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.

EGASP: the human ENCODE Genome Annotation Assessment Project.

BACKGROUND: We present the results of EGASP, a community experiment to assess the state-of-the-art in genome annotation within the ENCODE regions, which span 1% of the human genome sequence. The experiment had two major goals: the assessment of the accuracy of computational methods to predict protein coding genes; and the overall assessment of the completeness of the current human genome annotations as represented in the ENCODE regions. For the computational prediction assessment, eighteen groups contributed gene predictions. We evaluated these submissions against each other based on a 'reference set' of annotations generated as part of the GENCODE project. These annotations were not available to the prediction groups prior to the submission deadline, so that their predictions were blind and an external advisory committee could perform a fair assessment. RESULTS: The best methods had at least one gene transcript correctly predicted for close to 70% of the annotated genes. Nevertheless, the multiple transcript accuracy, taking into account alternative splicing, reached only approximately 40% to 50% accuracy. At the coding nucleotide level, the best programs reached an accuracy of 90% in both sensitivity and specificity. Programs relying on mRNA and protein sequences were the most accurate in reproducing the manually curated annotations. Experimental validation shows that only a very small percentage (3.2%) of the selected 221 computationally predicted exons outside of the existing annotation could be verified. CONCLUSION: This is the first such experiment in human DNA, and we have followed the standards established in a similar experiment, GASP1, in Drosophila melanogaster. We believe the results presented here contribute to the value of ongoing large-scale annotation projects and should guide further experimental methods when being scaled up to the entire human genome sequence.

Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions.

This report presents systematic empirical annotation of transcript products from 399 annotated protein-coding loci across the 1% of the human genome targeted by the Encyclopedia of DNA elements (ENCODE) pilot project using a combination of 5' rapid amplification of cDNA ends (RACE) and high-density resolution tiling arrays. We identified previously unannotated and often tissue- or cell-line-specific transcribed fragments (RACEfrags), both 5' distal to the annotated 5' terminus and internal to the annotated gene bounds for the vast majority (81.5%) of the tested genes. Half of the distal RACEfrags span large segments of genomic sequences away from the main portion of the coding transcript and often overlap with the upstream-annotated gene(s). Notably, at least 20% of the resultant novel transcripts have changes in their open reading frames (ORFs), most of them fusing ORFs of adjacent transcripts. A significant fraction of distal RACEfrags show expression levels comparable to those of known exons of the same locus, suggesting that they are not part of very minority splice forms. These results have significant implications concerning (1) our current understanding of the architecture of protein-coding genes; (2) our views on locations of regulatory regions in the genome; and (3) the interpretation of sequence polymorphisms mapping to regions hitherto considered to be "noncoding," ultimately relating to the identification of disease-related sequence alterations.

Factors affecting snow damage of trees with particular reference to European conditions

Summary

SPATIAL VARIABILITY AND VITALITY OF EPIGEOUS TERMITE MOUNDS IN PASTURES OF MATO GROSSO DO SUL, BRAZIL

Epigeous termite mounds are frequently observed in pasture areas, but the processes regulating their population dynamics are poorly known. This study evaluated epigeous termite mounds in cultivated grasslands used as pastures, assessing their spatial distribution by means of geostatistics and evaluating their vitality. The study was conducted in the Cerrado biome in the municipality of Rio Brilhante, Mato Grosso do Sul, Brazil. In two pasture areas (Pasture 1 and Pasture 2), epigeous mounds (nests) were georeferenced and analyzed for height, circumference and vitality (inhabited or not). The area occupied by the mounds was calculated and termite specimens were collected for taxonomic identification. The spatial distribution pattern of the mounds was analyzed with geostatistical procedures. In both pasture areas, all epigeous mounds were built by the same species, Cornitermes cumulans. The mean number of mounds per hectare was 68 in Pasture 1 and 127 in Pasture 2, representing 0.4 and 1 % of the entire area, respectively. A large majority of the mounds were active (vitality), 91 % in Pasture 1 and 84 % in Pasture 2. A “pure nugget effect” was observed in the semivariograms of height and nest circumference in both pastures reflecting randomized spatial distribution and confirming that the distribution of termite mounds in pastures had a non-standard distribution.

