A highly contiguous reference genome for the Steller's jay (Cyanocitta stelleri)

The Steller's jay is a familiar bird of western forests from Alaska south to Nicaragua. Here, we report a draft reference assembly for the species generated from PacBio HiFi long-read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project (CCGP). Sequenced reads were assembled into 352 scaffolds totaling 1.16 Gb in length. Assembly metrics indicate a highly contiguous and complete assembly with a contig N50 of 7.8 Mb, scaffold N50 of 25.8 Mb, and BUSCO completeness score of 97.2%. Repetitive elements span 16.6% of the genome including nearly 90% of the W chromosome. Compared with high-quality assemblies from other members of the family Corvidae, the Steller's jay genome contains a larger proportion of repetitive elements than 4 crow species (Corvus), but a lower proportion of repetitive elements than the California scrub-jay (Aphelocoma californica). This reference genome will serve as an essential resource for future studies on speciation, local adaptation, phylogeography, and conservation genetics in this species of significant biological interest.

Mechanical force regulates Sox9 expression at the developing enthesis

Entheses transmit force from tendons and ligaments to the skeleton. Regional organization of enthesis extracellular matrix (ECM) generates differences in stiffness required for force transmission. Two key transcription factors co-expressed in entheseal tenocytes, scleraxis (Scx) and Sox9, directly control production of enthesis ECM components. Formation of embryonic craniofacial entheses in zebrafish coincides with onset of jaw movements, possibly in response to the force of muscle contraction. We show dynamic changes in scxa and sox9a mRNA levels in subsets of entheseal tenocytes that correlate with their roles in force transmission. We also show that transcription of a direct target of Scxa, Col1a, in enthesis ECM is regulated by the ratio of scxa to sox9a expression. Eliminating muscle contraction by paralyzing embryos during early stages of musculoskeletal differentiation alters relative levels of scxa and sox9a in entheses, primarily owing to increased sox9a expression. Force-dependent TGF-β (TGFβ) signaling is required to maintain this balance of scxa and sox9a expression. Thus, force from muscle contraction helps establish a balance of transcription factor expression that controls specialized ECM organization at the tendon enthesis and its ability to transmit force.

Evolution of chemosensory and detoxification gene families across herbivorous Drosophilidae

Herbivorous insects are exceptionally diverse, accounting for a quarter of all known eukaryotic species, but the genomic basis of adaptations that enabled this dietary transition remains poorly understood. Many studies have suggested that expansions and contractions of chemosensory and detoxification gene families-genes directly mediating interactions with plant chemical defenses-underlie successful plant colonization. However, this hypothesis has been challenging to test because the origins of herbivory in many insect lineages are ancient (>150 million years ago (mya)), obscuring genomic evolutionary patterns. Here, we characterized chemosensory and detoxification gene family evolution across Scaptomyza, a genus nested within Drosophila that includes a recently derived (<15 mya) herbivore lineage of mustard (Brassicales) specialists and carnation (Caryophyllaceae) specialists, and several nonherbivorous species. Comparative genomic analyses revealed that herbivorous Scaptomyza has among the smallest chemosensory and detoxification gene repertoires across 12 drosophilid species surveyed. Rates of gene turnover averaged across the herbivore clade were significantly higher than background rates in over half of the surveyed gene families. However, gene turnover was more limited along the ancestral herbivore branch, with only gustatory receptors and odorant-binding proteins experiencing strong losses. The genes most significantly impacted by gene loss, duplication, or changes in selective constraint were those involved in detecting compounds associated with feeding on living plants (bitter or electrophilic phytotoxins) or their ancestral diet (fermenting plant volatiles). These results provide insight into the molecular and evolutionary mechanisms of plant-feeding adaptations and highlight gene candidates that have also been linked to other dietary transitions in Drosophila.

