Littérature scientifique sur le sujet « Gene PARL »
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Articles de revues sur le sujet "Gene PARL"
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Merhi, Rawan, Michael Kalyn, Amanda Zhu-Pawlowsky et Marc Ekker. « Loss of parla Function Results in Inactivity, Olfactory Impairment, and Dopamine Neuron Loss in Zebrafish ». Biomedicines 9, no 2 (18 février 2021) : 205. http://dx.doi.org/10.3390/biomedicines9020205.
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The presenilin-associated rhomboid-like (PARL) gene was found to contribute to mitochondrial morphology and function and was linked to familial Parkinson’s disease (PD). The PARL gene product is a mitochondrial intramembrane cleaving protease that acts on a number of mitochondrial proteins involved in mitochondrial morphology, apoptosis, and mitophagy. To date, functional and genetic studies of PARL have been mainly performed in mammals. However, little is known about PARL function and its role in dopaminergic (DA) neuron development in vertebrates. The zebrafish genome comprises two PARL paralogs: parla and parlb. Here, we established a loss-of-function mutation in parla via CRISPR/Cas9-mediated mutagenesis. We examined DA neuron numbers in the adult brain and expression of genes associated with DA neuron function in larvae and adults. We show that loss of parla function results in loss of DA neurons, mainly in the olfactory bulb. Changes in the levels of tyrosine hydroxylase transcripts supported this neuronal loss. Expression of fis1, a gene involved in mitochondrial fission, was increased in parla mutants. Finally, we showed that loss of parla function translates into impaired olfaction and altered locomotion parameters. These results suggest a role for parla in the development and/or maintenance of DA neuron function in zebrafish.
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Liu, J. F., S. L. Zhang, H. L. Tang, L. Z. Wu, L. J. Dong, L. D. Liu et W. L. Che. « Overexpression of an Aeluropus littoralis Parl. potassium transporter gene, AlHAK1, in cotton enhances potassium uptake and salt tolerance ». Euphytica 203, no 1 (26 novembre 2014) : 197–209. http://dx.doi.org/10.1007/s10681-014-1310-2.
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Istikharah, Rochmy, Aung Win Tun, Supannee Kaewsutthi, Pratibha Aryal, Bussaraporn Kunhapan, Wanphen Katanyoo, Wanicha Chuenkongkaew et Patcharee Lertrit. « Identification of the variants in PARL, the nuclear modifier gene, responsible for the expression of LHON patients in Thailand ». Experimental Eye Research 116 (novembre 2013) : 55–57. http://dx.doi.org/10.1016/j.exer.2013.08.007.
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Zhang, A.-Mei, Xiaoyun Jia, Qingjiong Zhang et Yong-Gang Yao. « No association between the SNPs (rs3749446 and rs1402000) in the PARL gene and LHON in Chinese patients with m.11778G>A ». Human Genetics 128, no 4 (14 août 2010) : 465–68. http://dx.doi.org/10.1007/s00439-010-0875-7.
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Ko, Kenton, Jeremy Guenther, Nicholas Ostan et Joshua Powles. « Analysis of the Arabidopsis organellar rhomboid At1g74140 transcript population uncovered splicing patterns different from its close relative At1g74130 ». F1000Research 8 (18 novembre 2019) : 1925. http://dx.doi.org/10.12688/f1000research.21219.1.
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Background: Four distinct rhomboid genes appear to function in Arabidopsis plastids, two “active” types from the secretases and presenilin-like associated rhomboid-like (PARL) categories (At1g25290 and At5g25752) and two “inactive” rhomboid forms (At1g74130 and At1g74140). The number of working rhomboids is further increased by alternative splicing, two reported for At1g25290 and three for At1g74130. Since At1g25290 and At1g74130 exist as alternative splice variants, it would be necessary to assess the splicing patterns of the other two plastid rhomboid genes, At5g25752 and At1g74140, before studying the Arabidopsis plastid rhomboid system as a whole. Methods: This study thus specifically focused on an analysis of the At1g74140 transcript population using various RT-PCR strategies. Results: The exon mapping results indicate splicing patterns different from the close relative At1g74130, despite similarity between the exonic sequences. The splicing patterns indicate a high level of sequence “discontinuity” in the At1g74140 transcript population with a significant portion of the discontinuity being generated by two regions of the gene. Conclusion: The overall discontinuous splicing pattern of At1g74140 may be reflective of its mode of involvement in activities like controlling gene expression.
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Powles, Joshua, Katharine Sedivy-Haley, Eric Chapman et Kenton Ko. « Characterization of three alternative splice variants associated with the Arabidopsis rhomboid protein gene At1g74130 ». Botany 91, no 12 (décembre 2013) : 840–49. http://dx.doi.org/10.1139/cjb-2013-0173.
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Rhomboid serine proteases are grouped into three main types — secretases, presenilin-like associated rhomboid-like (PARL) proteases, and “inactive” rhomboid proteins. Although the three rhomboid groups are distinct, the different types are likely to operate within the same cell or compartment, such as observed in the plastids of Arabidopsis. There are four distinct plastid rhomboid genes at play in Arabidopsis plastids, two for active types (At1g25290 and At5g25752) and two for inactive forms (At1g74130 and At1g74140). The number of working plastid rhomboids is further increased by alternative splicing, as reported for At1g25290. To understand how the plastid rhomboid system works, it is necessary to identify all rhomboid forms in play. To this end, this study was designed to examine the alternative splicing activities of At1g74130, one of the two genes encoding proteolytically “inactive” plastid rhomboids. The exon mapping and DNA sequencing results obtained here indicate the presence of three prominent alternative splice variants in the At1g74130 transcript population. The dominant splice variant, L, encodes the full-length protein. The other two splice variants, M and S, produce proteins lacking sections from the carboxyl transmembrane domain region. The splice variants M and S appear to be at levels with functional potential and appear to adjust relative to each other during development and in response to changes in the level of Tic40, a component of the plastid translocon. The splice variant proteins themselves exhibit different characteristics with respect to rhomboid protein–substrate interactions. These differences were observed in bacterial co-expression pull-down assays and in yeast mitochondrial studies. When considered together, the data suggest that the alternative splicing of At1g74130 bears functional significance in Arabidopsis and is likely to be part of a mechanism for diversifying plastid rhomboid function.
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Flores, Andrés, Javier López-Upton, Cristobal D. Rullán-Silva, Adriana E. Olthoff, Ricardo Alía, Cuauhtémoc Sáenz-Romero et José M. Garcia del Barrio. « Priorities for Conservation and Sustainable Use of Forest Genetic Resources in Four Mexican Pines ». Forests 10, no 8 (9 août 2019) : 675. http://dx.doi.org/10.3390/f10080675.
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The strategies for the conservation and sustainable use of forest genetic resources, which are essential for the future adaptation of forest species to changing environments, are also a source of valuable genetic resources for breeding and restoration activities. The first step to define and implement cost-effective strategies is to identify specific priority populations. Mexico, in spite of being characterized by high levels of tree species diversity, mostly lacks a combined strategy for the genetic conservation and use of forest genetic resources. The aims of this work are: (i) to identify areas for gene conservation, and (ii) to propose measures for the conservation and sustainable use of forest genetic resources of four pine species: Pinus greggii Engelm. ex Parl., Pinus oocarpa Schiede ex Schltdl., Pinus patula Schiede ex Schltdl. & Cham. and Pinus pseudostrobus Lindl. To do that, we use the existing information on the distribution, genetic variation and conservation and breeding efforts in Mexico. Overall, 51 areas for establishing genetic conservation units were prioritized and 6 genetic zones for the use of forest genetic resources in breeding and selection of forest reproductive material were identified. The current conservation efforts for the four priority Mexican pines should be improved to satisfy the needs of a national breeding and conservation network.
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Powles, Joshua, et Kenton Ko. « Alternative splice variants of rhomboid proteins : In silico analysis of database entries for select model organisms and validation of functional potential ». F1000Research 7 (1 février 2018) : 139. http://dx.doi.org/10.12688/f1000research.13383.1.
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Background: Rhomboid serine proteases are present in many species with sequenced genomes, and are often encoded in each species by more than one predicted gene. Based on protein sequence comparisons, rhomboids can be differentiated into groups - secretases, presenilin-like associated rhomboid-like (PARL) proteases, iRhoms, and “inactive” rhomboid proteins. Although these rhomboid groups are distinct, the different types can operate simultaneously. Studies in Arabidopsis showed that the number of rhomboid proteins working simultaneously can be further diversified by alternative splicing. This phenomenon was confirmed for the Arabidopsis plastid rhomboid proteins At1g25290 and At1g74130. Although alternative splicing was determined to be a significant mechanism for diversifying these two Arabidopsis plastid rhomboids, there has yet to be an assessment as to whether this mechanism extends to other rhomboids and to other species. Methods: We thus conducted a multi-year analysis of databases to determine if the alternative splicing mechanism observed for the two Arabidopsis plastid rhomboids was utilized in other species to expand the repertoire of rhomboid proteins. To help verify the in silico findings, select splice variants from different groups were tested for activity using transgenic- and additive-based assays. These assays aimed to uncover evidence that the selected splice variants display capacities to influence processes like antimicrobial sensitivity. Results: The multi-year in silico assessment for six model experimental species (human, mouse, Arabidopsis, Drosophila, nematode, and yeast) revealed robust usage of alternative splicing to diversify rhomboid protein structure across the various motifs or regions, especially in human, mouse and Arabidopsis. Subsequent validation studies uncover evidence that the splice variants selected for testing displayed functionality in the different activity assays. Conclusions: The combined results support the hypothesis that alternative splicing is likely used to diversify and expand rhomboid protein functionality, and this potentially occurred across the various motifs or regions of the protein.
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Powles, Joshua, et Kenton Ko. « Alternative splice variants of rhomboid proteins : Comparative analysis of database entries for select model organisms and validation of functional potential ». F1000Research 7 (31 mai 2018) : 139. http://dx.doi.org/10.12688/f1000research.13383.2.
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Background: Rhomboid serine proteases are present across many species and are often encoded in each species by more than one predicted gene. Based on protein sequence comparisons, rhomboids can be differentiated into groups - secretases, presenilin-like associated rhomboid-like (PARL) proteases, iRhoms, and “inactive” rhomboid proteins. Although these rhomboid groups are distinct, the different types can operate simultaneously. Studies in Arabidopsis showed that the number of rhomboid proteins working simultaneously can be further diversified by alternative splicing. This phenomenon was confirmed for the Arabidopsis plastid rhomboid proteins At1g25290 and At1g74130. Although alternative splicing was determined to be a significant mechanism for diversifying these two Arabidopsis plastid rhomboids, there has yet to be an assessment as to whether this mechanism extends to other rhomboids and to other species. Methods: We thus conducted a comparative analysis of select databases to determine if the alternative splicing mechanism observed for the two Arabidopsis plastid rhomboids was utilized in other species to expand the repertoire of rhomboid proteins. To help verify the in silico observations, select splice variants from different groups were tested for activity using transgenic- and additive-based assays. These assays aimed to uncover evidence that the selected splice variants display capacities to influence processes like antimicrobial sensitivity. Results: A comparison of database entries of six widely used eukaryotic experimental models (human, mouse, Arabidopsis, Drosophila, nematode, and yeast) revealed robust usage of alternative splicing to diversify rhomboid protein structure across the various motifs or regions, especially in human, mouse and Arabidopsis. Subsequent validation studies uncover evidence that the splice variants selected for testing displayed functionality in the different activity assays. Conclusions: The combined results support the hypothesis that alternative splicing is likely used to diversify and expand rhomboid protein functionality, and this potentially occurred across the various motifs or regions of the protein.
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Sawhney, Shikhar, Sandeep Bansal, Madhur Kalyan, Indu Verma, Ramandeep Singh Virk et Ashok Kumar Gupta. « Analysis of differential expression of protease-activated receptors in patients with allergic fungal rhinosinusitis ». Allergy & ; Rhinology 9 (janvier 2018) : 215265671876419. http://dx.doi.org/10.1177/2152656718764199.
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Background Ever since its characterization in the 1970s, allergic fungal rhinosinusitis (AFRS) has been the subject of much controversy, especially regarding its pathogenesis. In this study, we analyzed the differential expression of genes that encode protease-activated receptors (PAR) in patients with AFRS and patients with chronic rhinosinusitis, and tried to understand the pathogenic basis of this disease. Objective To analyze the differential expression of PAR genes in patients with AFRS and in patients with chronic rhinosinusitis. Methods Mucosa from ethmoid sinuses of 51 patients (tests and controls) was biopsied and evaluated for messenger RNA expression of PAR genes by using reverse transcriptase–polymerase chain reaction. Each of the four PAR genes, i.e., par1, par2, par3 and par4 was amplified, the final gene products were run on 1.8% agarose gel and analyzed by densitometry to calculate differential expression. The significance level was determined as p ≤ 0.05. Results It was observed that the expressions of all four par genes were higher in the test samples compared with the controls, but statistical significance was achieved only for par1 (p=0.004) and par2 (p=0.05). Comparative expression of the four PAR genes was also performed within the test and control groups, and a statistically significant difference was seen between par1 and par2 (p=0.007), par1 and par3 (p=0.029), par1 and par4 (p=0.0001), par2 and par4 (p=0.002), and par3 and par4 (p=0.009) in the test group. In the control group as well, par1, par2, and par3 exhibited a higher expression compared with par4 but the difference was significant between par3 and par4 genes only. Conclusion Patients with AFRS expressed increased levels of PAR genes in their nasal mucosa, and, of the four PAR genes, a higher expression of par1, par2, and par3 was observed in both the groups compared with par4. This information contributes toward our understanding of pathogenesis and possibly treatment of AFRS.
