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ABSTRACT Intracellular bacterial pathogens remodel cellular functions during their infectious cycle via the coordinated actions of effector molecules delivered through dedicated secretion systems. While the function of many individual effectors is known, how they interact to promote pathogenesis is rarely understood. The zoonotic bacterium Brucella abortus, the causative agent of brucellosis, delivers effector proteins via its VirB type IV secretion system (T4SS) which mediate biogenesis of the endoplasmic reticulum (ER)-derived replicative Brucella-containing vacuole (rBCV). Here, we show that T4SS effectors BspB and RicA display epistatic interactions in Brucella replication. Defects in rBCV biogenesis and Brucella replication caused by deletion of bspB were dependent on the host GTPase Rab2a and suppressed by the deletion of ricA, indicating a role of Rab2-binding effector RicA in these phenotypic defects. Rab2a requirements for rBCV biogenesis and Brucella intracellular replication were abolished upon deletion of both bspB and ricA, demonstrating that the functional interaction of these effectors engages Rab2-dependent transport in the Brucella intracellular cycle. Expression of RicA impaired host secretion and caused Golgi fragmentation. While BspB-mediated changes in ER-to-Golgi transport were independent of RicA and Rab2a, BspB-driven alterations in Golgi vesicular traffic also involved RicA and Rab2a, defining BspB and RicA’s functional interplay at the Golgi interface. Altogether, these findings support a model where RicA modulation of Rab2a functions impairs Brucella replication but is compensated by BspB-mediated remodeling of Golgi apparatus-associated vesicular transport, revealing an epistatic interaction between these T4SS effectors. IMPORTANCE Bacterial pathogens with an intracellular lifestyle modulate many host cellular processes to promote their infectious cycle. They do so by delivering effector proteins into host cells via dedicated secretion systems that target specific host functions. While the roles of many individual effectors are known, how their modes of action are coordinated is rarely understood. Here, we show that the zoonotic bacterium Brucella abortus delivers the BspB effector that mitigates the negative effect on bacterial replication that the RicA effector exerts via modulation of the host small GTPase Rab2. These findings provide an example of functional integration between bacterial effectors that promotes proliferation of pathogens.

Abstract Background The effects of environmental disturbances on livestock are often observed indirectly through the variability patterns of repeated performance records over time. Sheep are frequently exposed to diverse extensive environments but currently lack appropriate measures of resilience (or sensitivity) towards environmental disturbance. In this study, random regression models were used to analyse repeated records of the fibre diameter of wool taken along the wool staple (bundle of wool fibres) to investigate how the genetic and environmental variance of fibre diameter changes with different growing environments. Results A model containing a fifth, fourth and second-order Legendre polynomial applied to the fixed, additive and permanent environmental effects, respectively, was optimal for modelling fibre diameter along the wool staple. The additive genetic and permanent environmental variance both showed variability across the staple length trajectory. The ranking of sire estimated breeding values (EBV) for fibre diameter was shown to change along the staple and the genetic correlations decreased as the distance between measurements along the staple increased. This result suggests that some genotypes were potentially more resilient towards the changes in the growing environment compared to others. In addition, the eigenfunctions of the random regression model implied the ability to change the fibre diameter trajectory to reduce its variability along the wool staple. Conclusions These results show that genetic variation in fibre diameter measured along the wool staple exists and this could be used to provide greater insight into the ability to select for resilience in extensively raised sheep populations.

Multilingual speakers can find speech recognition in everyday environments like restaurants and open-plan offices particularly challenging. In a world where speaking multiple languages is increasingly common, effective clinical and educational interventions will require a better understanding of how factors like multilingual contexts and listeners' language proficiency interact with adverse listening environments. For example, word and phrase recognition is facilitated when competing voices speak different languages. Is this due to a "release from masking" from lower-level acoustic differences between languages and talkers, or higher-level cognitive and linguistic factors? To address this question, we created a "one-man bilingual cocktail party" selective attention task using English and Mandarin speech from one bilingual talker to reduce low-level acoustic cues. In Experiment 1, 58 listeners more accurately recognized English targets when distracting speech was Mandarin compared to English. Bilingual Mandarin-English listeners experienced significantly more interference and intrusions from the Mandarin distractor than did English listeners, exacerbated by challenging target-to-masker ratios. In Experiment 2, 29 Mandarin-English bilingual listeners exhibited linguistic release from masking in both languages. Bilinguals experienced greater release from masking when attending to English, confirming an influence of linguistic knowledge on the "cocktail party" paradigm that is separate from primarily energetic masking effects. Effects of higher-order language processing and expertise emerge only in the most demanding target-to-masker contexts. The "one-man bilingual cocktail party" establishes a useful tool for future investigations and characterization of communication challenges in the large and growing worldwide community of Mandarin-English bilinguals.

