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21.
22.
Anttila J Heinonen P Nenonen T Pino A Iwaï H Kauppi E Soliymani R Baumann M Saksi J Suni N Haltia T 《Biochimica et biophysica acta》2011,1807(3):311-318
Paracoccus denitrificans is a soil bacterium which can respire aerobically and also denitrify if oxygen is absent. Both processes are highly dependent on copper enzymes and copper is therefore likely to be an essential trace element for the bacterium. If copper is not easily available, a copper-acquisition mechanism would be highly beneficial. In this paper, we have addressed the question of whether Paracoccus secretes a copper-acquisition compound functionally analogous to that found in some methanotrophs. Bacteria were grown both in copper-containing and copper-deficient denitrification media, cells were removed by centrifugation and the supernatant was analysed using chromatography and spectroscopy. Bacterial growth yield in the absence of copper was 70-80% of that in the copper-containing medium. A notable difference between the two culture conditions was that spent copper-deficient medium was pigmented, whereas the copper-containing medium was not. Spectrophotometry indicated that a red compound with an absorption maximum at 405 nm was produced under copper-limited conditions. In addition to the strong 405 nm maximum, the visible spectrum of the purified red molecule had weaker maxima at 535 nm and 570 nm, features typical of metallated tetrapyrroles. Mass spectrometry showed that the purified pigment had a molecular mass of 716.18. Moreover, the fine structure of the mass spectrum suggested the presence of zinc and was consistent with the chemical formula of C(36)H(36)N(4)O(8)Zn. The presence of zinc was also demonstrated using inductively coupled plasma atomic emission spectroscopy. Fragmentation analysis with mass spectrometry showed the release of consecutive 59 Da fragments, assignable to four -CH(2)-COOH moieties. Thin layer chromatography as well as NMR analysis of the C-13/N-15 labelled red pigment suggested that it is predominantly zinc coproporphyrin III with a minor fraction of metal-free coproporphyrin III. We propose that in a copper-poor environment P. denitrificans secretes coproporphyrin III for copper chelation and subsequent uptake of the bound copper into the cell. Consistent with this idea, cell yields of copper-deficient cultures grown in the presence of 1 microM copper-coproporphyrin III were 90-95% of the yields of cultures grown in the normal copper-containing media. Coproporphyrin III may work as a copper-acquisition compound in P. denitrificans. 相似文献
23.
Leinonen T Herczeg G Cano JM Merilä J 《Evolution; international journal of organic evolution》2011,65(10):2916-2926
The transition from marine to freshwater life in the threespine stickleback (Gasterosteus aculeatus) is accompanied by complex morphological changes-including reduction in bony armor and change in body shape-but experimental evidence for the selective agents behind these evolutionary transitions is sparse. We investigated whether selection by predatory fish affects threespine stickleback morphology differentially when refuge is absent (pelagic lifestyle-ancestral condition) or present (benthic lifestyle-derived condition). Our results show that selection favors low numbers of lateral plates in habitats with refuge, whereas fully plated individuals have a selective advantage in habitats without refuge. We also found that a decrease in the length of the caudal peduncle increased survival probability, irrespective of habitat. The effect of spine lengths on survival was evident only in a multivariate analysis of selection, implying that it is essential to account for phenotypic and genetic correlations between traits before drawing conclusions about the effects of selection on single traits. Apart from uncovering targets and patterns of predator-induced selection on threespine stickleback morphology, our results provide direct evidence to support the hypothesis that differences in antipredator strategies in pelagic versus benthic sticklebacks could play a role in the repeated, independent cases of plate number reduction following freshwater colonization in this species. 相似文献
24.
Error-prone rolling circle amplification (RCA) is a promising alternative to error-prone PCR for random mutagenesis. The main disadvantage of error-prone RCA is the low transformation efficiency of the DNA concatemer produced in the amplification reaction. We improved the method by introducing loxP recombination site of bacteriophage P1 Cre recombinase into the target plasmid and reducing the concatemer by Cre recombinase to plasmid-sized units, increasing the number of transformants 50-fold in non-error-prone and 13-fold in error-prone conditions. The efficiency improvement was verified by obtaining 115 ± 57 ceftazidime resistant colonies per recombined RCA reaction from randomly mutated TEM-1 β-lactamase gene library whereas only 9 ± 11 colonies were gained without recombination. Supplementation of the error-prone RCA with Cre/loxP recombination is a simple and useful tool to increase the transformable library size. 相似文献
25.