Thèses sur le sujet "Gene PARL"
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Semir, Frappart David de. « Reparación de mutaciones en el gent CFTR como estrategia de terapia génica para la fibrosis quística ». Doctoral thesis, Universitat Pompeu Fabra, 2005. http://hdl.handle.net/10803/7084.
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La fibrosis quística (fq) es la enfermedad autosómica recesiva más frecuente en la población caucasoide con una frecuencia de portadores de 1/25. Las manifestaciones clínicas más importantes son las infecciones crónicas recurrentes del pulmón conllevando al deterioro del mismo. En esta tesis nos propusimos corregir dos mutaciones en el gen cftr, responsable de la fq, en la linea celular de epitelio bronquial ib3.1 de genotipo (f508del/w1282x). Para ello, mediante citometría de flujo y microscopía confocal pusimos a punto la incorporación no viral (vectores pei, geneporter y citofectina) de oligonucleótidos modificados (quimeraplastos y oligonucleótidos fosforotioato) y de fragmentos sfhr en estas células. Los quimeraplastos son oligonucléotidos quiméricos de rna y dna y los oligonucleótidos fosforotioato contienen enlaces fosforotioato para evitar su degradación además de enlaces fosfodiéster. Ambos, son capaces de estimular los mecanismos de reparación intrínsecos de las células para corregir a nivel de dna mutaciones puntuales. Los fragmentos sfhr (small fragment homologous replacement) son fragmentos de pcr de longitud variable con la secuencia salvaje del gen que se intercambian con las secuencias genómicas diana mutadas por recombinación homóloga para revertir mutaciones puntuales (cambios de 1 nucleótido, pequeñas inserciones o deleciones). Para estimar el porcentaje de corrección génica adaptamos la técnica diagnóstica de pcr-ola a nuestro modelo para utilizarla como metodología de cuantificación. Además, hemos confirmado que las células ib3.1 tienen los mecanismos de reparación de mutaciones puntuales activos tanto por rt-pcr como por un ensayo in vitro en e.coli con el plásmido pksm4021 que contiene el gen de resistencia a ampicilina y el gen de resistencia a kanamicina inactivado por una mutación puntual. Los resultados que se publicaron en los siguientes artículos nos han permitido extraer las siguientes conclusiones: las células Ib3.1 de epitelio bronquial de fq son competentes en cuanto al sistema de reparación mmr. La incorporación celular de quimeraplastos, oligonucleótidos monocadena y fragmentos sfhr es muy eficiente en las células ib3.1. El lípido catiónico citofectina, el policatión pei y la electroporación, aunque no el lípido catiónico geneporter, son sistemas de transfección eficientes para incorporar oligonucleótidos modificados en el núcleo de las células ib3.1. Los poliplejos de pei y los lipoplejos de citofectina son internalizados por distintos mecanismos aunque en ambos casos los oligonucleótidos modificados son degradados significativamente en las células ib3.1. El análisis genescan de electroferogramas fluorescentes constituye un sistema fiable, fácil, sensible y seguro para evaluar y cuantificar la degradación intracelular y extracelular de oligonucleótidos marcados con fluorescencia en fluidos biológicos. La tecnología de pcr-ola constituye un sistema fiable y preciso de cuantificación de reparación génica aplicable a modelos celulares heterocigotos. Los fragmentos sfhr pueden actuar como cebador artefactual en las reacciones de pcr y generar un artefacto que da lugar a falsos positivos en la detección de conversión génica. Es indispensable diseñar los cebadores de detección de la modificación génica fuera de la región de homología con los fragmentos sfhr. La corrección génica de mutaciones puntuales mediada por quimeraplastos, oligonucleótidos monocadena y fragmentos sfhr es un proceso ineficiente en las células ib3.1. Será necesario estimular los mecanismos endógenos de reparación génica para incrementar la frecuencia de reparación génica hasta niveles terapéuticos en dichas células.
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DASILIO, A. « Utilidade filogenética de genes nucleares em comparação com gene mitocondrial para Phyllostomidae (Chiroptera) ». Universidade Federal do Espírito Santo, 2016. http://repositorio.ufes.br/handle/10/3861.
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Previous issue date: 2016-02-25Phyllostomidae, da subordem Microchiroptera, é uma família com uma grande variedade morfológica e de hábitos alimentares, com mais gêneros do que qualquer outra família de morcegos. Porém um grande desafio tem sido a resolução de suas relações filogenéticas principalmente devido ao paralelismo evolutivo e convergência entre linhagens. Várias tentativas foram feitas para resgatar as relações dentro dessa família, a fim de reconstruir suas transições evolutivas e identificar as relações entre gêneros, desde estudos morfológicos a moleculares. Entretanto, estas pesquisas em sua maioria, tem usado principalmente o DNA mitocondrial, com pouco sucesso com marcadores nucleares. Estudos apresentando incongruências entre filogenias têm se expandido rapidamente, derivadas, principalmente, de dados morfológicos em face de análises moleculares, ou até mesmo entre as árvores baseadas em diferentes subconjuntos de seqüências moleculares. Diante deste cenário, este trabalho teve como objetivo fazer uma investigação filogenética de cinco genes (um mitocondrial e quatro nucleares) a fim de identificar marcadores nucleares que apresentassem os melhores resultados para Phyllostomidae. Isso ainda não havia sido reportado na literatura para filostomideos. Os genes selecionados para o estudo foram: dois éxons de genes nucleares recombination activating protein 2 (RAG2) e o gene for von Willebrand factor (VWF), dois íntrons Beta-Fibrinogênio (Fgb) e o B-spectrin non-erythrocytic 1 (SPTBN1), e um gene mitocondrial cytochrome oxidase subunit 1 (COI). A metodologia de obtenção das sequências nucleotídicas consistiu em extração do DNA total da célula, amplificação da região controle do DNA mitocondrial através da Reação em Cadeia da Polimerase, purificação do produto da PCR e sequenciamento. Sequências disponíveis no GenBank também foram utilizadas. Dentre os marcadores nucleares estudados os resultados das análises indicaram que o Beta-Fibrinogênio é o marcador nuclear mais promissor, estimulando futuros trabalhos moleculares com os morcegos filostomídeos utilizando esse gene. Palavras-chaves: Phyllostomidae, investigação filogenética, marcadores nucleares, DNA mitocondrial.
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Wagner, Priscilla Koch. « Uma nova abordagem para identificação da provável origem de genes exclusivos de bactérias ». Universidade de São Paulo, 2018. http://www.teses.usp.br/teses/disponiveis/100/100131/tde-24052018-175017/.
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A comparação de genomas, genes ou até sequências de nucleotídeos não condificantes é uma importante tarefa na qual a bioinformática pode ser aplicada, uma vez que ela auxiliar em diversas atividades, por exemplo, análises filogenéticas. Análise filogenética, por sua vez, busca analisar a relação evolutiva de cada espécie, considerando suas características genéticas. Esses processos e as técnicas que os implementam se baseiam em sequências de nucleotídeos sequenciadas e armazenadas em bancos de dados de genomas públicos. Com análise filogenética também é possível identificar possíveis origens de um gene. Essa tarefa é de grande importância, pois auxilia na identificação da origem de genes patogênicos, podendo auxiliar no combate e prevenção do surgimento de doenças. Um problema potencial dessas sequências é a possibilidade de haver erros nas anotações (marcações de sequências como genes). Esses erros são pouco explorados por pesquisadores atualmente. Outro tema pouco explorado é a análise filogenética de genes exclusivos, que são genes que se manifestam em apenas uma espécie, considerando um grupo de espécies próximas. A identificação de genes exclusivos de alguma espécie pode servir para a correta identificação de, por exemplo, a espécie que causa uma doença, de forma a permitir o uso do tratamento mais específico e adequado. A importância da descoberta de filogenias de genes exclusivos e a dificuldade de garantir a consistência nas anotações genéticas motivaram este trabalho, que teve como objetivo implementar ferramentas para interpretar dados de comparação genética, identificando potenciais erros em anotação de genes exclusivos e criando estratégias para identificar a origem desses genes. As origens de genes exclusivos exploradas neste trabalho envolvem a possibilidade dos genes exclusivos terem derivado de outras famílias de genes do próprio organismo, ou, os genes exclusivos se diferenciaram muito dos genes ancestrais. Essas hipóteses, juntamente com a hipótese da existência de erros de anotação, foram exploradas em experimentos utilizando as ferramentas desenvolvidas. Os experimentos visaram a analisar a aplicabilidade da estratégia desenvolvida. Foram utilizados genomas de bactérias do gênero Xanthomonas, que contém um grande grupo de bactérias que causam doenças em plantas. Os resultados obtidos demonstram que existe uma quantidade considerável de potenciais erros de anotação nos genomas considerados, provando a hipótese de que a inconsistência nas anotações genômicas possui grande influência para a dificuldade na identificação de filogenias (tanto de genes exclusivos como para não exclusivos). Os resultados também demonstraram que boa parte dos genes exclusivos possivelmente se originaram de outras famílias de genes do próprio genoma. Ou ainda, que esses genes sofreram modificações em relação aos genes ancestrais, mas ainda possuem certas semelhanças com sequências de nucleotídeos que não codificam genes em outras espécies mais distantes. Por fim, a estratégia desenvolvida se mostrou útil na análise filogenética das bactérias estudadas, sendo este um forte indício de que a mesma abordagem pode ser utilizada para problemas similares com outras espécies de seres vivosComparison of genomes, genes or even non-coding nucleotide sequences is an important task in which bioinformatics can be applied, since it allows the application of phylogenetic analyses. Phylogenetic analysis, in its turn, seeks to analyze the evolutionary relation of each species, considering its genetic characteristics. These processes and the techniques that implement them are based on nucleotide sequences sequenced and stores in databases of public genomes. With phylogenetic analysis it is also possible to identify possible origins of a gene. This task has a great importance, because it allows the identification of the origin of pathogenic genes, which may help to combat or prevent deseases. A potencial problem of these sequences is the possibility of having annotation errors (sequences marking as genes). These errors are little explored by researchers nowadays. Another unexplored topic is the phylogenetic analysis of exclusive genes, which are genes thaht manifest in only one species, considering a group of nearby species. The identification of exclusive genes of a species may serve to correctly identify, for example, a desease, in order to allow the use of a more especific and appropriate treatment. The importance of discovering phylogenies of exclusive genes and the difficulty of guaranteeing the consistency of genetic annotations motivated this work, whose objective was to implement tools to interpret data of genetic comparison, identifying annotation errors in exclusive genes and creating strategies to identify the origin of these genes.The origins of exclusive genes explored in this work involve the possibility of the exclusive genes have derived of other gene families of the organism itself, or, the exclusive genes differed a lot from the ancestral genes. Theses hypotheses, with the hypotesis of the existance of annotation errors, were explored in experiments using the developed tools. The experiments aimed to analyse the applicability of the developed strategy. Genomes of bacteria of the genus Xanthomonas were used, which contains a large group of bacteria that cause diseases in plants. The results show that there is a considerable amount of annotation errors on the genomes, proving the hypothesis that the inconsistency in genomic annotations has a great influence on the difficulty in identifying phylogenies (both exclusive and non-exclusive genes). The results also show that much of exclusive genes possibly originated from other gene families of the genome itself. Furthermore, these genes may have sufferedmodifications in relation to the ancestral genes, but still have certain similarities with nucleotide sequences that don\'t encode genes in other more distant species. Finally, the strategy developed proved useful on phylogenetic analysis of the studied bacteria, which is a strong indication that the same approach can be used for similar problems with other species of living beings
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Melo, Vinicius André Morais Rocha. « Construção de ferramentas para estudo da possível interação entre interferon-beta e p53 ». Universidade de São Paulo, 2009. http://www.teses.usp.br/teses/disponiveis/87/87131/tde-17082009-121304/.