In host evolution of Exophiala dermatitidis in cystic fibrosis lung micro-environment

Individuals with cystic fibrosis (CF) are susceptible to chronic lung infections that lead to inflammation and irreversible lung damage. While most respiratory infections that occur in CF are caused by bacteria, some are dominated by fungi such as the slow-growing black yeast Exophiala dermatitidis. Here, we analyze isolates of E. dermatitidis cultured from two samples, collected from a single subject 2 years apart. One isolate genome was sequenced using long-read Nanopore technology as an in-population reference to use in comparative single nucleotide polymorphism and insertion-deletion variant analyses of 23 isolates. We then used population genomics and phylo-genomics to compare the isolates to each other as well as the reference genome strain E. dermatitidis NIH/UT8656. Within the CF lung population, three E. dermatitidis clades were detected, each with varying mutation rates. Overall, the isolates were highly similar suggesting that they were recently diverged. All isolates were MAT 1-1, which was consistent with their high relatedness and the absence of evidence for mating or recombination between isolates. Phylogenetic analysis grouped sets of isolates into clades that contained isolates from both early and late time points indicating there are multiple persistent lineages. Functional assessment of variants unique to each clade identified alleles in genes that encode transporters, cytochrome P450 oxidoreductases, iron acquisition, and DNA repair processes. Consistent with the genomic heterogeneity, isolates showed some stable phenotype heterogeneity in melanin production, subtle differences in antifungal minimum inhibitory concentrations, and growth on different substrates. The persistent population heterogeneity identified in lung-derived isolates is an important factor to consider in the study of chronic fungal infections, and the analysis of changes in fungal pathogens over time may provide important insights into the physiology of black yeasts and other slow-growing fungi in vivo.

Species Delimitation, Phylogenomics, and Biogeography of Sulawesi Flying Lizards: A Diversification History Complicated by Ancient Hybridization, Cryptic Species, and Arrested Speciation

The biota of Sulawesi is noted for its high degree of endemism and for its substantial levels of in situ biological diversification. While the island's long period of isolation and dynamic tectonic history have been implicated as drivers of the regional diversification, this has rarely been tested in the context of an explicit geological framework. Here, we provide a tectonically informed biogeographical framework that we use to explore the diversification history of Sulawesi flying lizards (the Draco lineatus Group), a radiation that is endemic to Sulawesi and its surrounding islands. We employ a framework for inferring cryptic speciation that involves phylogeographic and genetic clustering analyses as a means of identifying potential species followed by population demographic assessment of divergence-timing and rates of bi-directional migration as means of confirming lineage independence (and thus species status). Using this approach, phylogenetic and population genetic analyses of mitochondrial sequence data obtained for 613 samples, a 50-SNP data set for 370 samples, and a 1249-locus exon-capture data set for 106 samples indicate that the current taxonomy substantially understates the true number of Sulawesi Draco species, that both cryptic and arrested speciations have taken place, and that ancient hybridization confounds phylogenetic analyses that do not explicitly account for reticulation. The Draco lineatus Group appears to comprise 15 species-9 on Sulawesi proper and 6 on peripheral islands. The common ancestor of this group colonized Sulawesi ~11 Ma when proto-Sulawesi was likely composed of two ancestral islands, and began to radiate ~6 Ma as new islands formed and were colonized via overwater dispersal. The enlargement and amalgamation of many of these proto-islands into modern Sulawesi, especially during the past 3 Ma, set in motion dynamic species interactions as once-isolated lineages came into secondary contact, some of which resulted in lineage merger, and others surviving to the present. [Genomics; Indonesia; introgression; mitochondria; phylogenetics; phylogeography; population genetics; reptiles.].

Biomechanical Phenotyping of Chronic Low Back Pain: Protocol for BACPAC

OBJECTIVE

Biomechanics represents the common final output through which all biopsychosocial constructs of back pain must pass, making it a rich target for phenotyping. To exploit this feature, several sites within the NIH Back Pain Consortium (BACPAC) have developed biomechanics measurement and phenotyping tools. The overall aims of this article were to: 1) provide a narrative review of biomechanics as a phenotyping tool; 2) describe the diverse array of tools and outcome measures that exist within BACPAC; and 3) highlight how leveraging these technologies with the other data collected within BACPAC could elucidate the relationship between biomechanics and other metrics used to characterize low back pain (LBP).

