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For most of the 20th century, Xanthomonas euvesicatoria was the only known bacterium associated with bacterial spot of tomato in Florida. X. perforans quickly replaced X. euvesicatoria, mainly because of production of three bacteriocins (BCNs) against X. euvesicatoria; however, X. perforans outcompeted X. euvesicatoria even when the three known BCNs were deleted. Surprisingly, we observed antimicrobial activity against X. euvesicatoria in the BCN triple mutant when the triple mutant was grown in Petri plates containing multiple spots but not in Petri plates containing only one spot. We determined that changes in the headspace composition (i.e., volatiles) rather than a diffusible signal in the agar were required for induction of the antimicrobial activity. Other Xanthomonas species also produced volatile-induced antimicrobial compounds against X. euvesicatoria and elicited antimicrobial activity by X. perforans. A wide range of plant pathogenic bacteria, including Clavibacter michiganensis subsp. michiganensis, Pantoea stewartii, and Pseudomonas cichorii, also elicited antimicrobial activity by X. perforans when multiple spots of the species were present. To identify potential antimicrobial compounds, we performed liquid chromatography with high-resolution mass spectrometry of the agar surrounding the spot in the high cell density Petri plates where the antimicrobial activity was present compared with agar surrounding the spot in Petri plates with one spot where antimicrobial activity was not observed. Among the compounds identified in the zone of inhibition were N-butanoyl-L-homoserine lactone and N-(3-hydroxy-butanoyl)-homoserine lactone, which are known quorum-sensing metabolites in other bacteria.

The U.S. is the world’s leading producer of highbush blueberries (Vaccinium corymbosum L.), and Michigan is ranked in the top five production states (USDA NASS, 2022). In June and July of 2021, 268 blueberry stem blight samples were collected for a pathogen survey across 22 total fields in Van Buren and Ottawa counties in Michigan. Current season stems with symptoms of necrosis and wilting were collected. Stems were cut just below the necrotic area and cross-sections (2-3 mm long) were surface disinfested in 10% bleach for 1 min, rinsed twice in sterile distilled water, and dried on sterile paper towels. Stem cross-sections were plated onto potato dextrose agar (PDA) amended with 100 µg/ml streptomycin sulfate and 50 µg/ml ampicillin. Plates were incubated at 21°C under a 12-h photoperiod for 5-6 days. Outgrowing fungi with morphology similar to Diaporthe spp. were transferred to new PDA plates 2 consecutive times after 7 days of similar incubation to ensure single colony isolation. After 7 days, colonies consisted of white and light brown mycelia that were mostly flat, with some isolates that had partially raised mycelia towards the center of the plate. After 3-4 weeks, colonies turned brown and gray and produced dark brown pycnidia. Aseptate, hyaline, fusiform to ellipsoid, biguttulate alpha conidia measuring 5.4 to 7.6 x 2.6 to 3.7 µm (n = 60) were produced. No beta conidia were observed. In total, 3 isolates, representing 3 different farms (37-95 km apart) and cultivars (‘Duke’, ‘Jersey’, and ‘Bluecrop’), as well as 2 counties, were identified as Diaporthe through colony morphology (Gomes et al. 2013, Udayanga et al. 2014). Amplification and subsequent Sanger sequencing were performed for the internal transcribed spacer (ITS) region and portions of the translation elongation factor (TEF) 1-α, β-tubulin (TUB), and histone H3 (HIS) genes using primers ITS5/ITS4 (White et al. 1990), EF1-728F/EF1-986R (Carbone and Kohn 1999), T1/Bt-2b (Glass and Donaldson 1995), and CYLH3F/H3-1b (Glass and Donaldson 1995), respectively. Representative sequences were deposited in NCBI GenBank (accession no. OQ507870-OQ507872 for ITS, and OQ550272-OQ550278 for TEF, HIS, and TUB). BLASTn results revealed 97-100% identity for all 4 genes across other established D. eres isolates reported in Gomes et al. (2013). For example, JMK047 had 99.8% (577/578 bp), 99.7% (327/328 bp), 100% (701/701 bp), and 100% (439/439 bp) homology with ITS, TEF, TUB, and HIS sequences, respectively, of D. eres CBS 439.82 (accession no. KC343090, KC343816, KC344058, KC343574). Koch’s Postulates were fulfilled via pathogenicity tests on 2-year-old potted ‘Blueray’ plants with 2 isolates. Stems were surface sterilized with 1% bleach then 8-mm long pieces of bark were removed using a sterile razor blade to expose the cambium. Plugs of sterile PDA (negative control) or mycelia from 7-day old cultures on PDA (5-mm diameter) were placed onto the cambium layer and sealed with Parafilm. Six stems on unique plants were inoculated per treatment. Plants were grown in a 20.5°C greenhouse with a 14-hr photoperiod. After 3 weeks, the stems inoculated with D. eres isolates showed similar stem blight symptoms to those observed in the field while control stems remained healthy. Re-isolation and sequencing of the ITS region of 3 replicates per treatment with the protocol described above confirmed symptoms correlated with D. eres isolates. This is the first report of D. eres associated with stem blight of highbush blueberry in Michigan, and the second report in the U.S. (Lombard et al. 2014). Increasing prevalence of D. eres in U.S. blueberries may affect disease management programs. References Carbone, I., and Kohn, L. M. 1999. Mycologia 91:553. 10.1080/00275514.1999.12061051. Glass, N. L., and Donaldson, G. C. 1995. Appl. Environ. Microbiol. 61:1323. 10.1128/aem.61.4.1323-1330.1995. Gomes, R. R., et al. 2013. Persoonia 31:1. 10.3767/003158513x666844. Lombard, L., et al. 2014. Phytopathol. Mediterr. 51(2):287. 10.14601/Phytopathol_Mediterr-14034. Udayanga, D., Castlebury, L. A., Rossman, A. Y., Chukeatirote, E., and Hyde, K. D. 2014. Fungal Divers. 67:203-229. 10.1007/s13225-014-0297-2. USDA NASS. 2022. Noncitrus Fruits and Nuts 2021 Summary. White, T. J., et al. 1990. Page 315 in: PCR Protocols: A Guide to Methods and Applications. Academic Press, Inc., San Diego, California, USA.