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Formação de tumores deve-se a combinações de fatores. A via de p53 tem um papel fundamental no controle de proliferação e apoptose. O interferon-beta (IFNb) é importante na modulação da resposta imunológica, no efeito antitumoral e no impacto apoptótico em células tumorais. Segundo a literatura, IFNb ativa a transcrição de p53 e componentes do sistema IFN efetuam sua função pela via p53/p14arf. Neste projeto, foi construída uma série de ferramentas para explorar interações entre p53 e IFNb. A primeira ferramenta, uma linhagem celular derivada de B16 com expressão de p53 reduzida por miRNA. Também construímos vetores plasmidiais e adenovirais portadores dos cDNAs para eGFP, Luciferase, p53 ou IFNb. Os vetores são utilizados para introduzir estes fatores, sozinho ou combinados, na célula alvo. Mesmo confirmando a atividade de p53 ou IFNb sozinho, não foi observado um efeito aditivo destes fatores em conjunto com este tipo de ensaio. Futuros estudos das possíveis interações entre as vias de p53 e IFNb terão o benefício das ferramentas construídas neste projeto.Formation of tumors it must to combinations of factors. The p53 pathway has an essential role in proliferation control and apoptosis. The interferon-beta (IFNb) is important in modulation of the immunologic response, in the antitumoral effect and in the apoptotic impact in tumor cells. According to literature, IFNb activate the p53 transcription and components of IFN system effect its function to p53/p14arf pathway. In this project, a series of tools was constructed to explore interactions between p53 and IFNb. The first tool, a cellular lineage derivative of B16 with expression of p53 reduced by miRNA. We also construct plasmidial and adenoviral vectors carriers of cDNAs for eGFP, Luciferase, p53 or IFNb. The vectors are used to introduce these factors, alone or agreed, in the target cell. Even confirming the activity of p53 or IFNb alone, an additive effect of these factors combined was not observed with this type of assay. Future studies of the possible interactions between p53 and IFNb pathways will have the benefit of the tools constructed in this project.
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Fernandes, Jussara Gonçalves. « Análise comparativa dos processos inflamatórios agudo e crônico no tecido subcutâneo e exsudato em camundongos selecionados para máxima ou mínima inflamação ». Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/42/42133/tde-30012013-092920/.
Texte intégralRésumé :
Linhagens de camundongos AIRmax e AIRmin diferem quanto a reatividade inflamatória aguda às partículas de Biogel. A AIR divergente nessas linhagens está bem estabelecida, no entanto, diferenças na resposta inflamatória crônica ao Biogel ainda não foram descritas. Assim, nós decidimos verificar se o processo de seleção que modificou a resposta inflamatória aguda nessas linhagens, também afetou o desenvolvimento da resposta inflamatória crônica. A infiltração de células no exsudado da linhagem AIRmax foi maior que na linhagem AIRmin em ambos os períodos avaliados (48h e 30d), e no período de 48 horas, os animais AIRmax apresentaram alta produção de citocinas no exsudato inflamatório. Essa linhagem mostrou ainda maior número de genes ativados envolvidos na transdução de sinal, resposta imune e inflamatória. Alguns genes envolvidos com a resposta inflamatória aguda, também apresentaram diferenças após 30 dias. Esses resultados indicam que o processo de seleção para a inflamação aguda pode ter afetado também o desenvolvimento da resposta inflamatória crônica ao Biogel.AIRmax and AIRmin mouse lines differ in terms of acute inflammatory response after Biogel injection. The distinct AIR in these lines is well established, however, differences in late or chronic inflammatory response to Biogel were not described yet. Thus, we decided to check if the genetic selection that modified the acute inflammatory response in these lines, also affected the development of a chronic inflammatory response. We found that AIRmax mice had higher cellular influx in the inflammatory exudate than AIRmin mice in both analyzed periods (48h and 30d) and that after 48 hours of Biogel injection, AIRmax mice showed higher cytokine levels in inflammatory exudates. This line also showed higher number of up regulated genes in AIRmax than in AIRmin mice involved with inflammatory response, immune response and signal transduction. Some acute inflammatory response genes also showed differences on day 30. Our results indicate that the genetic selection for acute inflammatory response may also have affected the chronic inflammatory response to Biogel.
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Jaskowiak, Pablo Andretta. « Estudo de coeficientes de correlação para medidas de proximidade em dados de expressão gênica ». Universidade de São Paulo, 2011. http://www.teses.usp.br/teses/disponiveis/55/55134/tde-05052011-143134/.
Texte intégralRésumé :
O desenvolvimento da tecnologia de microarray tornou possível a mediçao dos níveis de expressão de centenas ou até mesmo milhares de genes simultaneamente para diversas condições experimentais. A grande quantidade de dados disponível gerou a demanda por métodos computacionais que permitam sua análise de forma eficiente e automatizada. Em muitos dos métodos computacionais empregados durante a análise de dados de expressão gênica é necessária a escolha de uma medida de proximidade apropriada entre genes ou amostras. Dentre as medidas de proximidade disponíveis, coeficientes de correlação têm sido amplamente empregados, em virtude da sua capacidade em capturar similaridades entre tendências das sequências numéricas comparadas (genes ou amostras). O presente trabalho possui como objetivo comparar diferentes medidas de correlação para as três principais tarefas envolvidas na análise de dados de expressão gênica: agrupamento, seleção de atributos e classificação. Dessa forma, é apresentada nesta dissertação uma visão geral da análise de dados de expressão gênica e das diferentes medidas de correlação consideradas para tal comparação. São apresentados também resultados empíricos obtidos a partir da comparação dos coeficientes de correlação para agrupamento de genes, agrupamento de amostras, seleção de genes para o problema de classificação de amostras e classificação de amostrasThe development of microarray technology made possible the expression level measurement of hundreds or even thousands of genes simultaneously for various experimental conditions. The huge amount of available data generated the need for computational methods that allow its analysis in an effcient and automated way. In many of the computational methods employed during gene expression data analysis the choice of a proximity measure is necessary. Among the proximity measures available, correlation coefficients have been widely employed because of their ability to capture similarity trends among the compared numeric sequences (genes or samples). The present work has as objective to compare different correlation measures for the three major tasks involved in the analysis of gene expression data: clustering, feature selection and classification. To this extent, in this dissertation an overview of gene expression data analysis and the different correlation measures considered for this comparison are presented. In the present work are also presented empirical results obtained from the comparison of correlation coefficients for gene clustering, sample clustering, gene selection for sample classification and sample classification
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Araujo, Tânia Kawasaki de 1985. « Utilização da técnica de Open Array para investigação de genes associados a fendas labiopalatais em amostra da população brasileira ». [s.n.], 2015. http://repositorio.unicamp.br/jspui/handle/REPOSIP/313118.
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Orientador: Vera Lúcia Gil da Silva LopesTese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas
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Resumo: A fenda de labiopalatal (FLP) isolada é o defeito craniofacial mais comum em humanos. O objetivo deste estudo foi avaliar associações entre 39 genes e a etiologia de FLP isolada em uma amostra da população brasileira. Este estudo de associação do tipo caso-controle foi desenhado com um poder estatístico de 81,29% por meio de regressão logística. O grupo de casos foi composto por 182 pacientes com FLP isolada registrados na Base Brasileira de Dados Clínicos e Familiais de Fendas Orofaciais Típicas. O grupo controle foi formado por 355 indivíduos saudáveis, sem história de fendas orais em três gerações. Toda a amostra foi genotipada por meio do sistema OpenArray®TaqManTM para 253 polimorfismos de nucleotídeo único (SNPs) em 39 genes, incluindo dois genes que, recentemente, haviam sido descritos por este grupo de pesquisa. A seleção de SNPs foi feita com o programa SNPbrowser 4.0 (Applied Biosystems) para verificar o número e a localização dos SNPs apropriados para explorar a associação de cada gene com FLP isolada. A análise de associação foi realizada por meio de regressão logística e regressão stepwise. Os resultados foram corrigidos para múltiplos testes (correção de Bonferroni). Vinte e quatro SNPs em 16 genes foram significativamente associados com a etiologia da FLP isolada, incluindo MSX1, SPRY1, MSX2, PRSS35, TFAP2A, SHH, VAX1, TBX10, WNT11, PAX9, BMP4, JAG2, AXIN2, DVL2, KIF7 e TCBE3. A análise de regressão stepwise revelou que 11 genes contribuiram em 15,5% do fenótipo de FLP isolada nessa amostra. Este é o primeiro estudo a associar os genes KIF7 e TCEB3 à FLP isolada
Abstract: Nonsyndromic cleft lip and palate (NSCLP) is the most common craniofacial birth defect. The aim of this study was to evaluate associations between 39 genes and the etiology of NSCLP in a Brazilian population. This case-control association study was designed with 81.29% statistical power according to logistic regression. The case group was composed of 182 patients with NSCLP enrolled in the Brazilian Database on Orofacial Clefts. The controls included 355 healthy individuals with no history of oral clefting in the past three generations. All samples were genotyped by TaqMan®OpenArrayTM system for 253 single nucleotide polymorphisms (SNPs) in 39 genes, including two that had recently been associated with this process. The SNPs selection was made by SNPbrowser 4.0 (Applied Biosystems) in order to establish the best SNPs to explor the association between each gene and NSCLP. The association analysis was performed using logistic regression and stepwise regression. The results were corrected for multiple testing (Bonferroni correction). Twenty-four SNPs in 16 genes were significantly associated with the etiology of NSCLP, including MSX1, SPRY1, MSX2, PRSS35, TFAP2A, SHH, VAX1, TBX10, WNT11, PAX9, BMP4, JAG2, AXIN2, DVL2, KIF7 and TCBE3. Stepwise regression analysis revealed that 11 genes contributed to 15.5% of the phenotype of NSCLP in the sample. This is the first study to associate KIF7 and TCEB3 with NSCLP
Doutorado
Ciencias Biomedicas
Doutora em Ciências Médicas
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Pereira, Joana Filipa de Sousa. « Estudo do gene FOXE1 e identificação de novos genes de susceptibilidade para o cancro da tiróide familiar ». Master's thesis, Faculdade de Ciências e Tecnologia, 2012. http://hdl.handle.net/10362/9925.
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Dissertação para obtenção do Grau de Mestre em Genética Molecular e BiomedicinaAs formas familiares de carcinomas não-medulares da tiróide (FNMTC) representam 5% das neoplasias da tiróide. Foram já mapeados 8 loci de susceptibilidade para o FNMTC, no entanto, até à data, apenas o gene DICER1 foi identificado. O envolvimento de diferentes loci sugere a existência de heterogeneidade genética para o FNMTC, contudo, a sua base molecular, é essencialmente desconhecida. Os factores de transcrição NKX2-1, FOXE1, PAX8 e HHEX estão envolvidos na morfogénese e diferenciação da tiróide. Estudos recentes levaram à identificação de mutações germinais no gene NKX2-1 em famílas com FNMTC. No entanto, continua por esclarecer o papel destes factores de transcrição na etiologia do FNMTC. A nova tecnologia de sequenciação global do exoma (WES) tem facilitado a identificação de genes de susceptibilidade para diferentes doenças hereditárias. Este projecto teve como objectivos o estudo do papel do gene FOXE1 em FNMTC e a identificação de novos genes de susceptibilidade para esta doença, utilizando a WES. Desenvolveram-se estudos funcionais para a variante p.A248G do gene FOXE1, identificada numa família com FNMTC, usando como modelos células de tiróide normal (PCCL3) e uma linha celular de carcinoma papilar da tiróide (TPC-1). Nestes ensaios, observou-se que a variante p.A248G promovia a proliferação e migração celular, sugerindo que esta variante poderá contribuir para a tumorigénese na tiróide. Por WES, identificou-se uma nova variante (p.T22I) no gene C8orf48. Esta variante segregava com a doença na família. O gene C8orf48 interage com proteínas da via de sinalização WNT. Em estudos preliminares de expressão génica, identificaram-se alguns genes-alvo desta via (CCND1 e MYC) que apresentavam sobre-expressão no tumor da tiróide relativamente à tiróide normal no probando. Estudos funcionais poderão esclarecer o papel desta variante na tumorigénese. Neste trabalho, foram identificadas variantes genéticas, potencialmente patogénicas nos genes FOXE1 e C8orf48, que constituem a primeira evidência do seu envolvimento em FNMTC.
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Carvalho, Anna Carolina Pereira Vieira de. « Construção e caracterização de um vírus Adeno-associado com expressão direcionada para células em divisão ». Universidade de São Paulo, 2010. http://www.teses.usp.br/teses/disponiveis/87/87131/tde-18062010-125910/.
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A utilização do vírus adeno-associado recombinante (AAVr) como vetor de transferência gênica em células tumorais está crescendo. Neste trabalho, o promotor gênico de E2F-1, um promotor ativo durante a divisão celular, foi inserido no AAVr e utilizado para dirigir a expressão do HSV-tk ou luciferase e, simultaneamente, eGFP afim de direcionar a expressão viral para células em proliferação. Em paralelo, foram construídos vetores portadores do promotor constitutivo CMV para servir como controles. O promotor gênico de E2F-1 não foi eficiente em dirigir a expressão dos transgenes na linhagem celular HT1080, enquanto o promotor CMV apresentou uma alta expressão dos repórteres e do gene terapêutico. A baixa eficiência do promotor E2F-1 ainda não foi explorada, mas poderia ser relacionada com o desempenho intrínseco deste promotor, a biologia do vetor AAVr e especificidade celular. Contudo, o bom desempenho do vetor AAVr contendo o promotor CMV abre a possibilidade de realizar novos ensaios de transferência gênica para tratamento e visualização de células tumoraisThe utilization of recombinant adeno-associated virus (AAVr) as a gene transfer vector in tumor cells is increasing. In this work, the promoter of the E2F-1 gene, active during cell division, was inserted in an AAVr vector and used to drive the expression of HSV-tk or luciferase and, simultaneously, eGFP with the intent of limiting viral expression to proliferating cells. Also, vectors with the constitutive CMV promoter were constructed to be used as controls. The E2F-1 promoter was not efficient in driving the expression of the transgenes in the HT1080 cell line, while the CMV promoter shows high level expression of the reporter and the therapeutic genes. The low efficiency of E2F promoter has not yet been explored, though this problem could be related to the intrinsic performance of this promoter, the biology of the vector AAV and cell-specific factors. However, the performance of the AAVr containing the CMV promoter creates the possibility of performing new gene transfer protocols for the treatment and visualization of tumor cells.
