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41.
Mols CM van Oers K Witjes LM Lessells CM Drent PJ Visser ME 《Proceedings. Biological sciences / The Royal Society》2004,271(Z3):S85-S87
The relationship between the encounter rate of predators with prey and the density of this prey is fundamental to models of predator-prey interactions. The relationship determines, among other variables, the rate at which prey patches are depleted, and hence the impact of predator populations on their prey, and the optimal spatial distribution of foraging effort. Two central assumptions that are made in many models are that encounter rate is directly proportional to prey density and that it is independent of the proportion of prey already removed, other than via the decreased density. We show here, using captive great tits searching for winter moth caterpillars in their natural hiding positions, that neither of these assumptions hold. Encounter rate increased less than directly in proportion to prey density, and it depended not only on the current density of prey, but also on the proportion of prey already removed by previous foragers. Both of these effects are likely to have major consequences for the outcome of predator-prey interactions. 相似文献
42.
Cleavage of DNA without loss of genetic information by incorporation of a disaccharide nucleoside 下载免费PDF全文
Nauwelaerts K Vastmans K Froeyen M Kempeneers V Rozenski J Rosemeyer H Van Aerschot A Busson R Lacey JC Efimtseva E Mikhailov S Lescrinier E Herdewijn P 《Nucleic acids research》2003,31(23):6758-6769
A ribose residue inserted between the 3′-OH of one nucleotide and the 5′-phosphate group of the next nucleotide, functions as a site-specific cleavage site within DNA. This extra ribose does not interrupt helix formation and it protects duplex DNA against cleavage by restriction enzymes. Cleavage can be obtained with periodate and all ribose fragments can be removed with sodium hydroxide. As a result of this, an intact natural oligodeoxynucleotide is obtained after ligation reaction, which means that site-specific cleavage and recovering of intact DNA occurs without loss of genetic information. 相似文献
43.
Oomen CJ Hoogerhout P Bonvin AM Kuipers B Brugghe H Timmermans H Haseley SR van Alphen L Gros P 《Journal of molecular biology》2003,328(5):1083-1089
We present an in silico, structure-based approach for design and evaluation of conformationally restricted peptide-vaccines. In particular, we designed four cyclic peptides of ten or 11 residues mimicking the crystallographically observed beta-turn conformation of a predicted immunodominant loop of PorA from Neisseria meningitidis. Conformational correctness and stability of the peptide designs, as evaluated by molecular dynamics simulations, correctly predicted the immunogenicity of the peptides. We observed a peptide-induced functional antibody response that, remarkably, exceeded the response induced by the native protein in outer membrane vesicles, without losing specificity for related strains. The presented approach offers tools for a priori design and selection of peptide-vaccine candidates with full biological activity. This approach could be widely applicable: to outer membrane proteins of Gram-negative bacteria, and to other epitopes in a large range of pathogens. 相似文献
44.
Haouz A Vanheusden V Munier-Lehmann H Froeyen M Herdewijn P Van Calenbergh S Delarue M 《The Journal of biological chemistry》2003,278(7):4963-4971
The chemical synthesis of new compounds designed as inhibitors of Mycobacterium tuberculosis TMP kinase (TMPK) is reported. The synthesis concerns TMP analogues modified at the 5-position of the thymine ring as well as a novel compound with a six-membered sugar ring. The binding properties of the analogues are compared with the known inhibitor azido-TMP, which is postulated here to work by excluding the TMP-bound Mg(2+) ion. The crystallographic structure of the complex of one of the compounds, 5-CH(2)OH-dUMP, with TMPK has been determined at 2.0 A. It reveals a major conformation for the hydroxyl group in contact with a water molecule and a minor conformation pointing toward Ser(99). Looking for a role for Ser(99), we have identified an unusual catalytic triad, or a proton wire, made of strictly conserved residues (including Glu(6), Ser(99), Arg(95), and Asp(9)) that probably serves to protonate the transferred PO(3) group. The crystallographic structure of the commercially available bisubstrate analogue P(1)-(adenosine-5')-P(5)-(thymidine-5')-pentaphosphate bound to TMPK is also reported at 2.45 A and reveals an alternative binding pocket for the adenine moiety of the molecule compared with what is observed either in the Escherichia coli or in the yeast enzyme structures. This alternative binding pocket opens a way for the design of a new family of specific inhibitors. 相似文献
45.
ATP-dependent interactions between Escherichia coli Min proteins and the phospholipid membrane in vitro 下载免费PDF全文
Proper placement of the division apparatus in Escherichia coli requires pole-to-pole oscillation of the MinC division inhibitor. MinC dynamics involves a membrane association-dissociation cycle that is driven by the activities of the MinD ATPase and the MinE topological specificity factor, which themselves undergo coupled oscillatory localization cycles. To understand the biochemical mechanisms underlying Min protein dynamics, we studied the interactions of purified Min proteins with phospholipid vesicles and the role of ATP in these interactions. We show that (i) the ATP-bound form of MinD (MinD.ATP) readily associates with phospholipid vesicles in the presence of Mg(2+), whereas the ADP-bound form (MinD.ADP) does not; (ii) MinD.ATP binds membrane in a self-enhancing fashion; (iii) both MinC and MinE can be recruited to MinD.ATP-decorated vesicles; (iv) MinE stimulates dissociation of MinD.ATP from the membrane in a process requiring hydrolysis of the nucleotide; and (v) MinE stimulates dissociation of MinC from MinD.ATP-membrane complexes, even when ATP hydrolysis is blocked. The results support and extend recent work by Z. Hu et al. (Z. Hu, E. P. Gogol, and J. Lutkenhaus, Proc. Natl. Acad. Sci. USA 99:6761-6766, 2002) and support models of protein oscillation wherein MinE induces Min protein dynamics by stimulating the conversion of the membrane-bound form of MinD (MinD.ATP) to the cytoplasmic form (MinD.ADP). The results also indicate that MinE-stimulated dissociation of MinC from the MinC-MinD.ATP-membrane complex can, and may, occur prior to hydrolysis of the nucleotide. 相似文献
46.
