Transcriptional dysregulation of coding and non-coding genes in cellular models of Huntington's disease

HD (Huntington's disease) is a late onset heritable neurodegenerative disorder that is characterized by neuronal dysfunction and death, particularly in the cerebral cortex and medium spiny neurons of the striatum. This is followed by progressive chorea, dementia and emotional dysfunction, eventually resulting in death. HD is caused by an expanded CAG repeat in the first exon of the HD gene that results in an abnormally elongated polyQ (polyglutamine) tract in its protein product, Htt (Huntingtin). Wild-type Htt is largely cytoplasmic; however, in HD, proteolytic N-terminal fragments of Htt form insoluble deposits in both the cytoplasm and nucleus, provoking the idea that mutHtt (mutant Htt) causes transcriptional dysfunction. While a number of specific transcription factors and co-factors have been proposed as mediators of mutHtt toxicity, the causal relationship between these Htt/transcription factor interactions and HD pathology remains unknown. Previous work has highlighted REST [RE1 (repressor element 1)-silencing transcription factor] as one such transcription factor. REST is a master regulator of neuronal genes, repressing their expression. Many of its direct target genes are known or suspected to have a role in HD pathogenesis, including BDNF (brain-derived neurotrophic factor). Recent evidence has also shown that REST regulates transcription of regulatory miRNAs (microRNAs), many of which are known to regulate neuronal gene expression and are dysregulated in HD. Thus repression of miRNAs constitutes a second, indirect mechanism by which REST can alter the neuronal transcriptome in HD. We will describe the evidence that disruption to the REST regulon brought about by a loss of interaction between REST and mutHtt may be a key contributory factor in the widespread dysregulation of gene expression in HD.

A novel regeneration system for a wild passion fruit species (Passiflora cincinnata Mast.) based on somatic embryogenesis from mature zygotic embryos

The objective of the present work was to induce somatic embryogenesis from zygotic embryos of Passiflora cincinnata Masters. Zygotic embryos formed calli on media with different concentrations of 2,4-dichlorophenoxyacetic acid (2,4-D) and 4.5 mu M benzyladenine (BA) after 30 days of in vitro culture. A concentration of 18.1 mu M 2,4-D resulted in the largest number of somatic embryos. Embryogenic calli were yellowish and friable, forming whitish proembryogenic masses. Morphologically, embryogenic cells were small and had large nuclei and dense cytoplasm, whereas non-embryogenic cells were elongated, with small nuclei and less dense cytoplasm. Calli cultured under white light on basal Murashige and Skoog`s medium with activated charcoal produced embryos in all developmental stages. There were differences among the treatments, with some leading to the production of calli with embryos and some only to callus formation. Some abnormalities were associated with somatic embryos, including fused axes, fused cotyledons and polycotyledonary embryos. Production of secondary somatic embryos occurred in the first cycle of primary embryo development. Secondary embryos differentiated from the surface of the protodermal layer of primary embryos with intense cell proliferation, successive mitotic divisions in the initial phase of embryoid development, and a vascular system formed with no connection to the parental tissue. This secondary embryogenic system of P. cincinnata is characterized by intense proliferation and maintenance of embryogenic competence after successive subcultures. This reproducible protocol opens new prospects for massive propagation and is an alternative to the current organogenesis-based transformation protocol.

Oscheius tipulae as an example of eEF1A gene diversity in nematodes

We characterized four eEF1A genes in the alternative rhabditid nematode model organism Oscheius tipulae. This is twice the copy number of eEF1A genes in C. elegans, C. briggsae, and, probably, many other free-living and parasitic nematodes. The introns show features remarkably different from those of other metazoan eEF1A genes. Most of the introns in the eEF1A genes are specific to O. tipulae and are not shared with any of the other genes described in metazoans. Most of the introns are phase 0 (inserted between two codons), and few are inserted in protosplice sites (introns inserted between the nucleotide sequence A/CAG and G/A). Two of these phase 0 introns are conserved in sequence in two or more of the four eEF1A gene copies, and are inserted in the same position in the genes. Neither of these characteristics has been detected in any of the nematode eEF1A genes characterized to date. The coding sequences were also compared with other eEF1A cDNAs from 11 different nematodes to determine the variability of these genes within the phylum Nematoda. Parsimony and distance trees yielded similar topologies, which were similar to those created using other molecular markers. The presence of more than one copy of the eEF1A gene with nearly identical coding regions makes it difficult to define the orthologous cDNAs. As shown by our data on O. tipulae, careful and extensive examination of intron positions in the eEF1A gene across the phylum is necessary to define their potential for use as valid phylogenetic markers.

