FISHGLOB_data: an integrated dataset of fish biodiversity sampled with scientific bottom-trawl surveys.

Scientific bottom-trawl surveys are ecological observation programs conducted along continental shelves and slopes of seas and oceans that sample marine communities associated with the seafloor. These surveys report taxa occurrence, abundance and/or weight in space and time, and contribute to fisheries management as well as population and biodiversity research. Bottom-trawl surveys are conducted all over the world and represent a unique opportunity to understand ocean biogeography, macroecology, and global change. However, combining these data together for cross-ecosystem analyses remains challenging. Here, we present an integrated dataset of 29 publicly available bottom-trawl surveys conducted in national waters of 18 countries that are standardized and pre-processed, covering a total of 2,170 sampled fish taxa and 216,548 hauls collected from 1963 to 2021. We describe the processing steps to create the dataset, flags, and standardization methods that we developed to assist users in conducting spatio-temporal analyses with stable regional survey footprints. The aim of this dataset is to support research, marine conservation, and management in the context of global change.

A synthesis of meta-analyses of mindfulness-based interventions in pain.

ABSTRACT: Mindfulness interventions have become popular in recent decades, with many trials, systematic reviews, and meta-analyses of the impact of mindfulness-based interventions (MBIs) on pain. Although many meta-analyses provide support for MBIs, the results are more mixed than they at first appear. The aim of this umbrella review was to determine the strength of evidence for MBIs by synthesizing available meta-analyses in pain. We conducted a systematic search in 5 databases and extracted data from published meta-analyses as the unit of analysis. For each outcome, we reported the range of effect sizes observed across studies and identified the largest meta-analysis as the "representative" study. We separately analysed effect sizes for different pain conditions, different types of MBIs, different control groups, and different outcomes. We identified 21 meta-analyses that included 127 unique studies. According to Assessment of Multiple Systematic Review ratings, the meta-analyses ranged from very strong to weak. Overall, there was an impact of MBIs on pain severity, anxiety, and depression but not pain interference or disability. When conditions were considered in isolation, only fibromyalgia and headache benefited significantly from MBIs. Mindfulness-based interventions were more efficacious for pain severity than passive control conditions but not active control conditions. Only pain severity and anxiety were affected by MBIs at follow-up. Overall, our results suggest that individual meta-analyses of MBIs may have overestimated the efficacy of MBIs in a range of conditions. Mindfulness-based interventions likely have a role in pain management but should not be considered a panacea.

Evolution and connectivity influence the persistence and recovery of coral reefs under climate change in the Caribbean, Southwest Pacific, and Coral Triangle.

Corals are experiencing unprecedented decline from climate change-induced mass bleaching events. Dispersal not only contributes to coral reef persistence through demographic rescue but can also hinder or facilitate evolutionary adaptation. Locations of reefs that are likely to survive future warming therefore remain largely unknown, particularly within the context of both ecological and evolutionary processes across complex seascapes that differ in temperature range, strength of connectivity, network size, and other characteristics. Here, we used eco-evolutionary simulations to examine coral adaptation to warming across reef networks in the Caribbean, the Southwest Pacific, and the Coral Triangle. We assessed the factors associated with coral persistence in multiple reef systems to understand which results are general and which are sensitive to particular geographic contexts. We found that evolution can be critical in preventing extinction and facilitating the long-term recovery of coral communities in all regions. Furthermore, the strength of immigration to a reef (destination strength) and current sea surface temperature robustly predicted reef persistence across all reef networks and across temperature projections. However, we found higher initial coral cover, slower recovery, and more evolutionary lag in the Coral Triangle, which has a greater number of reefs and more larval settlement than the other regions. We also found the lowest projected future coral cover in the Caribbean. These findings suggest that coral reef persistence depends on ecology, evolution, and habitat network characteristics, and that, under an emissions stabilization scenario (RCP 4.5), recovery may be possible over multiple centuries.

Evolution reverses the effect of network structure on metapopulation persistence.