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Leal, Dora Yovana Barrios. « História Demográfica e Estrutura de Populações para a Espécie Cactófila Drosophila meridionalis ». Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/17/17135/tde-12062013-150608/.
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Drosophila meridionalis é uma espécie endêmica da América do Sul, sendo amplamente distribuída na Costa Atlântica do Brasil. Com o objetivo de elaborar uma hipótese filogeográfica para esta espécie foram obtidas sequências do gene nuclear period e do gene mitocondrial COI. Foram calculados os índices de diversidade nucleotídica e realizados os testes: AMOVA, testes de neutralidade, a Mismatch Distribution, Bayesian Skyline Plot, NCPA. Foram obtidas três redes pelo gene COI, denominadas A (populações do interior), B (populações do litoral sul) e C (populações do litoral sudeste e oriental) e uma única rede obtida para o gene period, esta rede divide as populações em dois grupos sendo o primeiro congruente com a rede A e o segundo compreendendo as redes B e C, do gene COI. A AMOVA mostrou uma estruturação alta e significativa entre as populações do interior e o litoral para os dois genes (ct=0,72 gene COI; ct=0,70 gene period), que pode ser explicada pela presença de barreiras geográficas, como a Serra do Mar. Eventos de expansão populacional e de fluxo gênico restrito com isolamento por distância foram detectados nas populações do litoral e o interior respectivamente. A expansão da área de ocorrência de D. meridionalis provavelmente teve inicio com as populações do litoral do Rio Grande de Sul, em direção ao litoral de Santa Catarina com posterior colonização a longa distância dos estados de São Paulo, Rio de Janeiro e Bahia. Migrações assincrônicas de indivíduos de populações litorâneas de São Paulo e Santa Catarina provavelmente colonizaram o interior de São Paulo, e a partir destas populações, se iniciara uma expansão populacional em direção ao sul pelo interior, colonizando o Paraná e Rio Grande do Sul. A análise bayesiana (MCCT) indicou que o tempo do ancestral comum mais recente (TMRCA) para todos os haplótipos de D. meridionalis é de 81.700 anos atrás, data que marca a separação das populações do interior e do litoral aproximadamente no final do Pleistoceno. Eventos similares têm sido sugeridos para explicar a distribuição geográfica de espécies do cluster D. buzzatii, que ocorrem em simpatria em grande parte com populações de D. meridionalis. Esta espécie, como as espécies do cluster D. buzzatii, apresentou indicativos de flutuações demográficas, podendo estar associadas à expansão e contração da distribuição da vegetação xerofítica, durante as oscilações paleoclimáticas do Pleistoceno.Drosophila meridionalis is an endemic species of South America, being widely distributed in the Atlantic Coast of Brazil. Aiming to develop a phylogeographic hypothesis for this species, sequences of mitochondrial COI and nuclear period genes were obtained. The diversity indexes, AMOVA, neutrality tests, Mismatch Distribution, Bayesan Skyline Plot and NCPA were calculated. We obtained three networks for the COI gene, denominated A (inland populations), B (south coast populations) and C (eastern and southeastern coast populations) and a single network obtained for the period gene, this network divides the population into two groups, being the first congruent with the network A of the COI gene and the second comprising the networks B and C of the COI gene. The AMOVA results, showed a high and significant structuring among inland and coastal populations, for both genes (ct=0,72 COI gene; ct=0,70 period gene), that can be explained by the presence of geographical barriers, such as Serra do Mar. Population expansion events and restricted gene flow with isolation by distance events were detected in coastal and inland populations respectively. The expansion of the area of occurrence of D. meridionalis probably was initiated with the populations of the coast of Rio Grande do Sul, towards the coast of Santa Catarina with subsequent long-distance colonization of the states of São Paulo, Rio de Janeiro and Bahia. Asynchronic migrations of individuals from coastal populations of São Paulo and Santa Catarina probably colonized the inland of São Paulo, and from these populations, a population expansion towards the south through the inland was initiated, colonizing the states of Paraná and Rio Grande do Sul. The bayesian analysis (MCCT) indicated that the time of the most recent common ancestor (TMRCA) for all haplotypes of D. meridionalis is from 81,700 years ago, a date that marks the separation of inland and coastal populations approximately at the end of the Pleistocene. Similar events have been suggested to explain the geographic distribution of species of the cluster D. buzzatii, occurring in sympatry largely with populations of D. meridionalis. This species, as the cluster D. buzzatii species, presented indicatives of demographic fluctuations, which can be associated with the expansion and contraction of the distribution of xerophytic vegetation, during the paleoclimatic fluctuations of the Pleistocene.
Livres sur le sujet "Gene PARL"
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Taman Nasional Gunung Gede Pangrango (Indonesia). Mt. Gede Pangrango National Park. 3e éd. Cipanas, Cianjur : Indonesian Ministry of Forestry, Directorate General Forest Protection and Nature Conservation, Gunung Gede Pangrango National Park, 2011.
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Taman Nasional Gunung Gede Pangrango (Indonesia), dir. Mt. Gede Pangrango National Park. [Cipanas, Cianjur] : Mt. Gede Pangrango National Park, 1996.
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Merryanto, Yohanes. Genetic variation and gene flow of hard coral population in Savu Sea Marine National Park, East Nusa Tenggara, Indonesia : Final report international research collaborative and publication (first year). Kupang] : Universitas Kristen Artha Wacana, 2010.
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J, Lamb Christopher, Beachy Roger N et UCLA Symposium on Plant Gene Transfer (1989 : Park City, Utah), dir. Plant gene transfer : Proceedings of a UCLA symposium held at Park City, Utah, April 1-7, 1989. New York : Wiley-Liss, 1990.
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Barlas, Nami. Para borçlarının ifasında borçlunun temerrüdü ve bu temerrüt açısından düzenlenen genel sonuçlar. İstanbul : Kazancı Kitap Ticaret, 1992.
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Gordon, Ringold, et University of California, Los Angeles., dir. Steroid hormone action : Proceedings of a UCLA symposium, held in Park City, Utah, January 17-23, 1987. New York : Liss, 1988.
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Sigue tu pasión : Consejos para un nuevo tipo de emprendedor. Argentina : Empresa Activa, 2012.
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Fogarty, Mary. Gene Kelly. Sous la direction de Melissa Blanco Borelli. Oxford University Press, 2014. http://dx.doi.org/10.1093/oxfordhb/9780199897827.013.008.
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This chapter explores the contemporary significance of Gene Kelly for street dance practitioners and cultural critics. Responses to a Volkswagen commercial remake of Kelly’s “Singin’ in the Rain” solo sequence raise questions about how creativity and originality are assessed in popular dance performances. By comparing the responses of film critics and hip-hop dance practitioners to both Gene Kelly’s performance in Singin’ in the Rain (Donen and Kelly 1952) and the commercial remake, a key theme emerges. Evaluations of creativity reveal how judgments about originality are as much a part of street dance practices as classic choreographic works. This chapter suggests that “remixes” of past popular dance performances reveal the pleasure created in aesthetic comparison. In fact, value judgments rooted in comparisons are a central component of popular dance assessment and appreciation.
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Franke, Barbara, et Jan K. Buitelaar. Gene–environment interactions. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198739258.003.0005.
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ADHD is highly heritable, but environmental factors also play significant roles in disease aetiology and outcome. Genetic and environmental influences are likely to show different types of interplay, with gene–environment interactions (G×E) playing a part. Different models of G×E exist, with the most frequently investigated in ADHD up to the present being the diathesis–stress and differential susceptibility models. The most frequently studied have been monoaminergic genes, often based on a single genetic variant. Only a single genome-wide study has been reported thus far. Environmental factors investigated include prenatal and postnatal risk factors for ADHD, in particular prenatal exposure to smoking or alcohol and aspects of parenting.
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(Editor), Detlev Ganten, Klaus Ruckpaul (Editor) et Josef Köhrle (Editor), dir. Molekularmedizinische Grundlagen von para- und autokrinen Regulationsstörungen (Molekulare Medizin). Springer, 2006.
Trouver le texte intégralChapitres de livres sur le sujet "Gene PARL"
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Tanaka, Motoyoshi, et H. Barton Grossman. « Tumor Suppressor Genes of Bladder Cancer and Potential for Gene Therapy ». Dans Bladder Disease, Part A, 185–91. Boston, MA : Springer US, 2003. http://dx.doi.org/10.1007/978-1-4419-8889-8_14.
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Landau, Alejandra, Franco Lencina, María Elizabeth Petterson, María Gabriela Pacheco, Susana Costoya, Vanina Brizuela et Alberto Prina. « The barley chloroplast mutator (cpm) mutant, an extraordinary source of plastome variability. » Dans Mutation breeding, genetic diversity and crop adaptation to climate change, 271–79. Wallingford : CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0027.
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Abstract The plastome is usually considered a highly conserved genome. Compared with the nuclear genome, it is small and has different genetic rules. Through different molecular methods (TILLING, candidate gene sequencing, amplicon massive sequencing and plastome re-sequencing) applied to barley chloroplast mutator (cpm) seedlings, we detected more than 60 polymorphisms affecting a wide variety of plastid genes and several intergenic regions. The genes affected belonged mostly to the plastid genetic machinery and the photosynthetic apparatus, but there were also genes like matK, whose functions are so far not clearly established. Among the isolated mutants, we found the first infA gene mutant in higher plants, two mutants in ycf3 locus and the first psbA gene mutant in barley. The latter is used in breeding barley cultivars where PSII is tolerant to toxic herbicides. Most of the molecular changes were substitutions, and small indels located in microsatellites. However, particular combinations of polymorphisms observed in the rpl23 gene and pseudogene suggest that, besides an increased rate of mutations, an augmented rate of illegitimate recombination also occurred. Although a few substitutions were observed in the mitochondria of cpm plants, we have not yet determined the implications of the cpm for mitochondrial stability. The spectrum of plastome polymorphisms highly suggests that the cpm gene is involved in plastid DNA repair, more precisely taking part in the mismatch repair system. All results show that the cpm mutant is an extraordinary source of plastome variability for plant research and/or plant breeding. This mutant also provides an interesting experimental system in which to investigate the mechanisms responsible for maintaining plastid stability.
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Joosten, M. H. A. J., G. Honée, J. A. A. Van Kan et P. J. G. M. De Wit. « The Gene-for-Gene Concept in Plant-Pathogen Interactions : Tomato-Cladosporium fulvum ». Dans Plant Relationships Part B, 3–16. Berlin, Heidelberg : Springer Berlin Heidelberg, 1997. http://dx.doi.org/10.1007/978-3-642-60647-2_1.
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Guo, Hui-jun, Yong-dun Xie, Lin-shu Zhao, Hong-chun Xiong, Jia-yu Gu, Shi-rong Zhao et Lu-xiang Liu. « Progress of mutant resource development and tilling on starch biosynthesis in wheat. » Dans Mutation breeding, genetic diversity and crop adaptation to climate change, 280–84. Wallingford : CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0028.
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Abstract Induced mutations have been widely utilized for the development of plant mutant germplasm and varieties since 1927 and have contributed to genetic diversity enhancement and food security in the world. Mutant resources are essential for gene identification and functional characterization by forward and reverse genetic strategies. The publishing of annotated wheat reference genomes is greatly promoting the progress of wheat functional genomic research. Mutant resources of a broad spectrum and diversified wild- types will be the prerequisites in this process, in part due to the polyploid nature of wheat. This review describes the progress of mutant resource development derived from the winter wheat cultivar 'Jing411'. The segregating M2 population has been used for mining functional mutant alleles of key genes involved in starch biosynthesis and could be further used for allele mining of any other target genes. The morphological mutant resources developed from various mutagens have been, and are going to be, used to develop genetic populations for gene mapping and the genetic analysis of biological functions.
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Ardelt, Peter, Ingo Kausch et Andreas Böhle. « Gene and Antisense Therapy of Bladder Cancer ». Dans Bladder Disease, Part A, 155–83. Boston, MA : Springer US, 2003. http://dx.doi.org/10.1007/978-1-4419-8889-8_13.
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Kral, Stefan, Markus Triska et Christoph W. Ueberhuber. « Compiler Technology for Blue Gene Systems ». Dans Euro-Par 2006 Parallel Processing, 279–88. Berlin, Heidelberg : Springer Berlin Heidelberg, 2006. http://dx.doi.org/10.1007/11823285_29.