Relationship between prion propensity and the rates of individual molecular steps of fibril assembly
Wang YQ Buell AK Wang XY Welland ME Dobson CM Knowles TP Perrett S 《The Journal of biological chemistry》2011,286(14):12101-12107
Peptides and proteins possess an inherent propensity to self-assemble into generic fibrillar nanostructures known as amyloid fibrils, some of which are involved in medical conditions such as Alzheimer disease. In certain cases, such structures can self-propagate in living systems as prions and transmit characteristic traits to the host organism. The mechanisms that allow certain amyloid species but not others to function as prions are not fully understood. Much progress in understanding the prion phenomenon has been achieved through the study of prions in yeast as this system has proved to be experimentally highly tractable; but quantitative understanding of the biophysics and kinetics of the assembly process has remained challenging. Here, we explore the assembly of two closely related homologues of the Ure2p protein from Saccharomyces cerevisiae and Saccharomyces paradoxus, and by using a combination of kinetic theory with solution and biosensor assays, we are able to compare the rates of the individual microscopic steps of prion fibril assembly. We find that for these proteins the fragmentation rate is encoded in the structure of the seed fibrils, whereas the elongation rate is principally determined by the nature of the soluble precursor protein. Our results further reveal that fibrils that elongate faster but fracture less frequently can lose their ability to propagate as prions. These findings illuminate the connections between the in vitro aggregation of proteins and the in vivo proliferation of prions, and provide a framework for the quantitative understanding of the parameters governing the behavior of amyloid fibrils in normal and aberrant biological pathways. 相似文献
26.
Heidi Hintsala Tuomas V. Kentt? Mikko Tulppo Antti Kiviniemi Heikki V. Huikuri Matti M?ntysaari Sirkka Kein?nen-Kiukaannemi Risto Bloigu Karl-Heinz Herzig Riitta Antikainen Hannu Rintam?ki Jouni J. K. Jaakkola Tiina M. Ik?heimo 《PloS one》2014,9(7)
Objectives
The aim of our study was to assess the effect of short-term cold exposure, typical in subarctic climate, on cardiac electrical function among untreated middle-aged hypertensive men.Methods
We conducted a population-based recruitment of 51 hypertensive men and a control group of 32 men without hypertension (age 55–65 years) who underwent whole-body cold exposure (15 min exposure to temperature −10°C, wind 3 m/s, winter clothes). Conduction times and amplitudes, vectorcardiography, arrhythmias, and heart rate variability (autonomic nervous function) were assessed.Results
Short-term cold exposure increased T-peak to T-end interval from 67 to 72 ms (p<0.001) and 71 to 75 ms (p<0.001) and T-wave amplitude from 0.12 to 0.14 mV (p<0.001) and from 0.17 to 0.21 mV (p<0.001), while QTc interval was shortened from 408 to 398 ms (p<0.001) and from 410 to 401 ms (p<0.001) among hypertensive men and controls, respectively. Cold exposure increased both low (from 390 to 630 ms2 (p<0.001) and 380 to 700 ms2 (p<0.001), respectively) and high frequency heart rate variability (from 90 to 190 ms2 (p<0.001) and 150 to 300 ms2 (p<0.001), respectively), while low-to-high frequency-ratio was reduced. In addition, the frequency of ventricular ectopic beats increased slightly during cold exposure. The cold induced changes were similar between untreated hypertensive men and controls.Conclusions
Short-term cold exposure with moderate facial and mild whole body cooling resulted in prolongation of T-peak to T-end interval and higher T-wave amplitude while QTc interval was shortened. These changes of ventricular repolarization may have resulted from altered cardiac autonomic regulation and were unaffected by untreated hypertension.Trial Registration
ClinicalTrials.gov NCT02007031相似文献27.
Selection for population‐specific adaptation shaped patterns of variation in the photoperiod pathway genes in Arabidopsis lyrata during post‐glacial colonization
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Tiina M. Mattila Esa A. Aalto Tuomas Toivainen Anne Niittyvuopio Susanna Piltonen Helmi Kuittinen Outi Savolainen 《Molecular ecology》2016,25(2):581-597
Spatially varying selection can lead to population‐specific adaptation, which is often recognized at the phenotypic level; however, the genetic evidence is weaker in many groups of organisms. In plants, environmental shifts that occur due to colonization of a novel environment may require adaptive changes in the timing of growth and flowering, which are often governed by location‐specific environmental cues such as day length. We studied locally varying selection in 19 flowering time loci in nine populations of the perennial herb Arabidopsis lyrata, which has a wide but patchy distribution in temperate and boreal regions of the northern hemisphere. The populations differ in their recent population demographic and colonization histories and current environmental conditions, especially in the growing season length. We searched for population‐specific molecular signatures of directional selection by comparing a set of candidate flowering time loci with a genomic reference set within each population using multiple approaches and contrasted the patterns of different populations. The candidate loci possessed approximately 20% of the diversity of the reference loci. On average the flowering time loci had more rare alleles (a smaller Tajima's D) and an excess of highly differentiated sites relative to the reference, suggesting positive selection. The strongest signal of selection was detected in photoperiodic pathway loci in the colonizing populations of Northwestern Europe, whereas no evidence of positive selection was detected in the Central European populations. These findings emphasized the population‐specific nature of selection and suggested that photoperiodic adaptation was important during postglacial colonization of the species. 相似文献
28.