ABSTRACT Brucella abortus, the bacterial agent of the worldwide zoonosis brucellosis, primarily infects host phagocytes, where it undergoes an intracellular cycle within a dedicated membrane-bound vacuole, the Brucella-containing vacuole (BCV). Initially of endosomal origin (eBCV), BCVs are remodeled into replication-permissive organelles (rBCV) derived from the host endoplasmic reticulum, a process that requires modulation of host secretory functions via delivery of effector proteins by the Brucella VirB type IV secretion system (T4SS). Following replication, rBCVs are converted into autophagic vacuoles (aBCVs) that facilitate bacterial egress and subsequent infections, arguing that the bacterium sequentially manipulates multiple cellular pathways to complete its cycle. The VirB T4SS is essential for rBCV biogenesis, as VirB-deficient mutants are stalled in eBCVs and cannot mediate rBCV biogenesis. This has precluded analysis of whether the VirB apparatus also drives subsequent stages of the Brucella intracellular cycle. To address this issue, we have generated a B. abortus strain in which VirB T4SS function is conditionally controlled via anhydrotetracycline (ATc)-dependent complementation of a deletion of the virB11 gene encoding the VirB11 ATPase. We show in murine bone marrow-derived macrophages (BMMs) that early VirB production is essential for optimal rBCV biogenesis and bacterial replication. Transient expression of virB11 prior to infection was sufficient to mediate normal rBCV biogenesis and bacterial replication but led to T4SS inactivation and decreased aBCV formation and bacterial release, indicating that these postreplication stages are also T4SS dependent. Hence, our findings support the hypothesis of additional, postreplication roles of type IV secretion in the Brucella intracellular cycle. IMPORTANCE Many intracellular bacterial pathogens encode specialized secretion systems that deliver effector proteins into host cells to mediate the multiple stages of their intracellular cycles. Because these intracellular events occur sequentially, classical genetic approaches cannot address the late roles that these apparatuses play, as secretion-deficient mutants cannot proceed past their initial defect. Here we have designed a functionally controllable VirB type IV secretion system (T4SS) in the bacterial pathogen Brucella abortus to decipher its temporal requirements during the bacterium’s intracellular cycle in macrophages. By controlling production of the VirB11 ATPase, which energizes the T4SS, we show not only that this apparatus is required early to generate the Brucella replicative organelle but also that it contributes to completion of the bacterium’s cycle and bacterial egress. Our findings expand upon the pathogenic functions of the Brucella VirB T4SS and illustrate targeting of secretion ATPases as a useful strategy to manipulate the activity of bacterial secretion systems.

Abstract Objectives Phenobarbital (PB) is a long‐acting GABA A‐agonist with favorable pharmacokinetics (long half‐life and duration of effect) that allows effective treatment of alcohol withdrawal (AW) after administration of a single loading dose. Current evidence suggests that in the setting of AW, PB administration may be associated with decreased hospital admissions and hospital length of stay. The aim of this study was to evaluate the safety outcomes of AW patients who were treated and discharged from the emergency department (ED) after receiving PB for AW. Methods This retrospective chart review included a convenience sample of 33 AW patients who presented to four EDs within an 18‐month span. Descriptive statistics (frequencies and percentages) were used to describe demographics, distribution of resources and referrals, and the safety outcomes of PB administration for low‐risk AW patients. Patients were selected for inclusion in consultation with a medical toxicologist, treated with PB, and discharged from the ED. Electronic medical records were utilized to gather information on the patient cohort. Results All patients were treated with at least a single loading dose of 5‒10 mg/kg (ideal body weight) of intravenous or per os PB during their ED stay. Only one patient had an unanticipated event after discharge, which was related to driving against advice. Two additional patients had ED revisits for recurrent alcohol use within 72 h, and 16 patients had recurrent alcohol use within 30 days. All 33 patients were provided with resources for linkage to treatment. None required hospital admission. Conclusion ED PB “load and go” may be a safe, effective AW treatment that could help treat AW, facilitate linkage to specific rehabilitation treatments, and decrease hospital admissions.

