An integrated encyclopedia of DNA elements in the human genome.

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.

Redução da influência da massa específica na determinação do teor de umidade de sementes de trigo

A medição da capacitância e da condutância de um capacitor contendo amostras de trigo permite a determinação de duas de suas propriedades dielétricas: a permissividade relativa (épsilon') e o fator de perda dielétrica (épsilon"). A utilização dessas propriedades, medidas simultaneamente em duas freqüências de oscilação do campo elétrico, permite reduzir ou eliminar o efeito da massa específica aparente na determinação do teor de umidade do trigo. Tal procedimento torna possível o monitoramento contínuo e em tempo real, sem a necessidade de retirar amostras, do teor de umidade de uma coluna de grãos em movimento, situação em que ocorrem as maiores variações na massa específica do produto. O objetivo deste trabalho consistiu na obtenção de equações que permitam reduzir ou eliminar o efeito da massa específica na determinação em linha do teor de umidade do trigo. Foram utilizadas amostras das variedades Hussar, Mercia e Hereward com teor de umidade entre 11% e 22% b.u. e massa específica no intervalo 666 kg m-3 <= ro <= 873 kg m-3. A equação que apresentou melhor desempenho permite calcular o teor de umidade do trigo com erros-padrão de calibração e de predição de 0,4 e 0,5 ponto percentual, respectivamente.

The GENCODE pseudogene resource.

BACKGROUND: Pseudogenes have long been considered as nonfunctional genomic sequences. However, recent evidence suggests that many of them might have some form of biological activity, and the possibility of functionality has increased interest in their accurate annotation and integration with functional genomics data. RESULTS: As part of the GENCODE annotation of the human genome, we present the first genome-wide pseudogene assignment for protein-coding genes, based on both large-scale manual annotation and in silico pipelines. A key aspect of this coupled approach is that it allows us to identify pseudogenes in an unbiased fashion as well as untangle complex events through manual evaluation. We integrate the pseudogene annotations with the extensive ENCODE functional genomics information. In particular, we determine the expression level, transcription-factor and RNA polymerase II binding, and chromatin marks associated with each pseudogene. Based on their distribution, we develop simple statistical models for each type of activity, which we validate with large-scale RT-PCR-Seq experiments. Finally, we compare our pseudogenes with conservation and variation data from primate alignments and the 1000 Genomes project, producing lists of pseudogenes potentially under selection. CONCLUSIONS: At one extreme, some pseudogenes possess conventional characteristics of functionality; these may represent genes that have recently died. On the other hand, we find interesting patterns of partial activity, which may suggest that dead genes are being resurrected as functioning non-coding RNAs. The activity data of each pseudogene are stored in an associated resource, psiDR, which will be useful for the initial identification of potentially functional pseudogenes.

Calculation of wood volume and stem taper using terrestrial single-image close-range photogrammetry and contemporary software tools

Abstract

Incidência de ascite em frangos de corte alimentados com rações comerciais de alto nível energético

O trabalho objetivou avaliar os efeitos de diferentes rações comerciais com alto nível energético na incidência de ascite em frangos de corte. Foram utilizadas 1.200 aves de uma mesma linhagem comercial (Hubbard), distribuídas em 12 boxes, segundo um delineamento inteiramente ao acaso, com quatro tratamentos e três repetições de 100 aves cada. Os tratamentos foram constituídos por três diferentes rações comerciais trituradas (B, C e D) comparadas com o controle, uma ração farelada inicial (A), do primeiro ao 39º dia de idade. Não houve diferenças entre os tratamentos quanto ao consumo, peso e ganho de peso das aves. Em relação à conversão alimentar, o tratamento C apresentou resultado significativamente melhor; entretanto, foi observada neste mesmo tratamento, a maior taxa de mortalidade. O maior motivo dos óbitos registrados foi a síndrome ascítica. Conclui-se que existe um favorecimento de surto de ascite pelas rações com melhor conversão alimentar nas aves.

