788 research outputs found
Use of split-dihydrofolate reductase for the detection of protein-protein interactions and simultaneous selection of multiple plasmids in Plasmodium falciparum
Defining protein-protein interactions is fundamental to the understanding of gene function. Protein-fragment complementation assays have been used for the analysis of protein-protein interactions in various organisms. The split-dihydrofolate reductase (DHFR) protein-fragment complementation assay utilises two complementary fragments of the enzyme fused to a pair of potentially interacting proteins. If these proteins interact, the DHFR fragments associate, fold into their native structure, reconstitute their function and confer resistance to antifolate drugs. We show that murine DHFR fragments fused to interacting proteins reconstitute a functional enzyme and confer resistance to the antifolate drug WR99210 in Plasmodium falciparum. These data demonstrate that the split-DHFR method can be used to detect in vivo protein-protein interactions in the parasite. Additionally, we show that split-DHFR fragments can be used as selection markers, permitting simultaneous selection of two plasmids in the presence of a single antifolate drug. Taken together, these experiments show that split-DHFR represents a valuable tool for the characterisation of Plasmodium protein function and genetic manipulation of the parasite
Magnetic Field Evolution in Accreting White Dwarfs
We discuss the evolution of the magnetic field of an accreting white dwarf.
We first show that the timescale for ohmic decay in the liquid interior is 8 to
12 billion years for a dipole field, and 4 to 6 billion years for a quadrupole
field. We then compare the timescales for ohmic diffusion and accretion at
different depths in the star, and for a simplified field structure and
spherical accretion, calculate the time-dependent evolution of the global
magnetic field at different accretion rates. In this paper, we neglect mass
loss by classical nova explosions and assume the white dwarf mass increases
with time. In this case, the field structure in the outer layers of the white
dwarf is significantly modified for accretion rates above the critical rate
(1-5) x 10^(-10) solar masses per year. We consider the implications of our
results for observed systems. We propose that accretion-induced magnetic field
changes are the missing evolutionary link between AM Her systems and
intermediate polars. The shorter ohmic decay time for accreting white dwarfs
provides a partial explanation of the lack of accreting systems with 10^9 G
fields. In rapidly accreting systems such as supersoft X-ray sources,
amplification of internal fields by compression may be important for Type Ia
supernova ignition and explosion. Finally, spreading matter in the polar cap
may induce complexity in the surface magnetic field, and explain why the more
strongly accreting pole in AM Her systems has a weaker field. We conclude with
speculations about the field evolution when classical nova explosions cause the
white dwarf mass to decrease with time.Comment: To appear in MNRAS (15 pages, 10 figures); minor revision
Two Bee-Pollinated Plant Species Show Higher Seed Production when Grown in Gardens Compared to Arable Farmland
Background Insect pollinator abundance, in particular that of bees, has been shown to be high where there is a super-abundance of floral resources; for example in association with mass-flowering crops and also in gardens where flowering plants are often densely planted. Since land management affects pollinator numbers, it is also likely to affect the resultant pollination of plants growing in these habitats. We hypothesised that the seed or fruit set of two plant species, typically pollinated by bumblebees and/or honeybees might respond in one of two ways: 1) pollination success could be reduced when growing in a floriferous environment, via competition for pollinators, or 2) pollination success could be enhanced because of increased pollinator abundance in the vicinity. Methodology/Principal Findings We compared the pollination success of experimental plants of Glechoma hederacea L. and Lotus corniculatus L. growing in gardens and arable farmland. On the farms, the plants were placed either next to a mass-flowering crop (oilseed rape, Brassica napus L. or field beans, Vicia faba L.) or next to a cereal crop (wheat, Triticum spp.). Seed set of G. hederacea and fruit set of L. corniculatus were significantly higher in gardens compared to arable farmland. There was no significant difference in pollination success of G. hederacea when grown next to different crops, but for L. corniculatus, fruit set was higher in the plants growing next to oilseed rape when the crop was in flower. Conclusions/Significance The results show that pollination services can limit fruit set of wild plants in arable farmland, but there is some evidence that the presence of a flowering crop can facilitate their pollination (depending on species and season). We have also demonstrated that gardens are not only beneficial to pollinators, but also to the process of pollination
Numerical instability of the Akhmediev breather and a finite-gap model of it
In this paper we study the numerical instabilities of the NLS Akhmediev
breather, the simplest space periodic, one-mode perturbation of the unstable
background, limiting our considerations to the simplest case of one unstable
mode. In agreement with recent theoretical findings of the authors, in the
situation in which the round-off errors are negligible with respect to the
perturbations due to the discrete scheme used in the numerical experiments, the
split-step Fourier method (SSFM), the numerical output is well-described by a
suitable genus 2 finite-gap solution of NLS. This solution can be written in
terms of different elementary functions in different time regions and,
ultimately, it shows an exact recurrence of rogue waves described, at each
appearance, by the Akhmediev breather. We discover a remarkable empirical
formula connecting the recurrence time with the number of time steps used in
the SSFM and, via our recent theoretical findings, we establish that the SSFM
opens up a vertical unstable gap whose length can be computed with high
accuracy, and is proportional to the inverse of the square of the number of
time steps used in the SSFM. This neat picture essentially changes when the