Phosphatidylinositol transfer protein alpha (PITP alpha) is a ubiquitous and highly conserved protein in multicellular eukaryotes that catalyzes the exchange of phospholipids between membranes in vitro and participates in cellular phospholipid metabolism, signal transduction and vesicular trafficking in vivo. Here we report the three-dimensional crystal structure of a phospholipid-free mouse PITP alpha at 2.0 A resolution. The structure reveals an open conformation characterized by a channel running through the protein. The channel is created by opening the phospholipid-binding cavity on one side by displacement of the C-terminal region and a hydrophobic lipid exchange loop, and on the other side by flattening of the central beta-sheet. The relaxed conformation is stabilized at the proposed membrane association site by hydrophobic interactions with a crystallographically related molecule, creating an intimate dimer. The observed open conformer is consistent with a membrane-bound state of PITP and suggests a mechanism for membrane anchoring and the presentation of phosphatidylinositol to kinases and phospholipases after its extraction from the membrane. Coordinates have been deposited in the Protein Data Bank (accession No. 1KCM). 相似文献
47.
The nuclear DNA of Trypanosoma brucei and other kinetoplastid flagellates contains the unusual base beta-d-glucosyl-hydroxymethyluracil, called J, replacing part of the thymine in repetitive sequences. We have described a 100 kDa protein that specifically binds to J in duplex DNA. We have now disrupted the genes for this J-binding protein (JBP) in T. brucei. The disruption does not affect growth, gene expression or the stability of some repetitive DNA sequences. Unexpectedly, however, the JBP KO trypanosomes contain only about 5% of the wild-type level of J in their DNA. Excess J, randomly introduced into T. brucei DNA by growing the cells in the presence of the J precursor 5-hydroxymethyldeoxyuridine, is lost by simple dilution as the KO trypanosomes multiply, showing that JBP does not protect J against removal. In contrast, cells containing JBP lose excess J only sluggishly. We conclude that JBP is able to activate the thymine modification enzymes to introduce additional J in regions of DNA already containing a basal level of J. We propose that JBP is a novel DNA modification maintenance protein. 相似文献
48.
49.
Vallero MV Lettinga G Lens PN 《Journal of industrial microbiology & biotechnology》2003,30(6):375-382
A laboratory-scale upflow anaerobic sludge bed (UASB) reactor was operated during 273 days at increasing NaCl concentrations (0.5–12.5 g NaCl l–1) to assess whether the stepwise addition of the salt NaCl results in the acclimation of that sludge. The 6.5-l thermophilic (55 °C), sulfidogenic [a chemical oxygen demand (COD) to SO42– ratio of 0.5] UASB reactor operated at an organic loading rate of 5 g COD l–1 day–1, a hydraulic retention time of 10 h and was fed with methanol as the sole electron donor. The results show that the adaptation of the thermophilic, sulfidogenic methanol-degrading biomass to a high osmolarity environment is unlikely to occur. Sulfide was the main mineralization product from methanol degradation, regardless of the NaCl concentration added to the influent. However, sulfide production in the reactor steadily decreased after the addition of 7.5 g NaCl l–1, whereas acetate production was stimulated at that influent NaCl concentration. Batch tests performed with sludge harvested from the UASB reactor when operating at different influent salinities confirmed that acetate is the main metabolic product at NaCl concentrations higher than 12.5 g l–1. The apparent order of NaCl toxicity towards the different trophic groups was found to be: sulfate-reducing bacteria > methane-producing archaea > acetogenic bacteria. 相似文献
50.
Fayman MS Potgieter E Becker PJ 《Plastic and reconstructive surgery》2003,111(2):676-84; discussion 685-7
Residual scars on occasion compromise patient satisfaction with breast reduction procedures. Periareolar breast reduction was proposed to minimize the scarring produced by the operation. This technique was criticized predominantly for producing a breast with low projection, for recurrence of ptosis after surgery, and for widening of the periareolar scar. The purpose of this study was to evaluate patient satisfaction from this technique. In the first branch of the study, 11 patients who had periareolar or circumareolar breast reduction were compared with 13 patients who had vertical scar reduction mammaplasty. The groups were matched for patient's age, size of reduction, and follow-up period. The patients were contacted by phone and requested to comment on four aspects of their operation: breast size, symmetry, quality of scars, and appearance and position of the nipple-areola complex. The replies were converted to numerical values and analyzed statistically. A panel of three women, prospective patients for breast reduction, were presented with standardized five-view before-and-after photographs and requested to score the results using the same criteria. Their responses were analyzed in the same manner. Both phases of the study produced similar results. Breast reduction done through a periareolar scar scored higher than a vertical scar technique. The operation did not differ with respect to shape, symmetry, or nipple-areola shape but did with respect to dissatisfaction with scars, which affected the overall result. This experimental model of assessing results of cosmetic operations is proposed as a tool to assess the patient's rather than the surgeon's perspective of a surgical technique, and it could find application in assessing other cosmetic operations. 相似文献