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991.
Lachlan H. Yee Vibeke Aagaard Angela Johnstone Matthew Lee Staffan J. Kjelleberg Mike Manefield 《Biodegradation》2010,21(6):947-956
The biodegradation of chlorinated organics in vadose zone soils is challenging owing to the presence of oxygen, which inhibits
reductive dehalogenation reactions and consequently the growth of dehalorespiring microbes. In addition, the hydraulic conductivity
of vadose zone soils is typically high, hence attempts to remediate such zones with biostimulation solutions are often unsuccessful
due to the short residence times for these solutions to act upon the native bacterial community. In this study we have identified
sodium alginate as a hydrogel polymer that can be used to increase the residence time of a nutrient solution in an unsaturated
sandy soil. Additionally we have identified neutral red as a redox active compound that can catalyse the reductive dechlorination
of the chlorinated organic hexachloro-1,3-butadiene by activated sludge fed with lactate and acetate. Finally we have shown
that a nutrient solution amended with neutral red and sodium alginate can lower the redox potential and reduce hexachloro-1,3-butadiene
concentrations in a contaminated vadose zone soil. 相似文献
992.
993.
994.
Ming‐Dong Zhang Amit Zeisel André Calas Marc Landry Matthew Fuszard Sally L Shirran Robert Schnell Árpád Dobolyi Márk Oláh Lauren Spence Jan Mulder Henrik Martens Miklós Palkovits Mathias Uhlen Harald H Sitte Catherine H Botting Ludwig Wagner Sten Linnarsson Tibor Harkany 《The EMBO journal》2015,34(1):36-54
995.
Predicting the emergence of new pathogenic strains is a key goal of evolutionary epidemiology. However, the majority of existing studies have focussed on emergence at the population level, and not within a host. In particular, the coexistence of pre-existing and mutated strains triggers a heightened immune response due to the larger total pathogen population; this feedback can smother mutated strains before they reach an ample size and establish. Here, we extend previous work for measuring emergence probabilities in non-equilibrium populations, to within-host models of acute infections. We create a mathematical model to investigate the emergence probability of a fitter strain if it mutates from a self-limiting strain that is guaranteed to go extinct in the long-term. We show that ongoing immune cell proliferation during the initial stages of infection causes a drastic reduction in the probability of emergence of mutated strains; we further outline how this effect can be accurately measured. Further analysis of the model shows that, in the short-term, mutant strains that enlarge their replication rate due to evolving an increased growth rate are more favoured than strains that suffer a lower immune-mediated death rate (‘immune tolerance’), as the latter does not completely evade ongoing immune proliferation due to inter-parasitic competition. We end by discussing the model in relation to within-host evolution of human pathogens (including HIV, hepatitis C virus, and cancer), and how ongoing immune growth can affect their evolutionary dynamics. 相似文献
996.
997.
Nicholas A Genthe James B Thoden Matthew M Benning Hazel M Holden 《Protein science : a publication of the Protein Society》2015,24(6):976-986
The existence of N-formylated sugars in the O-antigens of Gram-negative bacteria has been known since the middle 1980s, but only recently have the biosynthetic pathways for their production been reported. In these pathways, glucose-1-phosphate is first activated by attachment to a dTMP moiety. This step is followed by a dehydration reaction and an amination. The last step in these pathways is catalyzed by N-formyltransferases that utilize N10-formyltetrahydrofolate as the carbon source. Here we describe the three-dimensional structure of one of these N-formyltransferases, namely VioF from Providencia alcalifaciens O30. Specifically, this enzyme catalyzes the conversion of dTDP-4-amino-4,6-dideoxyglucose (dTDP-Qui4N) to dTDP-4,6-dideoxy-4-formamido-d-glucose (dTDP-Qui4NFo). For this analysis, the structure of VioF was solved to 1.9 Å resolution in both its apoform and in complex with tetrahydrofolate and dTDP-Qui4N. The crystals used in the investigation belonged to the space group R32 and demonstrated reticular merohedral twinning. The overall catalytic core of the VioF subunit is characterized by a six stranded mixed β-sheet flanked on one side by three α-helices and on the other side by mostly random coil. This N-terminal domain is followed by an α-helix and a β-hairpin that form the subunit:subunit interface. The active site of the enzyme is shallow and solvent-exposed. Notably, the pyranosyl moiety of dTDP-Qui4N is positioned into the active site by only one hydrogen bond provided by Lys 77. Comparison of the VioF model to that of a previously determined N-formyltransferase suggests that substrate specificity is determined by interactions between the protein and the pyrophosphoryl group of the dTDP-sugar substrate. 相似文献
998.