Genetic regulation of gene expression is a complex process, with genetic effects known to vary across cellular contexts such as cell types and environmental conditions. We developed SURGE, a method for unsupervised discovery of context-specific expression quantitative trait loci (eQTLs) from single-cell transcriptomic data. This allows discovery of the contexts or cell types modulating genetic regulation without prior knowledge. Applied to peripheral blood single-cell eQTL data, SURGE contexts capture continuous representations of distinct cell types and groupings of biologically related cell types. We demonstrate the disease-relevance of SURGE context-specific eQTLs using colocalization analysis and stratified LD-score regression.

Modern agricultural practices increase the potential for plant pathogen spread, while the advent of affordable whole genome sequencing enables in-depth studies of pathogen movement. Population genomic studies may decipher pathogen movement and population structure as a result of complex agricultural production systems. We used whole genome sequences of 281 Xanthomonas perforans strains collected within one tomato production season across Florida and southern Georgia fields to test for population genetic structure associated with tomato production system variables. We identified six clusters of X. perforans from core gene SNPs that corresponded with phylogenetic lineages. Using whole genome SNPs, we found genetic structure among farms, transplant facilities, cultivars, seed producers, grower operations, regions, and counties. Overall, grower operations that produced their own transplants were associated with genetically distinct and less diverse populations of strains compared to grower operations that received transplants from multiple sources. The degree of genetic differentiation among components of Florida’s tomato production system varied between clusters, suggesting differential dispersal of the strains, such as through seed or contaminated transplants versus local movement within farms. Overall, we showed that the genetic variation of a bacterial plant pathogen is shaped by the structure of the plant production system.