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Karagiannaki, Ioulia, Yannis Pantazis, Ekaterini Chatzaki et Ioannis Tsamardinos. « Pathway Activity Score Learning for Dimensionality Reduction of Gene Expression Data ». Dans Discovery Science, 246–61. Cham : Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-61527-7_17.
Texte intégralRésumé :
Abstract Molecular gene-expression datasets consist of samples with tens of thousands of measured quantities (e.g., high dimensional data). However, there exist lower-dimensional representations that retain the useful information. We present a novel algorithm for such dimensionality reduction called Pathway Activity Score Learning (PASL). The major novelty of PASL is that the constructed features directly correspond to known molecular pathways and can be interpreted as pathway activity scores. Hence, unlike PCA and similar methods, PASL’s latent space has a relatively straight-forward biological interpretation. As a use-case, PASL is applied on two collections of breast cancer and leukemia gene expression datasets. We show that PASL does retain the predictive information for disease classification on new, unseen datasets, as well as outperforming PLIER, a recently proposed competitive method. We also show that differential activation pathway analysis provides complementary information to standard gene set enrichment analysis. The code is available at https://github.com/mensxmachina/PASL.
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Trapnell, Bruce C., et Michael N. Pensiero. « Development of Viral Vectors for Human Gene Therapy : Retrovirus and Adenovirus (Part I) ». Dans Gene Transfer in the Cardiovascular System, 3–24. Boston, MA : Springer US, 1997. http://dx.doi.org/10.1007/978-1-4615-6277-1_1.
Texte intégral
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Moreira, José. « The Evolution of the Blue Gene/L Supercomputer ». Dans Euro-Par 2005 Parallel Processing, 13. Berlin, Heidelberg : Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/11549468_2.
Texte intégral
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Oulhen, Nathalie, Stephany Foster, Greg Wray et Gary Wessel. « Identifying gene expression from single cells to single genes ». Dans Echinoderms, Part B, 127–58. Elsevier, 2019. http://dx.doi.org/10.1016/bs.mcb.2018.11.018.
Texte intégralActes de conférences sur le sujet "Gene PARL"
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Da Silva, Carla Fernandes, Kuruvilla Joseph Abraham et Evandro Eduardo Seron Ruiz. « Correlacionando genes e doenças através de caminhos metabólicos ». Dans XVII Simpósio Brasileiro de Computação Aplicada à Saúde. Sociedade Brasileira de Computação - SBC, 2017. http://dx.doi.org/10.5753/sbcas.2017.3725.
Texte intégralRésumé :
Um dos principais desafios da ciência é identificar os fatores que causam essas doenças, dentre estes fatores estão os genes. Neste trabalho, será apresentada uma metodologia para priorizar genes e vias metabólicas relacionados a uma doença complexa, com o desafio de descobrir quais os genes podem contribuir para desencadear uma doença complexa. O objetivo é desenvolver uma metodologia para predição de gene-doença através da integração de dados de genes-doencas-vias metabólicas, visando a descoberta de novos genes associado a doença.
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Prates, Pedro Emílio Gomes. « AVALIAÇÃO DA TERAPIA GÊNICA DO SUICÍDIO COM USO DE GENES SUICIDAS PARA O COMBATE AO CÂNCER : REVISÃO INTEGRATIVA ». Dans II Congresso Brasileiro de Biologia Molecular On-line. Revista Multidisciplinar em Saúde, 2021. http://dx.doi.org/10.51161/rems/2334.
Texte intégralRésumé :
Introdução: Durante décadas os tratamentos quimioterápicos convencionais foram empregados no câncer devido à eficácia em matar as células tumorais. Diante disso, a terapia gênica com uso de genes suicidas surge como uma das abordagens mais inovadoras para o desenvolvimento de agentes antineoplásicos com maior seletividade tumoral. Assim, entre os genes suicidas disponíveis, a timidina quinase é investigada em vários modelos de tumor. Contudo, o uso dessa enzima apresenta limitações devido ao sistema de imunogenicidade. Recentemente, pesquisadores passaram a utilizar o sistema de gene suicida da Caspase-9 induzível, a qual apresentou resultados mais favoráveis se comparado à timidina quinase. Objetivo: Objetiva-se construir uma revisão integrativa da literatura sobre a terapia gênica do suicídio avaliando o uso de genes suicidas, sobretudo da timidina quinase e da caspase-9 induzível para o combate ao câncer. Material e Métodos: Foi realizada uma revisão integrativa de literatura por meio de uma pesquisa nos bancos de dados PubMed, Scopus e LILACS com os seguintes descritores “terapia gênica de genes suicidas”, “câncer”, “avaliação”, “timidina quinase” e “caspase-9 induzível” simultaneamente às correspondentes em inglês, em intervalo de 11 anos (2010-2021), com critérios de inclusão preestabelecidos. Para o cruzamento dos descritores, utilizou-se um protocolo com os seguintes booleanos: Gene Therapy of Suicide Gene AND Cancer AND Assessment AND Thymidine Kinase AND Inducible Caspase-9. Ao final, 4 artigos foram selecionados. Resultados: Foi selecionado 1 artigo (n = 25%) que abordava o tema da avaliação na terapia de genes suicidas. Em contrapartida, os critérios de exclusão foram estudos que não contemplavam o efeito avaliativo desses genes na terapia gênica, resumindo-se a 3 artigos selecionados (n = 75%). Com isso, observou-se que a avaliação do uso de genes suicidas ainda é uma abordagem recente, necessitando de mais estudos que contemplem essa temática. Conclusão: A avaliação da terapia gênica do suicídio pautada no uso de genes suicidas para o combate ao câncer é promissora, mesmo que recente e dos mínimos estudos publicados. Além disso, o sistema de entrega utilizando a caspase-9 induzível é mais viável do que o sistema de entrega da timidina quinase, já que esse sistema se limita à imunogenicidade do transgene viral.
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Huber, P., J. Dalmon, M. Laurent, G. Courtois, D. Thevenon et G. Marguerie. « CHARACTERIZATION OFTHE 5’FLANKING REGION FOR THE HUMAN FIBRINOGEN β GENE ». Dans XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642889.
Texte intégralRésumé :
Fibrinogen is coded by three separate genes located in a 50kb region of chromosome 4 and organized in a α - β - γ orientation with an inversion of the gene 3- A human genomic library was constructed using the EMBL4 phage and screened with cDNA probes coding for human fibrinogen Aα, Bβ and γ chains. Clones, covering the fibrinogen locus,were identified, and their organization was analyzed by means of hybridization and restriction mapping. Among these clones one recombinant phage containing the β gene and large 5’ and 3’ -flanking sequences was isolated.To identify the regulatory sequences Dpstream from the human β gene, a 1.5 kb fragment of the immediate 5’-flanking region was sequenced. The SI mapping experiments revealed three transcription initiation sites. PotentialTATA and CAAT sequences were identified upstream the initiation start points at the positions -21 and -58 from the first initiation start point.Comparison of this sequence with that previously reported for the same region upstream from the human γ gene revealed no significant homology which suggests that the potential promoting sequences of these genes are different. In contrast, comparison of the 5’flanking regions of human and rat β genes showed more than 80% homology for 142 bp upstream from the gene. This highly conserved region is a potential candidate for a regulatory sequence of the human β gene.To verify this activity, a β fibrinogen minigene was constructed by deletion of the internal part of the normal gene and including 3.4kb of the 5’flanking region and 1.4kb of the 3’flanking region. The minigene was transfected into HepG2, a human hepatoma cell line, to show whether the 5’flanking region of the human fibrinogen gene contains DNA sequences sufficient for efficient transcription in HepG2. Constructions of several parts of the sequenced 5’flanking region of the human β gene with the gene of the chloramphenical acetyl transferase have been also transfected in the HepG2 cells to determine the specificity of the gene expression and to localize the sequences controlling the transcription of the gene.
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Edenbrandt, C.-M., S. Gershagen, P. Femlund, R. Wydro, J. Stenflo et Å. Lundwall. « GENE STRUCTURE OF VITAMIN K-DEPENDENT PROTEIN S ; A REGION HOMOLOGOUS TO SEX HORMONE BINDING GLOBULIN (SHBG) REPLACES THE SERINE PROTEASE REGION OF FACTORS IX, X AND PROTEIN C ». Dans XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644640.
Texte intégralRésumé :
It has recently been shown that the similarity between coagulation factors IX, X and protein C in the protein sequence is also evident in the organization of their genes. To further elucidate the relation of protein S to the other vitamin K-dependent clotting factors, we are now characterizing the human protein S gene. The size of the gene was estimated to be more than 45 kb, by hybridization of a cDNA for human protein S with chromosomal DNA in a Southern blot.We have isolated three overlapping clones from a human genomic DNA library in bacteriophage λ Charon 4A, which cover approximately 40 kb of the gene. The clones have been mapped by single- and double restriction enzyme digestion. Genomic subclones in pUC 18 which hybridize with cDNA probes for protein S have been isolated and sequenced to establish the intron/exon structure of the gene. The 5’- part of the human protein S gene closely resembles the corresponding part of the genes for factors IX, X and protein C. However, the thrombin sensitive region (amino acids 46-75), which is unique for protein S among the vitamin K-dependent clotting factors, is coded for by a separate exon. The 3'- end of the protein S gene, coding for amino acids 247-635, is not homologous to the catalytic region of the vitamin K-dependent serine proteases but shows a significant homology to human sex hormone binding globulin (SHBG).
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Dantas, Joao Victor Jose de Barros, PAULO ROBERTO ELEUTÉRIO DE SOUZA et NARA SUZY AGUIAR FREITAS. « VARIAÇÃO E PADRÕES DE CONSERVAÇÃO ENTRE DIFERENTES CEPAS DE CAMPYLOBACTER JEJUNI PARA O GENE GYRA ». Dans I Congresso Nacional de Pesquisas e Estudos Genéticos On-line. Revista Multidisciplinar em Saúde, 2022. http://dx.doi.org/10.51161/geneticon/8298.
Texte intégralRésumé :
Introdução: Polimorfismos de nucleotídeo único no gene gyrA têm sido relacionados com resistência antimicrobiana à infecção por Campylobacter jejuni. Com o passar dos anos, a ciência avançou com diversos medicamentos, entre eles os antimicrobianos. Entretanto, concomitantemente ao advento dos antimicrobianos, mais especificamente os antibióticos, notou-se uma certa resistência aos diversos mecanismos de atuação desses aliados contra agentes patogênicos. O grupo abordado neste trabalho foi a espécie Campylobacter jejuni. Objetivo: O objetivo deste estudo foi avaliar, através de análises comparativas, procurando regiões de alta similaridade e pequenas variações em regiões específicas do gene gyrA de Campylobacter jejuni depositado em um banco de dados NCBI. Material e Método: Um total de 18 sequências genômicas completas do gene gyrA de Campylobacter jejuni foram baixadas e alinhadas pelo software Clustalw. As análises comparativas mostraram regiões com dois grupos distintos de genomas. Resultados: O primeiro grupo apresentou regiões com alto grau de similaridade e também regiões com pequena variação de bases. No segundo grupo, todos os genomas foram 100% semelhantes. Assim, sugerimos que essa variação está relacionada à localização geográfica e origem (organismo, hospedeiro e isolados da alimentação humana) dessas sequências. Conclusão: Em conclusão, é possível que variações e padrões de genes estejam associados à história evolutiva, genética e ecológica dos genomas. Além disso, percebe-se que os genótipos de Campylobacter jejuni que apresentavam o gene gyrA, estavam associados aos organismos que foram isolados de hospitais, criações bovinas e criações aviárias, demonstrando a alta relação desse agente patogênico com o uso exacerbado de antibióticos. Dado isto, é de suma importância estudos futuros para investigar mais genes de resistência à antimicrobianos, visando a melhor alternativa para contornar essa situação que impacta cada vez mais todos os cenários da sociedade.
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Neves, Dyenifer Sara Lopes, Augusto Borges Matos, Rafaella Moniza Bento Palmeira Figueiredo, Letícia de Castro Ottoni et Letícia Ariane Tanure. « RELAÇÃO CAUSAL ENTRE A SÍNDROME MIELODISPLÁSICA E LEUCEMIA MIELÓIDE AGUDA ». Dans I Congresso Brasileiro de Hematologia Clínico-laboratorial On-line. Revista Multidisciplinar em Saúde, 2021. http://dx.doi.org/10.51161/rems/636.
