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981.
Iacomino G Picariello G Sbrana F Di Luccia A Raiteri R D'Agostino L 《Biomacromolecules》2011,12(4):1178-1186
In the cell nucleus, putrescine, spermidine, and spermine self-assemble with phosphate ions to generate three forms of compounds, named nuclear aggregates of polyamines (NAPs), which may interact with DNA. In an in vitro setting mimicking the cell nucleus milieu, this molecular aggregation occurs within well-defined ratios. Structural and functional analogies exist between the in vitro NAPs (ivNAPs) and their extractive homologues. The present Article reports images of ivNAPs at different resolution levels. Independent of the DNA template, ivNAPs become hierarchically stacked to produce ultimately macroscopic filamentous structures. The ivNAP-DNA complexes arranged in long and repetitive structures that displayed the self-similar features of natural fractals when dehydrated onto glass slides. Atomic force microscopy showed that ivNAPs have a cyclic structure and dispose around the DNA in a tube-like arrangement. Overall, the images indicate that these aggregates envelope the genomic DNA, thus proving that NAPs play a crucial role in DNA compaction and functioning. 相似文献
982.
The structure of calcium-saturated alginate hydrogels has been studied by combining rheological determinations and relaxometry measurements. The mechanical spectroscopy analyses performed on alginate gel cylinders at different polysaccharide concentration allowed estimating their main structural features such as the average mesh size. The calculation was based on the introduction of a front factor in the classical rubber elasticity approach which was correlated to the average length of the Guluronic acid blocks along the polysaccharide chain. Transverse relaxation time (T(2)) determinations performed on the cylinders revealed the presence of two relaxation rates of the water entrapped within the hydrogel network. The cross-correlation of the latter data with the rheological measurements allowed estimating the mesh size distribution of the hydrogel network. The results obtained for the hydrogel cylinders were found to be consistent with the relaxometric analysis performed on the alginate microbeads where, however, only one type of water bound into the network structure was detected. A good correlation was found in the average mesh size determined by means of relaxometric measurements on alginate microbeads and by a statistical analysis performed on TEM micrographs. Finally, the addition of a solution containing calcium ions allowed investigating further the different water relaxation modes within alginate hydrogels. 相似文献
983.
Maddalo G Stenberg-Bruzell F Götzke H Toddo S Björkholm P Eriksson H Chovanec P Genevaux P Lehtiö J Ilag LL Daley DO 《Journal of proteome research》2011,10(4):1848-1859
The cell envelope of Escherichia coli is an essential structure that modulates exchanges between the cell and the extra-cellular milieu. Previous proteomic analyses have suggested that it contains a significant number of proteins with no annotated function. To gain insight into these proteins and the general organization of the cell envelope proteome, we have carried out a systematic analysis of native membrane protein complexes. We have identified 30 membrane protein complexes (6 of which are novel) and present reference maps that can be used for cell envelope profiling. In one instance, we identified a protein with no annotated function (YfgM) in a complex with a well-characterized periplasmic chaperone (PpiD). Using the guilt by association principle, we suggest that YfgM is also part of the periplasmic chaperone network. The approach we present circumvents the need for engineering of tags and protein overexpression. It is applicable for the analysis of membrane protein complexes in any organism and will be particularly useful for less-characterized organisms where conventional strategies that require protein engineering (i.e., 2-hybrid based approaches and TAP-tagging) are not feasible. 相似文献
984.