Template-based quadrilateral meshing

Generating quadrilateral meshes is a highly non-trivial task, as design decisions are frequently driven by specific application demands. Automatic techniques can optimize objective quality metrics, such as mesh regularity, orthogonality, alignment and adaptivity; however, they cannot make subjective design decisions. There are a few quad meshing approaches that offer some mechanisms to include the user in the mesh generation process; however, these techniques either require a large amount of user interaction or do not provide necessary or easy to use inputs. Here, we propose a template-based approach for generating quad-only meshes from triangle surfaces. Our approach offers a flexible mechanism to allow external input, through the definition of alignment features that are respected during the mesh generation process. While allowing user inputs to support subjective design decisions, our approach also takes into account objective quality metrics to produce semi-regular, quad-only meshes that align well to desired surface features. Published by Elsevier Ltd.

Fiedler trees for multiscale surface analysis

In this work we introduce a new hierarchical surface decomposition method for multiscale analysis of surface meshes. In contrast to other multiresolution methods, our approach relies on spectral properties of the surface to build a binary hierarchical decomposition. Namely, we utilize the first nontrivial eigenfunction of the Laplace-Beltrami operator to recursively decompose the surface. For this reason we coin our surface decomposition the Fiedler tree. Using the Fiedler tree ensures a number of attractive properties, including: mesh-independent decomposition, well-formed and nearly equi-areal surface patches, and noise robustness. We show how the evenly distributed patches can be exploited for generating multiresolution high quality uniform meshes. Additionally, our decomposition permits a natural means for carrying out wavelet methods, resulting in an intuitive method for producing feature-sensitive meshes at multiple scales. Published by Elsevier Ltd.

A powder X-ray diffraction method for detection of polyprenylated benzophenones in plant extracts associated with HPLC for quantitative analysis

A robust, direct, rapid and non-destructive X-ray diffraction crystallography method to detect the polyprenylated benzophenones 7-epi-clusianone (1) and guttiferone A (2) in extracts from Garcinia brasiliensis is presented. Powder samples of benzophenones 1 and 2, dried hexane extracts from G. brasiliensis seeds and fruit`s pericarp, and the dried ethanolic extract from G. brasiliensis seeds were unambiguously characterized by powder X-ray diffractometry. The calculated X-ray diffraction peaks from crystal structures of analytes 1 and 2, previously determined by single-crystal X-ray diffraction technique, were overlaid to those of the experimental powder diffractograms, providing a practical identification of these compounds in the analyzed material and confirming the pure contents of the powder samples. Using the X-ray diffraction crystallography method, the studied polyprenylated benzophenones were selectively and simultaneously detected in the extracts which were mounted directly on sample holder. In addition, reference materials of the analytes were not required for analyses since the crystal structures of the compounds are known. High performance liquid chromatography analyses also were comparatively carried out to quantify the analytes in the same plant extracts showing to be in agreement with X-ray diffraction crystallography method. (C) 2010 Elsevier B.V. All rights reserved.

Automatic camera control in virtual environments augmented using multiple sparse videos

Automated virtual camera control has been widely used in animation and interactive virtual environments. We have developed a multiple sparse camera based free view video system prototype that allows users to control the position and orientation of a virtual camera, enabling the observation of a real scene in three dimensions (3D) from any desired viewpoint. Automatic camera control can be activated to follow selected objects by the user. Our method combines a simple geometric model of the scene composed of planes (virtual environment), augmented with visual information from the cameras and pre-computed tracking information of moving targets to generate novel perspective corrected 3D views of the virtual camera and moving objects. To achieve real-time rendering performance, view-dependent textured mapped billboards are used to render the moving objects at their correct locations and foreground masks are used to remove the moving objects from the projected video streams. The current prototype runs on a PC with a common graphics card and can generate virtual 2D views from three cameras of resolution 768 x 576 with several moving objects at about 11 fps. (C)2011 Elsevier Ltd. All rights reserved.