METHODS

The narrative review highlights how biomechanical outcomes can discriminate between those with and without LBP, as well as among levels of severity of LBP. It also addresses how biomechanical outcomes track with functional improvements in LBP. Additionally, we present the clinical use case for biomechanical outcome measures that can be met via emerging technologies.

RESULTS

To answer the need for measuring biomechanical performance, our "Results" section describes the spectrum of technologies that have been developed and are being used within BACPAC.

CONCLUSION AND FUTURE DIRECTIONS

The outcome measures collected by these technologies will be an integral part of longitudinal and cross-sectional studies conducted in BACPAC. Linking these measures with other biopsychosocial data collected within BACPAC increases our potential to use biomechanics as a tool for understanding the mechanisms of LBP, phenotyping unique LBP subgroups, and matching these individuals with an appropriate treatment paradigm.

Deformation Rate-Adaptive Conducting Polymers and Composites

Materials are more easily damaged during accidents that involve rapid deformation. Here, a design strategy is described for electronic materials comprised of conducting polymers that defies this orthodox property, making their extensibility and toughness dynamically adaptive to deformation rates. This counterintuitive property is achieved through a morphology of interconnected nanoscopic core-shell micelles, where the chemical interactions are stronger within the shells than the cores. As a result, the interlinked shells retain material integrity under strain, while the rate of dissociation of the cores controls the extent of micelle elongation, which is a process that adapts to deformation rates. A prototype based on polyaniline shows a 7.5-fold increase in ultimate elongation and a 163-fold increase in toughness when deformed at increasing rates from 2.5 to 10 000% min-1 . This concept can be generalized to other conducting polymers and highly conductive composites to create "self-protective" soft electronic materials with enhanced durability under dynamic movement or deformation.

Dual chemical labeling enables nucleotide-resolution mapping of DNA abasic sites and common alkylation damage in human mitochondrial DNA

Mitochondrial DNA (mtDNA) modifications play an emerging role in innate immunity and inflammatory diseases. Nonetheless, relatively little is known regarding the locations of mtDNA modifications. Such information is critically important for deciphering their roles in mtDNA instability, mtDNA-mediated immune and inflammatory responses, and mitochondrial disorders. The affinity probe-based enrichment of lesion-containing DNA represents a key strategy for sequencing DNA modifications. Existing methods are limited in the enrichment specificity of abasic (AP) sites, a prevalent DNA modification and repair intermediate. Herein, we devise a novel approach, termed dual chemical labeling-assisted sequencing (DCL-seq), for mapping AP sites. DCL-seq features two designer compounds for enriching and mapping AP sites specifically at single-nucleotide resolution. For proof of principle, we mapped AP sites in mtDNA from HeLa cells under different biological conditions. The resulting AP site maps coincide with mtDNA regions with low TFAM (mitochondrial transcription factor A) coverage and with potential G-quadruplex-forming sequences. In addition, we demonstrated the broader applicability of the method in sequencing other DNA modifications in mtDNA, such as N7-methyl-2'-deoxyguanosine and N3-methyl-2'-deoxyadenosine, when coupled with a lesion-specific repair enzyme. Together, DCL-seq holds the promise to sequence multiple DNA modifications in various biological samples.

