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101.
Lucio Marcello Suraj Menon Pauline Ward Jonathan M Wilkes Nicola G Jones Mark Carrington J David Barry 《BMC bioinformatics》2007,8(1):143
Background
Trypanosomes are coated with a variant surface glycoprotein (VSG) that is so densely packed that it physically protects underlying proteins from effectors of the host immune system. Periodically cells expressing a distinct VSG arise in a population and thereby evade immunity. The main structural feature of VSGs are two long α-helices that form a coiled coil, and sets of relatively unstructured loops that are distal to the plasma membrane and contain most or all of the protective epitopes. The primary structure of different VSGs is highly variable, typically displaying only ~20% identity with each other. The genome has nearly 2000 VSG genes, which are located in subtelomeres. Only one VSG gene is expressed at a time, and switching between VSGs primarily involves gene conversion events. The archive of silent VSGs undergoes diversifying evolution rapidly, also involving gene conversion. The VSG family is a paradigm for α helical coiled coil structures, epitope variation and GPI-anchor signals. At the DNA level, the genes are a paradigm for diversifying evolutionary processes and for the role of subtelomeres and recombination mechanisms in generation of diversity in multigene families. To enable ready availability of VSG sequences for addressing these general questions, and trypanosome-specific questions, we have created VSGdb, a database of all known sequences. 相似文献102.
Vittoria Pagliarini Laura Pelosi Maria Blaire Bustamante Annalisa Nobili Maria Grazia Berardinelli Marcello D’Amelio Antonio Musarò Claudio Sette 《The Journal of cell biology》2015,211(1):77-90
Spinal muscular atrophy (SMA) is a neurodegenerative disease caused by loss of motor neurons in patients with null mutations in the SMN1 gene. The almost identical SMN2 gene is unable to compensate for this deficiency because of the skipping of exon 7 during pre–messenger RNA (mRNA) processing. Although several splicing factors can modulate SMN2 splicing in vitro, the physiological regulators of this disease-causing event are unknown. We found that knockout of the splicing factor SAM68 partially rescued body weight and viability of SMAΔ7 mice. Ablation of SAM68 function promoted SMN2 splicing and expression in SMAΔ7 mice, correlating with amelioration of SMA-related defects in motor neurons and skeletal muscles. Mechanistically, SAM68 binds to SMN2 pre-mRNA, favoring recruitment of the splicing repressor hnRNP A1 and interfering with that of U2AF65 at the 3′ splice site of exon 7. These findings identify SAM68 as the first physiological regulator of SMN2 splicing in an SMA mouse model. 相似文献
103.
The interplay between event and background sedimentation and the origin of fossil‐rich carbonate concretions: a case study in Permian rocks of the Paraná Basin,Brazil 下载免费PDF全文
João G. Bondioli Suzana A. Matos Lucas V. Warren Mário L. Assine Cláudio Riccomini Marcello G. Simões 《Lethaia: An International Journal of Palaeontology and Stratigraphy》2015,48(4):522-539
The Permian Serra Alta Formation was generated under transgressive conditions within a large, calm epeiric sea. A monotonous succession of ‘barren’, massive mudstones deposited under oxygen‐deficient conditions (mainly below storm wave base) is the main lithofacies of this unit. Fossils are generally rare and diluted in the matrix, but certain intervals contain shell‐rich concentrations with well‐preserved, closed articulated bivalves, mixed with shells and comminuted debris with variable quality of preservation, all encased in carbonate concretions. Two main scenarios may account for the origin of these bivalve‐rich concretions (i.e. unique events in sea‐water chemistry or unique burial‐starvation couplets). Sedimentological and taphonomic information indicates that the final deposition of the original shell‐rich mudstone intervals was probably tied to episodic influx of fine‐grained sediments in distal settings. Moderate bioturbation is also recorded suggesting low rates of sedimentation prior to early diagenesis. Hence, the fossil concentrations in concretions were formed due to the interplay of event and background sedimentation. These are internally simple concentrations with complex depositional histories. The concretion‐bearing beds are not randomly distributed in the Serra Alta Formation. Rather, they are found in the sparsely fossiliferous offshore deposits of the basal to intermediate portions of the unit. Thus, the concretionary mudstone beds and associated deposits are preserved in particular intervals and can be tracked for kilometres. This indicates that the conditions essential for concretion development existed only at particular stratigraphical intervals. Finally, our study strongly corroborates the idea that concretions are critical sources of sedimentological, taphonomic and stratigraphical information. 相似文献
104.
Vivian Flinte Ethel Hentz Barbara Mascarenhas Morgado Anne Caruliny do Monte Lima Gabriel Khattar Ricardo Ferreira Monteiro Margarete Valverde de Macedo 《ZooKeys》2015,(547):119-132
The population phenology of the cassidines, Coptocycla
arcuata and Omaspides
trichroa, and the chrysomeline, Platyphora
axillaris, was studied at Serra dos Órgãos National Park, State of Rio de Janeiro, southeast Brazil. Monthly surveys of larvae and adults were conducted between 2008 and 2011 at approximately 1000 m altitude on their respective host plants, Cordia
polycephala (Boraginaceae), Ipomoea
philomega (Convolvulaceae) and Solanum
scuticum (Solanaceae). This is the first observation of larviparity and host record for Platyphora
axillaris. Although having different life history traits, all species showed similar phenologies. They were abundant from October to March, months of high temperatures and intense rainfall, with two distinct reproductive peaks in the same season. Abundance dropped abruptly during the coldest and driest months, from May to August. Frequently none of these species were recorded during June and July. This phenological pattern is similar to other Chrysomelidae living in subtropical areas of Brazil. Temperature and rainfall appear to be the major factors influencing the fluctuation of these three species. 相似文献
105.