Análise de haplótipos intragênicos ao gene MJD1 em pacientes com doença de Machado-Joseph

A doença de Machado-Joseph (DMJ), ou ataxia espinocerebelar tipo 3 (SCA3), é uma desordem neurodegenerativa autossômica dominante, originalmente descrita em famílias de ancestralidade portuguesa-açoriana. Incordenação generalizada da marcha, dos membros e da fala podem estar presentes nos pacientes afetados por essa doença. O início das manifestações clínicas ocorre, em geral, entre os 30 e os 40 anos, apresentando uma progressão bastante lenta. O tempo médio de sobrevida depois do início da doença é de 14 a 17 anos. O gene associado à doença, denominado MJD1, foi identificado em 1994 e localiza-se no cromossomo 14. Este gene se caracteriza por apresentar uma repetição nucleotídica CAG na região 5` do exon 2. O número destas repetições é polimórfico na população, sendo que indivíduos normais apresentam de 12 a 37 repetições CAG, enquanto os afetados pela DMJ podem apresentar de 61 a 84 repetições. Um recente estudo mundial de haplótipos demonstrou a presença de dois diferentes haplótipos em famílias de origem açoriana, que são específicos à ilha de origem. Em famílias da porção continental de Portugal, os dois haplótipos foram encontrados. A maioria das famílias não portuguesas também compartilha o mesmo haplótipo encontrado em famílias originárias da ilha de Flores, mas três outros haplótipos foram encontrados nessas famílias. Até o momento, a hipótese mais forte declara que a difusão da mutação original está diretamente ligada à imigração portuguesa-açoriana No presente estudo, esta hipótese foi testada através da análise de disequilíbrio de ligação de três polimorfismos intragênicos (A669TG/C669TG, C987GG/G987GG, TAA1118/TAC1118). O polimorfismo na posição 669 foi identificado por PCR seguido de SSCP e confirmado por sequenciamento direto. Os polimorfismos nas posições 987 e 1118 foram detectados por PCR alelo-específico. Os resultados obtidos indicaram que o haplótipo intragênico A-C-A estava associado ao alelo com a expansão na maioria dos pacientes (92%). Estes resultados confirmam achados em outros estudos. Isto indica que uma única mutação na DMJ foi introduzida em várias populações, seguida de um efeito fundador local, e indicando também que provavelmente esta mutação é muito antiga. E, para finalizar, baseado neste estudo e comparando com dados gerados no estudo mundial de haplótipos, pode-se especular que a origem da mutação associada a DMJ nos pacientes do sul do Brasil é proveniente da ilha de Flores.

Análise molecular de indivíduos com doença de Machado-Joseph

As ataxias espinocerebelares (SCAs) constituem um grupo de doenças neurodegenerativas fatais que apresentam uma grande heterogeneidade clínica. A doença de Machado-Joseph (DMJ), ou ataxia espinocerebelar tipo 3 (SCA3), é causada por uma expansão de uma seqüência repetitiva CAG em um gene, denominado MJD1, localizado no braço longo do cromossomo 14, expansão codificadora de uma seqüência poliglutamínica constituinte da proteína ataxina 3. Indivíduos normais apresentam entre 12 a 41 repetições, enquanto indivíduos afetados apresentam 61 a 84 repetições CAGs neste gene. Este trabalho teve como objetivos principais a padronização de metodologias moleculares para o identificação e a quantificação do número de repetições CAG no gene responsável pela da DMJ. Um grupo de 112 pacientes, pertencentes a 77 famílias, com suspeita clínica de algum tipo de ataxia espinocerebelar foi avaliado no Hospital de Clínicas de Porto Alegre. Após a extração de DNA destes pacientes, este material foi amplificado por PCR utilizando oligonucleotídeos iniciadores específicos para a região de interesse e posterior transferência destes fragmentos (1) para uma membrana de nylon pelo método de Southern blot, visando ao estabelecimento de um protocolo não-radioativo para detectar a presença do alelo normal e/ou mutante; e (2) análise em gel de poliacrilamida para quantificação do número de repetições presentes no alelo mutante. As análises laboratoriais identificaram um total de 77 pacientes com uma expansão CAG no gene da MJD1. Considerando-se apenas indivíduos não relacionados, a freqüência encontrada foi de 61% (47 indivíduos). Os protocolos estabelecidos demonstraram-se bastante eficazes e sensíveis para o diagnóstico da DMJ e quantificação do alelo expandido da respectiva doença.

