A reference genome for ecological restoration of the sunflower sea star, Pycnopodia helianthoides.

Wildlife diseases, such as the sea star wasting (SSW) epizootic that outbroke in the mid-2010s, appear to be associated with acute and/or chronic abiotic environmental change; dissociating the effects of different drivers can be difficult. The sunflower sea star, Pycnopodia helianthoides, was the species most severely impacted during the SSW outbreak, which overlapped with periods of anomalous atmospheric and oceanographic conditions, and there is not yet a consensus on the cause(s). Genomic data may reveal underlying molecular signatures that implicate a subset of factors and, thus, clarify past events while also setting the scene for effective restoration efforts. To advance this goal, we used Pacific Biosciences HiFi long sequencing reads and Dovetail Omni-C proximity reads to generate a highly contiguous genome assembly that was then annotated using RNA-seq-informed gene prediction. The genome assembly is 484 Mb long, with contig N50 of 1.9 Mb, scaffold N50 of 21.8 Mb, BUSCO completeness score of 96.1%, and 22 major scaffolds consistent with prior evidence that sea star genomes comprise 22 autosomes. These statistics generally fall between those of other recently assembled chromosome-scale assemblies for two species in the distantly related asteroid genus Pisaster. These novel genomic resources for P. helianthoides will underwrite population genomic, comparative genomic, and phylogenomic analyses-as well as their integration across scales-of SSW and environmental stressors.

Embodying cognitive ethology.

Cognitive psychology considers the environment as providing information, not affecting fundamental information processes. Thus, cognitive psychology's traditional paradigms study responses to precisely timed stimuli in controlled environments. However, new research demonstrates the environment does influence cognitive processes and offers cognitive psychology new methods. The authors examine one such proposal: cognitive ethology. Cognitive ethology improves cognitive psychology's ecological validity through first drawing inspiration from robust phenomena in the real world, then moving into the lab to test those phenomena. To support such methods, cognitive ethologists appeal to embodied cognition, or 4E cognition, for its rich relationships between agents and environments. However, the authors note while cognitive ethology focuses on new methods (epistemology) inspired by embodied cognition, it preserves most traditional assumptions about cognitive processes (ontology). But embodied cognition-particularly its radical variants-also provides strong ontological challenges to cognitive psychology, which work against cognitive ethology. The authors argue cognitive ethology should align with the ontology of less radical embodied cognition, which produces epistemological implications, offering alternative methodologies. For example, cognitive ethology can explore differences between real-world and lab studies to fully understand how cognition depends on environments.

Species' attributes predict the relative magnitude of ecological and genetic recovery following mass mortality.

Theoretically, species' characteristics should allow estimation of dispersal potential and, in turn, explain levels of population genetic differentiation. However, a mismatch between traits and genetic patterns is often reported for marine species, and interpreted as evidence that life-history traits do not influence dispersal. Here, we couple ecological and genomic methods to test the hypothesis that species with attributes favouring greater dispersal potential-e.g., longer pelagic duration, higher fecundity and larger population size-have greater realized dispersal overall. We used a natural experiment created by a large-scale and multispecies mortality event which created a "clean slate" on which to study recruitment dynamics, thus simplifying a usually complex problem. We surveyed four species of differing dispersal potential to quantify the abundance and distribution of recruits and to genetically assign these recruits to probable parental sources. Species with higher dispersal potential recolonized a broader extent of the impacted range, did so more quickly and recovered more genetic diversity than species with lower dispersal potential. Moreover, populations of taxa with higher dispersal potential exhibited more immigration (71%-92% of recruits) than taxa with lower dispersal potential (17%-44% of recruits). By linking ecological with genomic perspectives, we demonstrate that a suite of interacting life-history and demographic attributes do influence species' realized dispersal and genetic neighbourhoods. To better understand species' resilience and recovery in this time of global change, integrative eco-evolutionary approaches are needed to more rigorously evaluate the effect of dispersal-linked attributes on realized dispersal and population genetic differentiation.

A chromosome-level reference genome for the giant pink sea star, Pisaster brevispinus, a species severely impacted by wasting.