Global environmental change is challenging species with novel conditions, such that demographic and evolutionary trajectories of populations are often shaped by the exchange of organisms and alleles across landscapes. Current ecological theory predicts that random networks with dispersal shortcuts connecting distant sites can promote persistence when there is no capacity for evolution. Here, we show with an eco-evolutionary model that dispersal shortcuts across environmental gradients instead hinder persistence for populations that can evolve because long-distance migrants bring extreme trait values that are often maladaptive, short-circuiting the adaptive response of populations to directional change. Our results demonstrate that incorporating evolution and environmental heterogeneity fundamentally alters theoretical predictions regarding persistence in ecological networks.

Unmasking latent inhibition in humans.

Presentations of a to-be-conditioned stimulus (CS) on its own impairs subsequent learning when that CS is paired with an unconditioned stimulus (US). Evidence for this latent inhibition (LI) effect in humans is said to require a "masking task" that diverts attention from the CS during preexposure. We present three experiments that demonstrate LI in humans without masking. Subjects performed a computerised task, making speeded responses to an imperative cue (the US) presented within a continuous stream of stimuli. During preexposure, a to-be-CS was presented 20 times among other stimuli, but excluding the US. Instructions ensured subjects actively monitored all stimuli at this time. This was immediately followed by the training phase, which included the US, the preexposed CS, and a novel CS. Both CSs were reliably followed by the US, but these associations were incidental to the instructed task. Nonetheless, some subjects learned the CS-US associations, responding faster when the US followed a CS than when it was unsignalled. All three experiments also found evidence for LI, in that subjects learned the novel CS-US association sooner than the preexposed CS-US association. We conclude that humans can show LI even when actively attending to the CS during preexposure.

Ibudilast reduces oxaliplatin-induced tactile allodynia and cognitive impairments in rats.

Chemotherapy can cause serious neurotoxic side effects, such as painful peripheral neuropathies and disabling cognitive impairments. Four experiments examined whether Ibudilast, a clinically approved neuroimmune therapy, would reduce tactile allodynia and memory impairments caused by oxaliplatin in laboratory rats. Rats received an intraperitoneal injection of oxaliplatin (6mg/kg i.p.) or vehicle and were assessed for tactile allodynia 3 or 5days after injection, memory impairments in the novel object and novel location recognition tests 10-12days after injection, and fear conditioning 14days after injection. Ibudilast (7.5mg/kg) or vehicle was administered prior to oxaliplatin (Experiments 1 and 3) or prior to behavioural testing (Experiments 2 and 4). Ibudilast treatment prior to oxaliplatin prevented the development of tactile allodynia and memory impairments. Ibudilast treatment prior to behavioural testing reduced oxaliplatin-induced tactile allodynia, memory impairments, and impaired renewal of fear conditioning. These results suggest that Ibudilast could be an effective treatment against oxaliplatin-induced neuropathies and cognitive impairments.

Lineage-specific biology revealed by a finished genome assembly of the mouse.

The mouse (Mus musculus) is the premier animal model for understanding human disease and development. Here we show that a comprehensive understanding of mouse biology is only possible with the availability of a finished, high-quality genome assembly. The finished clone-based assembly of the mouse strain C57BL/6J reported here has over 175,000 fewer gaps and over 139 Mb more of novel sequence, compared with the earlier MGSCv3 draft genome assembly. In a comprehensive analysis of this revised genome sequence, we are now able to define 20,210 protein-coding genes, over a thousand more than predicted in the human genome (19,042 genes). In addition, we identified 439 long, non-protein-coding RNAs with evidence for transcribed orthologs in human. We analyzed the complex and repetitive landscape of 267 Mb of sequence that was missing or misassembled in the previously published assembly, and we provide insights into the reasons for its resistance to sequencing and assembly by whole-genome shotgun approaches. Duplicated regions within newly assembled sequence tend to be of more recent ancestry than duplicates in the published draft, correcting our initial understanding of recent evolution on the mouse lineage. These duplicates appear to be largely composed of sequence regions containing transposable elements and duplicated protein-coding genes; of these, some may be fixed in the mouse population, but at least 40% of segmentally duplicated sequences are copy number variable even among laboratory mouse strains. Mouse lineage-specific regions contain 3,767 genes drawn mainly from rapidly-changing gene families associated with reproductive functions. The finished mouse genome assembly, therefore, greatly improves our understanding of rodent-specific biology and allows the delineation of ancestral biological functions that are shared with human from derived functions that are not.