Estudos de microsatélites em humanos: aplicações na identificação de indivíduos, genética de populações, datação de mutações e diagnóstico de doenças

Os microsatélites, também chamados STRs (Short Tandem Repeat), são pequenas sequências de DNA que consistem numa sequência de repetições de um motivo que varia de um a seis pares de bases. Existem em quase todos os cromossomas humanos e podem situar-se nos exões ou nos intrões. Estes últimos são altamente polimórficos e são por isso utilizados na identificação de indivíduos em testes de paternidade e também em estudos de genética de populações. A combinação dos vários genótipos possíveis faz com que cada indivíduo possua um perfil único, que permite a sua identificação. Existem também microsatélites associados a exões ou a regiões promotoras dos genes, normalmente repetições trinucleotídicas CGG/CCG ou CAG/CTG, associados a doenças neurodegenerativas como a síndrome do X-frágil e a doença de Huntington. Neste trabalho caracterizaram-se geneticamente várias populações humanas dos arquipélagos da Madeira, Açores e Cabo Verde. A partir do estudo dos microsatélites do cromossoma Y, foram definidas idades de coalescência que permitiram concluir que as cópias do gene DAZ situado no cromossoma Y são o resultado de um processo evolutivo estando a sua evolução associada a alguns haplogrupos. Verificou-se também a ocorrência de possíveis mutações nos SNPs que definem os haplogrupos, através da comparação dos microsatélites do cromossoma Y dentro de cada haplogrupo, especialmente no haplogrupo E3b. Verificou-se existir uma associação entre o número de repetições CAG e GGC do gene Receptor de Androgénios (AR), situado no cromossoma X, e a infertilidade especialmente quando combinados os dois polimorfismos, parecendo haver um efeito protector dos alelos maiores e alguma susceptibilidade para os alelos menores. Quando se estudou o número de repetições GGC do gene FMR1 em doentes com suspeita de síndrome de X-frágil observaram-se diferenças significativas quando comparadas com a população em geral e com um grupo de sobredotados. Essa diferença deveu-se principalmente à presença do alelo 29 em quase todos os indivíduos do primeiro grupo o que por si só não constitui um factor de risco mas poderá ser uma indicação da associação deste alelo com outra mutação no mesmo gene que possa ser responsável por este fenótipo.

Desempenho e rendimento de carcaça de frangos de corte alimentados com pectina na ração

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Identificação de híbridos de citros resistentes à mancha-marrom-de-alternária por meio de fAFLP e testes de patogenicidade

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Bidens mosaic virus: detecção via RT-PCR e identificação de Galinsoga parviflora como um novo hospedeiro natural do vírus

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Experimental investigation of smouldering in biomass

The smouldering process of wood logs was studied experimentally in a laboratory facility and in prescribed forest bums. The main goal was to check the parameters that initiate and control the stability of the smouldering process. To do so, sample temperatures at five different locations and concentrations of CO, CO2 and O-2 were measured and discussed. By varying the temperature and air supply of the flow tunnel apparatus, different rates of smoulder propagation were identified. In prescribed bums, the main characteristics of the self-sustained smouldering combustion front in logs of different sizes and species are reported. The average smouldering speed in the field is about one order of magnitude lower than that reported for different materials in laboratory experiments. (C) 2002 Elsevier B.V. Ltd. All rights reserved.

Log smoldering after an Amazonian deforestation fire

The characteristics of log smoldering after an Amazonian deforestation fire are described. The experiment was carried out in 2001 at the Caiabi farm, near the city of Alta Floresta, state of Mato Grosso, Brazil, as part of a set of tests that have been performed in the same area since 1997. A 200 x 200m(2) test area was slashed in the beginning of June and burned on 20 August. The area contained 507 logs with diameter at breast height (DBH) higher than 10 cm, per hectare. In the day following the main burn 59 logs were found to remain smoldering, a number that corresponds to 2.9% of the total in the area. We chose 11 of the 59 logs to have their smoldering process monitored. Their diameter, moisture content and CHN dry biomass composition after the plot burn and before smoldering were determined. Other parameters such as temperature distribution while smoldering, porosity, density and mass volatilized during thermogravimetric test were also determined. Average smoldering speeds were in the range from 0.8 to 1.5 cm h(-1) for logs that smoldered without transition to the flaming regime. The average speed increased to 2.1 cm h(-1) for those logs that oscillated between smoldering and flaming. The speeds were lower overnight as compared to values determined during daytime for the same log. Higher log moisture contents were found to produce decreased speeds. Micro-porous biomass was not observed in the set of the 11 selected logs. Smoldering was observed to occur at substantial intensity in crossing of logs, with no longitudinal propagation. (C) 2003 Elsevier Ltd. All rights reserved.