Optogenetic control of Wnt signaling models cell-intrinsic embryogenic patterning using 2D human pluripotent stem cell culture

In embryonic stem cell (ESC) models for early development, spatially and temporally varying patterns of signaling and cell types emerge spontaneously. However, mechanistic insight into this dynamic self-organization is limited by a lack of methods for spatiotemporal control of signaling, and the relevance of signal dynamics and cell-to-cell variability to pattern emergence remains unknown. Here, we combine optogenetic stimulation, imaging and transcriptomic approaches to study self-organization of human ESCs (hESC) in two-dimensional (2D) culture. Morphogen dynamics were controlled via optogenetic activation of canonical Wnt/β-catenin signaling (optoWnt), which drove broad transcriptional changes and mesendoderm differentiation at high efficiency (>99% cells). When activated within cell subpopulations, optoWnt induced cell self-organization into distinct epithelial and mesenchymal domains, mediated by changes in cell migration, an epithelial to mesenchymal-like transition and TGFβ signaling. Furthermore, we demonstrate that such optogenetic control of cell subpopulations can be used to uncover signaling feedback mechanisms between neighboring cell types. These findings reveal that cell-to-cell variability in Wnt signaling is sufficient to generate tissue-scale patterning and establish a hESC model system for investigating feedback mechanisms relevant to early human embryogenesis.

Association of nativity with survival among adults with hepatocellular carcinoma

INTRODUCTION

Immigrants comprise a considerable proportion of those diagnosed with hepatocellular carcinoma (HCC) in the United States. Nativity or birthplace affects incidence and risk factors for HCC, but little is known about its influence on survival after diagnosis.

METHODS

We identified 51 533 adults with HCC with available birthplace in the California Cancer Registry between 1988 and 2017. HCC cases were categorized as foreign born or US born and stratified by mutually exclusive race and ethnicity groups. Primary outcome was all-cause mortality. Race and ethnicity-specific Cox regression propensity score-weighted models evaluated the relationship between nativity and death as well as region of birth among foreign-born patients.

RESULTS

A total of 40% of all HCC cases were foreign born, and 92.2%, 45.2%, 9.1%, and 5.8% of Asian/Pacific Islander (API), Hispanic, White, and Black patients were foreign born, respectively. Five-year survival rates were higher in foreign-born patients compared with US-born patients: 12.9% vs 9.6% for White patients, 11.7% vs 9.8% for Hispanic patients, 12.8% vs 8.1% for Black patients, and 16.4% vs 12.4% for API patients. Nativity was associated with survival, with better survival in foreign-born patients: White patients: hazard ratio (HR) = 0.86 (95% confidence interval [CI] = 0.81 to 0.90), Hispanic patients: HR = 0.90 (95% CI = 0.86 to 0.93), Black patients: HR = 0.89 (95% CI = 0.76 to 1.05), and API patients: HR = 0.94 (95% CI = 0.88 to 1.00). Among foreign-born patients, lower mortality was observed in those from Central and South America compared with Mexico for Hispanic patients, East Asia compared with Southeast Asia for API patients, and East Europe and Greater Middle East compared with West/South/North Europe for White patients.

CONCLUSION

Foreign-born patients with HCC have better survival than US-born patients. Further investigation into the mechanisms of this survival disparity by nativity is needed.

Saccharomyces cerevisiae DNA polymerase IV overcomes Rad51 inhibition of DNA polymerase δ in Rad52-mediated direct-repeat recombination

Saccharomyces cerevisiae DNA polymerase IV (Pol4) like its homolog, human DNA polymerase lambda (Polλ), is involved in Non-Homologous End-Joining and Microhomology-Mediated Repair. Using genetic analysis, we identified an additional role of Pol4 also in homology-directed DNA repair, specifically in Rad52-dependent/Rad51-independent direct-repeat recombination. Our results reveal that the requirement for Pol4 in repeat recombination was suppressed by the absence of Rad51, suggesting that Pol4 counteracts the Rad51 inhibition of Rad52-mediated repeat recombination events. Using purified proteins and model substrates, we reconstituted in vitro reactions emulating DNA synthesis during direct-repeat recombination and show that Rad51 directly inhibits Polδ DNA synthesis. Interestingly, although Pol4 was not capable of performing extensive DNA synthesis by itself, it aided Polδ in overcoming the DNA synthesis inhibition by Rad51. In addition, Pol4 dependency and stimulation of Polδ DNA synthesis in the presence of Rad51 occurred in reactions containing Rad52 and RPA where DNA strand-annealing was necessary. Mechanistically, yeast Pol4 displaces Rad51 from ssDNA independent of DNA synthesis. Together our in vitro and in vivo data suggest that Rad51 suppresses Rad52-dependent/Rad51-independent direct-repeat recombination by binding to the primer-template and that Rad51 removal by Pol4 is critical for strand-annealing dependent DNA synthesis.