Non-allelic homologous recombination (NAHR) is a common mechanism for generating genome rearrangements and is implicated in numerous genetic disorders, but its detection in high-throughput sequencing data poses a serious challenge. We present a probabilistic model of NAHR and demonstrate its ability to find NAHR in low-coverage sequencing data from 44 individuals. We identify NAHR-mediated deletions or duplications in 109 of 324 potential NAHR loci in at least one of the individuals. These calls segregate by ancestry, are more common in closely spaced repeats, often result in duplicated genes or pseudogenes, and affect highly studied genes such as GBA and CYP2E1.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-015-0633-1) contains supplementary material, which is available to authorized users. 相似文献999.
Sexually selected UV signals in the tropical ornate jumping spider,Cosmophasis umbratica may incur costs from predation 下载免费PDF全文
Matthew W. Bulbert James C. O'Hanlon Shane Zappettini Shichang Zhang Daiqin Li 《Ecology and evolution》2015,5(4):914-920
Sexually selected ornaments and signals are costly to maintain if they are maladaptive in nonreproductive contexts. The jumping spider Cosmophasis umbratica exhibits distinct sexual dichromatism with males displaying elaborate UV body markings that signal male quality. Female C. umbratica respond favorably to UV‐reflecting males and ignore males that have their UV masked. However, Portia labiata, a UV‐sensitive spider‐eating specialist and a natural predator of C. umbratica, is known to use UV reflectance as a cue when hunting prey. We investigated the cost of these UV signals in C. umbratica in terms of their predation risk. Under experimental conditions, three choice scenarios were presented to P. labiata individuals. Choices by P. labiata were made between male C. umbratica with and without the UV signal; a UV‐reflecting male and non‐UV‐reflecting female; and a UV‐masked male and female. The presence and absence of UV signals was manipulated using an optical filter. Portia labiata exhibited a strong bias toward UV+ individuals. These results suggest the sexually selected trait of UV reflectance increases the visibility of males to UV‐sensitive predators. The extent of this male‐specific UV signal then is potentially moderated by predation pressure. Interestingly though, P. labiata still preferred males to females irrespective of whether UV reflectance was present or not. This suggests P. labiata can switch cues when conditions to detect UV reflectance are not optimal. 相似文献
1000.
Sandra Lavorel Matthew J. Colloff Sue Mcintyre Michael D. Doherty Helen T. Murphy Daniel J. Metcalfe Michael Dunlop Richard J. Williams Russell M. Wise Kristen J. Williams 《Global Change Biology》2015,21(1):12-31
Ecosystem services are typically valued for their immediate material or cultural benefits to human wellbeing, supported by regulating and supporting services. Under climate change, with more frequent stresses and novel shocks, 'climate adaptation services', are defined as the benefits to people from increased social ability to respond to change, provided by the capability of ecosystems to moderate and adapt to climate change and variability. They broaden the ecosystem services framework to assist decision makers in planning for an uncertain future with new choices and options. We present a generic framework for operationalising the adaptation services concept. Four steps guide the identification of intrinsic ecological mechanisms that facilitate the maintenance and emergence of ecosystem services during periods of change, and so materialise as adaptation services. We applied this framework for four contrasted Australian ecosystems. Comparative analyses enabled by the operational framework suggest that adaptation services that emerge during trajectories of ecological change are supported by common mechanisms: vegetation structural diversity, the role of keystone species or functional groups, response diversity and landscape connectivity, which underpin the persistence of function and the reassembly of ecological communities under severe climate change and variability. Such understanding should guide ecosystem management towards adaptation planning. 相似文献