Abstract Cognitive decline is a major health concern and identification of genes that may serve as drug targets to slow decline is important to adequately support an aging population. Whilst genetic studies of cross-sectional cognition have been carried out, cognitive change is less well-understood. Here, using data from the TOMMORROW trial, we investigate genetic associations with cognitive change in a cognitively normal older cohort. We conducted a genome-wide association study of trajectories of repeated cognitive measures (using generalised estimating equation (GEE) modelling) and tested associations with polygenic risk scores (PRS) of potential risk factors. We identified two genetic variants associated with change in attention domain scores, rs534221751 (p = 1 × 10−8 with slope 1) and rs34743896 (p = 5 × 10−10 with slope 2), implicating NCAM2 and CRIPT/ATP6V1E2 genes, respectively. We also found evidence for the association between an education PRS and baseline cognition (at >65 years of age), particularly in the language domain. We demonstrate the feasibility of conducting GWAS of cognitive change using GEE modelling and our results suggest that there may be novel genetic associations for cognitive change that have not previously been associated with cross-sectional cognition. We also show the importance of the education PRS on cognition much later in life. These findings warrant further investigation and demonstrate the potential value of using trial data and trajectory modelling to identify genetic variants associated with cognitive change.

In 2020, the COVID-19 pandemic interrupted all aspects of human activity, including environmental research and monitoring. Despite a lack of laboratory access and other restrictive measures, we adapted an existing community science monitoring program to continue through the summer of 2020. We worked with local community groups to recruit 58 volunteers who collected lake water samples from 60 sites on 16 lakes in south-central Ontario from June to September 2020. We organized drop-off depots and had volunteers freeze samples to monitor nearshore nutrients (phosphorus and nitrogen) and chlorophyll-a. A survey was distributed to volunteers to analyze lake-front property owners’ activities during the pandemic. We found spatial patterns in nearshore water quality across the lakes, with sub-watershed development being a significant predictor of nutrients and chlorophyll-a. Additionally, pre-pandemic (2019) and pandemic (2020 and 2021) nutrient concentrations were compared, but there was no clear impact of the pandemic on nearshore nutrient concentrations, despite changes in lake-front property owners activities. Overall, this study demonstrated the ability of community science to provide water quality data on a large spatial scale despite a major societal disruption, providing insight into regional nutrient trends during the first year of the pandemic.

Summary: Gain-of-function mutations in the LRRK2 gene cause Parkinson’s disease (PD), increasing phosphorylation of RAB GTPases through hyperactive kinase activity. We find that LRRK2-hyperphosphorylated RABs disrupt the axonal transport of autophagosomes by perturbing the coordinated regulation of cytoplasmic dynein and kinesin. In iPSC-derived human neurons, knockin of the strongly hyperactive LRRK2-p.R1441H mutation causes striking impairments in autophagosome transport, inducing frequent directional reversals and pauses. Knockout of the opposing protein phosphatase 1H (PPM1H) phenocopies the effect of hyperactive LRRK2. Overexpression of ADP-ribosylation factor 6 (ARF6), a GTPase that acts as a switch for selective activation of dynein or kinesin, attenuates transport defects in both p.R1441H knockin and PPM1H knockout neurons. Together, these findings support a model where a regulatory imbalance between LRRK2-hyperphosphorylated RABs and ARF6 induces an unproductive “tug-of-war” between dynein and kinesin, disrupting processive autophagosome transport. This disruption may contribute to PD pathogenesis by impairing the essential homeostatic functions of axonal autophagy.