Reference genome of an iconic lizard in western North America, Blainville's horned lizard Phrynosoma blainvillii

Genome assemblies are increasingly being used to identify adaptive genetic variation that can help prioritize the population management of protected species. This approach may be particularly relevant to species like Blainville's horned lizard, Phrynosoma blainvillii, due to its specialized diet on noxious harvester ants, numerous adaptative traits for avoiding predation (e.g. cranial horns, dorsoventrally compressed body, cryptic coloration, and blood squirting from the orbital sinuses), and status as Species of Special Concern in California. Rangewide decline since the early 20th century, the basis of its conservation status, has been driven mainly by habitat conversion, over-collecting, and invasion of a non-native ant that displaces its native ant prey base. Here, we report on a scaffold-level genome assembly for P. blainvillii as part of the California Conservation Genomics Project (CCGP), produced using Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology. The de novo assembly has 78 scaffolds, a total length of ~2.21 Gb, a scaffold N50 length of ~352 Mb, and BUSCO score of 97.4%. This is the second species of Phrynosoma for which a reference genome has been assembled and represents a considerable improvement in terms of contiguity and completeness. Combined with the landscape genomics data being compiled by the CCGP, this assembly will help strategize efforts to maintain and/or restore local genetic diversity, where interventions like genetic rescue, translocation, and strategic land preservation may be the only means by which P. blainvillii and other low-vagility species can survive in the fragmented habitats of California.

Reference genome of the Virginia rail, Rallus limicola

The Virginia rail, Rallus limicola, is a member of the family Rallidae, which also includes many other species of secretive and poorly studied wetland birds. It is recognized as a single species throughout its broad distribution in North America where it is exploited as a game bird, often with generous harvest limits, despite a lack of systematic population surveys and evidence of declines in many areas due to wetland loss and degradation. To help advance understanding of the phylogeography, biology, and ecology of this elusive species, we report the first reference genome assembly for the Virginia rail, produced as part of the California Conservation Genomics Project (CCGP). We produced a de novo genome assembly using Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology with an estimated sequencing error rate of 0.191%. The assembly consists of 1,102 scaffolds spanning 1.39 Gb, with a contig N50 of 11.0 Mb, scaffold N50 of 25.3 Mb, largest contig of 45 Mb, and largest scaffold of 128.4 Mb. It has a high BUSCO completeness score of 96.9% and represents the first genome assembly available for the genus Rallus. This genome assembly will help resolve questions about the complex evolutionary history of rails and evaluate the potential of rails for adaptive evolution in the face of growing threats from climate change and habitat loss and fragmentation. It will also provide a valuable resource for rail conservation efforts by quantifying Virginia rail vagility, population connectivity, and effective population sizes.

Reference genome of the black rail, Laterallus jamaicensis

The black rail, Laterallus jamaicensis, is one of the most secretive and poorly understood birds in the Americas. Two of its five subspecies breed in North America: the Eastern black rail (L. j. jamaicensis), found primarily in the southern and mid-Atlantic states, and the California black rail (L. j. coturniculus), inhabiting California and Arizona, are recognized across the highly disjunct distribution. Population declines, due primarily to wetland loss and degradation, have resulted in conservation status listings for both subspecies. To help advance understanding of the phylogeography, biology, and ecology of this elusive species, we report the first reference genome assembly for the black rail, produced as part of the California Conservation Genomics Project (CCGP). We produced a de novo genome assembly using Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology with an estimated sequencing error rate of 0.182%. The assembly consists of 964 scaffolds spanning 1.39 Gb, with a contig N50 of 7.4 Mb, scaffold N50 of 21.4 Mb, largest contig of 44.8 Mb, and largest scaffold of 101.2 Mb. The assembly has a high BUSCO completeness score of 96.8% and represents the first genome assembly available for the genus Laterallus. This genome assembly can help resolve questions about the complex evolutionary history of rails, assess black rail vagility and population connectivity, estimate effective population sizes, and evaluate the potential of rails for adaptive evolution in the face of growing threats from climate change, habitat loss and fragmentation, and disease.