round-off error is sufficiently large. Indeed experiments in standard double
precision show serious instabilities in both the periods and phases of the
recurrence. In contrast with it, as predicted by the theory, replacing the
exact Akhmediev Cauchy datum by its first harmonic approximation, we only
slightly modify the numerical output. Let us also remark, that the first rogue
wave appearance is completely stable in all experiments and is in perfect
agreement with the Akhmediev formula and with the theoretical prediction in
terms of the Cauchy data.Comment: 27 pages, 8 figures, Formula (30) at page 11 was corrected, arXiv
admin note: text overlap with arXiv:1707.0565
Can implementation of technology transform the management of Parkinson's? Lessons learnt from the Parkinson's KinetiGraph (TM) (PKG (TM)) service evaluation project
Mining the Gene Wiki for functional genomic knowledge
<p>Abstract</p> <p>Background</p> <p>Ontology-based gene annotations are important tools for organizing and analyzing genome-scale biological data. Collecting these annotations is a valuable but costly endeavor. The Gene Wiki makes use of Wikipedia as a low-cost, mass-collaborative platform for assembling text-based gene annotations. The Gene Wiki is comprised of more than 10,000 review articles, each describing one human gene. The goal of this study is to define and assess a computational strategy for translating the text of Gene Wiki articles into ontology-based gene annotations. We specifically explore the generation of structured annotations using the Gene Ontology and the Human Disease Ontology.</p> <p>Results</p> <p>Our system produced 2,983 candidate gene annotations using the Disease Ontology and 11,022 candidate annotations using the Gene Ontology from the text of the Gene Wiki. Based on manual evaluations and comparisons to reference annotation sets, we estimate a precision of 90-93% for the Disease Ontology annotations and 48-64% for the Gene Ontology annotations. We further demonstrate that this data set can systematically improve the results from gene set enrichment analyses.</p> <p>Conclusions</p> <p>The Gene Wiki is a rapidly growing corpus of text focused on human gene function. Here, we demonstrate that the Gene Wiki can be a powerful resource for generating ontology-based gene annotations. These annotations can be used immediately to improve workflows for building curated gene annotation databases and knowledge-based statistical analyses.</p
The ontogeny of bumblebee flight trajectories: From naïve explorers to experienced foragers
Understanding strategies used by animals to explore their landscape is essential to predict how they exploit patchy resources, and consequently how they are likely to respond to changes in resource distribution. Social bees provide a good model for this and, whilst there are published descriptions of their behaviour on initial learning flights close to the colony, it is still unclear how bees find floral resources over hundreds of metres and how these flights become directed foraging trips. We investigated the spatial ecology of exploration by radar tracking bumblebees, and comparing the flight trajectories of bees with differing experience. The bees left the colony within a day or two of eclosion and flew in complex loops of ever-increasing size around the colony, exhibiting Lévy-flight characteristics constituting an optimal searching strategy. This mathematical pattern can be used to predict how animals exploring individually might exploit a patchy landscape. The bees’ groundspeed, maximum displacement from the nest and total distance travelled on a trip increased significantly with experience. More experienced bees flew direct paths, predominantly flying upwind on their outward trips although forage was available in all directions. The flights differed from those of naïve honeybees: they occurred at an earlier age, showed more complex looping, and resulted in earlier returns of pollen to the colony. In summary bumblebees learn to find home and food rapidly, though phases of orientation, learning and searching were not easily separable, suggesting some multi-tasking
Landscape effects on wild Bombus terrestris (Hymenoptera: Apidae) queens visiting highbush blueberry fields in south-central Chile
Regulation of mammary gland branching morphogenesis by the extracellular matrix and its remodeling enzymes.
A considerable body of research indicates that mammary gland branching morphogenesis is dependent, in part, on the extracellular matrix (ECM), ECM-receptors, such as integrins and other ECM receptors, and ECM-degrading enzymes, including matrix metalloproteinases (MMPs) and their inhibitors, tissue inhibitors of metalloproteinases (TIMPs). There is some evidence that these ECM cues affect one or more of the following processes: cell survival, polarity, proliferation, differentiation, adhesion, and migration. Both three-dimensional culture models and genetic manipulations of the mouse mammary gland have been used to study the signaling pathways that affect these processes. However, the precise mechanisms of ECM-directed mammary morphogenesis are not well understood. Mammary morphogenesis involves epithelial 'invasion' of adipose tissue, a process akin to invasion by breast cancer cells, although the former is a highly regulated developmental process. How these morphogenic pathways are integrated in the normal gland and how they become dysregulated and subverted in the progression of breast cancer also remain largely unanswered questions
Double hadron leptoproduction in the nuclear medium
First measurement of double-hadron production in deep-inelastic scattering
has been measured with the HERMES spectrometer at HERA using a 27.6 GeV
positron beam with deuterium, nitrogen, krypton and xenon targets. The
influence of the nuclear medium on the ratio of double-hadron to single-hadron
yields has been investigated. Nuclear effects are clearly observed but with
substantially smaller magnitude and reduced -dependence compared to
previously measured single-hadron multiplicity ratios. The data are in fair
agreement with models based on partonic or pre-hadronic energy loss, while they
seem to rule out a pure absorptive treatment of the final state interactions.
Thus, the double-hadron ratio provides an additional tool for studying
modifications of hadronization in nuclear matter
- …