Summary: Despite the importance of understanding how variability across induced pluripotent stem cell (iPSC) lines due to non-genetic factors (clone and passage) influences their differentiation outcome, large-scale studies capable of addressing this question have not yet been conducted. Here, we differentiated 191 iPSC lines to generate iPSC-derived cardiovascular progenitor cells (iPSC-CVPCs). We observed cellular heterogeneity across the iPSC-CVPC samples due to varying fractions of two cell types: cardiomyocytes (CMs) and epicardium-derived cells (EPDCs). Comparing the transcriptomes of CM-fated and EPDC-fated iPSCs, we discovered that 91 signature genes and X chromosome dosage differences are associated with these two distinct cardiac developmental trajectories. In an independent set of 39 iPSCs differentiated into CMs, we confirmed that sex and transcriptional differences affect cardiac-fate outcome. Our study provides novel insights into how iPSC transcriptional and X chromosome gene dosage differences influence their response to differentiation stimuli and, hence, cardiac cell fate. : In this article, D'Antonio-Chronowska, Donovan and colleagues differentiated 191 iPSC lines to generate iPSC-derived cardiovascular progenitor cells (iPSC-CVPCs). The iPSC-CVPC samples showed cellular heterogeneity due to varying fractions of cardiomyocytes (CMs) and epicardium-derived cells (EPDCs). Donor sex and expression levels of signature genes in iPSCs played a role in the relative proportions of CMs and EPDCs present in the derived CVPCs. Keywords: iPSC, iPSC-derived cardiovascular progenitor cells, iPSC-derived cardiomyocytes, iPSC-derived epicardium, scRNA-seq, single-cell transcriptomics, X chromosome inactivation, X chromosome erosion, iPSC differentiation

Summary: We evaluate whether human induced pluripotent stem cell-derived retinal pigment epithelium (iPSC-RPE) cells can be used to prioritize and functionally characterize causal variants at age-related macular degeneration (AMD) risk loci. We generated iPSC-RPE from six subjects and show that they have morphological and molecular characteristics similar to those of native RPE. We generated RNA-seq, ATAC-seq, and H3K27ac ChIP-seq data and observed high similarity in gene expression and enriched transcription factor motif profiles between iPSC-RPE and human fetal RPE. We performed fine mapping of AMD risk loci by integrating molecular data from the iPSC-RPE, adult retina, and adult RPE, which identified rs943080 as the probable causal variant at VEGFA. We show that rs943080 is associated with altered chromatin accessibility of a distal ATAC-seq peak, decreased overall gene expression of VEGFA, and allele-specific expression of a non-coding transcript. Our study thus provides a potential mechanism underlying the association of the VEGFA locus with AMD. : Smith, D'Antonio-Chronowska, and colleagues integrate newly generated epigenetic and transcriptomic data from iPSC-derived retinal pigment epithelium with data from adult samples to prioritize potential causal variants associated with age-related macular degeneration. They prioritize rs943080 at the VEGFA locus and show that the risk allele may reduce VEGFA gene expression by altering activity of a distal regulatory region. Keywords: induced pluripotent stem cells, retinal pigment epithelium, age-related macular degeneration, VEGFA, chromatin accessibility, fine mapping, regulatory variants, genome-wide association, iPSC-RPE

Abstract Introduction Given the rapidly aging population in both the United States and Mexico, rates of Parkinson's disease (PD) are likely to rise in both countries, suggesting that the number of individuals providing informal care will also increase, and the healthcare system will have to consider the burden this places upon caregivers. Therefore, the purpose of the current study was to examine differences in PD caregiving and burden between the United States and Mexico. Methods Data were collected from PD caregivers in the Parkinson's Clinic at the Hospital Civil Fray Antonio Alcalde in Guadalajara, Mexico (N = 148) and the Parkinson's and Movement Disorders Center at Virginia Commonwealth University in Richmond, Virginia (N = 105) regarding caregiver demographics and self‐reported burden. Results Despite considerably more time spent in caregiving duties, higher rates in unemployment or underemployment, and lower education levels, Mexican PD caregivers reported significantly less personal strain and role strain than did their United States counterparts. Even after controlling for these and other demographic differences between the two sites, the differences in caregiver burden remained. Conclusions Latino cultural values in Mexico encouraging the importance of caring for family members with PD and respecting elders may promote caregiving and even make it a point of cultural pride, helping to overcome potential negative effects on caregivers seen in the United States. The scientific and medical communities should view caregiving as a culturally embedded and potentially positive role, rather than predominantly as burdensome as frequently conceptualized in Western or Eurocentric cultures.