A highly contiguous genome assembly for the California quail (Callipepla californica)

The California quail (Callipepla californica) is an iconic native bird of scrub and oak woodlands in California and the Baja Peninsula of Mexico. Here, we report a draft reference assembly for the species generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project (CCGP). Sequenced reads were assembled into 321 scaffolds totaling 1.08 Gb in length. Assembly metrics indicate a highly contiguous and complete assembly with a contig N50 of 5.5 Mb, scaffold N50 of 19.4 Mb, and BUSCO completeness score of 96.5%. Transposable elements (TEs) occupy 16.5% of the genome, more than previous Odontophoridae quail assemblies but in line with estimates of TE content for recent long-read assemblies of chicken and Peking duck. Together these metrics indicate that the present assembly is more complete than prior reference assemblies generated for Odontophoridae quail. This reference will serve as an essential resource for studies on local adaptation, phylogeography, and conservation genetics in this species of significant biological and recreational interest.

Reference genome for the American rubyspot damselfly, Hetaerina americana

Damselflies and dragonflies (Order: Odonata) play important roles in both aquatic and terrestrial food webs and can serve as sentinels of ecosystem health and predictors of population trends in other taxa. The habitat requirements and limited dispersal of lotic damselflies make them especially sensitive to habitat loss and fragmentation. As such, landscape genomic studies of these taxa can help focus conservation efforts on watersheds with high levels of genetic diversity, local adaptation, and even cryptic endemism. Here, as part of the California Conservation Genomics Project (CCGP), we report the first reference genome for the American rubyspot damselfly, Hetaerina americana, a species associated with springs, streams and rivers throughout California. Following the CCGP assembly pipeline, we produced two de novo genome assemblies. The primary assembly includes 1,630,044,487 base pairs, with a contig N50 of 5.4 Mb, a scaffold N50 of 86.2 Mb, and a BUSCO completeness score of 97.6%. This is the seventh Odonata genome to be made publicly available and the first for the subfamily Hetaerininae. This reference genome fills an important phylogenetic gap in our understanding of Odonata genome evolution, and provides a genomic resource for a host of interesting ecological, evolutionary, and conservation questions for which the rubyspot damselfly genus Hetaerina is an important model system.

Reference genome of the long-jawed orb-weaver, Tetragnatha versicolor (Araneae: Tetragnathidae)

Climate-driven changes in hydrological regimes are of global importance and are particularly significant in riparian ecosystems. Riparian ecosystems in California provide refuge to many native and vulnerable species within a xeric landscape. California Tetragnatha spiders play a key role in riparian ecosystems, serving as a link between terrestrial and aquatic elements. Their tight reliance on water paired with the widespread distributions of many species make them ideal candidates to better understand the relative role of waterways versus geographic distance in shaping the population structure of riparian species. To assist in better understanding population structure, we constructed a reference genome assembly for Tetragnatha versicolor using long-read sequencing, scaffolded with proximity ligation Omni-C data. The near-chromosome-level assembly is comprised of 174 scaffolds spanning 1.06 Gb pairs, with a scaffold N50 of 64.1 Mb pairs and BUSCO completeness of 97.6%. This reference genome will facilitate future study of T. versicolor population structure associated with the rapidly changing environment of California.