Burkholderia cenocepacia BC2L-C is a super lectin with dual specificity and proinflammatory activity
Sulák O Cioci G Lameignère E Balloy V Round A Gutsche I Malinovská L Chignard M Kosma P Aubert DF Marolda CL Valvano MA Wimmerová M Imberty A 《PLoS pathogens》2011,7(9):e1002238
Lectins and adhesins are involved in bacterial adhesion to host tissues and mucus during early steps of infection. We report the characterization of BC2L-C, a soluble lectin from the opportunistic pathogen Burkholderia cenocepacia, which has two distinct domains with unique specificities and biological activities. The N-terminal domain is a novel TNF-α-like fucose-binding lectin, while the C-terminal part is similar to a superfamily of calcium-dependent bacterial lectins. The C-terminal domain displays specificity for mannose and l-glycero-d-manno-heptose. BC2L-C is therefore a superlectin that binds independently to mannose/heptose glycoconjugates and fucosylated human histo-blood group epitopes. The apo form of the C-terminal domain crystallized as a dimer, and calcium and mannose could be docked in the binding site. The whole lectin is hexameric and the overall structure, determined by electron microscopy and small angle X-ray scattering, reveals a flexible arrangement of three mannose/heptose-specific dimers flanked by two fucose-specific TNF-α-like trimers. We propose that BC2L-C binds to the bacterial surface in a mannose/heptose-dependent manner via the C-terminal domain. The TNF-α-like domain triggers IL-8 production in cultured airway epithelial cells in a carbohydrate-independent manner, and is therefore proposed to play a role in the dysregulated proinflammatory response observed in B. cenocepacia lung infections. The unique architecture of this newly recognized superlectin correlates with multiple functions including bacterial cell cross-linking, adhesion to human epithelia, and stimulation of inflammation. 相似文献
985.
Alberto Magi Lorenzo Tattini Ingrid Cifola Romina D’Aurizio Matteo Benelli Eleonora Mangano Cristina Battaglia Elena Bonora Ants Kurg Marco Seri Pamela Magini Betti Giusti Giovanni Romeo Tommaso Pippucci Gianluca De Bellis Rosanna Abbate Gian Franco Gensini 《Genome biology》2013,14(10):R120
We developed a novel software tool, EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data. EXCAVATOR combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies genomic regions into five copy number states. We validate EXCAVATOR on three datasets and compare the results with three other methods. These analyses show that EXCAVATOR outperforms the other methods and is therefore a valuable tool for the investigation of CNVs in largescale projects, as well as in clinical research and diagnostics. EXCAVATOR is freely available at http://sourceforge.net/projects/excavatortool/. 相似文献
986.
987.
Gianluca Occhi Daniela Regazzo Giampaolo Trivellin Francesca Boaretto Denis Ciato Sara Bobisse Sergio Ferasin Filomena Cetani Elena Pardi Márta Korbonits Natalia S. Pellegata Viktoryia Sidarovich Alessandro Quattrone Giuseppe Opocher Franco Mantero Carla Scaroni 《PLoS genetics》2013,9(3)
The CDKN1B gene encodes the cyclin-dependent kinase inhibitor p27KIP1, an atypical tumor suppressor playing a key role in cell cycle regulation, cell proliferation, and differentiation. Impaired p27KIP1 expression and/or localization are often observed in tumor cells, further confirming its central role in regulating the cell cycle. Recently, germline mutations in CDKN1B have been associated with the inherited multiple endocrine neoplasia syndrome type 4, an autosomal dominant syndrome characterized by varying combinations of tumors affecting at least two endocrine organs. In this study we identified a 4-bp deletion in a highly conserved regulatory upstream ORF (uORF) in the 5′UTR of the CDKN1B gene in a patient with a pituitary adenoma and a well-differentiated pancreatic neoplasm. This deletion causes the shift of the uORF termination codon with the consequent lengthening of the uORF–encoded peptide and the drastic shortening of the intercistronic space. Our data on the immunohistochemical analysis of the patient''s pancreatic lesion, functional studies based on dual-luciferase assays, site-directed mutagenesis, and on polysome profiling show a negative influence of this deletion on the translation reinitiation at the CDKN1B starting site, with a consequent reduction in p27KIP1 expression. Our findings demonstrate that, in addition to the previously described mechanisms leading to reduced p27KIP1 activity, such as degradation via the ubiquitin/proteasome pathway or non-covalent sequestration, p27KIP1 activity can also be modulated by an uORF and mutations affecting uORF could change p27KIP1 expression. This study adds the CDKN1B gene to the short list of genes for which mutations that either create, delete, or severely modify their regulatory uORFs have been associated with human diseases. 相似文献
988.