Tuomas Huovinen Hanna Sanmark Jani Ylä-Pelto Markus Vehniäinen Urpo Lamminmäki 《Molecular biotechnology》2010,44(3):221-231
Efficient display of antibody on filamentous phage M13 coat is crucial for successful biopanning selections. We applied a
directed evolution strategy to improve the oligovalent display of a poorly behaving Fab fragment fused to phage gene-3 for
minor coat protein (g3p). The Fab displaying clones were enriched from a randomly mutated Fab gene library with polyclonal
anti-mouse IgG antibodies. Contribution of each mutation to the improved phenotype of one selected mutant was studied. It
was found out that two point mutations had significant contribution to the display efficiency of Fab clones superinfected
with hyperphage. The most dramatic effect was connected to a start codon mutation, from AUG to GUG, of the PelB signal sequence
preceding the heavy chain. The clone carrying this mutation, FabMGUG, displayed Fab 19-fold better and yielded twofold higher phage titers than the original Fab. 相似文献
29.
Alexander?K. Buell Peter Hung Xavier Salvatella Mark?E. Welland Christopher?M. Dobson Tuomas?P.J. Knowles 《Biophysical journal》2013,104(5):1116-1126
Electrostatic forces play a key role in mediating interactions between proteins. However, gaining quantitative insights into the complex effects of electrostatics on protein behavior has proved challenging, due to the wide palette of scenarios through which both cations and anions can interact with polypeptide molecules in a specific manner or can result in screening in solution. In this article, we have used a variety of biophysical methods to probe the steady-state kinetics of fibrillar protein self-assembly in a highly quantitative manner to detect how it is modulated by changes in solution ionic strength. Due to the exponential modulation of the reaction rate by electrostatic forces, this reaction represents an exquisitely sensitive probe of these effects in protein-protein interactions. Our approach, which involves a combination of experimental kinetic measurements and theoretical analysis, reveals a hierarchy of electrostatic effects that control protein aggregation. Furthermore, our results provide a highly sensitive method for the estimation of the magnitude of binding of a variety of ions to protein molecules. 相似文献
30.
On the separation of net ecosystem exchange into assimilation and ecosystem respiration: review and improved algorithm 总被引:13,自引:1,他引:13
Markus Reichstein Eva Falge Dennis Baldocchi Dario Papale Marc Aubinet Paul Berbigier Christian Bernhofer Nina Buchmann Tagir Gilmanov Andr Granier Thomas Grünwald Katka Havrnkov Hannu Ilvesniemi Dalibor Janous Alexander Knohl Tuomas Laurila Annalea Lohila Denis Loustau Giorgio Matteucci Tilden Meyers Franco Miglietta Jean‐Marc Ourcival Jukka Pumpanen Serge Rambal Eyal Rotenberg Maria Sanz John Tenhunen Günther Seufert Francesco Vaccari Timo Vesala Dan Yakir Riccardo Valentini 《Global Change Biology》2005,11(9):1424-1439
This paper discusses the advantages and disadvantages of the different methods that separate net ecosystem exchange (NEE) into its major components, gross ecosystem carbon uptake (GEP) and ecosystem respiration (Reco). In particular, we analyse the effect of the extrapolation of night‐time values of ecosystem respiration into the daytime; this is usually done with a temperature response function that is derived from long‐term data sets. For this analysis, we used 16 one‐year‐long data sets of carbon dioxide exchange measurements from European and US‐American eddy covariance networks. These sites span from the boreal to Mediterranean climates, and include deciduous and evergreen forest, scrubland and crop ecosystems. We show that the temperature sensitivity of Reco, derived from long‐term (annual) data sets, does not reflect the short‐term temperature sensitivity that is effective when extrapolating from night‐ to daytime. Specifically, in summer active ecosystems the long‐term temperature sensitivity exceeds the short‐term sensitivity. Thus, in those ecosystems, the application of a long‐term temperature sensitivity to the extrapolation of respiration from night to day leads to a systematic overestimation of ecosystem respiration from half‐hourly to annual time‐scales, which can reach >25% for an annual budget and which consequently affects estimates of GEP. Conversely, in summer passive (Mediterranean) ecosystems, the long‐term temperature sensitivity is lower than the short‐term temperature sensitivity resulting in underestimation of annual sums of respiration. We introduce a new generic algorithm that derives a short‐term temperature sensitivity of Reco from eddy covariance data that applies this to the extrapolation from night‐ to daytime, and that further performs a filling of data gaps that exploits both, the covariance between fluxes and meteorological drivers and the temporal structure of the fluxes. While this algorithm should give less biased estimates of GEP and Reco, we discuss the remaining biases and recommend that eddy covariance measurements are still backed by ancillary flux measurements that can reduce the uncertainties inherent in the eddy covariance data. 相似文献