Redundancy and specialization among plant microRNAs : role of the MIR164 family in developmental robustness

In plants, members of microRNA (miRNA) families are often predicted to target the same or overlapping sets of genes. It has thus been hypothesized that these miRNAs may act in a functionally redundant manner. This hypothesis is tested here by studying the effects of elimination of all three members of the MIR164 family from Arabidopsis. It was found that a loss of miR164 activity leads to a severe disruption of shoot development, in contrast to the effect of mutation in any single MIR164 gene. This indicates that these miRNAs are indeed functionally redundant. Differences in the expression patterns of the individual MIR164 genes imply, however, that redundancy among them is not complete, and that these miRNAs show functional specialization. Furthermore, the results of molecular and genetic analyses of miR164-mediated target regulation indicate that miR164 miRNAs function to control the transcript levels, as well as the expression patterns, of their targets, suggesting that they might contribute to developmental robustness. For two of the miR164 targets, namely CUP-SHAPED COTYLEDON1 (CUC1) and CUC2, we provide evidence for their involvement in the regulation of growth and show that their derepression in miR164 loss-of-function mutants is likely to account for most of the mutant phenotype

Derivation of Delay Equation Climate Models Using the Mori-Zwanzig Formalism

Models incorporating delay have been frequently used to understand climate variability phenomena, but often the delay is introduced through an ad-hoc physical reasoning, such as the propagation time of waves. In this paper, the Mori-Zwanzig formalism is introduced as a way to systematically derive delay models from systems of partial differential equations and hence provides a better justification for using these delay-type models. The Mori-Zwanzig technique gives a formal rewriting of the system using a projection onto a set of resolved variables, where the rewritten system contains a memory term. The computation of this memory term requires solving the orthogonal dynamics equation, which represents the unresolved dynamics. For nonlinear systems, it is often not possible to obtain an analytical solution to the orthogonal dynamics and an approximate solution needs to be found. Here, we demonstrate the Mori-Zwanzig technique for a two-strip model of the El Nino Southern Oscillation (ENSO) and explore methods to solve the orthogonal dynamics. The resulting nonlinear delay model contains an additional term compared to previously proposed ad-hoc conceptual models. This new term leads to a larger ENSO period, which is closer to that seen in observations.Comment: Submitted to Proceedings of the Royal Society A, 25 pages, 10 figure

Derivation of Delay Equation Climate Models Using the Mori-Zwanzig Formalism

This is the author accepted manuscript. The final version is available from The Royal Society via the DOI in this record.Data access: The codes supporting this article have been uploaded as part of the supplementary material. They can also be found on the online repository figshare: https://doi.org/10.6084/m9.figshare.8085683.v1Models incorporating delay have been frequently used to understand climate variability phenomena, but often the delay is introduced through an ad-hoc physical reasoning, such as the propagation time of waves. In this paper, the Mori-Zwanzig formalism is introduced as a way to systematically derive delay models from systems of partial differential equations and hence provides a better justification for using these delay-type models. The Mori-Zwanzig technique gives a formal rewriting of the system using a projection onto a set of resolved variables, where the rewritten system contains a memory term. The computation of this memory term requires solving the orthogonal dynamics equation, which represents the unresolved dynamics. For nonlinear systems, it is often not possible to obtain an analytical solution to the orthogonal dynamics and an approximate solution needs to be found. Here, we demonstrate the Mori-Zwanzig technique for a two-strip model of the El Nino Southern Oscillation (ENSO) and explore methods to solve the orthogonal dynamics. The resulting nonlinear delay model contains an additional term compared to previously proposed ad-hoc conceptual models. This new term leads to a larger ENSO period, which is closer to that seen in observations.European Union Horizon 2020Dutch Science Foundation (NWOEngineering and Physical Sciences Research Council (EPSRC

Intrinsic disorder in the common N-terminus of human adenovirus 5 E1B-55K and its related E1BN proteins indicated by studies on E1B-93R