Single-molecule approach to bacterial genomic comparisons via optical mapping.

Modern comparative genomics has been established, in part, by the sequencing and annotation of a broad range of microbial species. To gain further insights, new sequencing efforts are now dealing with the variety of strains or isolates that gives a species definition and range; however, this number vastly outstrips our ability to sequence them. Given the availability of a large number of microbial species, new whole genome approaches must be developed to fully leverage this information at the level of strain diversity that maximize discovery. Here, we describe how optical mapping, a single-molecule system, was used to identify and annotate chromosomal alterations between bacterial strains represented by several species. Since whole-genome optical maps are ordered restriction maps, sequenced strains of Shigella flexneri serotype 2a (2457T and 301), Yersinia pestis (CO 92 and KIM), and Escherichia coli were aligned as maps to identify regions of homology and to further characterize them as possible insertions, deletions, inversions, or translocations. Importantly, an unsequenced Shigella flexneri strain (serotype Y strain AMC[328Y]) was optically mapped and aligned with two sequenced ones to reveal one novel locus implicated in serotype conversion and several other loci containing insertion sequence elements or phage-related gene insertions. Our results suggest that genomic rearrangements and chromosomal breakpoints are readily identified and annotated against a prototypic sequenced strain by using the tools of optical mapping.

A microfluidic system for large DNA molecule arrays.

Single molecule approaches offer the promise of large, exquisitely miniature ensembles for the generation of equally large data sets. Although microfluidic devices have previously been designed to manipulate single DNA molecules, many of the functionalities they embody are not applicable to very large DNA molecules, normally extracted from cells. Importantly, such microfluidic devices must work within an integrated system to enable high-throughput biological or biochemical analysis-a key measure of any device aimed at the chemical/biological interface and required if large data sets are to be created for subsequent analysis. The challenge here was to design an integrated microfluidic device to control the deposition or elongation of large DNA molecules (up to millimeters in length), which would serve as a general platform for biological/biochemical analysis to function within an integrated system that included massively parallel data collection and analysis. The approach we took was to use replica molding to construct silastic devices to consistently deposit oriented, elongated DNA molecules onto charged surfaces, creating massive single molecule arrays, which we analyzed for both physical and biochemical insights within an integrated environment that created large data sets. The overall efficacy of this approach was demonstrated by the restriction enzyme mapping and identification of single human genomic DNA molecules.

An integrative approach for the optical sequencing of single DNA molecules.

A new approach for optically sequencing ensembles of single DNA molecules using DNA polymerase to mediate the consecutive incorporation of fluorochrome-labeled nucleotides into an array of large single DNA molecules is presented. The approach utilizes cycles of labeled fluorochrome addition, detection to count incorporations, and bleaching to reset the counter. These additions are imaged and analyzed to estimate the number of labeled additions and to correlate them on a per-locus basis along DNA backbones. Initial studies used precisely labeled polymerase chain reaction products to aid the development and validation of simple models of fluorochrome point spread functions within the imaging system. In complementary studies, nucleotides labeled with the fluorochrome R110 were incorporated into surface-elongated lambda DNA, and fluorescent signals corresponding to the addition of R110-dUTP were counted and assigned precise loci along DNA backbones. The labeled DNAs were then subjected to photobleaching and to a second cycle of addition of R110-labeled nucleotides-a second round of additions was correlated with the first to establish strings of addition histories among the ensemble of largely double-stranded templates. These results confirm the basic operational validity of this approach and point the way to the development of a practical system for optical sequencing.