Exotic pest insects: another perspective on coffee and conservation

Research on crop systems and biodiversity conservation in the tropics has mainly been concerned with how low to mid intensity agricultural systems can benefit from adjacent natural habitats by receiving ecosystem services from natural biodiversity. One intensively studied crop in this framework is coffee. Positive effects are relatively easy to quantify by comparing coffee yield and by recording native species diversity. However, a largely overlooked issue is how agricultural areas affect native organisms in adjacent natural habitats, for example through movement of pest species that could impose a risk of degrading these habitats. We give an example from Mauritius, where an introduced coffee pest severely reduces the reproductive success of a threatened endemic plant species. We argue that such effects may be more common than suggested by the literature, especially when crop and native plants are congeneric. In the long term, such negative effects may degrade natural habitats, thereby causing ecosystem services derived from these habitats to declin

Two-dimensional colloidal fluids exhibiting pattern formation

Fluids with competing short range attraction and long range repulsive interactions between the particles can exhibit a variety of microphase separated structures. We develop a lattice-gas (generalised Ising) model and analyse the phase diagram using Monte Carlo computer simulations and also with density functional theory (DFT). The DFT predictions for the structures formed are in good agreement with the results from the simulations, which occur in the portion of the phase diagram where the theory predicts the uniform fluid to be linearly unstable. However, the mean-field DFT does not correctly describe the transitions between the different morphologies, which the simulations show to be analogous to micelle formation. We determine how the heat capacity varies as the model parameters are changed. There are peaks in the heat capacity at state points where the morphology changes occur. We also map the lattice model onto a continuum DFT that facilitates a simplification of the stability analysis of the uniform fluid.Comment: 13 pages, 15 figure

Seed Dispersal and Establishment of Endangered Plants on Oceanic Islands: The Janzen-Connell Model, and the Use of Ecological Analogues

BACKGROUND: The Janzen-Connell model states that plant-specific natural enemies may have a disproportionately large negative effect on progeny close to maternal trees. The majority of experimental and theoretical studies addressing the Janzen-Connell model have explored how it can explain existing patterns of species diversity in tropical mainland areas. Very few studies have investigated how the model's predictions apply to isolated oceanic islands, or to the conservation management of endangered plants. Here, we provide the first experimental investigation of the predictions of the Janzen-Connell model on an oceanic island, in a conservation context. In addition, we experimentally evaluate the use of ecological analogue animals to resurrect the functional component of extinct frugivores that could have dispersed seeds away from maternal trees. METHODOLOGY/PRINCIPAL FINDINGS: In Mauritius, we investigated seed germination and seedling survival patterns of the critically endangered endemic plant Syzygium mamillatum (Myrtaceae) in relation to proximity to maternal trees. We found strong negative effects of proximity to maternal trees on growth and survival of seedlings. We successfully used giant Aldabran tortoises as ecological analogues for extinct Mauritian frugivores. Effects of gut-passage were negative at the seed germination stage, but seedlings from gut-passed seeds grew taller, had more leaves, and suffered less damage from natural enemies than any of the other seedlings. CONCLUSIONS/SIGNIFICANCE: We provide the first experimental evidence of a distance-dependent Janzen-Connell effect on an oceanic island. Our results potentially have serious implications for the conservation management of rare plant species on oceanic islands, which harbour a disproportionately large fraction of the world's endemic and endangered plants. Furthermore, in contrast to recent controversy about the use of non-indigenous extant megafauna for re-wilding projects in North America and elsewhere, we argue that Mauritius and other oceanic islands are ideal study systems in which to empirically explore the use of ecological analogue species in restoration ecology

An expectation-maximization framework for comprehensive prediction of isoform-specific functions.

