TFBSs modules) on promoter regions, in view of order and distance, lead to a common specific expression pattern within a set of genes. To gain insights into transcriptional regulation of hESCs, we selected promoter regions of eleven common expressed hESC genes including SOX2, LIN28, STAT3, NANOG, LEFTB, TDGF1, POU5F1, FOXD3, TERF1, REX1 and GDF3 to predict activating regulatory modules on promoters and discover key corresponding transcription factors. Then, promoter regions in human genome were explored for modules and 328 genes containing the same modules were detected. Using microarray data, we verified that 102 of 328 genes commonly upregulate in hESCs. Also, using output data of DNA-protein interaction assays, we found that 42 of all predicted genes are targets of SOX2...

Kausale Zusammenhänge der Expression des Transkriptionsfaktorgens TEC1, des Regulatorgens BCR1 und des Agglutiningens ALS3 in Candida albicans; Causal links between gene expression of the transcription factor TEC1, gene regulator BCR1 and Agglutinin ALS3 in Candida albicans

Ley, Claudia
Fonte: Universidade de Tubinga Publicador: Universidade de Tubinga
Tipo: Dissertação
Português
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C. albicans ist der häufigste humanpathogene Pilz. Dabei ermöglicht ihm insbesondere seine Fähigkeit zur Ausprägung zweier unterschiedlicher morphologischer Wachstumsformen (Hyphen- und Hefeform) eine spezifische Anpassung an die jeweiligen Umgebungsverhältnisse im Wirt. Zum einen wird durch die Ausbildung von Hyphen eine bessere Adhärenz und auch eine erleichterte Invasion der äußeren Zellbarriere erreicht, zum anderen erfolgt in der Hefeform eine effizientere Dissemination im menschlichen Blutkreislauf. Der Übergang zwischen den verschiedenen Wachstumsformen wird durch ein komplexes Netzwerk verschiedener Signaltransduktionswege reguliert. Eine tragende Rolle kommt hierbei dem Transkriptionsfaktor Tec1p, einem Mitglied der TEA/ATTS-Transkriptionsfaktoren-Familie, zu. Dieser übt einen regulativen Effekt auf zahlreiche hyphenspezifische Gene aus, unter anderem auf BCR1 und ALS3. Dabei ist nach wie vor unklar, durch welche Wechselwirkung auf DNA-Ebene Tec1p diesen Effekt entfaltet. Es sind sowohl eine direkte Bindung über spezifische TCS-Motive als auch indirekte Wirkungen über Induktion anderer Transkriptionsfaktoren denkbar. So geht man zwar davon aus, dass Bcr1p einen direkten Effekt auf die ALS3-Expression hat (Argimón et al...

A screen for transcription factor targets of glycogen synthase kinase-3 highlights an inverse correlation of NFκB and androgen receptor signaling in prostate cancer

Campa Fernández, Víctor Manuel; Baltziskueta, Eder; Bengoa Vergniory, Nora; Gorroño Etxebarria, Irantzu; Wesołowski, Radosław; Waxman, Jonathan; Kypta, Robert M.
Fonte: Impact Journals Publicador: Impact Journals
Tipo: info:eu-repo/semantics/article; publishedVersion
Português
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Expression of Glycogen Synthase Kinase-3 (GSK-3) is elevated in prostate cancer and its inhibition reduces prostate cancer cell proliferation, in part by reducing androgen receptor (AR) signaling. However, GSK-3 inhibition can also activate signals that promote cell proliferation and survival, which may preclude the use of GSK-3 inhibitors in the clinic. To identify such signals in prostate cancer, we screened for changes in transcription factor target DNA binding activity in GSK-3-silenced cells. Among the alterations was a reduction in AR DNA target binding, as predicted from previous studies, and an increase in NFκB DNA target binding. Consistent with the latter, gene silencing of GSK-3 or inhibition using the GSK-3 inhibitor CHIR99021 increased basal NFκB transcriptional activity. Activation of NFκB was accompanied by an increase in the level of the NFκB family member RelB. Conversely, silencing RelB reduced activation of NFκB by CHIR99021. Furthermore, the reduction of prostate cancer cell proliferation by CHIR99021 was potentiated by inhibition of NFκB signaling using the IKK inhibitor PS1145. Finally, stratification of human prostate tumor gene expression data for GSK3 revealed an inverse correlation between NFκB-dependent and androgen-dependent gene expression...

