The ISO SWS on-line system

The software which is currently being developed for the Short Wavelength Spectrometer (SWS) of the Infrared Space Observatory (ISO) is described. The spectrometer has a wide range of capabilities in the 2-45 micron infrared band. SWS contains two independent gratings, one for the long and one for the short wavelength section of the band. With the gratings a spectral resolution of approximately 1000 to approximately 2500 can be obtained. The instrument also contains two Fabry-Perault's yielding a resolution between approximately 1000 and approximately 20000. Software is currently being developed for the acquisition, calibration, and analysis of SWS data. The software is firstly required to run in a pipeline mode without human interaction, to process data as they are received from the telescope. However, both for testing and calibration of the instrument as well as for evaluation of the planned operating procedures the software should also be suitable for interactive use. Thirdly the same software will be used for long term characterization of the instrument. The software must work properly within the environment designed by the European Space Agency (ESA) for the spacecraft operations. As a result strict constraints are put on I/O devices, throughput etc

Finite-gap Solutions of the Vortex Filament Equation: Isoperiodic Deformations

We study the topology of quasiperiodic solutions of the vortex filament equation in a neighborhood of multiply covered circles. We construct these solutions by means of a sequence of isoperiodic deformations, at each step of which a real double point is "unpinched" to produce a new pair of branch points and therefore a solution of higher genus. We prove that every step in this process corresponds to a cabling operation on the previous curve, and we provide a labelling scheme that matches the deformation data with the knot type of the resulting filament.Comment: 33 pages, 5 figures; submitted to Journal of Nonlinear Scienc

Rappemonads are haptophyte phytoplankton

20年以上謎だった生物の正体が判明 --光合成生物進化解明のカギに--. 京都大学プレスリリース. 2021-03-29.Rapidly accumulating genetic data from environmental sequencing approaches have revealed an extraordinary level of unsuspected diversity within marine phytoplankton, which is responsible for around 50% of global net primary production.However, the phenotypic identity of many of the organisms distinguished by environmental DNA sequences remains unclear. The rappemonads represent a plastid-bearing protistan lineage that to date has only been identified by environmental plastid 16S rRNA sequences.The phenotypic identity of this group, which does not confidently cluster in any known algal clades in 16S rRNA phylogenetic reconstructions, has remained unknown since the first report of environmental sequences over two decades ago. We show that rappemonads are closely related to a haptophyte microalga, Pavlomulina ranunculiformis gen. nov. et sp. nov., and belong to a new haptophyte class, the Rappephyceae. Organellar phylogenomic analyses provide strong evidence for the inclusion of this lineage within the Haptophyta as a sister group to the Prymnesiophyceae. Members of this new class have a cosmopolitan distribution in coastal and oceanic regions. The relative read abundance of Rappephyceae in a large environmental barcoding dataset was comparable to, or greater than, those of major haptophyte species, such as the bloom-forming Gephyrocapsa huxleyi and Prymnesium parvum, and this result indicates that they likely have a significant impact as primary producers. Detailed characterization of Pavlomulina allowed for reconstruction of the ancient evolutionary history of the Haptophyta, a group that is one of the most important components of extant marine phytoplankton communities

The Ecm11-Gmc2 complex promotes synaptonemal complex formation through assembly of transverse filaments in budding yeast

During meiosis, homologous chromosomes pair at close proximity to form the synaptonemal complex (SC). This association is mediated by transverse filament proteins that hold the axes of homologous chromosomes together along their entire length. Transverse filament proteins are highly aggregative and can form an aberrant aggregate called the polycomplex that is unassociated with chromosomes. Here, we show that the Ecm11-Gmc2 complex is a novel SC component, functioning to facilitate assembly of the yeast transverse filament protein, Zip1. Ecm11 and Gmc2 initially localize to the synapsis initiation sites, then throughout the synapsed regions of paired homologous chromosomes. The absence of either Ecm11 or Gmc2 substantially compromises the chromosomal assembly of Zip1 as well as polycomplex formation, indicating that the complex is required for extensive Zip1 polymerization. We also show that Ecm11 is SUMOylated in a Gmc2-dependent manner. Remarkably, in the unSUMOylatable ecm11 mutant, assembly of chromosomal Zip1 remained compromised while polycomplex formation became frequent. We propose that the Ecm11-Gmc2 complex facilitates the assembly of Zip1 and that SUMOylation of Ecm11 is critical for ensuring chromosomal assembly of Zip1, thus suppressing polycomplex formation