Background: The case count for coronavirus disease 2019 (COVID-19) is the predominant measure used to track epidemiological dynamics and inform policy decision-making. Case counts, however, are influenced by testing rates and strategies, which have varied over time and space. A method to interpret COVID-19 case counts consistently in the context of other surveillance data is needed, especially for data-limited settings in low- and middle-income countries (LMICs). Methods: Statistical analyses were used to detect changes in COVID-19 surveillance data. The pruned exact linear time change detection method was applied for COVID-19 case counts, number of tests, and test positivity rate over time. With this information, change points were categorized as likely driven by epidemiological dynamics or non-epidemiological influences, such as noise. Findings: Higher rates of epidemiological change detection are more associated with open testing policies than with higher testing rates. This study quantified alignment of non-pharmaceutical interventions with epidemiological changes. LMICs have the testing capacity to measure prevalence with precision if they use randomized testing. Rwanda stands out as a country with an efficient COVID-19 surveillance system. Subnational data reveal heterogeneity in epidemiological dynamics and surveillance. Interpretation: Relying solely on case counts to interpret pandemic dynamics has important limitations. Normalizing counts by testing rate mitigates some of these limitations, and an open testing policy is key to efficient surveillance. The study findings can be leveraged by public health officials to strengthen COVID-19 surveillance and support programmatic decision-making.

Abstract Jurassic to Eocene sedimentary rocks in central Arabia have been deformed by faulting and jointing. We measured these structures in the field. Paleostress directions from these data demonstrate that successive extensional events occurred. Introduction The effects on platforms of distal tectonic events can be used to study the deformation in front of mountain belts (Bergerat, 1987) or between more highly deformed regions (Bergerat et al., 1992). These studies may yield clues to the directions of plate motion which may be difficult to decipher within the mountain belts due to the complexity of the deformation, or they may aid in determining the deformation process. Unlike regions previously studied in this context, the Arabian Platform is not just in front of a mountain belt such as the West European Platform (Bergerat, 1987) nor trapped between deformed zones such as the Colorado Plateau (Bergerat et al., 1992), but is the foreland of the Bitlis/Zagros/Oman deformation belt and is also near the Red Sea/Gulf of Aden which have been forming as small ocean basins simultaneously with convergence in the mountain belt. Previous workers have argued that the Red Sea/Gulf of Aden could not have formed as a "passive" rift related to the formation of the Bitlis/Zagros belt because the Arabian Platform is undeformed. In this paper, we show that the central Arabian platform has indeed been deformed and we link its deformation to tectonic events occurring on the margins of the Arabian plate supporting models for a passive origin of the Red Sea/Gulf of Aden (Gordon and Hempton, 1986; Hempton, 1987; Bohannon et al., 1989).

Tomato is an important crop grown worldwide. Various plant diseases cause massive losses in tomato plants due to diverse biotic agents. Bacterial spot of tomato (BST) is a worldwide disease that results in high losses in processed and fresh tomato. Xanthomonas perforans, an aerobic, single-flagellated, rod-shaped, Gram-negative plant pathogenic bacterium, is one of the leading causes of BST. Over the past three decades, X. perforans has increasingly been reported from tomato-growing regions and became a major bacterial disease. X. perforans thrives under high humidity and high temperature, which is commonplace in tropical and subtropical climates. Distinguishing symptoms of BST are necrotic lesions that can coalesce and cause a shot-hole appearance. X. perforans can occasionally cause fruit symptoms depending on disease pressure during fruit development. Short-distance movement in the field is mainly dependent on wind-driven rain, whereas long distance movement occurs through contaminated seed or plant material. X. perforans harbors a suite of effectors that increase pathogen virulence, fitness, and dissemination. BST management mainly relies on copper-based compounds; however, resistance is widespread. Alternative compounds, such as nanomaterials, are currently being evaluated and show high potential for BST management. Resistance breeding remains difficult to attain due to limited resistant germplasm. While the increased genetic diversity and gain and loss of effectors in X. perforans limits the success of single-gene resistance, the adoption of effector-specific transgenes and quantitative resistance may lead to durable host resistance. However, further research that aims to more effectively implement novel management tools is required to curb disease spread. KEY POINTS: • Xanthomonas perforans causes bacterial spot on tomato epidemics through infected seedlings and movement of plant material. • Genetic diversity plays a major role in shaping populations which is evident in loss and gain of effectors. • Management relies on copper sprays, but nanoparticles are a promising alternative to reduce copper toxicity.