Transcription factor-based biosensors enlightened by the analyte

Fernández López, Raúl; Ruiz González, Raúl; Cruz Calahorra, Fernando de la; Moncalián Montes, Gabriel
Fonte: Frontiers Publicador: Frontiers
Tipo: info:eu-repo/semantics/article; publishedVersion
Português
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Whole cell biosensors (WCBs) have multiple applications for environmental monitoring, detecting a wide range of pollutants. WCBs depend critically on the sensitivity and specificity of the transcription factor (TF) used to detect the analyte. We describe the mechanism of regulation and the structural and biochemical properties of TF families that are used, or could be used, for the development of environmental WCBs. Focusing on the chemical nature of the analyte, we review TFs that respond to aromatic compounds (XylS-AraC, XylR-NtrC, and LysR), metal ions (MerR, ArsR, DtxR, Fur, and NikR) or antibiotics (TetR and MarR). Analyzing the structural domains involved in DNA recognition, we highlight the similitudes in the DNA binding domains (DBDs) of these TF families. Opposite to DBDs, the wide range of analytes detected by TFs results in a diversity of structures at the effector binding domain. The modular architecture of TFs opens the possibility of engineering TFs with hybrid DNA and effector specificities. Yet, the lack of a crisp correlation between structural domains and specific functions makes this a challenging task.

BOLITA, an Arabidopsis AP2/ERF-like transcription factor that affects cell expansion and proliferation/differentiation pathways

Marsch-Martinez, Nayelli; Greco, Raffaella; Becker, Jorg D.; Dixit, Shital; Bergervoet, Jan H. W.; Karaba, Aarati Aarati; de Folter, Stefan; Pereira, Andy
Fonte: Springer Publicador: Springer
Tipo: Artigo de Revista Científica
Publicado em /12/2006 Português
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The BOLITA (BOL) gene, an AP2/ERF transcription factor, was characterized with the help of an activation tag mutant and overexpression lines in Arabidopsis and tobacco. The leaf size of plants overexpressing BOL was smaller than wild type plants due to a reduction in both cell size and cell number. Moreover, severe overexpressors showed ectopic callus formation in roots. Accordingly, global gene expression analysis using the overexpression mutant reflected the alterations in cell proliferation, differentiation and growth through expression changes in RBR, CYCD, and TCP genes, as well as genes involved in cell expansion (i.e. expansins and the actin remodeling factor ADF5). Furthermore, the expression of hormone signaling (i.e. auxin and cytokinin), biosynthesis (i.e. ethylene and jasmonic acid) and regulatory genes was found to be perturbed in bol-D mutant leaves

Elucidation of a peribacteroid membrane-bound bHLH transcription factor required for legume nitrogen fixation.

Loughlin, Patrick Charles
Fonte: Universidade de Adelaide Publicador: Universidade de Adelaide
Tipo: Tese de Doutorado
Publicado em //2007 Português
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65.95%
Many legumes, including soybean, are agriculturally important crop plants. Legumes are unique in their ability to form an endo-symbiosis with soil borne bacteria collectively called rhizobia, which allows the plant to access atmospheric di-nitrogen via the bacteria. The interface between the legume and differentiated, intracellular rhizobia (called bacteroids) is a plant derived membrane called the peribacteroid membrane (PBM). This membrane has a unique complement of proteins, which are required to maintain the bacteroids' environment and allow bi-directional transport of solutes. One such PBM protein from soybean is GmSAT1 (Glycine max symbiotic ammonium transporter 1) which was initially characterised as a PBM-Iocalised ammonium transporter based on its ability to complement an ammonium transport-deficient yeast strain 26972c (Kaiser et al., 1998). Subsequent research however, has suggested that GmSA T1 is not directly involved in ammonium transport (Marini et al., 2000). This project sought to shed some light on the functional role of this intriguing protein. GmSAT1 is unusual in that it has both high homology with known transcription factors of the basic Helix-Loop-Helix (bHLH) family, as well as a predicted C-terminal transmembrane domain. Conservative amino acid substitutions within the bHLH transcription factor domain of GmSAT1 completely abolished the ability of the protein to complement growth of the ammonium transport-deficient yeast 26972c on low ammonium medium. The localisation of GmSAT1 in both soybean and a yeast expression system were examined in depth using immunolocalisation...

Regulation of the neuronal transcription factor NPAS4 by REST and microRNAs

Bersten, D.; Wright, J.; McCarthy, P.; Whitelaw, M.
Fonte: Elsevier BV Publicador: Elsevier BV
Tipo: Artigo de Revista Científica
Publicado em //2014 Português
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65.92%
NPAS4 is a brain restricted, activity-induced transcription factor which regulates the expression of inhibitory synapse genes to control homeostatic excitatory/inhibitory balance in neurons. NPAS4 is required for normal social interaction and contextual memory formation in mice. Protein and mRNA expression of NPAS4 is tightly coupled to neuronal depolarization and most prevalent in the cortical and hippocampal regions in the brain, however the precise mechanisms by which the NPAS4 gene is controlled remain unexplored. Here we show that expression of NPAS4 mRNA is actively repressed by RE-1 silencing transcription factor/neuron-restrictive silencer factor (REST/NRSF) in embryonic stem cells and non-neuronal cells by binding multiple sites within the promoter and Intron I of NPAS4. Repression by REST also appears to correlate with the binding of the zinc finger DNA binding protein CTCF within Intron I of NPAS4. In addition, we show that the 3' untranslated region (3'UTR) of NPAS4 can be targeted by two microRNAs, miR-203 and miR-224 to further regulate its expression. miR-224 is a midbrain/hypothalamus enriched microRNA which is expressed from an intron within the GABAA receptor epsilon (GABRE) gene and may further regionalize NPAS4 expression. Our results reveal REST and microRNA dependent mechanisms that restrict NPAS4 expression to the brain.; David C. Bersten...