Predicting the shape, size, and placement of adult human pubic symphyses

OBJECTIVES

When reconstructing fossil pelves, the articulation of the pelvic bones largely relies on subjective decisions by researchers. Different positionings at the pubic symphysis can affect the overall morphology of the pelvis and the subsequent biological interpretation associated with that individual or species. This study aims to reduce this subjectivity using quantitative models to predict pubic symphysis morphology.

METHODS

We collected 3D landmarks and semilandmarks on the pubic symphysis and adjacent aspects on the CT scans of 103 adults. Using geometric morphometrics we, (1) quantified pubic symphysis morphology, (2) trained simple and two-stage least-squares linear regression models to predict pubic symphysis shape, and (3) assessed the shape variation in the sample. The model with the lowest prediction error was identified as the best model. Principal components analysis was used to explore the effects of each variable on shape and hypothetical shapes were generated from the model to illustrate these effects.

RESULTS

The best model is a two-stage least-squares model that predicts pubic symphysis size at the first stage using additive effects of sex and age, then subsequently interacts pubic symphysis size with sex and age at the second stage to predict pubic symphysis shape. Other models with low prediction errors included variables reflecting pelvic size and breadth.

CONCLUSION

Linear regression modeling can be used to systematically predict pubic symphysis morphology. This method can be used in addition to other techniques to improve fossil reconstructions by more accurately estimating the morphology of this region of the pelvis.

Exposure to quasi-ultrafine particulate matter accelerates memory impairment and Alzheimer's disease-like neuropathology in the AppNL-G-F knock-in mouse model

Exposure to traffic-related air pollution consisting of particulate matter (PM) is associated with cognitive decline leading to Alzheimer's disease (AD). In this study, we sought to examine the neurotoxic effects of exposure to ultrafine PM and how it exacerbates neuronal loss and AD-like neuropathology in wildtype (WT) mice and a knock-in mouse model of AD (AppNL-G-F/+-KI) when the exposure occurs at a prepathologic stage or at a later age with the presence of neuropathology. AppNL-G-F/+-KI and WT mice were exposed to concentrated ultrafine PM from local ambient air in Irvine, California, for 12 weeks, starting at 3 or 9 months of age. Particulate matter-exposed animals received concentrated ultrafine PM up to 8 times above the ambient levels, whereas control animals were exposed to purified air. Particulate matter exposure resulted in a marked impairment of memory tasks in prepathologic AppNL-G-F/+-KI mice without measurable changes in amyloid-β pathology, synaptic degeneration, and neuroinflammation. At aged, both WT and AppNL-G-F/+-KI mice exposed to PM showed a significant memory impairment along with neuronal loss. In AppNL-G-F/+-KI mice, we also detected an increased amyloid-β buildup and potentially harmful glial activation including ferritin-positive microglia and C3-positive astrocytes. Such glial activation could promote the cascade of degenerative consequences in the brain. Our results suggest that exposure to PM impairs cognitive function at both ages while exacerbation of AD-related pathology and neuronal loss may depend on the stage of pathology, aging, and/or state of glial activation. Further studies will be required to unveil the neurotoxic role of glial activation activated by PM exposure.

Distinct neural activations correlate with maximization of reward magnitude versus frequency

Choice selection strategies and decision-making are typically investigated using multiple-choice gambling paradigms that require participants to maximize expected value of rewards. However, research shows that performance in such paradigms suffers from individual biases towards the frequency of gains such that users often choose smaller frequent gains over larger rarely occurring gains, also referred to as melioration. To understand the basis of this subjective tradeoff, we used a simple 2-choice reward task paradigm in 186 healthy human adult subjects sampled across the adult lifespan. Cortical source reconstruction of simultaneously recorded electroencephalography suggested distinct neural correlates for maximizing reward magnitude versus frequency. We found that activations in the parahippocampal and entorhinal areas, which are typically linked to memory function, specifically correlated with maximization of reward magnitude. In contrast, maximization of reward frequency was correlated with activations in the lateral orbitofrontal cortices and operculum, typical areas involved in reward processing. These findings reveal distinct neural processes serving reward frequency versus magnitude maximization that can have clinical translational utility to optimize decision-making.

