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A novel meroterpenoid cabagranin D was isolated with related neolignans cabagranins A–C from the leaves ofPiper cabagranum(Costa Rica). Cabagranins A–C represent the first examples of 3,3′-neolignans isolated from the plant genusPiper, and the meroterpenoid cabagranin D displays an unprecedented Diels–Alder conjugate of an unsubstituted phenylpropenone and α-phellandrene. Details of the full structural elucidation of these compounds and a discussion of their potential biosynthetic relationships are presented.

 

Thiolutin is a natural product transcription inhibitor with an unresolved mode of action. Thiolutin and the related dithiolopyrrolone holomycin chelate Zn2+ and previous studies have concluded that RNA Polymerase II (Pol II) inhibition in vivo is indirect. Here, we present chemicogenetic and biochemical approaches to investigate thiolutin's mode of action in Saccharomyces cerevisiae. We identify mutants that alter sensitivity to thiolutin. We provide genetic evidence that thiolutin causes oxidation of thioredoxins in vivo and that thiolutin both induces oxidative stress and interacts functionally with multiple metals including Mn2+ and Cu2+, and not just Zn2+. Finally, we show direct inhibition of RNA polymerase II (Pol II) transcription initiation by thiolutin in vitro in support of classical studies that thiolutin can directly inhibit transcription in vitro. Inhibition requires both Mn2+ and appropriate reduction of thiolutin as excess DTT abrogates its effects. Pause prone, defective elongation can be observed in vitro if inhibition is bypassed. Thiolutin effects on Pol II occupancy in vivo are widespread but major effects are consistent with prior observations for Tor pathway inhibition and stress induction, suggesting that thiolutin use in vivo should be restricted to studies on its modes of action and not as an experimental tool.

 

Understanding the strong interaction dynamics that govern the emergence of hadron mass (EHM) represents a challenging open problem in the Standard Model. In this paper we describe new opportunities for gaining insight into EHM from results on nucleon resonance (N*) electroexcitation amplitudes (i.e., γvpN* electrocouplings) in the mass range up to 1.8 GeV for virtual photon four-momentum squared (i.e., photon virtualities Q2) up to 7.5 GeV2 available from exclusive meson electroproduction data acquired during the 6-GeV era of experiments at Jefferson Laboratory (JLab). These results, combined with achievements in the use of continuum Schwinger function methods (CSMs), offer new opportunities for charting the momentum dependence of the dressed quark mass from results on the Q2-evolution of the γvpN* electrocouplings. This mass function is one of the three pillars of EHM and its behavior expresses influences of the other two, viz. the running gluon mass and momentum-dependent effective charge. A successful description of the Δ(1232)3/2+ and N(1440)1/2+ electrocouplings has been achieved using CSMs with, in both cases, common momentum-dependent mass functions for the dressed quarks, for the gluons, and the same momentum-dependent strong coupling. The properties of these functions have been inferred from nonperturbative studies of QCD and confirmed, e.g., in the description of nucleon and pion elastic electromagnetic form factors. Parameter-free CSM predictions for the electrocouplings of the Δ(1600)3/2+ became available in 2019. The experimental results obtained in the first half of 2022 have confirmed the CSM predictions. We also discuss prospects for these studies during the 12-GeV era at JLab using the CLAS12 detector, with experiments that are currently in progress, and canvass the physics motivation for continued studies in this area with a possible increase of the JLab electron beam energy up to 22 GeV. Such an upgrade would finally enable mapping of the dressed quark mass over the full range of distances (i.e., quark momenta) where the dominant part of hadron mass and N* structure emerge in the transition from the strongly coupled to perturbative QCD regimes. 

