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991.
Background
Meiotic recombination between homologous chromosomes provides natural combinations of genetic variations and is a main driving force of evolution. It is initiated via programmed DNA double-strand breaks (DSB) and involves a specific axial chromosomal structure. So far, recombination regions have been mainly determined by experiments, both expensive and time-consuming.Results
SPoRE is a mathematical model that describes the non-uniform localisation of DSB and axis proteins sites, and distinguishes high versus low protein density. It is based on a combination of genomic signals, based on what is known from wet-lab experiments, whose contribution is precisely quantified. It models axis proteins accumulation at gene 5’-ends with a discrete approximation of their diffusion and convection along genes. It models DSB accumulation at approximated gene promoter positions with intergenic region length and GC-content. SPoRE can be used for prediction and it is parameterised in an obvious way that makes it easy to understand from a biological viewpoint.Conclusions
When compared to Saccharomyces cerevisiae experimental data, SPoRE predicts axis protein and DSB positions with high sensitivity and precision, axis protein density with an average local correlation r=0.63 and DSB density with an average local correlation r=0.62. SPoRE outbreaks previous DSB predictors, which are based on nucleotide patterning, and it reaches 85% of success rate in DSB prediction compared to 54% obtained by available tools on a benchmarked dataset.SPoRE is available at the address http://www.lcqb.upmc.fr/SPoRE/.Electronic supplementary material
The online version of this article (doi:10.1186/s12859-014-0391-1) contains supplementary material, which is available to authorized users. 相似文献992.
Phosphatidylinositol 3‐kinase inhibition potentiates glucocorticoid response in B‐cell acute lymphoblastic leukemia 下载免费PDF全文
Cecilia Evangelisti Alessandra Cappellini Mariana Oliveira Rita Fragoso João T. Barata Alice Bertaina Franco Locatelli Carolina Simioni Luca M. Neri Francesca Chiarini Annalisa Lonetti Francesca Buontempo Ester Orsini Andrea Pession Lucia Manzoli Alberto Maria Martelli Camilla Evangelisti 《Journal of cellular physiology》2018,233(3):1796-1811
993.
Bruzzese F Leone A Rocco M Carbone C Piro G Caraglia M Di Gennaro E Budillon A 《Journal of cellular physiology》2011,226(9):2378-2390
994.
Paola Braghetta Alessandra Ferrari Paola de Gemmis Miriam Zanetti Dino Volpin Paolo Bonaldo Giorgio M Bressan 《Matrix biology》2002,21(7):603-609
Expression of EMILIN-1, the first member of a newly discovered family of extracellular matrix genes, has been investigated during mouse development. EMILIN-1 mRNA is detectable in morula and blastocyst by RT-PCR. First expression of the gene is found by in situ hybridization in ectoplacental cone in embryos of 6.5 days and in extraembryonic visceral endoderm at 7.5 days. The allantois is also labeled. Staining of ectoplacental cone-derived secondary trophoblast giant cells and spongiotrophoblast is strong up to 11.5 days and then declines. In the embryo, high levels of mRNA are initially expressed in blood vessels, perineural mesenchyme and somites at 8.5 days. Later on, intense labeling is identified in the mesenchymal component of organs anlage (i.e. lung and liver) and different mesenchymal condensations (i.e. limb bud and branchial arches). At late gestation staining is widely distributed in interstitial connective tissue and smooth muscle cell-rich tissues. The data suggest that EMILIN-1 may have a function in placenta formation and initial organogenesis and a later role in interstitial connective tissue. 相似文献
995.
996.
? Arbuscular mycorrhizal fungi (AMF) are ubiquitous organisms that benefit ecosystems through the establishment of an association with the roots of most plants: the mycorrhizal symbiosis. Despite their ecological importance, however, these fungi have been poorly studied at the genome level. ? In this study, total DNA from the AMF Gigaspora margarita was subjected to a combination of 454 and Illumina sequencing, and the resulting reads were used to assemble its mitochondrial genome de novo. This genome was annotated and compared with those of other relatives to better comprehend the evolution of the AMF lineage. ? The mitochondrial genome of G. margarita is unique in many ways, exhibiting a large size (97 kbp) and elevated GC content (45%). This genome also harbors molecular events that were previously unknown to occur in fungal mitochondrial genomes, including trans-splicing of group I introns from two different genes coding for the first subunit of the cytochrome oxidase and for the small subunit of the rRNA. ? This study reports the second published genome from an AMF organelle, resulting in relevant DNA sequence information from this poorly studied fungal group, and providing new insights into the frequency, origin and evolution of trans-spliced group I introns found across the mitochondrial genomes of distantly related organisms. 相似文献
997.
