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Stops making sense: translational trade-offs and stop codon reassignment
Background
Efficient gene expression involves a trade-off between (i) premature termination of protein synthesis; and (ii) readthrough, where the ribosome fails to dissociate at the terminal stop. Sense codons that are similar in sequence to stop codons are more susceptible to nonsense mutation, and are also likely to be more susceptible to transcriptional or translational errors causing premature termination. We therefore expect this trade-off to be influenced by the number of stop codons in the genetic code. Although genetic codes are highly constrained, stop codon number appears to be their most volatile feature.
Results
In the human genome, codons readily mutable to stops are underrepresented in coding sequences. We construct a simple mathematical model based on the relative likelihoods of premature termination and readthrough. When readthrough occurs, the resultant protein has a tail of amino acid residues incorrectly added to the C-terminus. Our results depend strongly on the number of stop codons in the genetic code. When the code has more stop codons, premature termination is relatively more likely, particularly for longer genes. When the code has fewer stop codons, the length of the tail added by readthrough will, on average, be longer, and thus more deleterious. Comparative analysis of taxa with a range of stop codon numbers suggests that genomes whose code includes more stop codons have shorter coding sequences.
Conclusions
We suggest that the differing trade-offs presented by alternative genetic codes may result in differences in genome structure. More speculatively, multiple stop codons may mitigate readthrough, counteracting the disadvantage of a higher rate of nonsense mutation. This could help explain the puzzling overrepresentation of stop codons in the canonical genetic code and most variants
Medicalization of eating and feeding
A variety of developments over the past century have produced the conditions in which eating and feeding are transformed from practices embedded in social or cultural relations into explicit medical practices. The rise of medical science, expansion of the pharmaceutical and food industries, escalating concern over diet‐related diseases and conditions, and growing anxiety over infant and childhood development have contributed to a process of medicalization. Medicalization is a sociological concept that analyses the expansion of medical terminology, interventions, or practitioners into areas of the life that were previously considered outside the medical sphere. For instance, under‐eating has previously been defined using theological language, as an act of fasting demonstrating a saintly character. Such practices are now understood through medical terms of anorexia nervosa, malnutrition, or general diagnoses such as “eating disorders not otherwise specified.” Individuals engaged in under‐ or over‐eating practices are increasingly defined by medical concepts (anorexia nervosa and obesity) and treated in medical spaces (hospitals, clinics, or rehabilitation centres) through medical interventions (pharmaceuticals, surgery, psychotherapy, or dietary regimens). Likewise, infant feeding (breast or formula) is understood as a practice that requires monitoring and instruction from medical practitioners. Further, eating in general is progressively invested with medical significance. Foods and diets are touted as possessing a therapeutic or health enhancing capacity that indicates an individual’s or population’s present and future health. Due to the high regard for, and influence of, medical science in the West, medicalization studies primarily focus on Western contexts. Medicalization does have an impact on non‐Western societies and the developing world, however its influence emanates from Western biomedicine, industries, and policies. There is important work to be done in examining the process of medicalization in non‐Western contexts, however this article is limited to the Western context ( Hunt, 1999). To analyse the medicalization of eating and feeding it is important to first sketch the theoretical and historical background of medicalization as a sociological concept. The relationship between eating and medicine is extensive. In order to focus the discussion, three examples are used – under‐eating, over‐ eating and infant feeding. This background focuses the analysis of the forces driving the medicalization of eating and feeding. Finally, in elaborating the influences and consequences of the medicalization of eating and feeding, some of the central ethical implications are identified and discusse
Assessment of technological options and economical feasibility for cyanophycin biopolymer and high-value amino acid production
Major transitions can be expected within the next few decades aiming at the reduction of pollution and global warming and at energy saving measures. For these purposes, new sustainable biorefinery concepts will be needed that will replace the traditional mineral oil-based synthesis of specialty and bulk chemicals. An important group of these chemicals are those that comprise N-functionalities. Many plant components contained in biomass rest or waste stream fractions contain these N-functionalities in proteins and free amino acids that can be used as starting materials for the synthesis of biopolymers and chemicals. This paper describes the economic and technological feasibility for cyanophycin production by fermentation of the potato waste stream Protamylasse™ or directly in plants and its subsequent conversion to a number of N-containing bulk chemicals
Lambda and Antilambda polarization from deep inelastic muon scattering
We report results of the first measurements of Lambda and Antilambda
polarization produced in deep inelastic polarized muon scattering on the
nucleon. The results are consistent with an expected trend towards positive
polarization with increasing x_F. The polarizations of Lambda and Antilambda
appear to have opposite signs. A large negative polarization for Lambda at low
positive x_F is observed and is not explained by existing models.A possible
