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971.
Erich Schuster Anne-Marie Hermansson Camilla ?hgren Mats Rudemo Niklas Lorén 《Biophysical journal》2014,106(1):253-262
The effects of electrostatic interactions and obstruction by the microstructure on probe diffusion were determined in positively charged hydrogels. Probe diffusion in fine-stranded gels and solutions of β-lactoglobulin at pH 3.5 was determined using fluorescence recovery after photobleaching (FRAP) and binding, which is widely used in biophysics. The microstructures of the β-lactoglobulin gels were characterized using transmission electron microscopy. The effects of probe size and charge (negatively charged Na2-fluorescein (376Da) and weakly anionic 70kDa FITC-dextran), probe concentration (50 to 200 ppm), and β-lactoglobulin concentration (9% to 12% w/w) on the diffusion properties and the electrostatic interaction between the negatively charged probes and the positively charged gels or solutions were evaluated. The results show that the diffusion of negatively charged Na2-fluorescein is strongly influenced by electrostatic interactions in the positively charged β-lactoglobulin systems. A linear relationship between the pseudo-on binding rate constant and the β-lactoglobulin concentration for three different probe concentrations was found. This validates an important assumption of existing biophysical FRAP and binding models, namely that the pseudo-on binding rate constant equals the product of the molecular binding rate constant and the concentration of the free binding sites. Indicators were established to clarify whether FRAP data should be analyzed using a binding-diffusion model or an obstruction-diffusion model. 相似文献
972.
Olivier Duss Erich Michel Nana Diarra dit Konté Mario Schubert Frédéric H.-T. Allain 《Nucleic acids research》2014,42(8):5332-5346
The carbon storage regulator/regulator of secondary metabolism (Csr/Rsm) type of small non-coding RNAs (sRNAs) is widespread throughout bacteria and acts by sequestering the global translation repressor protein CsrA/RsmE from the ribosome binding site of a subset of mRNAs. Although we have previously described the molecular basis of a high affinity RNA target bound to RsmE, it remains unknown how other lower affinity targets are recognized by the same protein. Here, we have determined the nuclear magnetic resonance solution structures of five separate GGA binding motifs of the sRNA RsmZ of Pseudomonas fluorescens in complex with RsmE. The structures explain how the variation of sequence and structural context of the GGA binding motifs modulate the binding affinity for RsmE by five orders of magnitude (∼10 nM to ∼3 mM, Kd). Furthermore, we see that conformational adaptation of protein side-chains and RNA enable recognition of different RNA sequences by the same protein contributing to binding affinity without conferring specificity. Overall, our findings illustrate how the variability in the Csr/Rsm protein–RNA recognition allows a fine-tuning of the competition between mRNAs and sRNAs for the CsrA/RsmE protein. 相似文献
973.
Nicolay Leme da Cunha Erich Fischer Aline P. Lorenz-Lemke Spencer C. H. Barrett 《Annals of botany》2014,114(8):1637-1649
MethodsStyle morph frequencies were sampled from 73 populations distributed across four flooding regimes differing in depth and duration. Measurements of flower size, sex-organ dimension, pollen size and pollen production were made in selected populations, and pollinator assemblages and their functional traits were recorded.ConclusionsThe similar morph structure and evenness of populations, regardless of flooding regime, suggest that sexual reproduction and clonal dispersal are sufficiently common to prevent the signature of founder events from dominating in a region. However, the pervasive occurrence of biased morph ratios in most populations suggests that many are in a non-equilibrium state. The reduced frequency of the mid-styled morph in trimorphic and dimorphic populations may be associated with the weak self-incompatibility of this morph resulting in selfing and inbreeding depression. Clonality in E. azurea and the weak self-incompatibility of the mid-styled morph may make it more vulnerable to geitonogamous selfing. 相似文献
974.
Susanne Horn Stefan Prost Mathias Stiller Daniel Makowiecki Tatiana Kuznetsova Norbert Benecke Erich Pucher Anne K. Hufthammer Charles Schouwenburg Beth Shapiro Michael Hofreiter 《Molecular ecology》2014,23(7):1717-1729
After centuries of human hunting, the Eurasian beaver Castor fiber had disappeared from most of its original range by the end of the 19th century. The surviving relict populations are characterized by both low genetic diversity and strong phylogeographical structure. However, it remains unclear whether these attributes are the result of a human‐induced, late Holocene bottleneck or already existed prior to this reduction in range. To investigate genetic diversity in Eurasian beaver populations during the Holocene, we obtained mitochondrial control region DNA sequences from 48 ancient beaver samples and added 152 modern sequences from GenBank. Phylogeographical analyses of the data indicate a differentiation of European beaver populations into three mitochondrial clades. The two main clades occur in western and eastern Europe, respectively, with an early Holocene contact zone in eastern Europe near a present‐day contact zone. A divergent and previously unknown clade of beavers from the Danube Basin survived until at least 6000 years ago, but went extinct during the transition to modern times. Finally, we identify a recent decline in effective population size of Eurasian beavers, with a stronger bottleneck signal in the western than in the eastern clade. Our results suggest that the low genetic diversity and the strong phylogeographical structure in recent beavers are artefacts of human hunting‐associated population reductions. While beaver populations have been growing rapidly since the late 19th century, genetic diversity within modern beaver populations remains considerably reduced compared to what was present prior to the period of human hunting and habitat reduction. 相似文献
975.
