A reference genome for the long-term kleptoplast-retaining sea slug Elysia crispata morphotype clarki

Several species of sacoglossan sea slugs possess the incredible ability to sequester chloroplasts from the algae they consume. These "photosynthetic animals" incorporate stolen chloroplasts, called kleptoplasts, into the epithelial cells of tubules that extend from their digestive tracts throughout their bodies. The mechanism by which these slugs maintain functioning kleptoplasts in the absence of an algal nuclear genome is unknown. Here, we report a draft genome of the sacoglossan slug Elysia crispata morphotype clarki, a morphotype native to the Florida Keys that can retain photosynthetically active kleptoplasts for several months without feeding. We used a combination of Oxford Nanopore Technologies long reads and Illumina short reads to produce a 786-Mb assembly (N50 = 0.459 Mb) containing 68,514 predicted protein-coding genes. A phylogenetic analysis found no evidence of horizontal acquisition of genes from algae. We performed gene family and gene expression analyses to identify E. crispata genes unique to kleptoplast-containing slugs that were more highly expressed in fed versus unfed developmental life stages. Consistent with analyses in other kleptoplastic slugs, our investigation suggests that genes encoding lectin carbohydrate-binding proteins and those involved in regulation of reactive oxygen species and immunity may play a role in kleptoplast retention. Lastly, we identified four polyketide synthase genes that could potentially encode proteins producing UV- and oxidation-blocking compounds in slug cell membranes. The genome of E. crispata is a quality resource that provides potential targets for functional analyses and enables further investigation into the evolution and mechanisms of kleptoplasty in animals.

Ecological generalism drives hyperdiversity of secondary metabolite gene clusters in xylarialean endophytes

Although secondary metabolites are typically associated with competitive or pathogenic interactions, the high bioactivity of endophytic fungi in the Xylariales, coupled with their abundance and broad host ranges spanning all lineages of land plants and lichens, suggests that enhanced secondary metabolism might facilitate symbioses with phylogenetically diverse hosts. Here, we examined secondary metabolite gene clusters (SMGCs) across 96 Xylariales genomes in two clades (Xylariaceae s.l. and Hypoxylaceae), including 88 newly sequenced genomes of endophytes and closely related saprotrophs and pathogens. We paired genomic data with extensive metadata on endophyte hosts and substrates, enabling us to examine genomic factors related to the breadth of symbiotic interactions and ecological roles. All genomes contain hyperabundant SMGCs; however, Xylariaceae have increased numbers of gene duplications, horizontal gene transfers (HGTs) and SMGCs. Enhanced metabolic diversity of endophytes is associated with a greater diversity of hosts and increased capacity for lignocellulose decomposition. Our results suggest that, as host and substrate generalists, Xylariaceae endophytes experience greater selection to diversify SMGCs compared with more ecologically specialised Hypoxylaceae species. Overall, our results provide new evidence that SMGCs may facilitate symbiosis with phylogenetically diverse hosts, highlighting the importance of microbial symbioses to drive fungal metabolic diversity.

The case against memory consolidation in REM sleep

We present evidence disputing the hypothesis that memories are processed or consolidated in REM sleep. A review of REM deprivation (REMD) studies in animals shows these reports to be about equally divided in showing that REMD does, or does not, disrupt learning/memory. The studies supporting a relationship between REM sleep and memory have been strongly criticized for the confounding effects of very stressful REM deprivation techniques. The three major classes of antidepressant drugs, monoamine oxidase inhibitors (MAOIs), tricyclic antidepressants (TCAs), and selective serotonin reuptake inhibitors (SSRIs), profoundly suppress REM sleep. The MAOIs virtually abolish REM sleep, and the TCAs and SSRIs have been shown to produce immediate (40-85%) and sustained (30-50%) reductions in REM sleep. Despite marked suppression of REM sleep, these classes of antidepressants on the whole do not disrupt learning/memory. There have been a few reports of patients who have survived bilateral lesions of the pons with few lingering complications. Although these lesions essentially abolished REM sleep, the patients reportedly led normal lives. Recent functional imaging studies in humans have revealed patterns of brain activity in REM sleep that are consistent with dream processes but not with memory consolidation. We propose that the primary function of REM sleep is to provide periodic endogenous stimulation to the brain which serves to maintain requisite levels of central nervous system (CNS) activity throughout sleep. REM is the mechanism used by the brain to promote recovery from sleep. We believe that the cumulative evidence indicates that REM sleep serves no role in the processing or consolidation of memory.

Bistability in the perception of motion and stationarity: effects of temporal asymmetry

Evidence for bistability in the perception of motion and stationarity was obtained for a displaced dot-figure embedded in a background of randomly moving noise dots. In the temporal symmetry condition, the figure was presented for the same duration in its two locations; either figure motion or random motion was perceived, depending on the number of noise dots. In the temporal asymmetry condition, the figure was presented for different durations in its two locations; figure motion, a single, stationary figure in a fixed position, or random noise was perceived, again depending on the number of noise dots. Competition between these percepts was established by an analysis of switching rates and by an experiment demonstrating the presence of hysteresis as noise levels were gradually increased and decreased across the figure-motion and figure-stationarity boundaries. This evidence for bistability in the perception of figure motion and figure stationarity (one or the other, but not both, was perceived for the same stimulus) suggested the presence of strong inhibitory competition between motion- and position-detecting mechanisms.

Cooperative interactions and the perception of motion and stationarity for directionally ambiguous apparent-motion stimuli

Evidence is reported that stationarity rather than motion can be perceived for displaced stimuli, not because of insufficient motion energy for the stimulus to activate individual motion detectors, but because of cooperative interactions that actively suppress the perception of motion. A long row of evenly spaced dots was presented in counterphase; the dots presented during each 180 ms frame were located midway between the dots presented during the previous frame. When either a blank interval as brief as 15 ms was inserted between successive frames or the luminance polarity of the dots was reversed on successive frames, the unidirectional motion pattern perceived for small interdot distances (small displacements) was replaced by the perception of stationarity. However, when under the same conditions a single dot was displaced over the same small distances, motion rather than stationarity was perceived. The contrasting results for the long row of displaced dots and the single displaced dot indicated that when the activation of motion detectors is weakened (by nonzero interframe intervals and/or the reversal of luminance polarity), the perception of motion can be actively suppressed by the collective effects of inhibitory interactions among the large ensemble of detectors that is activated by the long row of dots.

Context effects on perceived position: sustained and transient temporal influences on spatial interactions

The effects of sustained and transient responses to inducing lines on the perceived position of nearby test lines were measured as constant errors in the vernier alignment of the test lines. The sustained response to the continued presence of the inducing lines had no effect on the perceived position of the test lines for very small inducing/test-line distances, and a repulsive effect for larger distances. Transient responses to the onset of the inducing lines had attractive effects for small distances, whereas transient responses to the offset of the inducing lines had repulsive effects for all distances tested. Attraction and repulsion effects on perceived position are accounted for by facilitating and inhibiting interactions that influence the relative sensitivities of an ensemble of position-selective detecting units.