AbstractThe E1B transcription unit of human adenovirus encodes at least five different proteins generated by alternative splicing of a common E1B precursor mRNA. E1B-156R, -93R and -84R contain individual carboxy termini but share a common amino terminus. To acquire data on the structure of the amino terminus we performed biophysical analyses on E1B-93R. We show that E1B-93R is mostly unstructured and fulfills the criteria of an intrinsically disordered protein (IDP). The intrinsic disorder in the amino terminus of these proteins is evolutionary conserved in all seven human adenovirus species. As IDPs comprise a rapidly growing family of proteins which, despite their lack of a well defined structure, often fulfill essential regulatory functions, the observations described here might open up a new avenue for the understanding of the regulation and functions of E1B proteins, in particular the multifunctional E1B-55K oncoprotein

Taijiquan the 'Taiji World' way: Towards a cosmopolitan vision of ecology.

In this article, we present a case study analysis of data gathered on the practice of the art of Taijiquan (Tai Chi Chuan) in one UK context. Our interest in looking at this physical culture was in exploring if/how physical cultures of shared embodied experience and practice may help “sow the seeds of environmental awareness”. In so doing, we illustrate certain affinities between this interpretation of the art and Beck’s idea of a “cosmopolitan vision of ecology”. We present an analysis of documentary and interview data of one English Taijiquan organisation and how it currently promotes the idea of interconnectedness, wellbeing and an alternative meta-narrative for living through the practice of Taijiquan. We conclude that, while further research is needed, there is evidence that a cosmopolitan vision for ecology is emerging in physical cultures such as Taijiquan

Interstellar Scintillation Observations of 146 Extragalactic Radio Sources

From 1979--1996 the Green Bank Interferometer was used by the Naval Research Laboratory to monitor the flux density from 146 compact radio sources at frequencies near 2 and 8 GHz. We filter the ``light curves'' to separate intrinsic variations on times of a year or more from more rapid interstellar scintilation (ISS) on times of 5--50 d. Whereas the intrinsic variation at 2 GHz is similar to that at 8 GHz (though diminished in amplitude), the ISS variation is much stronger at 2 than at 8 GHz. We characterize the ISS variation by an rms amplitude and a timescale and examine the statistics of these parameters for the 121 sources with significant ISS at 2 GHz. We model the scintillations using the NE2001 Galactic electron model assuming the sources are brightness-limited. We find the observed rms amplitude to be in general agreement with the model, provided that the compact components of the sources have about 50% of their flux density in a component with maximum brightness temperatures $10^{11}$--$10^{12}$K. Thus our results are consistent with cm-wavelength VLBI studies of compact AGNs, in that the maximum brightness temperatures found are consistent with the inverse synchrotron limit at $3 \times 10^{11}$ K, boosted in jet configurations by Doppler factors up to about 20. The average of the observed 2 GHz ISS timescales is in reasonable agreement with the model at Galactic latitudes above about 10\de. At lower latitudes the observed timescales are too fast, suggesting that the transverse plasma velocity increases more than expected beyond about 1 kpc.Comment: 32 pages, 16 figures. Submitted to Ap

The early extra petals1 Mutant Uncovers a Role for MicroRNA miR164c in Regulating Petal Number in Arabidopsis

Background: MicroRNAs (miRNAs) are small 20–25 nucleotide non-protein-coding RNAs that negatively regulate expression of genes in many organisms, ranging from plants to humans. The MIR164 family of miRNAs in Arabidopsis consists of three members that share sequence complementarity to transcripts of NAC family transcription factors, including CUP-SHAPED COTYLEDON1 (CUC1) and CUC2. CUC1 and CUC2 are redundantly required for the formation of boundaries between organ primordia. The analysis of transgenic plants that either overexpress miR164a or miR164b or express a miRNA-resistant version of CUC1 or CUC2 has shown that miRNA regulation of CUC1 and CUC2 is necessary for normal flower development. A loss-of-function allele of MIR164b did not result in a mutant phenotype, possibly because of functional redundancy among the three members of the MIR164 family. Results: In this study, we describe the characterization of the early extra petals1 (eep1) Arabidopsis mutant, whose predominant phenotype is the formation of extra petals in early-arising flowers. We demonstrate that eep1 is a loss-of-function allele of MIR164c, one of three known members of the MIR164 family. Our analyses of miR164c function and eep1 mir164b double mutants reveal that miR164c controls petal number in a nonredundant manner by regulating the transcript accumulation of the transcription factors CUC1 and CUC2. Conclusions: The data presented in this study indicate that closely related miRNA family members that are predicted to target the same set of genes can have different functions during development, possibly because of nonoverlapping expression patterns