Texte intégralRésumé :
Introdução: As síndromes mielodisplásicas (SMD) são resultado de alteração em um ou mais genes que controlam o desenvolvimento de células sanguíneas, causando displasia em pelo menos uma linhagem celular. A SMD afeta em sua maioria os idosos, podendo variar de um impacto mínimo ou se estender a um curso muito agressivo com progressão para leucemia mielóide aguda (LMA), que se dá através de mutações em determinados genes, em especial as que envolvem cariótipo complexo. Objetivos: Discutir, com base na literatura utilizada, a relação causal entre a SMD e LMA. Material e métodos: Foi realizada uma revisão integrativa da literatura de artigos das plataformas Scielo, PubMed e Nature, na busca por análise, registro e interpretação acerca dos resultados visando artigos de relevância para o resumo. Resultados: Há diferenças no padrão de progressão da SMD para LMA. Isso ocorre devido às diferentes mutações no curso da mielodisplasia. Assim, SMDs com mutações somáticas heterozigotas no gene SF3B1 (splicing fator 3b, subunit 1) apresentam uma característica de progressão lenta e crônica, raramente evoluindo para LMA. Quando ocorre a progressão, ela se deve a aquisições ou expansões de mutações somáticas com inativação dos genes RUNX1 ou EZH2. Em contrapartida, as SMDs com combinações de genes mutados, sobretudo os genes codificadores de splicing de RNA SRSF2 e U2AF1, evoluem com grande presença de blastos desde o início da doença e progridem, frequentemente, para LMA, quando a contagem de blastos na medula óssea supera 20%. Conclusão: Apesar de raros casos de SMD com mutações no gene SF3B1 evoluírem para LMA, outros genes comprovaram a relação causal entre SMD e LMA. Translocações envolvidas na patogênese da LMA também estão associadas à SMD, evidenciando um padrão de continuidade entre as doenças.
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Ploos van Amstel, J. K., A. L. van der Zanden, P. H. Reitsma et R. M. Bertina. « RESTRICTION ANALYSIS AND SOUTHERN BLOTTING OF TOTAL HUMAN DNA REVEALS THE EXISTENCE OF MORE THAN ONE GENE HOMOLOGOUS WITH PROTEIN S cDNA ». Dans XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644639.
Texte intégralRésumé :
A deficiency in protein S, the cofactor of activated protein C, is associated with an increased risk for the development of venous thrombosis. It is inherited as an autosomal dominant disorder. To improve the detection of heterozygotes in affected families, we have started to search for restriction fragment length polymorphism (RFLP) in the protein S gene. This study revealed the existence of two genes containing sequences homologous to protein S cDNA.Three non-overlapping fragments of clone pSUL5, which codes for the carboxy-terminal part of protein S and contains the complete 3' untranslated region, were isolated and used as probes in search for RFLP of the protein S gene.Surprisingly the non-overlapping probes shared more than one hybridizing band. The hybridization took place under stringent assay conditions.This observation is contradictory to the intron-exon organization of a gene and suggests the existence of two genes, containing sequences homologous with pSUL5. Both genes could be assigned to chromosome 3 by mapping through somatic cell hybrids. Whether two functional protein S genes are present in the human genome remains to be established.
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Shaposhnikov, A. I., N. A. Vishnevskaya, V. Yu Shakhnazarova, D. S. Syrova, E. V. Borodina, O. N. Kovaleva et O. K. Strunnikova. « Activation of protective reactions in barley plants during colonization of roots with the phytopathogenic fungus Fusarium culmorum in the presence of Pseudomonas fluorescens 2137 ». Dans CURRENT STATE, PROBLEMS AND PROSPECTS OF THE DEVELOPMENT OF AGRARIAN SCIENCE. Federal State Budget Scientific Institution “Research Institute of Agriculture of Crimea”, 2020. http://dx.doi.org/10.33952/2542-0720-2020-5-9-10-118.
Texte intégralRésumé :
The expression of the PAL gene, one of the host protection genes, in sterile barley plants and colonized F. culmorum and P. fluorescens 2137 were assessed. The obtained results indicate that strain 2137 may cause a more active protective response (1.5-2.1 fold) in barley than a phytopathogenic fungus.
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Martins, Amanda Pezzini. « A IMPORTÂNCIA DOS MÉTODOS DE EDIÇÃO GÊNICA NA DIMINUIÇÃO DOS CASOS DE CÂNCER DECORRENTES DA MUTAÇÃO DO GENE TP53 : UMA REVISÃO ». Dans I Congresso Nacional de Pesquisas e Estudos Genéticos On-line. Revista Multidisciplinar em Saúde, 2022. http://dx.doi.org/10.51161/geneticon/7330.
Texte intégralRésumé :
Introdução: Alternativas diversas vêm sendo testadas, como método de adição gênica na busca da substituição de genes TP53 mutantes de potencialidade cancerosa por similaridades que não causem qualquer efeito genotóxico no indivíduo. Tais genes se localizam no cromossomo 17, e tem sido associados à diferentes tipos de neoplasias devido ao grande número de variações apresentadas, principalmente entre os éxons 5 e 8. Objetivos: Alternativas diversas vêm sendo testadas, como método de adição gênica na busca da substituição de genes TP53 mutantes de potencialidade cancerosa por similaridades que não causem qualquer efeito genotóxico no indivíduo. A CRISPR/Cas9 é um dos mecanismos de edição gênica mais utilizados, que consiste na clivagem do gene afetado e substituição por um gene normal guiada pelo mecanismo de reparo DSB (Clivagem da dupla cadeia). Materiais e Métodos:: Revisão biliográfica de pesquisas envolvendo métodos genéticos para redução da expressão tumoral através da análise de artigos e publicações em revistas científicas, recursos disponíveis no National Center for Biotechnology Information (NCBI), PUBMED e Mouse Models of Human Cancer Database (MMHCdb). Foram palavras chave para a pesquisa das publicações: p53; biologia de tumores em camundongos; CRISPR e o câncer; supressão de tumor p53, dentre outros. Resultados e Discussão: Um número significativo de publicações é encontrado na literatura envolvendo papel do gene p53 no funcionamento celular normal e neoplásico, envolvendo praticamente todos os tipos de células. Outros recursos têm sido explorados em busca de uma alternativa clínica para a supressão tumoral e o controle de crescimento celular. Uma dessas possibilidades envolve o método de edição gênica CRISPR Cas9, tendo como principal foco o silenciamento de oncogenes, avaliando a supressão tumoral in vitro e in vivo. Conclusão: Os avanços científicos têm auxiliado no combate à cânceres, seja com o diagnóstico precoce, descoberta de novas drogas ou imunoterapia. Muitas técnicas tem sido aplicadas nas pesquisas e o cenário é otimista, sendo necessário mais estudos e recursos para que no futuro haja a possibilidade da redução drástica das mais de 9.6 milhões de mortes em todo o mundo.
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Oliveira, Letícia Eduarda de, Mariana Souza Bezerra Cavalcanti, Maria Eduarda de Albuquerque Borborema et Jaqueline de Azevêdo Silva. « POLIMORFISMO NO GENE GNB3 E O DESENVOLVIMENTO DA DIABETES MELLITUS TIPO II : UMA REVISÃO DE LITERATURA ». Dans XXVII Semana de Biomedicina Inovação e Ciência. Editora IME, 2021. http://dx.doi.org/10.51161/9786588884119/9.
Texte intégralRésumé :
Introdução: O diabetes mellitus (DM) destaca-se, atualmente, como importante causa de morbidade e mortalidade. Estimativas globais indicam que 382 milhões de pessoas vivem com DM (8,3%), e esse número poderá chegar a 592 milhões em 2035(1). Com destaque para o diabetes mellitus tipo II (DM2), doença multifatorial associada a fatores genéticos e ambientais(2). Caracterizado pela resistência à insulina e hiperglicemia, o DM2 é alvo de diversos estudos para compreender os principais fatores genéticos envolvidos em seu desenvolvimento(3). Dentre eles, os polimorfismos em certos genes estão relacionados a uma maior susceptibilidade ao desenvolvimento da doença, com destaque para alterações no gene da subunidade beta 3 da proteína G humana (GNB3), uma molécula sinalizadora envolvida na regulação dos níveis de glicose pela sinalização da via metabólica da insulina. Já foi comprovado que polimorfismos nesse gene estariam associados ao desenvolvimento da doença e de suas complicações(4). Objetivos: Este resumo tem como objetivo relacionar o impacto do polimorfismo no gene GNB3 contribuindo para a DM2. Métodos: Foi realizada pesquisa nas bases públicas de dados de artigos científicos: PubMed e Google Acadêmico usando os descritores ‘’type 2 diabetes mellitus’’ e ‘’type 2 diabetes mellitus and genetics’’ durante o período de 26 de agosto à 4 de setembro. Resultados: O marcador rs5443 localizado no gene GNB3 foi associado a uma série de condições metabólicas, incluindo a obesidade, doença arterial coronariana, resistência à insulina e DM2(3). A alteração no gene GNB3 devido a alguma mutação ou polimorfismo pode levar a defeitos na proteína G codificada por este gene. Essas alterações polimórficas estão associadas ao desenvolvimento de DM2, bem como às complicações secundárias associadas(4). Conclusão: O polimorfismo GNB3 rs5443 pode conferir efeitos no DM2 tais como algumas condições metabólicas associadas como a obesidade, hipertensão e arteriosclerose. Desta forma sua detecção nos indivíduos indicam maior risco para o desenvolvimento da doença.
Rapports d'organisations sur le sujet "Gene PARL"
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Pichersky, Eran, Alexander Vainstein et Natalia Dudareva. Scent biosynthesis in petunia flowers under normal and adverse environmental conditions. United States Department of Agriculture, janvier 2014. http://dx.doi.org/10.32747/2014.7699859.bard.
Texte intégralRésumé :
The ability of flowering plants to prosper throughout evolution, and for many crop plants to set fruit, is strongly dependent on their ability to attract pollinators. To that end many plants synthesize a spectrum of volatile compounds in their flowers. Scent is a highly dynamic trait that is strongly influenced by the environment. However, with high temperature conditions becoming more common, the molecular interplay between this type of stress and scent biosynthesis need to be investigated. Using petunia as a model system, our project had three objectives: (1) Determine the expression patterns of genes encoding biosynthetic scent genes (BSGs) and of several genes previously identified as encoding transcription factors involved in scent regulation under normal and elevated temperature conditions. (2) Examine the function of petunia transcription factors and a heterologous transcription factor, PAPl, in regulating genes of the phenylpropanoid/benzenoid scent pathway. (3) Study the mechanism of transcriptional regulation by several petunia transcription factors and PAPl of scent genes under normal and elevated temperature conditions by examining the interactions between these transcription factors and the promoters of target genes. Our work accomplished the first two goals but was unable to complete the third goal because of lack of time and resources. Our general finding was that when plants grew at higher temperatures (28C day/22C night, vs. 22C/16C), their scent emission decreased in general, with the exception of a few volatiles such as vanillin. To understand why, we looked at gene transcription levels, and saw that generally there was a good correlation between levels of transcriptions of gene specifying enzymes for specific scent compounds and levels of emission of the corresponding scent compounds. Enzyme activity levels, however, showed little difference between plants growing at different temperature regimes. Plants expressing the heterologous gene PAPl showed general increase in scent emission in control temperature conditions but emission decreased at the higher temperature conditions, as seen for control plants. Finally, expression of several transcription factor genes decreased at high temperature, but expression of new transcription factor, EOB-V, increased, implicating it in the decrease of transcription of BSGs. The major conclusion of this work is that high temperature conditions negatively affect scent emission from plants, but that some genetic engineering approaches could ameliorate this problem.
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Reisch, Bruce, Avichai Perl, Julie Kikkert, Ruth Ben-Arie et Rachel Gollop. Use of Anti-Fungal Gene Synergisms for Improved Foliar and Fruit Disease Tolerance in Transgenic Grapes. United States Department of Agriculture, août 2002. http://dx.doi.org/10.32747/2002.7575292.bard.