Efforts to protect the ecologically and economically significant California Current Ecosystem from global change will greatly benefit from data about patterns of local adaptation and population connectivity. To facilitate that work, we present a reference-quality genome for the giant pink sea star, Pisaster brevispinus, a species of ecological importance along the Pacific west coast of North America that has been heavily impacted by environmental change and disease. We used Pacific Biosciences HiFi long sequencing reads and Dovetail Omni-C proximity reads to generate a highly contiguous genome assembly of 550 Mb in length. The assembly contains 127 scaffolds with a contig N50 of 4.6 Mb and a scaffold N50 of 21.4 Mb; the BUSCO completeness score is 98.70%. The P. brevispinus genome assembly is comparable to the genome of the congener species P. ochraceus in size and completeness. Both Pisaster assemblies are consistent with previously published karyotyping results showing sea star genomes are organized into 22 autosomes. The reference genome for P. brevispinus is an important first step toward the goal of producing a comprehensive, population genomics view of ecological and evolutionary processes along the California coast. This resource will help scientists, managers, and policy makers in their task of understanding and protecting critical coastal regions from the impacts of global change.

Reference genome for the California ribbed mussel, Mytilus californianus, an ecosystem engineer.

The California ribbed mussel, Mytilus californianus, is an ecosystem engineer crucial for the survival of many marine species inhabiting the intertidal zone of California. Here, we describe the first reference genome for M. californianus and compare it to previously published genomes from three other Mytilus species: M. edulis, M. coruscus, and M. galloprovincialis. The M. californianus reference genome is 1.65 Gb in length, with N50 sequence length of 118 Mb, and an estimated 86.0% complete single copy genes. Compared with the other three Mytilus species, the M. californianus genome assembly is the longest, has the highest N50 value, and the highest percentage complete single copy genes. This high-quality genome assembly provides a foundation for population genetic analyses that will give insight into future conservation work along the coast of California.

Preliminary Evaluation of the Effect of Mechanotactile Feedback Location on Myoelectric Prosthesis Performance Using a Sensorized Prosthetic Hand.

A commonly cited reason for the high abandonment rate of myoelectric prostheses is a lack of grip force sensory feedback. Researchers have attempted to restore grip force sensory feedback by stimulating the residual limb's skin surface in response to the prosthetic hand's measured grip force. Recent work has focused on restoring natural feedback to the missing digits directly through invasive surgical procedures. However, the functional benefit of utilizing somatotopically matching feedback has not been evaluated. In this paper, we propose an experimental protocol centered on a fragile object grasp and lift task using a sensorized myoelectric prosthesis to evaluate sensory feedback techniques. We formalized a suite of outcome measures related to task success, timing, and strategy. A pilot study (n = 3) evaluating the effect of utilizing a somatotopically accurate feedback stimulation location in able-bodied participants was conducted to evaluate the feasibility of the standardized platform, and to inform future studies on the role of feedback stimulation location in prosthesis use. Large between-participant effect sizes were observed in all outcome measures, indicating that the feedback location likely plays a role in myoelectric prosthesis performance. The success rate decreased, and task timing and task focus metrics increased, when using somatotopically-matched feedback compared to non-somatotopically-matched feedback. These results were used to conduct a power analysis, revealing that a sample size of n = 8 would be sufficient to achieve significance in all outcome measures.

Landscape analyses using eDNA metabarcoding and Earth observation predict community biodiversity in California.

Ecosystems globally are under threat from ongoing anthropogenic environmental change. Effective conservation management requires more thorough biodiversity surveys that can reveal system-level patterns and that can be applied rapidly across space and time. Using modern ecological models and community science, we integrate environmental DNA and Earth observations to produce a time snapshot of regional biodiversity patterns and provide multi-scalar community-level characterization. We collected 278 samples in spring 2017 from coastal, shrub, and lowland forest sites in California, a complex ecosystem and biodiversity hotspot. We recovered 16,118 taxonomic entries from eDNA analyses and compiled associated traditional observations and environmental data to assess how well they predicted alpha, beta, and zeta diversity. We found that local habitat classification was diagnostic of community composition and distinct communities and organisms in different kingdoms are predicted by different environmental variables. Nonetheless, gradient forest models of 915 families recovered by eDNA analysis and using BIOCLIM variables, Sentinel-2 satellite data, human impact, and topographical features as predictors, explained 35% of the variance in community turnover. Elevation, sand percentage, and photosynthetic activities (NDVI32) were the top predictors. In addition to this signal of environmental filtering, we found a positive relationship between environmentally predicted families and their numbers of biotic interactions, suggesting environmental change could have a disproportionate effect on community networks. Together, these analyses show that coupling eDNA with environmental predictors including remote sensing data has capacity to test proposed Essential Biodiversity Variables and create new landscape biodiversity baselines that span the tree of life.