Venous thromboembolism (VTE) is a frequent complication in patients with cancer. Homozygous carriers of the fibrinogen gamma gene (FGG) rs2066865 have a moderately increased risk of VTE, but the effect of the FGG variant in cancer is unknown. We aimed to investigate the effect of the FGG variant and active cancer on the risk of VTE. Cases with incident VTE (n=640) and a randomly selected age-weighted sub-cohort (n=3,734) were derived from a population-based cohort (the Tromsø study). Cox-regression was used to estimate hazard ratios (HR) with 95% confidence intervals (CI) for VTE according to categories of cancer and FGG. In those without cancer, homozygosity at the FGG variant was associated with a 70% (HR 1.7, 95% CI: 1.2–2.3) increased risk of VTE compared to non-carriers. Cancer patients homozygous for the FGG variant had a two-fold (HR 2.0, 95% CI: 1.1–3.6) higher risk of VTE than cancer patients without the variant. Moreover, the six-months cumulative incidence of VTE among cancer patients was 6.4% (95% CI: 3.5–11.6) in homozygous carriers of FGG and 3.1% (95% CI: 2.3–4.7) in those without risk alleles. A synergistic effect was observed between rs2066865 and active cancer on the risk of VTE (synergy index: 1.81, 95% CI: 1.02–3.21, attributable proportion: 0.43, 95% CI: 0.11–0.74). In conclusion, homozygosity at the FGG variant and active cancer yielded a synergistic effect on the risk of VTE.

Abstract Background Genomic interaction studies use next-generation sequencing (NGS) to examine the interactions between two loci on the genome, with subsequent bioinformatics analyses typically including annotation, intersection, and merging of data from multiple experiments. While many file types and analysis tools exist for storing and manipulating single locus NGS data, there is currently no file standard or analysis tool suite for manipulating and storing paired-genomic-loci: the data type resulting from “genomic interaction” studies. As genomic interaction sequencing data are becoming prevalent, a standard file format and tools for working with these data conveniently and efficiently are needed. Results This article details a file standard and novel software tool suite for working with paired-genomic-loci data. We present the paired-genomic-loci (PGL) file standard for genomic-interactions data, and the accompanying analysis tool suite “pgltools”: a cross platform, pypy compatible python package available both as an easy-to-use UNIX package, and as a python module, for integration into pipelines of paired-genomic-loci analyses. Conclusions Pgltools is a freely available, open source tool suite for manipulating paired-genomic-loci data. Source code, an in-depth manual, and a tutorial are available publicly at www.github.com/billgreenwald/pgltools , and a python module of the operations can be installed from PyPI via the PyGLtools module.

Summary: Large-scale collections of induced pluripotent stem cells (iPSCs) could serve as powerful model systems for examining how genetic variation affects biology and disease. Here we describe the iPSCORE resource: a collection of systematically derived and characterized iPSC lines from 222 ethnically diverse individuals that allows for both familial and association-based genetic studies. iPSCORE lines are pluripotent with high genomic integrity (no or low numbers of somatic copy-number variants) as determined using high-throughput RNA-sequencing and genotyping arrays, respectively. Using iPSCs from a family of individuals, we show that iPSC-derived cardiomyocytes demonstrate gene expression patterns that cluster by genetic background, and can be used to examine variants associated with physiological and disease phenotypes. The iPSCORE collection contains representative individuals for risk and non-risk alleles for 95% of SNPs associated with human phenotypes through genome-wide association studies. Our study demonstrates the utility of iPSCORE for examining how genetic variants influence molecular and physiological traits in iPSCs and derived cell lines. : Working as part of the NHLBI NextGen consortium, Panopoulos and colleagues report the derivation and characterization of 222 publicly available iPSCs from ethnically diverse individuals with corresponding genomic data including SNP arrays, RNA-seq, and whole-genome sequencing. This collection provides a powerful resource to investigate the function of genetic variants. Keywords: iPSCORE, iPSC, GWAS, molecular traits, physiological traits, cardiac disease, NHLBI Next Gen, LQT2, KCNH2, iPSC-derived cardiomyocytes