Aberrant repair and fibrosis development in skeletal muscle

The repair process of damaged tissue involves the coordinated activities of several cell types in response to local and systemic signals. Following acute tissue injury, infiltrating inflammatory cells and resident stem cells orchestrate their activities to restore tissue homeostasis. However, during chronic tissue damage, such as in muscular dystrophies, the inflammatory-cell infiltration and fibroblast activation persists, while the reparative capacity of stem cells (satellite cells) is attenuated. Abnormal dystrophic muscle repair and its end stage, fibrosis, represent the final common pathway of virtually all chronic neurodegenerative muscular diseases. As our understanding of the pathogenesis of muscle fibrosis has progressed, it has become evident that the muscle provides a useful model for the regulation of tissue repair by the local microenvironment, showing interplay among muscle-specific stem cells, inflammatory cells, fibroblasts and extracellular matrix components of the mammalian wound-healing response. This article reviews the emerging findings of the mechanisms that underlie normal versus aberrant muscle-tissue repair.

Níveis protéicos na ração de frangos de corte na fase de crescimento

O objetivo deste trabalho foi determinar o nível mínimo de proteína bruta para atender às exigências nutricionais de frangos de corte Hubbard, machos e fêmeas, na fase de crescimento. Oitocentos e oitenta pintos machos e fêmeas de 22 a 42 dias de idade foram distribuídos ao acaso em esquema fatorial 5x2 (níveis de proteína bruta x sexos), com quatro repetições de 22 aves. Os níveis de proteína testados foram 15%, 17%, 19%, 21% e 23%. Houve efeito quadrático dos níveis de proteína no ganho de peso e na conversão alimentar dos machos. Em relação às fêmeas, o efeito foi quadrático no ganho de peso e linear na conversão. A relação entre o rendimento de carcaça e o nível de proteína bruta da ração foi linear e independente do sexo. O consumo de ração, a gordura abdominal e o rendimento de peito foram influenciados apenas pelo sexo. Recomenda-se 21,70% de proteína bruta para os machos e 19,00% para as fêmeas, na fase de crescimento.

Suscetibilidade de linhagens de frangos de corte à síndrome ascítica

O objetivo deste trabalho foi estudar a suscetibilidade à síndrome ascítica de machos e fêmeas em linhagens comerciais de frango de corte. Todas as aves receberam ração ad libitum com 3.050 kcal/ME. Foram comparadas as linhagens comerciais representadas pela Cobb, Hubbard e Ross, machos e fêmeas. O delineamento utilizado foi o inteiramente casualizado, em esquema fatorial. As aves foram aleatoriamente alojadas em um galpão experimental de 8x76 m, com 18 boxes de 3x3,5 m cada e 100 aves por divisão, num total de 1.800 aves. Os resultados revelaram que a incidência de ascite independe da linhagem comercial dos frangos de corte, entretanto, os machos foram mais suscetíveis.

Potential detrimental effects of a phytoestrogen-rich diet on male fertility in mice.

Soy and soy-based products are widely consumed by infants and adult individuals. There has been speculation that the presence of isoflavone phytoestrogens in soybean cause adverse effects on the development and function of the male reproductive system. The purpose of this study was to examine the influence of dietary soy and phytoestrogens on testicular and reproductive functions. Male mice were fed from conception to adulthood with either a high soy-containing diet or a soy-free diet. Although adult mice fed a soy-rich diet exhibited normal male behaviour and were fertile, we observed a reduced proportion of haploid germ cells in testes correlating with a 25% decrease in epididymal sperm counts and a 21% reduction in litter size. LH and androgens levels were not affected but transcripts coding for androgen-response genes in Sertoli cells and Gapd-s, a germ cell-specific gene involved in sperm glycolysis and mobility were significantly reduced. In addition, we found that dietary soy decreased the size of the seminal vesicle but without affecting its proteolytic activity. Taken together, these studies show that long-term exposure to dietary soy and phytoestrogens may affect male reproductive function resulting in a small decrease in sperm count and fertility.