Decimation by sea star wasting disease and rapid genetic change in a keystone species, Pisaster ochraceus.

Standing genetic variation enables or restricts a population's capacity to respond to changing conditions, including the extreme disturbances expected to increase in frequency and intensity with continuing anthropogenic climate change. However, we know little about how populations might respond to extreme events with rapid genetic shifts, or how population dynamics may influence and be influenced by population genomic change. We use a range-wide epizootic, sea star wasting disease, that onset in mid-2013 and caused mass mortality in Pisaster ochraceus to explore how a keystone marine species responded to an extreme perturbation. We integrated field surveys with restriction site-associated DNA sequencing data to (i) describe the population dynamics of mortality and recovery, and (ii) compare allele frequencies in mature P. ochraceus before the disease outbreak with allele frequencies in adults and new juveniles after the outbreak, to identify whether selection may have occurred. We found P. ochraceus suffered 81% mortality in the study region between 2012 and 2015, and experienced a concurrent 74-fold increase in recruitment beginning in late 2013. Comparison of pre- and postoutbreak adults revealed significant allele frequency changes at three loci, which showed consistent changes across the large majority of locations. Allele frequency shifts in juvenile P. ochraceus (spawned from premortality adults) were consistent with those seen in adult survivors. Such parallel shifts suggest detectable signals of selection and highlight the potential for persistence of this change in subsequent generations, which may influence the resilience of this keystone species to future outbreaks.

An initial comparative genomic autopsy of wasting disease in sea stars.

Beginning in 2013, sea stars throughout the Eastern North Pacific were decimated by wasting disease, also known as "asteroid idiopathic wasting syndrome" (AIWS) due to its elusive aetiology. The geographic extent and taxonomic scale of AIWS meant events leading up to the outbreak were heterogeneous, multifaceted, and oftentimes unobserved; progression from morbidity to death was rapid, leaving few tell-tale symptoms. Here, we take a forensic genomic approach to discover candidate genes that may help explain sea star wasting syndrome. We report the first genome and annotation for Pisaster ochraceus, along with differential gene expression (DGE) analyses in four size classes, three tissue types, and in symptomatic and asymptomatic individuals. We integrate nucleotide polymorphisms associated with survivors of the wasting disease outbreak, DGE associated with temperature treatments in P. ochraceus, and DGE associated with wasting in another asteroid Pycnopodia helianthoides. In P. ochraceus, we found DGE across all tissues, among size classes, and between asymptomatic and symptomatic individuals; the strongest wasting-associated DGE signal was in pyloric caecum. We also found previously identified outlier loci co-occur with differentially expressed genes. In cross-species comparisons of symptomatic and asymptomatic individuals, consistent responses distinguish genes associated with invertebrate innate immunity and chemical defence, consistent with context-dependent stress responses, defensive apoptosis, and tissue degradation. Our analyses thus highlight genomic constituents that may link suspected environmental drivers (elevated temperature) with intrinsic differences among individuals (age/size, alleles associated with susceptibility) that elicit organismal responses (e.g., coelomocyte proliferation) and manifest as sea star wasting mass mortality.

Direct modifications of the cyclic peptide Polymyxin B leading to analogues with enhanced in vitro antibacterial activity.

Synthetic modifications have been made directly to the cyclic peptide core of polymyxin B, enabling the further understanding of structure activity relationships of this antimicrobial peptide. Such modified polymyxins are also substrates for enzymic hydrolysis, enabling the synthesis of a variety of semi-synthetic analogues, resulting in compounds with increased in vitro antibacterial activity.

Microbes and macro-invertebrates show parallel ß-diversity but contrasting α-diversity patterns in a marine natural experiment.