A common CNS architecture is observed in all chordates, from vertebrates to basal chordates like the ascidian Ciona. Ciona stands apart among chordates in having a complete larval connectome. Starting with visuomotor circuits predicted by the Ciona connectome, we used expression maps of neurotransmitter use with behavioral assays to identify two parallel visuomotor circuits that are responsive to different components of visual stimuli. The first circuit is characterized by glutamatergic photoreceptors and responds to the direction of light. These photoreceptors project to cholinergic motor neurons, via two tiers of cholinergic interneurons. The second circuit responds to changes in ambient light and mediates an escape response. This circuit uses GABAergic photoreceptors which project to GABAergic interneurons, and then to cholinergic interneurons. Our observations on the behavior of larvae either treated with a GABA receptor antagonist or carrying a mutation that eliminates photoreceptors indicate the second circuit is disinhibitory.

Transcription controls splicing and other gene regulatory processes, yet mechanisms remain obscure due to our fragmented knowledge of the molecular connections between the dynamically phosphorylated RNA polymerase II (Pol II) C-terminal domain (CTD) and regulatory factors. By systematically isolating phosphorylation states of the CTD heptapeptide repeat (Y1S2P3T4S5P6S7), we identify hundreds of protein factors that are differentially enriched, revealing unappreciated connections between the Pol II CTD and co-transcriptional processes. These data uncover a role for threonine-4 in 3′ end processing through control of the transition between cleavage and termination. Furthermore, serine-5 phosphorylation seeds spliceosomal assembly immediately downstream of 3′ splice sites through a direct interaction with spliceosomal subcomplex U1. Strikingly, threonine-4 phosphorylation also impacts splicing by serving as a mark of co-transcriptional spliceosome release and ensuring efficient post-transcriptional splicing genome-wide. Thus, comprehensive Pol II interactomes identify the complex and functional connections between transcription machinery and other gene regulatory complexes.

This study seeks to understand the psychological factors that may contribute to the development and endorsement of ageist belief systems. Dual process theory is used to examine how one’s worldview, beliefs in social hierarchy, authoritarian aggression, authoritarian submission, and conventionalism predict ageist attitudes. Participants living in the United States (n = 407) in 49 states and territories were recruited through this online national study and completed surveys of their ageist beliefs, epistemological style, social dominance orientation (SDO), and right-wing authoritarianism (RWA). RWA, SDO, and naïve realism were all positively associated with ageist beliefs. A hypothesized path model and two alternative models suggested the retention of a model whereby naïve realism led to RWA, which led to SDO, and finally to ageism. All possible direct and indirect effects were significant within the retained model, suggesting the presence of a multiple mediation. The fit of this model was superior to that of models testing alternative theoretical causal chains. Naïve realism may lead to authoritarian aggression, authoritarian submission, and conventionalism, which may then increase the value that people place on social hierarchies, and this may influence the development and retention of ageist beliefs. Helping people to understand what their basic beliefs about the world are and how they may play a role in the development of ageism may assist in reducing ageist attitudes.

BACKGROUND: Nonvariceal upper gastrointestinal bleeding (NVUGIB) is associated with significant mortality.

Venous thromboembolism occurs frequently in cancer patients. Two variants in the factor 5 gene (F5), rs6025 encoding for the factor V Leiden mutation R506Q, and rs4524 encoding K858R, have been found to be associated with venous thromboembolism. We assessed the joint effect of active cancer and these two F5 variants on venous thromboembolism risk in a case-cohort study. Cases with a first venous thromboembolism (n=609) and a randomly selected age-weighted cohort (n=1,691) were sampled from the general population in Tromsø, Norway. Venous thromboembolism was classified as cancer-related if it occurred in the period 6 months before to 2 years after a diagnosis of cancer. Active cancer was associated with an 8.9-fold higher risk of venous thromboembolism (95% CI 7.2–10.9). The risk of cancer-related venous thromboembolism was 16.7-fold (95% CI 9.9–28.0) higher in subjects heterozygous for rs6025 compared with non-carriers of this variant without active cancer. In subjects with active cancer the risk of venous thromboembolism was 15.9-fold higher (95% CI 9.1–27.9) in those with one risk allele at rs4524, and 21.1-fold (95% CI 12.4–35.8) higher in those with two risk alleles compared with non-carriers without active cancer. A synergistic interaction was observed between active cancer and factor V Leiden (relative excess risk due to interaction 7.0; 95% CI 0.5–14.4) and rs4524 (relative excess risk due to interaction 15.0; 95% CI 7.5–29.2). The incidence of venous thromboembolism during the initial 6 months following a diagnosis of cancer was particularly high in subjects with risk alleles at these loci. This implies that the combination of cancer and F5 variants synergistically increases venous thromboembolism risk.