Principles of meiotic chromosome assembly revealed in S. cerevisiae

During meiotic prophase, chromosomes organise into a series of chromatin loops emanating from a proteinaceous axis, but the mechanisms of assembly remain unclear. Here we use Saccharomyces cerevisiae to explore how this elaborate three-dimensional chromosome organisation is linked to genomic sequence. As cells enter meiosis, we observe that strong cohesin-dependent grid-like Hi-C interaction patterns emerge, reminiscent of mammalian interphase organisation, but with distinct regulation. Meiotic patterns agree with simulations of loop extrusion with growth limited by barriers, in which a heterogeneous population of expanding loops develop along the chromosome. Importantly, CTCF, the factor that imposes similar features in mammalian interphase, is absent in S. cerevisiae, suggesting alternative mechanisms of barrier formation. While grid-like interactions emerge independently of meiotic chromosome synapsis, synapsis itself generates additional compaction that matures differentially according to telomere proximity and chromosome size. Collectively, our results elucidate fundamental principles of chromosome assembly and demonstrate the essential role of cohesin within this evolutionarily conserved process

Composition and Habitability of Europa’s Ocean Over Time

Introduction: Europa is proposed to host a global liquid water ocean that is in contact with a silicate interior [1]. Understanding the composition of this ocean and the underlying rock is crucial for evaluating the habitability of Europa. However, the presence of an ice shell impedes direct observation or analysis of the ocean and rock, leaving their compositions largely unknown. Previous modelling work has shown that, if Europa accreted entirely from CI or CM chondritic material, sufficient volatiles could be released during prograde metamorphism to account for the current size of the hydrosphere [2]. However, thermal models predict that temperatures in Europa’s interior would gradually increase over billions of years [e.g. 3], where the progressive release of volatiles would change the ocean composition over time. In this study, possible ocean compositions were explored using computer modelling to simulate the thermal evolution of Europa’s interior over its ~4.5 Gyr lifetime and assess the volatiles released from the starting material as it is heated. Methods: The composition of Murchison (a CM chondrite) was chosen to represent the silicate material that accreted to form Europa because the CMs: formed close to early Jupiter (unlike the CIs [4]), contain sufficient water (largely held within hydrated silicates [5]), and can produce fluid compositions consistent with salts observed on Europa’s surface [2, 6]. A 1-dimensional thermal evolution code was used to model the temperatures achieved within Europa’s interior [3]. Temperature-depth profiles were then extracted at two points in time to reflect the formation of the proto-ocean (i.e. ~1600 Myr since the calcium-aluminium-rich inclusions (CAIs)) and the current-day ocean (~4568 Myr since the CAIs). Rcrust [7] and Perple_X [8] were used to predict the electrolytic fluid speciation from the starting material when heated to the temperatures predicted by the first temperature-depth profile (Stage 1; 4 – ~1600 Myr) and then the second (Stage 2; ~1600 – ~4568 Myr). Pyrrhotite was extracted from the starting material past the Fe-FeS eutectic temperature (which was also calculated using Rcrust and Perple_X) to approximate core formation. The volatiles forming the proto-ocean (i.e. those released in Stage 1) were then equilibrated using CHIM-XPT [9], where supersaturated gases were exsolved and minerals precipitated. The further volatiles (i.e. those released in Stage 2) were then added to the proto-ocean in CHIM-XPT, forming the current-day ocean. Results and Discussion: Released volatiles for the proto-ocean are predicted to form a ~77.9 km deep layer around Europa. With the addition of the further volatiles, the current-day ocean would be ~84.8 km deep. The extraction of pyrrhotite, which occurs after proto-ocean formation, would form a metallic core of ~271.5 km radius by the current day. The current-day ocean depth and core radius predicted here agree with those inferred for current-day Europa based on observations [3]. The model predicts that both the proto- and current-day oceans would be rich in Na+, Cl-, and CO32-, which may explain the recent observation of NaCl and CO2 in geologically-disrupted regions of Europa’s surface [10, 11]. Large concentrations of NH3 and NH4+ are predicted for both the proto- and current-day oceans, despite the lack of any clear detection of nitrogen species on the surface. However, this abundance may be explained by the absence of thermodynamic data for solid nitrogen-bearing phases in the model resulting in an overestimation of nitrogen release during metamorphism (mainly as NH3). A key difference between the proto- and current-day oceans is their HS- concentration, where the current-day ocean has only ~0.2% that of the proto-ocean. This is due to the addition of the iron-rich Stage 2 volatiles to the proto-ocean causing the precipitation of pyrite (removing HS- from solution). Conclusion: We find that Europa’s ocean composition would have varied over time as a result of continued prograde metamorphism, with particular changes in HS- concentration. The significant decrease in HS- content could affect the potential for energy generation by sulfide-oxidising microbes in the current-day ocean and, thus, would have implications for Europa’s continuous habitability. References: [1] Běhounková M. et al. (2021) Geophys. Res. Lett., 48. [2] Melwani Daswani M. et al. (2021) Geophys. Res. Lett., 48. [3] Trinh K. T. et al. (2023) Sci. Adv., 9, eadf3955. [4] Desch S. J. et al. (2018), ApJS. 238, 11. [5] Howard K. T. et al. (2011) Geochim. Cosmochim. Acta., 75, 2735–2751. [6] Fanale F. P. et al. (2001) J. Geophys. Res., 106, 14595–14600. [7] Mayne M. J. et al. (2016), J. Metamorph. Geol., 34, 663–682. [8] Connolly J. A. D. (2005) Earth Planet. Sci. Lett., 236, 524–541. [9] Reed M. H. et al. (2010) J. Chem. Inf. Model., 53, 1689–1699. [10] Trumbo S. K. et al. (2019) Sci. Adv., 5, eaaw7123. [11] Villanueva G. L. et al. (2023) Science., 381, 1305–1308. Part of this work was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under contract to the National Aeronautics and Space Administration