Giovannini M Verduci E Radaelli G Lammardo A Minghetti D Cagnoli G Salvatici E Riva E 《Prostaglandins, leukotrienes, and essential fatty acids》2011,84(1-2):39-42
IntroductionThe aim of the present study was to examine whether hyperphenylalaninemic children on unrestricted diet (MHP) may exhibit a different LCPUFA profile from PKU or healthy children in plasma phospholipids.Patients and methodsForty-five MHP children (age 9–14 years) were age and sex matched with 45 PKU and 45 healthy children. Fatty acids were determined and expressed as % of total fatty acids.ResultsMHP children showed docosahexaenoic acid (DHA) levels higher than PKU children (mean difference, 0.2%; 95% confidence interval, 0.02%–0.38%), although difference was not significant after correction for multiple comparisons, and lower levels than healthy children (?0.8%; ?1.01% to ?0.59%). Concentration of n-3 PUFA was higher in MHP than PKU children (0.6%; 0.4% to 0.8%),ConclusionsThe results suggest that low DHA levels in plasma phospholipids not only are evident in PKU but also may occur in MHP children, who are on unrestricted diet, as compared to healthy children. 相似文献
106.
The possibility of introducing a computationally assisted method to study aptamer-protein interaction was evaluated with the aim of streamlining the screening and selection of new aptamers. Starting from information on the 15-mer (5'-GGTTGGTGTGGTTGG-3') thrombin binding aptamer (TBA), a library of mutated DNA sequences (994 elements) was generated and screened using shapegauss a shape-based scoring function from openeye software to generate computationally derived binding scores. The TBA and three other mutated oligonucleotides, selected on the basis of their binding score (best, medium, worst), were incorporated into surface plasmon resonance (SPR) biosensors. By reducing the ionic strength (binding buffer, 50 mM TrisHCl pH 7.4, 140 mM NaCl, 1mM MgCl?, diluted 1:50) in order to match the simulated condition, the analytical performances of the four oligonucleotide sequences were compared using signal amplitude, sensitivity (slope), linearity (R2) and reproducibility (CVav %). The experimental results were in agreement with the simulation findings. 相似文献
107.
108.
109.
Dall'Acqua S Linardi MA Maggi F Nicoletti M Petitto V Innocenti G Basso G Viola G 《Bioorganic & medicinal chemistry》2011,19(19):5876-5885
Plants of the genera Ferula and Ferulago are known for their complex content in bioactive secondary metabolites such as coumarins, phenylpropanoids, and sesquiterpenes. We used the ground parts of Ferula communis subsp. communis, Ferula glauca subsp. glauca and Ferulago campestris as natural sources for the isolation of four coumarins (CU-1 to CU-4), two phenylpropanoids (PE-1 and PE-2), one polyacetylene (PA-1) and 16 daucane esters (DE-1 to DE-16). The cytotoxic activity of the isolated compounds was evaluated against a panel of seven human tumor cell lines. Fourteen of the daucane derivatives showed antiproliferative activity at least against one of the human tumor cell lines tested, four compounds (DE-5, DE-8, DE-11, and DE-16) were active against all the tested cell lines. Among them DE-11 was the most cytotoxic compound against HeLa (4.4 ± 0.7 μM), A549 (2.8 ± 1.4 μM), HL-60 (2.6 ± 0.4 μM), K562 (26.5 ± 6.0 μM) RS 4;11 (1.7 ± 0.3 μM) and SEM (2.4 ± 0.1 μM) cell lines, while DE-8 was the most active against Jurkat (3.3 ± 0.8 μM). Preliminary structure-activity relationship suggests that the most active compounds in the daucane series present the trans fusion of the penta- and hepta-atomic cycles, and lipophylic ester groups linked to position 6. Isomeric derivatives such as DE-8 and DE-9 or DE-3, DE-4, and DE-5 exhibited significant differences in their IC(50) supporting that the β orientation for the ester group in the position 2 enhances the cytotoxic activity. Furthermore, the pro-apoptotic effect of the most active compounds evaluated in Jurkat cell line showed that these compounds are able to induce apoptosis in a time and concentration-dependent manner. Our findings suggest the potential role of daucane derivatives as models for the development of proapoptotic compounds. 相似文献
110.
Giovanni Ciotta Helmut Hofemeister Marcello Maresca Jun Fu Mihail Sarov Konstantinos Anastassiadis A. Francis Stewart 《Methods (San Diego, Calif.)》2011,53(2):113-119
Protein tagging offers many advantages for proteomic and regulomic research, particularly due to the use of generic and highly sensitive methods that can be applied with reasonable throughput. Ideally, protein tagging is equivalent to having a high affinity antibody for every chosen protein. However, these advantages are compromised if the tagged protein is overexpressed, which is usually the case from cDNA expression vectors. BAC (bacterial artificial chromosome) transgenes present a way to express a chosen protein at physiological levels with all regulatory elements in their native configurations, including cell cycle, alternative splicing and microRNA regulation. Recombineering has become the method of choice for modifying large constructs like BACs. Here, we present a method for protein tagging by recombineering BACs, transfecting cells and evaluating tagged protein expression. 相似文献