interpretation is presented.Comment: 9 pages, 2 figure
Development and validation of a short version of the Partnership Self-Assessment Tool (PSAT) among professionals in Dutch disease-management partnerships
Background: The extent to which partnership synergy is created within quality improvement programmes in the Netherlands is unknown. In this article, we describe the psychometric testing of the Partnership Self-Assessment Tool (PSAT) among professionals in twenty-two disease-management partnerships participating in quality improvement projects focused on chronic care in the Netherlands. Our objectives are to validate the PSAT in the Netherlands and to reduce the number of items of the original PSAT while maintaining validity and reliability. Methods. The Dutch version of the PSAT was tested in twenty-two disease-management partnerships with 218 professionals. We tested the instrument by means of structural equation modelling, and examined its validity and reliability. Results: After eliminating 14 items, the confirmatory factor analyses revealed good indices of fit with the resulting 15-item PSAT-Short version (PSAT-S). Internal consistency as represented by Cronbach's alpha ranged from acceptable (0.75) for the 'efficiency' subscale to excellent for the 'leadership' subscale (0.87). Convergent validity was provided with high correlations of the partnership dimensions and partnership synergy (ranged from 0.512 to 0.609) and high correlations with chronic illness care (ranged from 0.447 to 0.329). Conclusion: The psychometric properties and convergent validity of the PSAT-S were satisfactory rendering it a valid and reliable instrument for assessing partnership syne
Search for gamma-ray emission from magnetars with the Fermi Large Area Telescope
We report on the search for 0.1-10 GeV emission from magnetars in 17 months
of Fermi Large Area Telescope (LAT) observations. No significant evidence for
gamma-ray emission from any of the currently-known magnetars is found. The most
stringent upper limits to date on their persistent emission in the Fermi-LAT
energy range are estimated between ~10^{-12}-10^{-10} erg/s/cm2, depending on
the source. We also searched for gamma-ray pulsations and possible outbursts,
also with no significant detection. The upper limits derived support the
presence of a cut-off at an energy below a few MeV in the persistent emission
of magnetars. They also show the likely need for a revision of current models
of outer gap emission from strongly magnetized pulsars, which, in some
realizations, predict detectable GeV emission from magnetars at flux levels
exceeding the upper limits identified here using the Fermi-LAT observations.Comment: ApJ Letters in press; Corresponding authors: Caliandro G. A., Hadasch
D., Rea N., Burnett
Fermi Gamma-ray Imaging of a Radio Galaxy
The Fermi Gamma-ray Space Telescope has detected the gamma-ray glow emanating
from the giant radio lobes of the radio galaxy Centaurus A. The resolved
gamma-ray image shows the lobes clearly separated from the central active
source. In contrast to all other active galaxies detected so far in high-energy
gamma-rays, the lobe flux constitutes a considerable portion (>1/2) of the
total source emission. The gamma-ray emission from the lobes is interpreted as
inverse Compton scattered relic radiation from the cosmic microwave background
(CMB), with additional contribution at higher energies from the
infrared-to-optical extragalactic background light (EBL). These measurements
provide gamma-ray constraints on the magnetic field and particle energy content
in radio galaxy lobes, and a promising method to probe the cosmic relic photon
fields.Comment: 27 pages, includes Supplementary Online Material; corresponding
authors: C.C. Cheung, Y. Fukazawa, J. Knodlseder, L. Stawar
Fermi Large Area Telescope observations of PSR J1836+5925
The discovery of the gamma-ray pulsar PSR J1836+5925, powering the formerly
unidentified EGRET source 3EG J1835+5918, was one of the early accomplishments
of the Fermi Large Area Telescope (LAT). Sitting 25 degrees off the Galactic
plane, PSR J1836+5925 is a 173 ms pulsar with a characteristic age of 1.8
million years, a spindown luminosity of 1.1 erg s, and a
large off-peak emission component, making it quite unusual among the known
gamma-ray pulsar population. We present an analysis of one year of LAT data,
including an updated timing solution, detailed spectral results and a long-term
light curve showing no indication of variability. No evidence for a surrounding
pulsar wind nebula is seen and the spectral characteristics of the off-peak
emission indicate it is likely magnetospheric. Analysis of recent XMM
observations of the X-ray counterpart yields a detailed characterization of its
spectrum, which, like Geminga, is consistent with that of a neutron star
showing evidence for both magnetospheric and thermal emission.Comment: Accepted to Astrophysical Journa
A change in the optical polarization associated with a gamma-ray flare in the blazar 3C 279
It is widely accepted that strong and variable radiation detected over all
accessible energy bands in a number of active galaxies arises from a
relativistic, Doppler-boosted jet pointing close to our line of sight. The size
of the emitting zone and the location of this region relative to the central
supermassive black hole are, however, poorly known, with estimates ranging from
light-hours to a light-year or more. Here we report the coincidence of a
gamma-ray flare with a dramatic change of optical polarization angle. This
provides evidence for co-spatiality of optical and gamma-ray emission regions
and indicates a highly ordered jet magnetic field. The results also require a
non-axisymmetric structure of the emission zone, implying a curved trajectory
for the emitting material within the jet, with the dissipation region located
at a considerable distance from the black hole, at about 10^5 gravitational
radii.Comment: Published in Nature issued on 18 February 2010. Corresponding
authors: Masaaki Hayashida and Greg Madejsk
The genomes of two key bumblebee species with primitive eusocial organization
Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation
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