Documenting ecological patterns across spatially, temporally and taxonomically diverse ecological communities is necessary for a general understanding of the processes shaping biodiversity. A major gap in our understanding remains the comparison of diversity patterns across a broad spectrum of evolutionarily and functionally diverse organisms, particularly in the marine realm. Here, we aim to narrow this gap by comparing the diversity patterns of free-living microbes and macro-invertebrates across a natural experiment provided by the marine lakes of Palau: geographically discrete and environmentally heterogeneous bodies of seawater with comparable geological and climatic history, and a similar regional species pool. We find contrasting patterns of α-diversity but remarkably similar patterns of ß-diversity between microbial and macro-invertebrate communities among lakes. Pairwise dissimilarities in community composition among lakes are positively correlated between microbes and macro-invertebrates, and influenced to a similar degree by marked gradients in oxygen concentration and salinity. Our findings indicate that a shared spatio-temporal and environmental context may result in parallel patterns of ß-diversity in microbes and macro-invertebrates, in spite of key trait differences between these organisms. This raises the possibility that parallel processes also influence transitions among regional biota across the tree of life, at least in the marine realm.

Introducing GIST and Dieulafoy - Think of Them in GI Bleeding and Anemia.

Common presentations of gastrointestinal bleeding include hematemesis, melena, and history of dizziness, fatigue, or syncope; yet, bleeds may present in many uncommon ways. This review discusses two cases of gastrointestinal bleeds (GIBs) in middle-aged female patients who presented with anemia and recurrent unexplained GIBs. Both patients were misdiagnosed for several years before the cause of their bleeding was established. Dieulafoy lesion is said to be rare, although its precise incidence is difficult to establish due to its anatomically inaccessible location, small size, and lack of symptoms prior to presentation. This condition can result in gastrointestinal hemorrhage and quickly pose life-threatening complications. Gastrointestinal stromal tumors (GISTs) are likewise difficult to diagnose due to their location in the submucosa and lack of good diagnostic tools. Depending on tumor size, location, and spread, GISTs can have a poor prognosis even with early intervention. By presenting the two cases, this review aims to bring attention to Dieulafoy lesion and GIST as arguably not-so-rare but potentially fatal sources of GIBs. Especially troublesome is the uncommon complication of GIST to perforate and the elusive nature of Dieulafoy lesions that require diligent evaluation. For these reasons, both should be considered in the differential diagnosis in patients with recurrent unexplained GIBs and anemia.

Microbial community diversity, structure and assembly across oxygen gradients in meromictic marine lakes, Palau.

Microbial communities consume oxygen, alter biogeochemistry and compress habitat in aquatic ecosystems, yet our understanding of these microbial-biogeochemical-ecological interactions is limited by a lack of systematic analyses of low-oxygen ecosystems. Marine lakes provide an ideal comparative system, as they range from well-mixed holomictic lakes to stratified, anoxic, meromictic lakes that vary in their vertical extent of anoxia. We examined microbial communities inhabiting six marine lakes and one ocean site using pyrosequencing of 16S rRNA genes. Microbial richness and evenness was typically highest in the anoxic monimolimnion of meromictic lakes, with common marine bacteria present in mixolimnion communities replaced by anoxygenic phototrophs, sulfate-reducing bacteria and SAR406 in the monimolimnion. These sharp changes in community structure were linked to environmental gradients (constrained variation in redundancy analysis = 68%-76%) - particularly oxygen and pH. However, in those lakes with the steepest oxygen gradients, salinity and dissolved nutrients were important secondary constraining variables, indicating that subtle but substantive differences in microbial communities occur within similar low-oxygen habitats. Deterministic processes were a dominant influence on whole community assembly (all nearest taxon index values >4), demonstrating that the strong environmental gradients present in meromictic marine lakes drive microbial community assembly.

Microbiological assessment of aerosol generated during debond of fixed orthodontic appliances.

INTRODUCTION: The aims of this study were to describe bacterial load and diversity of the aerosol created during enamel cleanup after the removal of fixed orthodontic appliances and to assess the effect of a preprocedural mouth rinse. METHODS: The study involved the sampling of ambient air adjacent to the patient's mouth during adhesive removal using a slow-speed handpiece and a spiral fluted tungsten carbide bur without water irrigation. Sampling was carried out during enamel cleanup with or without a preprocedural mouth rinse of either sterile water or chlorhexidine. Airborne particles were collected using a viable inertial impactor simulating the human respiratory tree. The bacteria collected were analyzed using both culture and molecular techniques. RESULTS: Bacteria produced during debond and enamel cleanup can reach all levels of the respiratory tree. The use of a preprocedural mouth rinse, either sterile water or chlorhexidine, increased the numbers and diversity of the bacteria in the air. CONCLUSIONS: When using a slow-speed handpiece and a spiral fluted tungsten carbide bur for enamel cleanup after orthodontic treatment, the bacterial load and diversity of the aerosol produced are lower when a preprocedural mouth rinse is not used.