Texte intégralRésumé :
Original objectives . 1. Test anti-fungal gene products for activity against Uncinula necator, Aspergillus niger, Rhizopus stolonifer and Botrytis cinerea. 2. For Agrobacterium transformation, design appropriate vectors with gene combinations. 3. Use biolistic bombardment and Agrobacterium for transformation of important cultivars. 4. Characterize gene expression in transformants, as well as level of powdery mildew and Botrytis resistance in foliage of transformed plants. Background The production of new grape cultivars by conventional breeding is a complex and time-consuming process. Transferring individual traits via single genes into elite cultivars was proposed as a viable strategy, especially for vegetatively propagated crops such as grapevines. The availability of effective genetic transformation procedures, the existence of genes able to reduce pathogen stress, and improved in vitro culture methods for grapes, were combined to serve the objective of this proposal. Effective deployment of resistance genes would reduce production costs and increase crop quality, and several such genes and combinations were used in this project. Progress The efficacy of two-way combinations of Trichoderma endochitinase (CHIT42), synthetic peptide ESF12 and resveratrol upon the control of growth of Botrytis cinerea and Penicillium digitatum were evaluated in vitro. All pairwise interactions were additive but not synergistic. Per objective 2, suitable vectors with important gene combinations for Agrobacterium transformation were designed. In addition, multiple gene co-transformation by particle bombardment was also tested successfully. In New York, transformation work focused on cultivars Chardonnay and Merlot, while the technology in Israel was extended to 41B, R. 110, Prime, Italia, Gamay, Chardonnay and Velika. Transgenic plant production is summarized in the appendix. Among plants developed in Israel, endochitinase expression was assayed via the MuchT assay using material just 1-5 days after co-cultivation. Plants of cv. Sugraone carrying the gene coding for ESF12, a short anti-fungal lytic peptide under the control of the double 358 promoter, were produced. Leaf extracts of two plants showed inhibition zones that developed within 48 h indicating the inhibitory effect of the leaf extracts on the six species of bacteria. X fastidiosa, the causal organism of Pierce's disease, was very sensitive to leaf extracts from ESF12 transformed plants. Further work is needed to verify the agricultural utility of ESF12 transformants. In New York, some transformants were resistant to powdery mildew and Botrytis fruit rot. Major conclusions, solutions, achievements and implications The following scientific achievements resulted from this cooperative BARD project: 1. Development and improvement of embryogenesis and tissue culture manipulation in grape, while extending these procedures to several agriculturally important cultivars both in Israel and USA. 2. Development and improvement of novel transformation procedures while developing transformation techniques for grape and other recalcitrant species. 3. Production of transgenic grapevines, characterization of transformed vines while studying the expression patterns of a marker gene under the control of different promoter as the 35S CaMV in different part of the plants including flowers and fruits. 4. Expression of anti-fungal genes in grape: establishment of transgenic plants and evaluation of gene expression. Development of techniques to insert multiple genes. 5. Isolation of novel grape specific promoter to control the expression of future antimicrobial genes. It is of great importance to report that significant progress was made in not only the development of transgenic grapevines, but also in the evaluation of their potential for increased resistance to disease as compared with the non engineered cultivar. In several cases, increased disease resistance was observed. More research and development is still needed before a product can be commercialized, yet our project lays a framework for further investigations.
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Friedman, Haya, Julia Vrebalov, James Giovannoni et Edna Pesis. Unravelling the Mode of Action of Ripening-Specific MADS-box Genes for Development of Tools to Improve Banana Fruit Shelf-life and Quality. United States Department of Agriculture, janvier 2010. http://dx.doi.org/10.32747/2010.7592116.bard.
Texte intégralRésumé :
Fruit deterioration is a consequence of a genetically-determined fruit ripening and senescence programs, in which developmental factors lead to a climacteric rise of ethylene production in ethylene-sensitive fruits such as tomato and banana. Breeding of tomato with extended fruit shelf life involves the incorporation of a mutation in RIN, a MADS-box transcription factor participating in developmental control signalling of ripening. The RIN mode of action is not fully understood, and it may be predicted to interact with other MADS-box genes to execute its effects. The overall goal of this study was to demonstrate conservation of ripening control functions between banana and tomato and thus, the potential to genetically extend shelf-life in banana based on tools developed in tomato. The specific objectives were: 1. To increase the collection of potential RIN-like genes from banana; 2. To verify their action as developmental regulators; 3. To elucidate MADS-box gene mode of action in ripening control; 4. To create transgenic banana plants that express low levels of endogenous Le-RIN- like, MaMADS- gene(s). We have conducted experiments in banana as well as in tomato. In tomato we have carried out the transformation of the tomato rin mutant with the MaMADS1 and MaMADS2 banana genes. We have also developed a number of domain swap constructs to functionally examine the ripening-specific aspects of the RIN gene. Our results show the RIN-C terminal region is essential for the gene to function in the ripening signalling pathway. We have further explored the tomato genome databases and recovered an additional MADS-box gene necessary for fruit ripening. This gene has been previously termed TAGL1 but has not been functionally characterized in transgenic plants. TAGL1 is induced during ripening and we have shown via RNAi repression that it is necessary for both fleshy fruit expansion and subsequent ripening. In banana we have cloned the full length of six MaMADS box genes from banana and determined their spatial and temporal expression patterns. We have created antibodies to MaMADS2 and initiated ChI assay. We have created four types of transgenic banana plants designed to reduce the levels of two of the MaMADS box genes. Our results show that the MaMADS-box genes expression in banana is dynamically changing after harvest and most of them are induced at the onset of the climacteric peak. Most likely, different MaMADS box genes are active in the pulp and peel and they are differently affected by ethylene. Only the MaMADS2 box gene expression is not affected by ethylene indicating that this gene might act upstream to the ethylene response pathway. The complementation analysis in tomato revealed that neither MaMADS1 nor MaMADS2 complement the rin mutation suggesting that they have functionally diverged sufficiently to not be able to interact in the context of the tomato ripening regulatory machinery. The developmental signalling pathways controlling ripening in banana and tomato are not identical and/or have diverged through evolution. Nevertheless, at least the genes MaMADS1 and MaMADS2 constitute part of the developmental control of ripening in banana, since transgenic banana plants with reduced levels of these genes are delayed in ripening. The detailed effect on peel and pulp, of these transgenic plants is underway. So far, these transgenic bananas can respond to exogenous ethylene, and they seem to ripen normally. The response to ethylene suggest that in banana the developmental pathway of ripening is different than that in tomato, because rin tomatoes do not ripen in response to exogenous ethylene, although they harbor the ethylene response capability This study has a major contribution both in scientific and agricultural aspects. Scientifically, it establishes the role of MaMADS box genes in a different crop-the banana. The developmental ripening pathway in banana is similar, but yet different from that of the model plant tomato and one of the major differences is related to ethylene effect on this pathway in banana. In addition, we have shown that different components of the MaMADS-box genes are employed in peel and pulp. The transgenic banana plants created can help to further study the ripening control in banana. An important and practical outcome of this project is that we have created several banana transgenic plants with fruit of extended shelf life. These bananas clearly demonstrate the potential of MaMADS gene control for extending shelf-life, enhancing fruit quality, increasing yield in export systems and for improving food security in areas where Musaspecies are staple food crops.
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Sessa, Guido, et Gregory Martin. Role of GRAS Transcription Factors in Tomato Disease Resistance and Basal Defense. United States Department of Agriculture, 2005. http://dx.doi.org/10.32747/2005.7696520.bard.
Texte intégralRésumé :
The research problem: Bacterial spot and bacterial speck diseases of tomato are causedby strains of Xanthomonas campestris pv. vesicatoria (Xcv) and Pseudomonas syringae pv.tomato (Pst), respectively. These bacteria colonize aerial parts of the plant and causesignificant losses in tomato production worldwide. Protection against Xcv and Pst bycultural practices or chemical control has been unsuccessful and there are only limitedsources of genetic resistance to these pathogens. In previous research supported in part byBARD IS-3237-01, we extensively characterized changes in tomato gene expression uponthe onset of spot and speck disease resistance. A remarkable finding of these studies wasthe inducibility in tomato leaves by both Xcv and Pst strains of genes encodingtranscriptional activator of the GRAS family, which has not been previously linked todisease resistance. Goals: Central goals of this research were to investigate the role of GRAS genes in tomatoinnate immunity and to assess their potential use for disease control.Specific objectives were to: 1. Identify GRAS genes that are induced in tomato during thedefense response and analyze their role in disease resistance by loss-of-function experiments.2. Overexpress GRAS genes in tomato and characterize plants for possible broad-spectrumresistance. 3. Identify genes whose transcription is regulated by GRAS family. Our main achievements during this research program are in three major areas:1. Identification of tomato GRAS family members induced in defense responses andanalysis of their role in disease resistance. Genes encoding tomato GRAS family memberswere retrieved from databases and analyzed for their inducibility by Pst avirulent bacteria.Real-time RT-PCR analysis revealed that six SlGRAS transcripts are induced during theonset of disease resistance to Pst. Further expression analysis of two selected GRAS genesshowed that they accumulate in tomato plants in response to different avirulent bacteria orto the fungal elicitor EIX. In addition, eight SlGRAS genes, including the Pst-induciblefamily members, were induced by mechanical stress in part in a jasmonic acid-dependentmanner. Remarkably, SlGRAS6 gene was found to be required for tomato resistance to Pstin virus-induced gene silencing (VIGS) experiments.2. Molecular analysis of pathogen-induced GRAS transcriptional activators. In aheterologous yeast system, Pst-inducible GRAS genes were shown to have the ability toactivate transcription in agreement with their putative function of transcription factors. Inaddition, deletion analysis demonstrated that short sequences at the amino-terminus ofSlGRAS2, SlGRAS4 and SlGRAS6 are sufficient for transcriptional activation. Finally,defense-related SlGRAS proteins were found to localize to the cell nucleus. 3. Disease resistance and expression profiles of transgenic plants overexpressing SlGRASgenes. Transgenic plants overexpressing SlGRAS3 or SlGRAS6 were generated. Diseasesusceptibility tests revealed that these plants are not more resistant to Pst than wild-typeplants. Gene expression profiles of the overexpressing plants identified putative direct orindirect target genes regulated by SlGRAS3 and SlGRAS6. Scientific and agricultural significance: Our research activities established a novel linkbetween the GRAS family of transcription factors, plant disease resistance and mechanicalstress response. SlGRAS6 was found to be required for disease resistance to Pstsuggesting that this and possibly other GRAS family members are involved in thetranscriptional reprogramming that takes place during the onset of disease resistance.Their nuclear localization and transcriptional activation ability support their proposed roleas transcription factors or co-activators. However, the potential of utilizing GRAS familymembers for the improvement of plant disease resistance in agriculture has yet to bedemonstrated.
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Heifetz, Yael, et Michael Bender. Success and failure in insect fertilization and reproduction - the role of the female accessory glands. United States Department of Agriculture, décembre 2006. http://dx.doi.org/10.32747/2006.7695586.bard.
Texte intégralRésumé :
The research problem. Understanding of insect reproduction has been critical to the design of insect pest control strategies including disruptions of mate-finding, courtship and sperm transfer by male insects. It is well known that males transfer proteins to females during mating that profoundly affect female reproductive physiology, but little is known about the molecular basis of female mating response and no attempts have yet been made to interfere with female post-mating responses that directly bear on the efficacy of fertilization. The female reproductive tract provides a crucial environment for the events of fertilization yet thus far those events and the role of the female tract in influencing them are poorly understood. For this project, we have chosen to focus on the lower reproductive tract because it is the site of two processes critical to reproduction: sperm management (storage, maintenance, and release from storage) and fertilization. E,fforts during this project period centered on the elucidation of mating responses in the female lower reproductive tract The central goals of this project were: 1. To identify mating-responsive genes in the female lower reproductive tract using DNA microarray technology. 2. In parallel, to identify mating-responsive genes in these tissues using proteomic assays (2D gels and LC-MS/MS techniques). 3. To integrate proteomic and genomic analyses of reproductive tract gene expression to identify significant genes for functional analysis. Our main achievements were: 1. Identification of mating-responsive genes in the female lower reproductive tract. We identified 539 mating-responsive genes using genomic and proteomic approaches. This analysis revealed a shift from gene silencing to gene activation soon after mating and a peak in differential gene expression at 6 hours post-mating. In addition, comparison of the two datasets revealed an expression pattern consistent with the model that important reproductive proteins are pre-programmed for synthesis prior to mating. This work was published in Mack et al. (2006). Validation experiments using real-time PCR techniques suggest that microarray assays provide a conservativestimate of the true transcriptional activity in reproductive tissues. 2.lntegration of proteomics and genomics data sets. We compared the expression profiles from DNA microarray data with the proteins identified in our proteomic experiments. Although comparing the two data sets poses analyical challenges, it provides a more complete view of gene expression as well as insights into how specific genes may be regulated. This work was published in Mack et al. (2006). 3. Development of primary reproductive tract cell cultures. We developed primary cell cultures of dispersed reproductive tract cell types and determined conditions for organ culture of the entire reproductive tract. This work will allow us to rapidly screen mating-responsive genes for a variety of reproductive-tract specifi c functions. Scientific and agricultural significance. Together, these studies have defined the genetic response to mating in a part of the female reproductive tract that is critical for successful fertllization and have identified alarge set of mating-responsive genes. This work is the first to combine both genomic and proteomic approaches in determining female mating response in these tissues and has provided important insights into insect reproductive behavior.
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Ohad, Nir, et Robert Fischer. Regulation of plant development by polycomb group proteins. United States Department of Agriculture, janvier 2008. http://dx.doi.org/10.32747/2008.7695858.bard.
Texte intégralRésumé :
Our genetic and molecular studies have indicated that FIE a WD-repeat Polycomb group (PcG) protein takes part in multi-component protein complexes. We have shown that FIE PcG protein represses inappropriate programs of development during the reproductive and vegetative phases of the Arabidopsis life cycle. Moreover, we have shown that FIE represses the expression of key regulatory genes that promote flowering (AG and LFY), embryogenesis (LEC1), and shoot formation (KNAT1). These results suggest that the FIE PcG protein participates in the formation of distinct PcG complexes that repress inappropriate gene expression at different stages of plant development. PcG complexes modulate chromatin compactness by modifying histones and thereby regulate gene expression and imprinting. The main goals of our original project were to elucidate the biological functions of PcG proteins, and to understand the molecular mechanisms used by FIE PcG complexes to repress the expression of its gene targets. Our results show that the PcG complex acts within the central cell of the female gametophyte to maintain silencing of MEA paternal allele. Further more we uncovered a novel example of self-imprinting mechanism by the PgG complex. Based on results obtained in the cures of our research program we extended our proposed goals and elucidated the role of DME in regulating plant gene imprinting. We discovered that in addition to MEA,DME also imprints two other genes, FWA and FIS2. Activation of FWA and FIS2 coincides with a reduction in 5-methylcytosine in their respective promoters. Since endosperm is a terminally differentiated tissue, the methylation status in the FWA and FIS2 promoters does not need to be reestablished in the following generation. We proposed a “One-Way Control” model to highlight differences between plant and animal genomic imprinting. Thus we conclude that DEMETER is a master regulator of plant gene imprinting. Future studies of DME function will elucidate its role in processes and disease where DNA methylation has a key regulatory role both in plants and animals. Such information will provide valuable insight into developing novel strategies to control and improve agricultural traits and overcome particular human diseases.