Gloria Brusotti Mohammed Farhad Ibrahim Alessandra Dentamaro Gianluca Gilardoni Solveig Tosi Pietro Grisoli Cesare Dacarro Maria Lidia Guglielminetti Faiq Hama Saeed Hussain Gabriele Caccialanza Giovanni Vidari 《化学与生物多样性》2013,10(2):274-280
The volatile fractions isolated from Prangos peucedanifolia Fenzl leaves and flowers were investigated for their phytochemical composition and biological properties. Flower and leaf hydrodistillation afforded 3.14 and 0.49 g of yellowish oils in 1.25 and 0.41% yields, respectively, from dry vegetable materials. According to the GC‐FID and GC/MS analyses, 36 (99.35% of the total oil composition) and 26 compounds (89.12%) were identified in the two oils, respectively. The major constituents in the flower volatile fraction were β‐pinene (35.58%), α‐pinene (22.13%), and β‐phellandrene (12.54%), while m‐cresol (50.38%) was the main constituent of the leaf volatile fraction. The antimicrobial activity was evaluated against several bacterial and fungal strains, on the basis of the minimum inhibitory concentration (MIC) by the micro‐ and macrodilution methods. The two volatile fractions showed moderate antifungal and antibacterial activities, especially against Trichophyton rubrum (MIC of 2×103 μg/ml), Streptococcus mutans, Streptococcus pyogenes, and Staphylococcus aureus (MIC≤1.9×103 μg/ml for all). 相似文献
989.
Wenming?Zhang Douglas?B?Menke Meisheng?Jiang Hui?Chen David?Warburton Gianluca?Turcatel Chi-Han?Lu Wei?Xu Yongfeng?Luo Wei?ShiEmail author 《BMC biology》2013,11(1):111
Background
Reciprocal interactions between lung mesenchymal and epithelial cells play essential roles in lung organogenesis and homeostasis. Although the molecular markers and related animal models that target lung epithelial cells are relatively well studied, molecular markers of lung mesenchymal cells and the genetic tools to target and/or manipulate gene expression in a lung mesenchyme-specific manner are not available, which becomes a critical barrier to the study of lung mesenchymal biology and the related pulmonary diseases.Results
We have identified a mouse Tbx4 gene enhancer that contains conserved DNA sequences across many vertebrate species with lung or lung-like gas exchange organ. We then generate a mouse line to express rtTA/LacZ under the control of the Tbx4 lung enhancer, and therefore a Tet-On inducible transgenic system to target lung mesenchymal cells at different developmental stages. By combining a Tbx4-rtTA driven Tet-On inducible Cre expression mouse line with a Cre reporter mouse line, the spatial-temporal patterns of Tbx4 lung enhancer targeted lung mesenchymal cells were defined. Pulmonary endothelial cells and vascular smooth muscle cells were targeted by the Tbx4-rtTA driver line prior to E11.5 and E15.5, respectively, while other subtypes of lung mesenchymal cells including airway smooth muscle cells, fibroblasts, pericytes could be targeted during the entire developmental stage.Conclusions
Developmental lung mesenchymal cells can be specifically marked by Tbx4 lung enhancer activity. With our newly created Tbx4 lung enhancer-driven Tet-On inducible system, lung mesenchymal cells can be specifically and differentially targeted in vivo for the first time by controlling the doxycycline induction time window. This novel system provides a unique tool to study lung mesenchymal cell lineages and gene functions in lung mesenchymal development, injury repair, and regeneration in mice.990.
The egg behaves as a prospective cell sustaining the developmental processes of the future embryo. In biosemiotic terms, this apparent teleonomic behaviour can be accounted for without referring to the exclusive causal role played by its genetic makeup. We envision two different processes that are uniquely found in the oocyte: (1) the first involves the mechanisms by which large amounts of mRNA accumulate in the ooplasm to establish the embryo axes prior to fertilization; (2) the second involves transfer of an excess of maternally supplied ribosomes to the oocyte to provide the future embryo with newly synthesized proteins. In this paper, we argue that the information required to sustain embryonic development is not due to any physical properties of the zygotic DNA and the maternal mRNAs, but to their spatially and temporally ordered relationship in the zygote’s internal space. 相似文献