The Ciona notochord displays planar cell polarity (PCP), with anterior localization of Prickle (Pk) and Strabismus (Stbm). We report that a myosin is polarized anteriorly in these cells and strongly colocalizes with Stbm. Disruption of the actin/myosin machinery with cytochalasin or blebbistatin disrupts polarization of Pk and Stbm, but not of myosin complexes, suggesting a PCP-independent aspect of myosin localization. Wash out of cytochalasin restored Pk polarization, but not if done in the presence of blebbistatin, suggesting an active role for myosin in core PCP protein localization. On the other hand, in the pk mutant line, aimless, myosin polarization is disrupted in approximately one third of the cells, indicating a reciprocal action of core PCP signaling on myosin localization. Our results indicate a complex relationship between the actomyosin cytoskeleton and core PCP components in which myosin is not simply a downstream target of PCP signaling, but also required for PCP protein localization.

Infection with Babesia microti has not been well-described in eastern Pennsylvania, USA, despite the vector of this organism being prevalent. We report 3 cases of babesiosis in eastern Pennsylvania in persons without recent travel outside the region or history of blood transfusions, suggesting emergence of this infection.

Primary central nervous system lymphomas (PCNSL) have a dramatically increased prevalence among persons living with AIDS and are known to be associated with human Epstein Barr virus (EBV) infection. Previous work suggests that in some cases, co-infection with other viruses may be important for PCNSL pathogenesis. Viral transcription in tumor samples can be measured using next generation transcriptome sequencing. We demonstrate the ability of transcriptome sequencing to identify viruses, characterize viral expression, and identify viral variants by sequencing four archived AIDS-related PCNSL tissue samples and analyzing raw sequencing reads. EBV was detected in all four PCNSL samples and cytomegalovirus (CMV), JC polyomavirus (JCV), and HIV were also discovered, consistent with clinical diagnoses. CMV was found to express three long non-coding RNAs recently reported as expressed during active infection. Single nucleotide variants were observed in each of the viruses observed and three indels were found in CMV. No viruses were found in several control tumor types including 32 diffuse large B-cell lymphoma samples. This study demonstrates the ability of next generation transcriptome sequencing to accurately identify viruses, including DNA viruses, in solid human cancer tissue samples.

Recent advances in the ability to efficiently characterize tumor genomes is enabling targeted drug development, which requires rigorous biomarker-based patient selection to increase effectiveness. Consequently, representative DNA biomarkers become equally important in pre-clinical studies. However, it is still unclear how well these markers are maintained between the primary tumor and the patient-derived tumor models. Here, we report the comprehensive identification of somatic coding mutations and copy number aberrations in four glioblastoma (GBM) primary tumors and their matched pre-clinical models: serum-free neurospheres, adherent cell cultures, and mouse xenografts. We developed innovative methods to improve the data quality and allow a strict comparison of matched tumor samples. Our analysis identifies known GBM mutations altering PTEN and TP53 genes, and new actionable mutations such as the loss of PIK3R1, and reveals clear patient-to-patient differences. In contrast, for each patient, we do not observe any significant remodeling of the mutational profile between primary to model tumors and the few discrepancies can be attributed to stochastic errors or differences in sample purity. Similarly, we observe ∼96% primary-to-model concordance in copy number calls in the high-cellularity samples. In contrast to previous reports based on gene expression profiles, we do not observe significant differences at the DNA level between in vitro compared to in vivo models. This study suggests, at a remarkable resolution, the genome-wide conservation of a patient's tumor genetics in various pre-clinical models, and therefore supports their use for the development and testing of personalized targeted therapies.