A perspective on the next generation of antibacterial agents derived by manipulation of natural products.

Natural products have been a major source of anti-infective drugs for many decades. With urgent need for new antibacterial agents to combat drug-resistant bacteria, the investigation of both new and existing classes of natural products has once again become an important focus. In this review, we highlight how a medicinal chemistry/semi-synthetic approach to natural product manipulation continues to offer a valuable strategy to overcome limitations in current therapy. Approaches to address toxicity and to improve the solubility, bioavailability and the spectrum of activity are demonstrated. Examples are drawn from aminoglycosides, glycopeptides, tetracyclines, macrolides, thiazolyl peptides, pleuromutilins and polymyxins and are taken from the current literature, patents and abstracts of symposia. In many cases, this approach has led to drug candidates currently in late stages of clinical development.

Feasibility of a sensory-adapted dental environment for children with autism.

OBJECTIVE: To provide an example of an occupational therapy feasibility study and evaluate the implementation of a randomized controlled pilot and feasibility trial examining the impact of a sensory-adapted dental environment (SADE) to enhance oral care for children with autism spectrum disorder (ASD). METHOD: Twenty-two children with ASD and 22 typically developing children, ages 6-12 yr, attended a dental clinic in an urban hospital. Participants completed two dental cleanings, 3-4 mo apart, one in a regular environment and one in a SADE. Feasibility outcome measures were recruitment, retention, accrual, dropout, and protocol adherence. Intervention outcome measures were physiological stress, behavioral distress, pain, and cost. RESULTS: We successfully recruited and retained participants. Parents expressed satisfaction with research study participation. Dentists stated that the intervention could be incorporated in normal practice. Intervention outcome measures favored the SADE condition. CONCLUSION: Preliminary positive benefit of SADE in children with ASD warrants moving forward with a large-scale clinical trial.

Investigating Penetration and Antimicrobial Activity of Vector-Bicycle Conjugates.

Growing antibiotic resistance is rapidly threatening the efficacy of treatments for Gram-negative infections. Bicycle molecules, constrained bicyclic peptides from diverse libraries generated by bacteriophage display that bind with high affinity to a chosen target are a potential new class of antibiotics. The generally impermeable bacterial outer membrane currently limits the access of peptides to bacteria. The conjugation of membrane active peptides offers an avenue for outer membrane penetration. Here, we investigate which physicochemical properties of a specific membrane active peptide (MAP), derived from ixosin-B, could be tweaked to enhance the penetration of conjugates by generating multiple MAP-Bicycle conjugate variants. We demonstrate that charge and hydrophobicity are important factors, which enhance penetration and, therefore, antimicrobial potency. Interestingly, we show that induction of secondary structure, but not a change in amphipathicity, is vital for effective penetration of the Gram-negative outer membrane. These results offer insights into the ways vectors could be designed to deliver Bicycle molecules (and other cargos) through biological membranes.

Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature.

This review presents recommended nomenclature for the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), a rapidly growing class of natural products. The current knowledge regarding the biosynthesis of the >20 distinct compound classes is also reviewed, and commonalities are discussed.

Get out of the corner: Inhibition and the effect of location type and number on perceptron and human reorientation.

Spatial learning and navigation have frequently been investigated using a reorientation task paradigm (Cheng, Cognition, 23(2), 149-78, 1986). However, implementing this task typically involves making tacit assumptions about the nature of spatial information. This has important theoretical consequences: Theories of reorientation typically focus on angles at corners as geometric cues and ignore information present at noncorner locations. We present a neural network model of reorientation that challenges these assumptions and use this model to generate predictions in a novel variant of the reorientation task. We test these predictions against human behavior in a virtual environment. Networks and humans alike exhibit reorientation behavior even when goal locations are not present at corners. Our simulated and our experimental results suggest that angles are processed in a manner more similar to features, acting as a focal point for reorientation, and that the mechanisms governing reorientation behavior may be inhibitory rather than excitatory.