RPA-Approach to the Excitations of the Nucleon, Part II: Phenomenology

The tensor-RPA approach developed previously in part I is applied to the Nambu-Jona-Lasinio (NJL) model. As a first step we investigate the structure of Dirac-Hartree-Fock solutions for a rotationally and isospin invariant ground-state density. Whereas vacuum properties can be reproduced, no solitonic configuration for a system with unit baryon number is found. We then solve the tensor-RPA equation employing simple models of the nucleon ground state. In general the ph interaction effects a decrease of the excited states to lower energies. Due to an enhanced level density at low energies the obtained spectra cannot be matched with the experimental data when a standard MIT-bag configuration is used. However, when the size of the nucleon quark core is reduced to approximately 0.3 fm a fair description of the baryon spectrum in the positive-parity channel is achieved. For this purpose the residual interaction turns out to be crucial and leads to a significant improvement compared with the mean-field spectra.Comment: 33 pages, Latex, 9 Postscpript figures, section on the excited states has been completely rewritten after error was detected, results are now much more encouragin

Prograde and retrograde metasomatic reactions in mineralised magnesium-silicate skarn in the Cu-Au Ertsberg East Skarn System, Ertsberg, Papua Province, Indonesia

The 2.7–2.9 Ma Ertsberg East Skarn System (EESS) is a world-class Cu-Au skarn that formed within and adjacent to an intrusion within a paleodepth of 0.5 km and >2.5 km. Its economic mineralisation developed by sustained reaction of magmatic fluid with contact metamorphosed siliciclastic and carbonate rocks at the margin of the adjacent Ertsberg quartz monzodiorite intrusion. Based on high-resolution mineral mapping, chemical analysis and thermodynamic calculations, the multistage formation processes of the exoskarn components of the EESS are examined in the context of changing pressure, temperature, fluid composition and fluid phase. We show that contact metamorphism of dolomitic sediments occurred at 51 ± 5 MPa, between 700 °C and 800 °C and in the presence of a H2O-CO2-fluid containing ~10 to ~70 mol% CO2. This prograde metamorphism formed a forsterite + diopside + calcite + phlogopite + spinel assemblage. Such forsterite-dominated skarns account for ~55 vol% of the EESS exoskarns. Rare pargasite (previously unrecognized in this deposit) formed locally in the metamorphosed carbonate sequence where the protolith was composed of supratidal evaporites with dolomitic carbonate and interlayered calc-silicate rocks. The subsequent flux of a lower pressure magmatic gas containing SO2(g) caused sulphate metasomatism. This high temperature gas alteration of the metamorphic assemblage also caused skarn Cu-Fe-sulphide mineralisation. The influx of a SO2 gas through fracture permeability occurred at a temperature between ~600 and 700 °C and caused calcite to be replaced by anhydrite, with the coupled release of H2S(g). This in-situ release of H2S(g) scavenged trace Cu from the gas phase to deposit Cu-Fe-sulphides, which make the economic value of the distinct. We demonstrate that the formation of metal sulphides within forsterite skarns of the Ertsberg East Skarn System required a minimum flux of ~1,050 Mt SO2(g) and show that volcanic degassing may have occurred over a time span of ~3,900 years. As the system waned, the ambient fluid resulted in partial retrograde serpentinization of olivine and diopside without carbonation, and at temperatures sufficiently high to preserve anhydrite.This study was partially supported by Australian Research Council funding to P. King (DP150104604 and FT130101524)