Bonamore A Gentili P Ilari A Schininà ME Boffi A 《The Journal of biological chemistry》2003,278(25):22272-22277
Escherichia coli flavohemoglobin (HMP) is shown to be capable of catalyzing the reduction of several alkylhydroperoxide substrates into their corresponding alcohols using NADH as an electron donor. In particular, HMP possesses a high catalytic activity and a low Km toward cumyl, linoleic acid, and tert-butyl hydroperoxides, whereas it is a less efficient hydrogen peroxide scavenger. An analysis of UV-visible spectra during the stationary state reveals that at variance with classical peroxidases, HMP turns over in the ferrous state. In particular, an iron oxygen adduct intermediate whose spectrum is similar to that reported for the oxo-ferryl derivative in peroxidases (Compound II), has been identified during the catalysis of hydrogen peroxide reduction. This finding suggests that hydroperoxide cleavage occurs upon direct binding of a peroxide oxygen atom to the ferrous heme iron. Competitive inhibition of the alkylhydroperoxide reductase activity by carbon monoxide has also been observed, thus confirming that heme iron is directly involved in the catalytic mechanism of hydroperoxide reduction. The alkylhydroperoxide reductase activity taken together with the unique lipid binding properties of HMP suggests that this protein is most likely involved in the repair of the lipid membrane oxidative damage generated during oxidative/nitrosative stress. 相似文献
998.
Sergio Barni Luigi Sciola Alessandra Spano Proto Pippia 《Biotechnic & histochemistry》1996,71(2):66-70
The shape, distribution, and content of mitochondria in individual cells were examined during the cell cycle phases (G0/G1, S, G2 mitosis) in living human fibroblasts by static cytofluorometry and fluorescence microscopy. The morphocytochemical evaluations were performed in cell cultures submitted to double supravital fluorochrome staining with Hoechst 33342 and DiOC6 to label DNA and mitochondria, respectively. The staining modalities were based on the stability of mitochondrial labeling. The G1 to early S phases were characterized by the presence of filamentous mitochondria, except during the early postmitotic period. During late S, G2, and mitotic phases, mitochondrial mass reached its highest value and mitochondria became short and numerous. During the last stage of mitosis, mitochondria were distributed among daughter cells through a cytoplasmic bridge. 相似文献
999.
1000.
Antonio Gasbarrini Alessandra Colantoni Cristiana Di Campli Stefania De Notariis Michele Masetti Elio Iovine Alighieri Mazziotti Irene Massari Giovanni Gasbarrini Paolo Pola Mauro Bernardi 《Free radical biology & medicine》1997,23(7):1067-1072
The sensitivity of liver cells to anoxia is a major problem afflicting liver preservation and transplantation. Intermittent ischemia has been proposed to reduce reperfusion injury. The aim of the study was to assess oxygen free radical formation and cell injury during continuous or intermittent anoxia/reoxygenation in rat hepatocytes. Anion superoxide was measured by lucigenin-enhanced chemiluminescence and cell damage by LDH release and trypan blue uptake. During anoxia, superoxide generation dropped to background level in both groups; trypan blue uptake and LDH release, which increased progressively, were significantly greater in hepatocytes exposed to continuous compared to intermittent anoxia. During reoxygenation, a massive generation of superoxide anion formation, followed by a sharp increase in LDH release, was observed in both groups. However, both oxyradical generation and cell injury were significantly greater in cells exposed to continuous compared to intermittent anoxia. The data, showing that intermittent oxygen deprivation reduce liver cell injury and oxygen free radical formation determined by anoxia/reoxygenation, suggest a novel possible approach to the reduction of reperfusion injury. 相似文献