Toni Luge Michael Kube Anja Freiwald David Meierhofer Erich Seemüller Sascha Sauer 《Proteomics》2014,14(16):1882-1889
Phytoplasmas are pathogenic bacteria within the class of Mollicutes, which are associated with more than 1000 plant diseases. In this study, we applied quantitative mass spectrometry to analyse affected pathways of the model plant tobacco (Nicotiana occidentalis) upon Candidatus Phytoplasma mali strain AT infection. Using tissue obtained from leaf midribs, 1466 plant‐assigned proteins were identified. For 1019 of these proteins, we could reproducibly quantify the expression changes of infected versus noninfected plants, of which 157 proteins were up‐ and 173 proteins were downregulated. Differential expression took place in a number of pathways, among others strong downregulation of porphyrin and chlorophyll metabolism and upregulation of alpha‐linolenic acid metabolism, which was consistent with observed increased levels of jasmonic acid, a key signal molecule of plant defence. Our data shed light on the molecular networks that are involved in defence of plants against phytoplasma infection and provide a resource for further studies. 相似文献
976.
977.
Jie Cui Wei Zhao Zhiyong Huang Erich D Jarvis M Thomas P Gilbert Peter J Walker Edward C Holmes Guojie Zhang 《Genome biology》2014,15(12)
Background
Mammalian genomes commonly harbor endogenous viral elements. Due to a lack of comparable genome-scale sequence data, far less is known about endogenous viral elements in avian species, even though their small genomes may enable important insights into the patterns and processes of endogenous viral element evolution.Results
Through a systematic screening of the genomes of 48 species sampled across the avian phylogeny we reveal that birds harbor a limited number of endogenous viral elements compared to mammals, with only five viral families observed: Retroviridae, Hepadnaviridae, Bornaviridae, Circoviridae, and Parvoviridae. All nonretroviral endogenous viral elements are present at low copy numbers and in few species, with only endogenous hepadnaviruses widely distributed, although these have been purged in some cases. We also provide the first evidence for endogenous bornaviruses and circoviruses in avian genomes, although at very low copy numbers. A comparative analysis of vertebrate genomes revealed a simple linear relationship between endogenous viral element abundance and host genome size, such that the occurrence of endogenous viral elements in bird genomes is 6- to 13-fold less frequent than in mammals.Conclusions
These results reveal that avian genomes harbor relatively small numbers of endogenous viruses, particularly those derived from RNA viruses, and hence are either less susceptible to viral invasions or purge them more effectively.Electronic supplementary material
The online version of this article (doi:10.1186/s13059-014-0539-3) contains supplementary material, which is available to authorized users. 相似文献978.
Claudia C Weber Bastien Boussau Jonathan Romiguier Erich D Jarvis Hans Ellegren 《Genome biology》2014,15(12)
Background
While effective population size (Ne) and life history traits such as generation time are known to impact substitution rates, their potential effects on base composition evolution are less well understood. GC content increases with decreasing body mass in mammals, consistent with recombination-associated GC biased gene conversion (gBGC) more strongly impacting these lineages. However, shifts in chromosomal architecture and recombination landscapes between species may complicate the interpretation of these results. In birds, interchromosomal rearrangements are rare and the recombination landscape is conserved, suggesting that this group is well suited to assess the impact of life history on base composition.Results
Employing data from 45 newly and 3 previously sequenced avian genomes covering a broad range of taxa, we found that lineages with large populations and short generations exhibit higher GC content. The effect extends to both coding and non-coding sites, indicating that it is not due to selection on codon usage. Consistent with recombination driving base composition, GC content and heterogeneity were positively correlated with the rate of recombination. Moreover, we observed ongoing increases in GC in the majority of lineages.Conclusions
Our results provide evidence that gBGC may drive patterns of nucleotide composition in avian genomes and are consistent with more effective gBGC in large populations and a greater number of meioses per unit time; that is, a shorter generation time. Thus, in accord with theoretical predictions, base composition evolution is substantially modulated by species life history.Electronic supplementary material
The online version of this article (doi:10.1186/s13059-014-0549-1) contains supplementary material, which is available to authorized users. 相似文献979.
Background
Visual exploration of the surroundings during locomotion at heights has not yet been investigated in subjects suffering from fear of heights.Methods
Eye and head movements were recorded separately in 16 subjects susceptible to fear of heights and in 16 non-susceptible controls while walking on an emergency escape balcony 20 meters above ground level. Participants wore mobile infrared eye-tracking goggles with a head-fixed scene camera and integrated 6-degrees-of-freedom inertial sensors for recording head movements. Video recordings of the subjects were simultaneously made to correlate gaze and gait behavior.Results
Susceptibles exhibited a limited visual exploration of the surroundings, particularly the depth. Head movements were significantly reduced in all three planes (yaw, pitch, and roll) with less vertical head oscillations, whereas total eye movements (saccade amplitudes, frequencies, fixation durations) did not differ from those of controls. However, there was an anisotropy, with a preference for the vertical as opposed to the horizontal direction of saccades. Comparison of eye and head movement histograms and the resulting gaze-in-space revealed a smaller total area of visual exploration, which was mainly directed straight ahead and covered vertically an area from the horizon to the ground in front of the feet. This gaze behavior was associated with a slow, cautious gait.Conclusions
The visual exploration of the surroundings by susceptibles to fear of heights differs during locomotion at heights from the earlier investigated behavior of standing still and looking from a balcony. During locomotion, anisotropy of gaze-in-space shows a preference for the vertical as opposed to the horizontal direction during stance. Avoiding looking into the abyss may reduce anxiety in both conditions; exploration of the “vertical strip” in the heading direction is beneficial for visual control of balance and avoidance of obstacles during locomotion. 相似文献980.
Jessamine P. Winer-Jones Behrad Vahidi Norma Arquilevich Cong Fang Samuel Ferguson Darren Harkins Cory Hill Erich Klem Paul C. Pagano Chrissy Peasley Juan Romero Robert Shartle Robert C. Vasko William M. Strauss Paul W. Dempsey 《PloS one》2014,9(1)