Filamin depletion blocks endoplasmic spreading and destabilizes force-bearing adhesions

Cell motility is an essential process that depends on a coherent, cross-linked actin cytoskeleton that physically coordinates the actions of numerous structural and signaling molecules. The actin cross-linking protein, filamin (Fln), has been implicated in the support of three-dimensional cortical actin networks capable of both maintaining cellular integrity and withstanding large forces. Although numerous studies have examined cells lacking one of the multiple Fln isoforms, compensatory mechanisms can mask novel phenotypes only observable by further Fln depletion. Indeed, shRNA-mediated knockdown of FlnA in FlnB¿/¿ mouse embryonic fibroblasts (MEFs) causes a novel endoplasmic spreading deficiency as detected by endoplasmic reticulum markers. Microtubule (MT) extension rates are also decreased but not by peripheral actin flow, because this is also decreased in the Fln-depleted system. Additionally, Fln-depleted MEFs exhibit decreased adhesion stability that appears in increased ruffling of the cell edge, reduced adhesion size, transient traction forces, and decreased stress fibers. FlnA¿/¿ MEFs, but not FlnB¿/¿ MEFs, also show a moderate defect in endoplasm spreading, characterized by initial extension followed by abrupt retractions and stress fiber fracture. FlnA localizes to actin linkages surrounding the endoplasm, adhesions, and stress fibers. Thus we suggest that Flns have a major role in the maintenance of actin-based mechanical linkages that enable endoplasmic spreading and MT extension as well as sustained traction forces and mature focal adhesions.

Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.

Within the ENCODE Consortium, GENCODE aimed to accurately annotate all protein-coding genes, pseudogenes, and noncoding transcribed loci in the human genome through manual curation and computational methods. Annotated transcript structures were assessed, and less well-supported loci were systematically, experimentally validated. Predicted exon-exon junctions were evaluated by RT-PCR amplification followed by highly multiplexed sequencing readout, a method we called RT-PCR-seq. Seventy-nine percent of all assessed junctions are confirmed by this evaluation procedure, demonstrating the high quality of the GENCODE gene set. RT-PCR-seq was also efficient to screen gene models predicted using the Human Body Map (HBM) RNA-seq data. We validated 73% of these predictions, thus confirming 1168 novel genes, mostly noncoding, which will further complement the GENCODE annotation. Our novel experimental validation pipeline is extremely sensitive, far more than unbiased transcriptome profiling through RNA sequencing, which is becoming the norm. For example, exon-exon junctions unique to GENCODE annotated transcripts are five times more likely to be corroborated with our targeted approach than with extensive large human transcriptome profiling. Data sets such as the HBM and ENCODE RNA-seq data fail sampling of low-expressed transcripts. Our RT-PCR-seq targeted approach also has the advantage of identifying novel exons of known genes, as we discovered unannotated exons in ~11% of assessed introns. We thus estimate that at least 18% of known loci have yet-unannotated exons. Our work demonstrates that the cataloging of all of the genic elements encoded in the human genome will necessitate a coordinated effort between unbiased and targeted approaches, like RNA-seq and RT-PCR-seq.

Recent skin injuries in children with motor disabilities.

OBJECTIVE: To determine the frequency of recent skin injuries in children with neuromotor disabilities and its association with disability. DESIGN: Cross-sectional study of 168 children with neuromotor disabilities aged 2-16 years. SETTING: Two outpatient child rehabilitation centres. MAIN OUTCOME MEASURES: Children were classified as unrestricted walkers, restricted walkers or wheelchair dependent. Each participant's body surface was systematically examined for recent skin injuries with the exception of the anal-genital area. RESULTS: The mean age of our sample was 7.8 (SD 3.7) years with a 3:2 male/female ratio. Overall, 64% had cerebral palsy, 17% a neuromuscular disease and 19% other motor disabilities. Participants had on average 5.3 (SD 4.5) recent skin injuries (max 19), of which 2.5 were bruises (SD 3.3, max 16), 2.4 were abrasions, scratches or cuts (SD 3.0, max 16) and 0.4 were pressure lesions (SD 0.8, max 4). There was a significant decrease in the frequency of recent skin injuries and of bruises with increasing severity of motor disability. Most of this variation was accounted for by injuries to the lower limbs. There were no significant effects of gender, learning disabilities or other comorbidities. CONCLUSIONS: Children with neuromotor disabilities present a progressive reduction in the number of skin injuries with decreasing mobility. Therefore, recent skin injuries in this population which are unusual by their number, appearance or distribution, should raise at least the same level of suspicion for physical abuse as in children without disabilities.