MOTIVATION: Advances in RNA sequencing technologies have achieved an unprecedented accuracy in the quantification of mRNA isoforms, but our knowledge of isoform-specific functions has lagged behind. There is a need to understand the functional consequences of differential splicing, which could be supported by the generation of accurate and comprehensive isoform-specific gene ontology annotations. RESULTS: We present isoform interpretation, a method that uses expectation-maximization to infer isoform-specific functions based on the relationship between sequence and functional isoform similarity. We predicted isoform-specific functional annotations for 85 617 isoforms of 17 900 protein-coding human genes spanning a range of 17 430 distinct gene ontology terms. Comparison with a gold-standard corpus of manually annotated human isoform functions showed that isoform interpretation significantly outperforms state-of-the-art competing methods. We provide experimental evidence that functionally related isoforms predicted by isoform interpretation show a higher degree of domain sharing and expression correlation than functionally related genes. We also show that isoform sequence similarity correlates better with inferred isoform function than with gene-level function. AVAILABILITY AND IMPLEMENTATION: Source code, documentation, and resource files are freely available under a GNU3 license at https://github.com/TheJacksonLaboratory/isopretEM and https://zenodo.org/record/7594321

Photofragment Translational Spectroscopy Studies of H Atom Loss Following Ultraviolet Photoexcitation of Methimazole in the Gas Phase

The ultraviolet (UV) photodissociation of gas-phase methimazole has been investigated by H Rydberg atom photofragment translational spectroscopy methods at many wavelengths in the range of 222.5–275 nm and by complementary electronic structure calculations. Methimazole is shown to exist predominantly as the thione tautomer, 1-methyl-2­(3H)-imidazolinethione, rather than the commonly given thiol form, 2-mercapto-1-methylimidazole. The UV absorption spectrum of methimazole is dominated by the S4 ← S0 transition of the thione tautomer, which involves electron promotion from an a′ (py) orbital localized on the sulfur atom to a σ* orbital localized around the N–H bond. Two H atom formation pathways are identified following UV photoexcitation. One, involving prompt, excited-state N–H bond fission, yields vibrationally cold but rotationally excited methimazolyl (Myl) radicals in their first excited (Ã) electronic state. The second yields H atoms with an isotropic recoil velocity distribution peaking at low kinetic energies but extending to the energetic limit allowed by energy conservation given a ground-state dissociation energy D0(Myl–H) ∼24 000 cm–1. These latter H atoms are attributed to the unimolecular decay of highly vibrationally excited S0 parent molecules. The companion electronic structure calculations provide rationales for both fragmentation pathways and the accompanying product energy disposals and highlight similarities and differences between the UV photochemistry of methimazole and that of other azoles (e.g., imidazole) and with molecules like thiourea and thiouracil that contain similar N–CS motifs

5-hydroxytryptamine (5-HT) cellular sequestration during chronic exposure delays 5-HT₃ receptor resensitization due to Its subsequent release

The serotonergic synapse is dynamically regulated by serotonin (5-hydroxytryptamine (5-HT)) with elevated levels leading to the down-regulation of the serotonin transporter and a variety of 5-HT receptors, including the 5-HT type-3 (5-HT(3)) receptors. We report that recombinantly expressed 5-HT(3) receptor binding sites are reduced by chronic exposure to 5-HT (IC(50) of 154.0 ± 45.7 μm, t(½) = 28.6 min). This is confirmed for 5-HT(3) receptor-induced contractions in the guinea pig ileum, which are down-regulated after chronic, but not acute, exposure to 5-HT. The loss of receptor function does not involve endocytosis, and surface receptor levels are unaltered. The rate and extent of down-regulation is potentiated by serotonin transporter function (IC(50) of 2.3 ± 1.0 μm, t(½) = 3.4 min). Interestingly, the level of 5-HT uptake correlates with the extent of down-regulation. Using TX-114 extraction, we find that accumulated 5-HT remains soluble and not membrane-bound. This cytoplasmically sequestered 5-HT is readily releasable from both COS-7 cells and the guinea pig ileum. Moreover, the 5-HT level released is sufficient to prevent recovery from receptor desensitization in the guinea pig ileum. Together, these findings suggest the existence of a novel mechanism of down-regulation where the chronic release of sequestered 5-HT prolongs receptor desensitization