Before 1991, Xanthomonas euvesicatoria was the causal agent of bacterial spot of tomato in Florida but was quickly replaced by X. perforans. The X. perforans population has changed in genotype and phenotype despite lack of a clear selection pressure. To determine the current Xanthomonas population in Florida, we collected 585 Xanthomonas strains from 70 tomato fields, representing 22 farms across eight counties, in the Florida tomato production region. Strains were isolated from 23 cultivars across eight seed producers and were associated with eight transplant facilities during the fall 2017 season. Our collection was phenotypically and genotypically characterized. Only X. perforans was identified, and all strains except one (99.8%) were tolerant to copper sulfate and 25% of strains were resistant to streptomycin sulfate. Most of the strains (99.3%) that were resistant to streptomycin sulfate were sequence type 1. The X. perforans population consisted of tomato races 3 (8%) and 4 (92%) and all three previously reported sequence types, ranging from 22 to 46% frequency. Approximately half of all strains, none of which were sequence type 2, produced bacteriocins against X. euvesicatoria. Effector profiles were highly variable among strains, which could impact the strains’ host range. The effector xopJ4, which was previously thought to be conserved in X. perforans tomato pathogens, was absent in 19 strains. Nonmetric multidimensional scaling and network analyses show how strains and strain traits were associated with production system variables, including anonymized farms and transplant facilities. These analyses show that the composition of the Florida X. perforans population is diverse and complex.

The SARS-CoV-2 pandemic has reemphasized the importance of genomic epidemiology to track the evolution of the virus, dynamics of epidemics, geographic origins, and the emerging variants. It is vital in understanding the epidemiological spread of the virus on global, national, and local scales. Several analytical (bioinformatics) resources have been developed for molecular surveillance. However, a resource that combines genetic mutations and functional annotations on the impact of these mutations has been lacking in SARS-CoV-2 genomics surveillance. COVID-MVP provides an interactive visualization application that summarizes the mutations and their prevalence in SARS-CoV-2 viral lineages and provides functional annotations from the literature curated in an ongoing effort, Pokay. COVID-MVP is a tool that can be used for routine surveillance including spatio-temporal analyses. We have powered the visualization through a scalable and reproducible genomic analysis workflow nf-ncov-voc wrapped in Nextflow. COVID-MVP allows users to interactively explore data and download summarized surveillance reports. COVID-MVP, Pokay, and nf-ncov-voc are open-source tools available under the Massachusetts Institute of Technology (MIT) and GPL-3.0 licenses. COVID-MVP source code is available at https://github.com/cidgoh/COVID-MVP and an instance is hosted at https://covidmvp.cidgoh.ca.

Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease. Knowledge of circulating immune cell types and states associated with SLE remains incomplete. We profiled more than 1.2 million peripheral blood mononuclear cells (162 cases, 99 controls) with multiplexed single-cell RNA sequencing (mux-seq). Cases exhibited elevated expression of type 1 interferon–stimulated genes (ISGs) in monocytes, reduction of naïve CD4(+) T cells that correlated with monocyte ISG expression, and expansion of repertoire-restricted cytotoxic GZMH(+) CD8(+) T cells. Cell type–specific expression features predicted case-control status and stratified patients into two molecular subtypes. We integrated dense genotyping data to map cell type–specific cis–expression quantitative trait loci and to link SLE-associated variants to cell type–specific expression. These results demonstrate mux-seq as a systematic approach to characterize cellular composition, identify transcriptional signatures, and annotate genetic variants associated with SLE. INTRODUCTION: Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease with elevated prevalence in women and individuals of Asian, African, and Hispanic ancestry. Bulk transcriptomic profiling has implicated increased type 1 interferon signaling, dysregulated lymphocyte activation, and failure of apoptotic clearance as hallmarks of disease. Many genes participating in these processes are proximal to the ~100 loci associated with SLE. Despite this progress, a comprehensive census of circulating immune cells in SLE remains incomplete, and annotating the cell types and contexts that mediate genetic associations remains challenging. RATIONALE: Historically, flow cytometry and bulk transcriptomic analyses were used to profile the composition and gene expression of circulating immune cells in SLE. However, flow cytometry is biased by its use of a limited set of known markers, whereas bulk transcriptomic profiling does not have sufficient power to detect cell type–specific expression differences. Single-cell RNA sequencing (scRNA-seq) of peripheral blood mononuclear cells (PBMCs) holds potential as a comprehensive and unbiased approach to simultaneously profile the composition and transcriptional states of circulating immune cells. However, application of scRNA-seq to population cohorts has been limited by sample throughput, cost, and susceptibility to technical variability. To overcome these limitations, we previously developed multiplexed scRNA-seq (mux-seq) to enable systematic and cost-effective scRNA-seq of population cohorts. RESULTS: We used mux-seq to profile more than 1.2 million PBMCs from 162 SLE cases and 99 healthy controls of either Asian or European ancestry. SLE cases exhibited differences in both the composition and state of PBMCs. Analysis of lymphocyte composition revealed a reduction in naïve CD4(+) T cells and an increase in repertoire-restricted GZMH(+) CD8(+) T cells. Analysis of transcriptomic profiles across eight cell types revealed that classical monocytes expressed the highest levels of both pan–cell type and myeloid-specific type 1 interferon-stimulated genes (ISGs). The expression of ISGs in monocytes was inversely correlated with naïve CD4(+) T cell abundance. Cell type–specific expression features accurately predicted case-control status and stratified patients into molecular subtypes. By integrating genotyping data and using a novel matrix decomposition method, we mapped shared and cell type–specific cis–expression quantitative trait loci (cis-eQTLs) across eight cell types. Cell type–specific cis-eQTLs were enriched for regions of open chromatin specific to the same or related cell types. Joint analysis of cis-eQTLs and genome-wide association study results enabled identification of cell types relevant to immune-mediated diseases, fine-mapping of disease-associated loci, and discovery of novel SLE associations. Interaction analysis identified variants whose effects on gene expression are further modified by interferon activation across patients. CONCLUSION: SLE remains challenging to diagnose and treat. The heterogeneity of disease manifestations and treatment response highlight the need for improved molecular characterization. In a large multiethnic cohort, we demonstrate mux-seq as a systematic approach to characterize cellular composition, identify cell type–specific transcriptomic signatures, and annotate genetic variants associated with SLE.