Gross-Neveu Models, Nonlinear Dirac Equations, Surfaces and Strings

Recent studies of the thermodynamic phase diagrams of the Gross-Neveu model (GN2), and its chiral cousin, the NJL2 model, have shown that there are phases with inhomogeneous crystalline condensates. These (static) condensates can be found analytically because the relevant Hartree-Fock and gap equations can be reduced to the nonlinear Schr\"odinger equation, whose deformations are governed by the mKdV and AKNS integrable hierarchies, respectively. Recently, Thies et al have shown that time-dependent Hartree-Fock solutions describing baryon scattering in the massless GN2 model satisfy the Sinh-Gordon equation, and can be mapped directly to classical string solutions in AdS3. Here we propose a geometric perspective for this result, based on the generalized Weierstrass spinor representation for the embedding of 2d surfaces into 3d spaces, which explains why these well-known integrable systems underlie these various Gross-Neveu gap equations, and why there should be a connection to classical string theory solutions. This geometric viewpoint may be useful for higher dimensional models, where the relevant integrable hierarchies include the Davey-Stewartson and Novikov-Veselov systems.Comment: 27 pages, 1 figur

Pch2 Links Chromosome Axis Remodeling at Future Crossover Sites and Crossover Distribution during Yeast Meiosis

Segregation of homologous chromosomes during meiosis I depends on appropriately positioned crossovers/chiasmata. Crossover assurance ensures at least one crossover per homolog pair, while interference reduces double crossovers. Here, we have investigated the interplay between chromosome axis morphogenesis and non-random crossover placement. We demonstrate that chromosome axes are structurally modified at future crossover sites as indicated by correspondence between crossover designation marker Zip3 and domains enriched for axis ensemble Hop1/Red1. This association is first detected at the zygotene stage, persists until double Holliday junction resolution, and is controlled by the conserved AAA+ ATPase Pch2. Pch2 further mediates crossover interference, although it is dispensable for crossover formation at normal levels. Thus, interference appears to be superimposed on underlying mechanisms of crossover formation. When recombination-initiating DSBs are reduced, Pch2 is also required for viable spore formation, consistent with further functions in chiasma formation. pch2Δ mutant defects in crossover interference and spore viability at reduced DSB levels are oppositely modulated by temperature, suggesting contributions of two separable pathways to crossover control. Roles of Pch2 in controlling both chromosome axis morphogenesis and crossover placement suggest linkage between these processes. Pch2 is proposed to reorganize chromosome axes into a tiling array of long-range crossover control modules, resulting in chiasma formation at minimum levels and with maximum spacing

Budding yeast ATM/ATR control meiotic double-strand break (DSB) levels by down-regulating Rec114, an essential component of the DSB-machinery

An essential feature of meiosis is Spo11 catalysis of programmed DNA double strand breaks (DSBs). Evidence suggests that the number of DSBs generated per meiosis is genetically determined and that this ability to maintain a pre-determined DSB level, or "DSB homeostasis", might be a property of the meiotic program. Here, we present direct evidence that Rec114, an evolutionarily conserved essential component of the meiotic DSB-machinery, interacts with DSB hotspot DNA, and that Tel1 and Mec1, the budding yeast ATM and ATR, respectively, down-regulate Rec114 upon meiotic DSB formation through phosphorylation. Mimicking constitutive phosphorylation reduces the interaction between Rec114 and DSB hotspot DNA, resulting in a reduction and/or delay in DSB formation. Conversely, a non-phosphorylatable rec114 allele confers a genome-wide increase in both DSB levels and in the interaction between Rec114 and the DSB hotspot DNA. These observations strongly suggest that Tel1 and/or Mec1 phosphorylation of Rec114 following Spo11 catalysis down-regulates DSB formation by limiting the interaction between Rec114 and DSB hotspots. We also present evidence that Ndt80, a meiosis specific transcription factor, contributes to Rec114 degradation, consistent with its requirement for complete cessation of DSB formation. Loss of Rec114 foci from chromatin is associated with homolog synapsis but independent of Ndt80 or Tel1/Mec1 phosphorylation. Taken together, we present evidence for three independent ways of regulating Rec114 activity, which likely contribute to meiotic DSBs-homeostasis in maintaining genetically determined levels of breaks