Analysis of optimized DNase-seq reveals intrinsic bias in transcription factor footprint identification

He, Housheng Hansen; Meyer, Clifford A.; Hu, Sheng'en Shawn; Chen, Mei-Wei; Zang, Chongzhi; Liu, Yin; Rao, Prakash K.; Fei, Teng; Xu, Han; Long, Henry; Liu, X. Shirley; Brown, Myles
Fonte: Harvard University Publicador: Harvard University
Tipo: Artigo de Revista Científica
Português
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66%
DNase-seq is a powerful technique for identifying cis-regulatory elements across the genome. We studied the key experimental parameters to optimize the performance of DNase-seq. We found that sequencing short 50-100bp fragments that accumulate in long inter-nucleosome linker regions is more efficient for identifying transcription factor binding sites than using longer fragments. We also assessed the potential of DNase-seq to predict transcription factor occupancy through the generation of nucleotide-resolution transcription factor footprints. In modeling the sequence-specific DNaseI cutting bias we found a surprisingly strong effect that varied over more than two orders of magnitude. This confounds DNaseI footprint analysis to the extent that the nucleotide resolution cleavage patterns at most transcription factor binding sites are derived from intrinsic DNaseI cleavage bias rather than from specific protein-DNA interactions. In contrast, quantitative comparison of DNaseI hypersensitivity between states can predict transcription factor occupancy associated with particular biological perturbations.

Transcription factor Ap-2 alpha is necessary for development of embryonic melanophores, autonomic neurons and pharyngeal skeleton in zebrafish

d’Alencon, Claudia; Eisen, Judith S.; Yelon, Deborah; Cornell, Robert A.; Bonde, Gregory; Gelb, Bruce D.; Allende Connelly, Miguel Luis; Li, Wei; Schoenebeck, Jeff; O’Brien, Erin K.
Fonte: ACADEMIC PRESS INC ELSEVIER SCIENCE Publicador: ACADEMIC PRESS INC ELSEVIER SCIENCE
Tipo: Artículo de revista
Português
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The genes that control development of embryonic melanocytes are poorly defined. Although transcription factor Ap-2a is expressed in neural crest (NC) cells, its role in development of embryonic melanocytes and other neural crest derivatives is unclear because mouse Ap-2a mutants die before melanogenesis. We show that zebrafish embryos injected with morpholino antisense oligonucleotides complementary to ap-2a (ap-2a MO) complete early morphogenesis normally and have neural crest cells. Expression of c-kit, which encodes the receptor for the Steel ligand, is reduced in these embryos, and, similar to zebrafish c-kit mutant embryos, embryonic melanophores are reduced in number and migration. The effects of ap-2a MO injected into heterozygous and homozygous c-kit mutants support the notion that Ap-2a works through C-kit and additional target genes to mediate melanophore cell number and migration. In contrast to c-kit mutant embryos, in ap-2a MO-injected embryos, melanophores are small and under-pigmented, and unexpectedly, analysis of mosaic embryos suggests Ap-2a regulates melanophore differentiation through cell non-autonomous targets. In addition to melanophore phenotypes, we document reduction of other neural crest derivatives in ap-2a MO-injected embryos...

A statistical model relating transcription factor concentrations to positional information in the early Drosophila embryo

Ilsley, Garth Robert
Fonte: Berkeley Drosophila Transcription Network Project (for associated data file); University of Cambridge; European Bioinformatics Institute Publicador: Berkeley Drosophila Transcription Network Project (for associated data file); University of Cambridge; European Bioinformatics Institute
Tipo: Thesis; doctoral; PhD
Português
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The idea of morphogen gradients encoding positional information for a developing organism has long been discussed in the field of developmental biology, but only recently have quantitative models been proposed that relate measured transcription factor concentrations to enhancer activity. However, successful models are typically computationally time-consuming, thus limiting full exploration and interpretation of the data. This thesis addresses these problems using standard statistical techniques applied to a comprehensive data set with the even skipped (eve) locus as a test case. The first part of the thesis introduces the data set. This is the precellular Virtual Embryo from the Berkeley Drosophila Transcription Network project. It comprises expression measurements of almost 100 genes in more than 6,000 individual nuclei at six time points. Different modelling approaches are evaluated in the context of this data set leading to a justification of logistic regression and the methods used to prepare the data set for further analysis. The second part applies logistic regression to describe the response of the eve enhancers to known regulating transcription factors such as Hunchback. Predictions of behaviour under regulator perturbation are consistent with experimental results and the functional form is shown not to be arbitrarily flexible...