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Stern, David, et Gadi Schuster. Manipulation of Gene Expression in the Chloroplast. United States Department of Agriculture, septembre 2000. http://dx.doi.org/10.32747/2000.7575289.bard.
Texte intégralRésumé :
The steady-state level of a given mRNA is determined by its rates of transcription and degradation. The stabilities of chloroplast mRNAs vary during plant development, in part regulating gene expression. Furthermore, the fitness of the organelle depends on its ability to destroy non-functional transcripts. In addition, there is a resurgent interest by the biotechnology community in chloroplast transformation due to the public concerns over pollen transmission of introduced traits or foreign proteins. Therefore, studies into basic gene expression mechanisms in the chloroplast will open the door to take advantage of these opportunities. This project was aimed at gaining mechanistic insights into mRNA processing and degradation in the chloroplast and to engineer transcripts of varying stability in Chlamydomonas reinhardtii cells. This research uncovered new and important information on chloroplast mRNA stability, processing, degradation and translation. In particular, the processing of the 3' untranslated regions of chloroplast mRNAs was shown to be important determinants in translation. The endonucleolytic site in the 3' untranslated region was characterized by site directed mutagensis. RNA polyadenylation has been characterized in the chloroplast of Chlamydomonas reinhardtii and chloroplast transformants carrying polyadenylated sequences were constructed and analyzed. Data obtained to date suggest that chloroplasts have gene regulatory mechanisms which are uniquely adapted to their post-endosymbiotic environment, including those that regulate RNA stability. An exciting point has been reached, because molecular genetic studies have defined critical RNA-protein interactions that participate in these processes. However, much remains to be learned about these multiple pathways, how they interact with each other, and how many nuclear genes are consecrated to overseeing them. Chlamydomonas is an ideal model system to extend our understanding of these areas, given its ease of manipulation and the existing knowledge base, some of which we have generated.
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Lichter, Amnon, Gopi K. Podila et Maria R. Davis. Identification of Genetic Determinants that Facilitate Development of B. cinerea at Low Temperature and its Postharvest Pathogenicity. United States Department of Agriculture, mars 2011. http://dx.doi.org/10.32747/2011.7592641.bard.
Texte intégralRésumé :
Botrytis cinerea is the postharvest pathogen of many agricultural produce with table grapes, strawberries and tomatoes as major targets. The high efficiency with which B. cinerea causes disease on these produce during storage is attributed in part due to its exceptional ability to develop at very low temperature. Our major goal was to understand the genetic determinants which enable it to develop at low temperature. The specific research objectives were: 1. Identify expression pattern of genes in a coldenriched cDNA library. 2. Identify B. cinerea orthologs of cold-induced genes 3. Profile protein expression and secretion at low temperature on strawberry and grape supplemented media. 4. Test novel methods for the functional analysis of coldresponsive genes. Objective 1 was modified during the research because a microarray platform became available and it allowed us to probe the whole set of candidate genes according to the sequence of 2 strains of the fungus, BO5.10 and T4. The results of this experiment allowed us to validate some of our earlier observations which referred to genes which were the product of a SSH suppression-subtraction library. Before the microarray became available during 2008 we also analyzed the expression of 15 orthologs of cold-induced genes and some of these results were also validated by the microarray experiment. One of our goals was also to perform functional analysis of cold-induced genes. This goal was hampered for 3 years because current methodology for transformation with ‘protoplasts’ failed to deliver knockouts of bacteriordopsin-like (bR) gene which was our primary target for functional analysis. Consequently, we developed 2 alternative transformation platforms, one which involves an air-gun based technique and another which involves DNA injection into sclerotia. Both techniques show great promise and have been validated using different constructs. This contribution is likely to serve the scientific community in the near future. Using these technologies we generated gene knockout constructs of 2 genes and have tested there effect on survival of the fungus at low temperature. With reference to the bR genes our results show that it has a significant effect on mycelial growth of the B. cinerea and the mutants have retarded development at extreme conditions of ionic stress, osmotic stress and low temperature. Another gene of unknown function, HP1 is still under analysis. An ortholog of the yeast cold-induced gene, CCH1 which encodes a calcium tunnel and was shown to be cold-induced in B. cinerea was recently cloned and used to complement yeast mutants and rescue them from cold-sensitivity. One of the significant findings of the microarray study involves a T2 ribonuclease which was validated to be cold-induced by qPCR analysis. This and other genes will serve for future studies. In the frame of the study we also screened a population of 631 natural B. cinerea isolates for development at low temperature and have identified several strains with much higher and lower capacity to develop at low temperature. These strains are likely to be used in the future as candidates for further functional analysis. The major conclusions from the above research point to specific targets of cold-induced genes which are likely to play a role in cold tolerance. One of the most significant observations from the microarray study is that low temperature does not induce ‘general stress response in B. cinerea, which is in agreement to its exceptional capacity to develop at low temperature. Due to the tragic murder of the Co-PI Maria R. Davis and GopiPodila on Feb. 2010 it is impossible to deliver their contribution to the research. The information of the PI is that they failed to deliver objective 4 and none of the information which relates to objective 3 has been delivered to the PI before the murder or in a visit to U. Alabama during June, 2010. Therefore, this report is based solely on the IS data.
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Prusky, Dov, Nancy P. Keller et Amir Sherman. global regulation of mycotoxin accumulation during pathogenicity of Penicillium expansum in postharvest fruits. United States Department of Agriculture, janvier 2014. http://dx.doi.org/10.32747/2014.7600012.bard.
Texte intégralRésumé :
Background to the topic- Penicilliumas a postharvest pathogen and producer of the mycotoxin PAT. Penicilliumspp. are destructive phytopathogens, capable of causing decay in many deciduous fruits, during postharvest handling and storage; and the resulting losses can amount to 10% of the stored produce and the accumulation of large amounts of the mycotoxinpatulin. The overall goal of this proposal is to identify critical host and pathogen factors that modulate P. expansummycotoxin genes and pathways which are required for PAT production and virulence. Our preliminary results indicated that gluconic acid are strongly affecting patulin accumulation during colonization. P. expansumacidifies apple fruit tissue during colonization in part through secretion of gluconic acid (GLA). Several publications suggested that GLA accumulation is an essential factor in P. expansumpathogenicity. Furthermore, down regulation of GOX2 significantly reduced PAT accumulation and pathogenicity. PAT is a polyketide and its biosynthesis pathway includes a 15-gene cluster. LaeA is a global regulator of mycotoxin synthesis. It is now known that patulin synthesis might be subjected to LaeA and sometimes by environmental sensing global regulatory factors including the carbon catabolite repressor CreA as well as the pH regulator factor PacC and nitrogen regulator AreA. The mechanisms by which LaeA regulates patulin synthesis was not fully known and was part of our work. Furthermore, the regulatory system that controls gene expression in accordance with ambient pH was also included in our work. PacC protein is in an inactive conformation and is unable to bind to the promoter sites of the target genes; however, under alkaline growth conditions activated PacC acts as both an activator of alkaline-expressed genes and a repressor of acid-expressed genes. The aims of the project- This project aims to provide new insights on the roles of LaeA and PacC and their signaling pathways that lead to GLA and PAT biosynthesis and pathogenicity on the host. Specifically, our specific aims were: i) To elucidate the mechanism of pH-controlled regulation of GLA and PAT, and their contribution to pathogenesis of P. expansum. We are interested to understanding how pH and/or GLA impact/s under PacC regulation affect PAT production and pathogenesis. ii) To characterize the role of LaeA, the global regulator of mycotoxin production, and its effect on PAT and PacC activity. iii) To identify the signaling pathways leading to GLA and PAT synthesis. Using state- of-the-art RNAseq technologies, we will interrogate the transcriptomes of laeAand pacCmutants, to identify the common signaling pathways regulating synthesis of both GLA and PAT. Major conclusions, solutions, achievements- In our first Aim our results demonstrated that ammonia secreted at the leading edge of the fungal colony induced transcript activation of the global pH modulator PacC and PAT accumulation in the presence of GLA. We assessed these parameters by: (i) direct exogenous treatment of P. expansumgrowing on solid medium; (ii) direct exogenous treatment on colonized apple tissue; (iii) growth under self-ammonia production conditions with limited carbon; and (iv) analysis of the transcriptional response to ammonia of the PAT biosynthesis cluster. Ammonia induced PAT accumulation concurrently with the transcript activation of pacCand PAT biosynthesis cluster genes, indicating the regulatory effect of ammonia on pacCtranscript expression under acidic conditions. Transcriptomic analysis of pH regulated processes showed that important genes and BARD Report - Project 4773 Page 2 of 10 functionalities of P. expansumwere controlled by environmental pH. The differential expression patterns of genes belonging to the same gene family suggest that genes were selectively activated according to their optimal environmental conditions to enable the fungus to cope with varying conditions and to make optimal use of available enzymes. Concerning the second and third Aims, we demonstrated that LaeA regulates several secondary metabolite genes, including the PAT gene cluster and concomitant PAT synthesis invitro. Virulence studies of ΔlaeAmutants of two geographically distant P. expansumisolates (Pe-21 from Israel and Pe-T01 from China) showed differential reduction in disease severity in freshly harvested fruit ranging from no reduction for Ch-Pe-T01 strains in immature fruit to 15–25% reduction for both strains in mature fruit, with the ΔlaeAstrains of Is-Pe-21 always showing a greater loss in virulence. Results suggest the importance of LaeA regulation of PAT and other secondary metabolites on pathogenicity. Our work also characterized for the first time the role of sucrose, a key nutritional factor present in apple fruit, as a negative regulator of laeAexpression and consequent PAT production in vitro. This is the first report of sugar regulation of laeAexpression, suggesting that its expression may be subject to catabolite repression by CreA. Some, but not all of the 54 secondary metabolite backbone genes in the P. expansumgenome, including the PAT polyketide backbone gene, were found to be regulated by LaeA. Together, these findings enable for the first time a straight analysis of a host factor that potentially activates laeAand subsequent PAT synthesis.
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Fluhr, Robert, et Volker Brendel. Harnessing the genetic diversity engendered by alternative gene splicing. United States Department of Agriculture, décembre 2005. http://dx.doi.org/10.32747/2005.7696517.bard.
Texte intégralRésumé :
Our original objectives were to assess the unexplored dimension of alternative splicing as a source of genetic variation. In particular, we sought to initially establish an alternative splicing database for Arabidopsis, the only plant for which a near-complete genome has been assembled. Our goal was to then use the database, in part, to advance plant gene prediction programs that are currently a limiting factor in annotating genomic sequence data and thus will facilitate the exploitation of the ever increasing quantity of raw genomic data accumulating for plants. Additionally, the database was to be used to generate probes for establishing high-throughput alternative transcriptome analysis in the form of a splicing-specific oligonucleotide microarray. We achieved the first goal and established a database and web site termed Alternative Splicing In Plants (ASIP, http://www.plantgdb.org/ASIP/). We also thoroughly reviewed the extent of alternative splicing in plants (Arabidopsis and rice) and proposed mechanisms for transcript processing. We noted that the repertoire of plant alternative splicing differs from that encountered in animals. For example, intron retention turned out to be the major type. This surprising development was proven by direct RNA isolation techniques. We further analyzed EST databases available from many plants and developed a process to assess their alternative splicing rate. Our results show that the lager genome-sized plant species have enhanced rates of alternative splicing. We did advance gene prediction accuracy in plants by incorporating scoring for non-canonical introns. Our data and programs are now being used in the continuing annotation of plant genomes of agronomic importance, including corn, soybean, and tomato. Based on the gene annotation data developed in the early part of the project, it turned out that specific probes for different exons could not be scaled up to a large array because no uniform hybridization conditions could be found. Therefore, we modified our original objective to design and produce an oligonucleotide microarray for probing alternative splicing and realized that it may be reasonable to investigate the extent of alternative splicing using novel commercial whole genome arrays. This possibility was directly examined by establishing algorithms for the analysis of such arrays. The predictive value of the algorithms was then shown by isolation and verification of alternative splicing predictions from the published whole genome array databases. The BARD-funded work provides a significant advance in understanding the extent and possible roles of alternative splicing in plants as well as a foundation for advances in computational gene prediction.