The human immune system displays substantial variation between individuals, leading to differences in susceptibility to autoimmune disease. We present single-cell RNA sequencing (scRNA-seq) data from 1,267,758 peripheral blood mononuclear cells from 982 healthy human subjects. For 14 cell types, we identified 26,597 independent cis-expression quantitative trait loci (eQTLs) and 990 trans-eQTLs, with most showing cell type–specific effects on gene expression. We subsequently show how eQTLs have dynamic allelic effects in B cells that are transitioning from naïve to memory states and demonstrate how commonly segregating alleles lead to interindividual variation in immune function. Finally, using a Mendelian randomization approach, we identify the causal route by which 305 risk loci contribute to autoimmune disease at the cellular level. This work brings together genetic epidemiology with scRNA-seq to uncover drivers of interindividual variation in the immune system.

SummaryTissue- and organism-level biological processes often involve coordinated action of multiple distinct cell types. Current computational methods for the analysis of single-cell RNA-sequencing (scRNA-seq) data, however, are not designed to capture co-variation of cell states across samples, in part due to the low number of biological samples in most scRNA-seq datasets. Recent advances in sample multiplexing have enabled population-scale scRNA-seq measurements of tens to hundreds of samples. To take advantage of such datasets, here we introduce a computational approach called single-cell Interpretable Tensor Decomposition (scITD). This method extracts “multicellular gene expression patterns” that vary across different biological samples. These patterns capture how changes in one cell type are connected to changes in other cell types. The multicellular patterns can be further associated with known covariates (e.g., disease, treatment, or technical batch effects) and used to stratify heterogeneous samples. We first validated the performance of scITD usingin vitroexperimental data and simulations. We then applied scITD to scRNA-seq data on peripheral blood mononuclear cells (PBMCs) from 115 patients with systemic lupus erythematosus and 56 healthy controls. We recapitulated a well-established pan-cell-type signature of interferon-signaling that was associated with the presence of anti-dsDNA autoantibodies and a disease activity index. We further identified a novel multicellular pattern that appears to potentiate renal involvement for patients with anti-dsDNA autoantibodies. This pattern was characterized by an expansion of activated memory B cells along with helper T cell activation and is predicted to be mediated by an increase in ICOSLG-ICOS interaction between monocytes and helper T cells. Finally, we applied scITD to two PBMC datasets from patients with COVID-19 and identified reproducible multicellular patterns that stratify patients by disease severity. Overall, scITD is a flexible method for exploring co-variation of cell states in multi-sample single-cell datasets, which can yield new insights into complex non-cell-autonomous dependencies that define and stratify disease.

