Post-transcriptional gene silencing triggered by sense transgenes involves uncapped antisense RNA and differs from silencing intentionally triggered by antisense transgenes

Although post-transcriptional gene silencing (PTGS) has been studied for more than a decade, there is still a gap in our understanding of how de novo silencing is initiated against genetic elements that are not supposed to produce double-stranded (ds)RNA. Given the pervasive transcription occurring throughout eukaryote genomes, we tested the hypothesis that unintended transcription could produce antisense (as)RNA molecules that participate to the initiation of PTGS triggered by sense transgenes (S-PTGS). Our results reveal a higher level of asRNA in Arabidopsis thaliana lines that spontaneously trigger S-PTGS than in lines that do not. However, PTGS triggered by antisense transgenes (AS-PTGS) differs from S-PTGS. In particular, a hypomorphic ago1 mutation that suppresses S-PTGS prevents the degradation of asRNA but not sense RNA during AS-PTGS, suggesting a different treatment of coding and non-coding RNA by AGO1, likely because of AGO1 association to polysomes. Moreover, the intended asRNA produced during AS-PTGS is capped whereas the asRNA produced during S-PTGS derives from 3' maturation of a read-through transcript and is uncapped. Thus, we propose that uncapped asRNA corresponds to the aberrant RNA molecule that is converted to dsRNA by RNA-DEPENDENT RNA POLYMERASE 6 in siRNA-bodies to initiate S-PTGS, whereas capped asRNA must anneal with sense RNA to produce dsRNA that initiate AS-PTGS

Two-Pion Exchange in Proton-Proton Scattering

The contribution of the box and crossed two-pion-exchange diagrams to proton-proton scattering at 90$^{\circ}_{c.m.}$ is calculated in the laboratory momentum range up to 12 GeV/c. Relativistic form factors related to the nucleon and pion size and representing the pion source distribution based on the quark structure of the hadronic core are included at each vertex of the pion-nucleon interaction. These form factors depend on the four-momenta of the exchanged pions and scattering nucleons. Feynman-diagram amplitudes calculated without form factors are checked against those derived from dispersion relations. In this comparison, one notices that a very short-range part of the crossed diagram, neglected in dispersion-relation calculations of the two-pion-exchange nucleon-nucleon potential, gives a sizable contribution. In the Feynman-diagram calculation with form factors the agreement with measured spin-separated cross sections, as well as amplitudes in the lower part of the energy range considered, is much better for pion-nucleon pseudo-vector vis \`a vis pseudo-scalar coupling. While strengths of the box and crossed diagrams are comparable for laboratory momenta below 2 GeV/c, the crossed diagram dominates for larger momenta, largely due to the kinematics of the crossed diagram allowing a smaller momentum transfer in the nucleon center of mass. An important contribution arises from the principal-value part of the integrals which is non-zero when form factors are included. It seems that the importance of the exchange of color singlets may extend higher in energy than expected

Tractability in Constraint Satisfaction Problems: A Survey

International audienceEven though the Constraint Satisfaction Problem (CSP) is NP-complete, many tractable classes of CSP instances have been identified. After discussing different forms and uses of tractability, we describe some landmark tractable classes and survey recent theoretical results. Although we concentrate on the classical CSP, we also cover its important extensions to infinite domains and optimisation, as well as #CSP and QCSP

How much afterhyperpolarization conductance is recruited by an action potential? A dynamic-clamp study in cat lumbar motoneurons.

We accurately measured the conductance responsible for the afterhyperpolarization (medium AHP) that follows a single spike in spinal motoneurons of anesthetized cats. This was done by using the dynamic-clamp method. We injected an artificial current in the neurons that increased the AHP amplitude, and we made use of the fact that the intensity of the natural AHP current at the trough of the voltage trajectory was related linearly to the AHP amplitude. We determined at the same time the conductance and the reversal potential of the AHP current. This new method was validated by a simple theoretical model incorporating AHP and hyperpolarization-activated (Ih) currents and could be applied when the decay time constant of the AHP conductance was at least five times shorter than the estimated Ih activation time. This condition was fulfilled in 33 of 44 motoneurons. The AHP conductance varied from 0.3 to 1.4 microS in both slow- and fast-type motoneurons, which was approximately the same range as the input conductance of the entire population. However, AHP and input conductances were not correlated. The larger AHP in slow-type motoneurons was mainly attributable to their smaller input conductance compared with fast motoneurons. The likeness of the AHP conductance in both types of motoneurons is in sharp contrast to differences in AHP decay time and explains why slow- and fast-type motoneurons have similar gain

Virtual arc consistency for weighted csp

Optimizing a combination of local cost functions on discrete variables is a central problem in many formalisms such as in probabilistic networks, maximum satisfiability, weighted CSP or factor graphs. Recent results have shown that maintaining a form of local consistency in a Branch and Bound search provides bounds that are strong enough to solve many practical instances. In this paper, we introduce Virtual Arc Consistency (VAC) which iteratively identifies and applies sequences of cost propagation over rational costs that are guaranteed to transform a WCSP in another WCSP with an improved constant cost. Although not as strong as Optimal Soft Arc Consistency, VAC is faster and powerful enough to solve submodular problems. Maintaining VAC inside branch and bound leads to important improvements in efficiency on large difficult problems and allowed us to close two famous frequency assignment problem instances

Flexible Management of Large-Scale Integer Domains in CSPs

Most research on Constraint Programming concerns the (exponential) search space of Constraint Satisfaction Problems (CSPs) and intelligent algorithms that reduce and explore it. This work proposes a different way, not of solving a problem, but of storing the domains of its variables, an important—and less focused—issue especially when they are large. The new data structures that are used are proved theoretically and empirically to adapt better to large domains, than the commonly used ones. The experiments of this work display the contrast between the most popular Constraint Programming systems and a new system that uses the data structures proposed in order to solve CSP instances with wide domains, such as known Bioinformatics problems

Genome-wide patterns of transposon proliferation in an evolutionary young hybrid fish

Hybridization can induce transposons to jump into new genomic positions, which may result in their accumulation across the genome. Alternatively, transposon copy numbers may increase through non-allelic (ectopic) homologous recombination in highly repetitive regions of the genome. The relative contribution of transposition bursts versus recombination-based mechanisms to evolutionary processes remains unclear because studies on transposon dynamics in natural systems are rare. We assessed the genome-wide distribution of transposon insertions in a young hybrid lineage ("invasive Cottus", n=11) and its parental species Cottus rhenanus (n=17) and Cottus perifretum (n=9) using a reference genome assembled from long single molecule PacBio reads. An inventory of transposable elements was reconstructed from the same data and annotated. Transposon copy numbers in the hybrid lineage increased in 120 (15.9%) out of 757 transposons studied here. The copy number increased on average by 69% (range: 10 - 197%). Given the age of the hybrid lineage, this suggests that they have proliferated within a few hundred generations since admixture began. However, frequency spectra of transposon insertions revealed no increase of novel and rare insertions across assembled parts of the genome. This implies that transposons were added to repetitive regions of the genome that remain difficult to assemble. Future studies will need to evaluate whether recombination-based mechanisms rather than genome-wide transposition may explain the majority of the recent transposon proliferation in the hybrid lineage. Irrespectively of the underlying mechanism, the observed over-abundance in repetitive parts of the genome suggests that gene-rich regions are unlikely to be directly affected. This article is protected by copyright. All rights reserved