In situ oxygen analysis of garnet in eclogite and related rocks is increasingly being used to probe the composition of subduction fluids. However, in many cases, these samples contain textural signs of both fluid flow and retrograde metamorphism, some of which may take place outside the garnet stability field. In order to test the connection between polymetamorphism and fluid infiltration, rutile rimmed by titanite from high‐grade tectonic blocks of the Franciscan Formation (California, USA) was analysed for oxygen isotope ratios and trace element concentrations. Zirconium concentrations in rutile yield temperatures of ~600°C for eclogite and hornblende eclogite from three well‐studied localities (Junction School, Tiburon and Ward Creek). Rutile trace element concentrations are generally low and consistent with a mafic protolith. Titanite surrounding rutile has inherited much of its trace element content from rutile, and Zr‐in‐titanite temperatures are spuriously high. Titanite in rutile‐free samples (blueschist and eclogite from Jenner beach) have similar compositions suggesting that they were formed at the expense of rutile as well. Oxygen isotope ratios from rutile and titanite in the same sample are fortuitously similar, indicating disequilibrium between these minerals, which formed at different times and temperatures but in equilibrium with the same oxygen reservoir. Rutile in blocks with garnets zoned in oxygen isotopes are generally in equilibrium with the rims rather than the cores. Slow oxygen diffusion in rutile and the low temperatures of formation require that rutile recrystallized after fluid interaction and before blueschist facies metamorphism. External fluid interaction of Franciscan eclogites took place near the peak of metamorphism.

 

Recent mass loss from ice sheets and ice shelves is now persistent and prolonged enough that it impacts downstream oceanographic conditions. To demonstrate this, we use an ensemble of coupled GISS‐E2.1‐G simulations forced with historical estimates of anomalous freshwater, in addition to other climate forcings, from 1990 through 2019. There are detectable differences in zonal‐mean sea surface temperatures (SST) and sea ice in the Southern Ocean, and in regional sea level around Antarctica and in the western North Atlantic. These impacts mostly improve the model's representation of historical changes, including reversing the forced trends in Antarctic sea ice. The changes in SST may have implications for estimates of the SST pattern effect on climate sensitivity and for cloud feedbacks. We conclude that the changes are sufficiently large that model groups should strive to include more accurate estimates of these drivers in all‐forcing historical simulations in future coupled model intercomparisons.

 

Plant–insect interactions are common and important in basic and applied biology. Trait and genetic variation can affect the outcome and evolution of these interactions, but the relative contributions of plant and insect genetic variation and how these interact remain unclear and are rarely subject to assessment in the same experimental context. Here, we address this knowledge gap using a recent host-range expansion onto alfalfa by the Melissa blue butterfly. Common garden rearing experiments and genomic data show that caterpillar performance depends on plant and insect genetic variation, with insect genetics contributing to performance earlier in development and plant genetics later. Our models of performance based on caterpillar genetics retained predictive power when applied to a second common garden. Much of the plant genetic effect could be explained by heritable variation in plant phytochemicals, especially saponins, peptides, and phosphatidyl cholines, providing a possible mechanistic understanding of variation in the species interaction. We find evidence of polygenic, mostly additive effects within and between species, with consistent effects of plant genotype on growth and development across multiple butterfly species. Our results inform theories of plant–insect coevolution and the evolution of diet breadth in herbivorous insects and other host-specific parasites. 

The R programming language is one of the most widely used programming languages for transforming raw genomic datasets into meaningful biological conclusions through analysis and visualization, which has been largely facilitated by infrastructure and tools developed by the Bioconductor project. However, existing plotting packages rely on relative positioning and sizing of plots, which is often sufficient for exploratory analysis but is poorly suited for the creation of publication-quality multi-panel images inherent to scientific manuscript preparation.

We present plotgardener, a coordinate-based genomic data visualization package that offers a new paradigm for multi-plot figure generation in R. Plotgardener allows precise, programmatic control over the placement, esthetics and arrangements of plots while maximizing user experience through fast and memory-efficient data access, support for a wide variety of data and file types, and tight integration with the Bioconductor environment. Plotgardener also allows precise placement and sizing of ggplot2 plots, making it an invaluable tool for R users and data scientists from virtually any discipline.

Package: https://bioconductor.org/packages/plotgardener, Code: https://github.com/PhanstielLab/plotgardener, Documentation: https://phanstiellab.github.io/plotgardener/.

Supplementary data are available at Bioinformatics online.