The prognosis for people with the high-grade brain tumor glioblastoma is very poor, due largely to low cell death in response to genotoxic therapy. The transcription factor BCL6, a protein that normally suppresses the DNA damage response during immune cell maturation, and a known driver of B-cell lymphoma, was shown to mediate the survival of glioblastoma cells. Expression was observed in glioblastoma tumor specimens and cell lines. When BCL6 expression or activity was reduced in these lines, increased apoptosis and a profound loss of proliferation was observed, consistent with gene expression signatures suggestive of anti-apoptotic and pro-survival signaling role for BCL6 in glioblastoma. Further, treatment with the standard therapies for glioblastoma-ionizing radiation and temozolomide-both induced BCL6 expression in vitro, and an in vivo orthotopic animal model of glioblastoma. Importantly, inhibition of BCL6 in combination with genotoxic therapies enhanced the therapeutic effect. Together these data demonstrate that BCL6 is an active transcription factor in glioblastoma, that it drives survival of cells, and that it increased with DNA damage, which increased the survival rate of therapy-treated cells. This makes BCL6 an excellent therapeutic target in glioblastoma-by increasing sensitivity to standard DNA damaging therapy, BCL6 inhibitors have real potential to improve the outcome for people with this disease.

Composite laminate thickness tapering is essential for weight efficient structures. This is achieved by terminating specific plies, but these can in turn act as sites for delamination initiation. One area of importance is the spacing between adjacent ply drops, which can have a significant impact on the delamination stress. In this work, a novel tape scarfing method that applies a tapered profile to dropped ply ends was used on unidirectional tapered laminate specimens with multiple ply drops. The effect of ply drop spacing on the delamination stress of both conventional and scarfed plies in tension was studied experimentally. The results showed that the scarfed ply drop configurations can completely suppress delamination in certain configurations. The scarfed ply drops also retained higher performance with smaller ply drop spacings. This indicates that in using scarfed plies, conventional laminate design rules could be relaxed and the weight of the structure could be further reduced. The underlying failure mechanisms were also investigated using both analytical and numerical methods. A simple stress-based formula for estimating the delamination stress of scarfed plies was introduced and shown to be consistent with both experimental and numerical results, which could be used (and further developed) to make tapered laminate design easier.

Psychosis in Alzheimer's disease (AD) represents a distinct disease subtype with a more rapid progression of illness evidenced by an increased velocity of cognitive decline and a hastened mortality. Previous biomarker and post-mortem studies have implicated tau neuropathology as a possible mediator of the accelerated decline in AD psychosis. Tau positron emission tomography (PET) neuroimaging provides the opportunity to evaluate tau pathology in-vivo, so that clinical symptomatology can be correlated with disease pathology. [

Introduction This study aimed to investigate potential factors, including delay to surgical stabilisation, affecting mortality in older patients sustaining pelvic or acetabular (PA) fractures. Method A retrospective review of the Trauma Audit and Research Network (TARN) database was performed to identify older patients (aged 65 and over) sustaining PA fractures treated surgically in a UK Major Trauma Centre (MTC) between 2015 and 2019. Chi-squared and Fisher tests were used to compare 1-year mortality rates following operative intervention between patients treated within 72-hours and after 72-hours. Kaplan-Meier curves were used to visualise survival probability; significant predictors of survival were found using Cox proportional hazard models. Results Of 564 older patients with PA fractures, 70 met the inclusion criteria. The mean age was 76.1 years. The overall 1-year mortality rate was 20%. When patients were grouped by time to surgery, there was no statistically significant difference in 1-year mortality. Patients whose surgery was delayed more than 72-hours were more likely to have longer hospital stays (p = 0.002) or to have suffered from polytrauma (p = 0.025). Age, Charlson Co-morbidities Index and pre-op mobility status were associated with statistically significant differences in overall mortality. Patient gender, mechanism of injury, polytrauma and head injury were not significant predictors of mortality. Conclusions Surgical intervention within 72-hours of injury did not result in decreased mortality in older patients with PA fractures. The 1–year mortality rate between older PA fractures and hip fractures was comparable. Consideration should be given to a combined multidisciplinary approach to managing these patients.