INTERVALO HÍDRICO ÓTIMO EM SOLO CONSTRUÍDO APÓS MINERAÇÃO DE CARVÃO EM DIFERENTES LIMITES CRÍTICOS DE RESISTÊNCIA À PENETRAÇÃO E UMIDADE

Na quantificação do intervalo hídrico ótimo (IHO), são utilizados diferentes limites críticos de resistência à penetração (RP) e umidade na capacidade de campo (θCC). Para solos agrícolas, esses valores estão sendo documentados na literatura. Entretanto, para solos construídos após mineração de carvão, constata-se grande lacuna de informações. O objetivo deste trabalho foi quantificar a faixa de variação do intervalo hídrico ótimo de um solo construído sob diferentes plantas de cobertura na área de mineração de carvão de Candiota, sul do Brasil, considerando diferentes limites críticos de umidade do solo na capacidade de campo e de resistência à penetração. Foram avaliadas no experimento, em blocos casualizados com quatro repetições, as seguintes plantas de cobertura: Hemártria (Hemarthria altissima (Poir.) Stapf & C. E. Hubbard), tratamento 1 (T1); Pensacola (Paspalum notatum Flüggé), tratamento 2 (T2); Grama Tifton (Cynodon dactilon (L.) Pers.), tratamento 3 (T3); Controle (Urochloa brizantha (Hochst.) Stapf), tratamento 4 (T4); e sem plantas de cobertura, tratamento 5 (T5). Para determinar o IHO, foram utilizados diferentes valores críticos de θCC referentes às tensões de 0,006; 0,01; e 0,033 MPa e RP de 1,5; 2,0; 2,5; e 3,0 MPa, mantendo-se sempre constante a umidade do solo no ponto de murcha permanente (θPMP) como sendo igual ao valor retido na tensão de 1,5 MPa e a umidade do solo em que a porosidade de aeração (PA) é de 10 %. A faixa de variação do IHO foi maior no solo construído cultivado com Urochloa brizantha; e a menor com Pensacola, independentemente dos limites críticos de θCC e de RP. Os limites críticos de θCC e de RP utilizados na definição do IHO originaram diferentes valores de densidade critica (Dsc) para o solo construído sob diferentes plantas de cobertura. Os menores e maiores valores de Dsc foram obtidos quando utilizados como limites críticos na definição do IHO, o θCC = 0,033 MPa e a RP = 3 MPa. O solo construído cultivado com Urochloa brizantha e Hemártria apresentou valor de Ds muito próximo ao de Dsc.

LSI-R Assessment is Valid for Iowa Offenders, Data Download, Iowa Department of Corrections, September 2006

Welcome to the first issue of the ICON Data Download, a periodic report intended to communicate findings relevant to those who work directly with offenders, as well as those involved in planning, policy and budgeting. This issue highlights work conducted by research partner Christopher Lowenkamp, Ph.D., of the University of Cincinnati and his research associate, Kristin Bechtel, M.S. Data for this analysis was provided from the Iowa Justice Data Warehouse – and takes advantage of the link between ICON and ICIS (the court database) to readily track offender recidivism.

EGASP: the human ENCODE Genome Annotation Assessment Project

Background: Non-long terminal repeat (non-LTR) retrotransposons have contributed to shaping the structure and function of genomes. In silico and experimental approaches have been used to identify the non-LTR elements of the urochordate Ciona intestinalis. Knowledge of the types and abundance of non-LTR elements in urochordates is a key step in understanding their contribution to the structure and function of vertebrate genomes. Results: Consensus elements phylogenetically related to the I, LINE1, LINE2, LOA and R2 elements of the 14 eukaryotic non-LTR clades are described from C. intestinalis. The ascidian elements showed conservation of both the reverse transcriptase coding sequence and the overall structural organization seen in each clade. The apurinic/apyrimidinic endonuclease and nucleic-acid-binding domains encoded upstream of the reverse transcriptase, and the RNase H and the restriction enzyme-like endonuclease motifs encoded downstream of the reverse transcriptase were identified in the corresponding Ciona families. Conclusions: The genome of C. intestinalis harbors representatives of at least five clades of non-LTR retrotransposons. The copy number per haploid genome of each element is low, less than 100, far below the values reported for vertebrate counterparts but within the range for protostomes. Genomic and sequence analysis shows that the ascidian non-LTR elements are unmethylated and flanked by genomic segments with a gene density lower than average for the genome. The analysis provides valuable data for understanding the evolution of early chordate genomes and enlarges the view on the distribution of the non-LTR retrotransposons in eukaryotes.

Valor agregado à informação: da teoria à prática

O objetivo deste trabalho é demonstrar como o valor pode ser agregado à informação. A atual situação de sobrecarga de informação vivenciada por todos nós no trabalho será descrita. Descrever-se-á também um modelo teórico para agregar valor à informação, assim como os modos de aplicação do modelo no DTI Market Service/Dinamarca.