The non-canonical Wnt receptor Ror2 is required for cartilage cell polarity and morphogenesis of the craniofacial skeleton in zebrafish

Non-canonical/β-catenin-independent Wnt signaling plays crucial roles in tissue/cell polarity in epithelia, but its functions have been less well studied in mesenchymal tissues, such as the skeleton. Mutations in non-canonical Wnt signaling pathway genes cause human skeletal diseases such as Robinow syndrome and Brachydactyly Type B1, which disrupt bone growth throughout the endochondral skeleton. Ror2 is one of several non-canonical Wnt receptor/co-receptors. Here, we show that ror2-/- mutant zebrafish have craniofacial skeletal defects, including disruptions of chondrocyte polarity. ror1-/- mutants appear to be phenotypically wild type, but loss of both ror1 and ror2 leads to more severe cartilage defects, indicating partial redundancy. Skeletal defects in ror1/2 double mutants resemble those of wnt5b-/- mutants, suggesting that Wnt5b is the primary Ror ligand in zebrafish. Surprisingly, the proline-rich domain of Ror2, but not its kinase domain, is required to rescue its function in mosaic transgenic experiments in ror2-/- mutants. These results suggest that endochondral bone defects in ROR-related human syndromes reflect defects in cartilage polarity and morphogenesis.

Disparities in cancer incidence by rurality in California

BACKGROUND

Cancer rates in rural areas across the United States have different patterns than in urban areas. This study examines associations between rurality and incidence for the top 5 cancers in California and evaluates whether these associations vary jointly by sex, race, and ethnicity.

METHODS

We used 2015-2019 California Cancer Registry data to compare incidence rate ratios (IRRs) and trends for breast, prostate, lung, colorectal, and skin (melanoma) cancers. We leveraged census tract aggregation zones and 7 levels of percentage rural population (0%, >0% to <10%, 10% to <20%, 20% to <30%, 30% to <40%, 40% to <50%, and 50+%).

RESULTS

Zones with higher proportions of rural population were significantly associated with lower incidence of female breast cancer and prostate cancer, though the trends were not statistically significant overall. Zones with higher proportions of rural population were significantly associated with higher incidence of lung cancer and melanoma. There were no statistically significant trends for colorectal cancer overall. Comparing areas with 50% and over rural population with areas with 0% rural population, the IRR for lung cancer in Hispanic females was higher (IRR = 1.43, 95% confidence interval [CI] = 1.17 to 1.74) than in Hispanic males (IRR = 0.90, 95% CI = 0.72 to 1.11). Also, in areas with 50% or more rural population, the IRR for melanoma was higher in Hispanic females (IRR = 1.75, 95% CI = 1.23 to 2.45) than non-Hispanic White females (IRR = 0.87, 95% CI = 0.80 to 0.95).

CONCLUSIONS

Our findings show that rurality is associated with cancer incidence and underscore the importance of jointly examining rural disparities with sex, race, and ethnicity by cancer site.

Reference genome of the Woolly Sculpin, Clinocottus analis

Sculpins (Family Cottidae) are generally cold-temperate intertidal reef fishes most commonly found in the North Pacific. As part of the California Conservation Genomics Project (CCGP), we sequenced the genome of the Woolly Sculpin, Clinocottus analis, to establish a genomic model for understanding phylogeographic structure of inshore marine taxa along the California coast. These patterns, in turn, should further inform the design of marine protected areas using dispersal models based on genomic data. The small genome of C. analis is typical of marine fishes at less than 1 Gb (genome size = 538 Mb), and our assembly is near-chromosome level (contig N50 = 9.1 Mb, scaffold N50 = 21 Mb, BUSCO completeness = 97.9%). Within the context of the CCGP, the Woolly Sculpin genome will be used as a reference for future whole-genome resequencing projects aimed at enhancing our knowledge of the population structure of the species, and efficacy of marine protected areas across the state.