Genome-wide association studies (GWASs) have identified a large number of variants (SNPs) associating with an increased risk of coronary artery disease (CAD). Recently, the CARDIoGRAM consortium published a GWAS based on the largest study population so far. They successfully replicated twelve already known associations and discovered thirteen new SNPs associating with CAD. We examined whether the genetic profiling of these variants improves prediction of subclinical atherosclerosis--i.e., carotid intima-media thickness (CIMT) and carotid artery elasticity (CAE)--beyond classical risk factors.We genotyped 24 variants found in a population of European ancestry and measured CIMT and CAE in 2001 and 2007 from 2,081, and 2,015 subjects (aged 30-45 years in 2007) respectively, participating in the Cardiovascular Risk in Young Finns Study (YFS). The Bogalusa Heart Study (BHS; n = 1179) was used as a replication cohort (mean age of 37.5). For additional replication, a sub-sample of 5 SNPs was genotyped for 1,291 individuals aged 46-76 years participating in the Health 2000 population survey. We tested the impact of genetic risk score (GRS(24SNP/CAD)) calculated as a weighted (by allelic odds ratios for CAD) sum of CAD risk alleles from the studied 24 variants on CIMT, CAE, the incidence of carotid atherosclerosis and the progression of CIMT and CAE during a 6-year follow-up.CIMT or CAE did not significantly associate with GRS(24SNP/CAD) before or after adjusting for classical CAD risk factors (p>0.05 for all) in YFS or in the BHS. CIMT and CAE associated with only one SNP each in the YFS. The findings were not replicated in the replication cohorts. In the meta-analysis CIMT or CAE did not associate with any of the SNPs.Genetic profiling, by using known CAD risk variants, should not improve risk stratification for subclinical atherosclerosis beyond conventional risk factors among healthy young adults.

Genome-wide association studies (GWAS) have identified multiple common variants associated with body mass index (BMI). In this study, we tested 23 genotyped GWAS-significant SNPs (p-value

To identify genetic factors that would be predictive of individuals who require an implantable cardioverter-defibrillator (ICD), we conducted a genome-wide association study among individuals with an ICD who experienced a life-threatening arrhythmia (LTA; cases) vs. those who did not over at least a 3-year period (controls).Most individuals that receive implantable cardioverter-defibrillators never experience a life-threatening arrhythmia. Genetic factors may help identify who is most at risk.Patients with an ICD and extended follow-up were recruited from 34 clinical sites with the goal of oversampling those who had experienced LTA, with a cumulative 607 cases and 297 controls included in the analysis. A total of 1,006 Caucasian patients were enrolled during a time period of 13 months. Arrhythmia status of 904 patients could be confirmed and their genomic data were included in the analysis. In this cohort, there were 704 males, 200 females, and the average age was 73.3 years. We genotyped DNA samples using the Illumina Human660 W Genotyping BeadChip and tested for association between genotype at common variants and the phenotype of having an LTA.We did not find any associations reaching genome-wide significance, with the strongest association at chromosome 13, rs11856574 at P = 5×10⁻⁶. Loci previously implicated in phenotypes such as QT interval (measure of the time between the start of the Q wave and the end of the T wave as measured by electrocardiogram) were not found to be significantly associated with having an LTA. Although powered to detect such associations, we did not find common genetic variants of large effect associated with having a LTA in those of European descent. This indicates that common gene variants cannot be used at this time to guide ICD risk-stratification.ClinicalTrials.gov NCT00664807.

Cardiovascular disease (CVD) is the leading cause of death worldwide. Recent genome-wide association (GWA) studies have pinpointed many loci associated with CVD risk factors in adults. It is unclear, however, if these loci predict trait levels at all ages, if they are associated with how a trait develops over time, or if they could be used to screen individuals who are pre-symptomatic to provide the opportunity for preventive measures before disease onset. We completed a genome-wide association study on participants in the longitudinal Bogalusa Heart Study (BHS) and have characterized the association between genetic factors and the development of CVD risk factors from childhood to adulthood. We report 7 genome-wide significant associations involving CVD risk factors, two of which have been previously reported. Top regions were tested for replication in the Young Finns Study (YF) and two associations strongly replicated: rs247616 in CETP with HDL levels (combined P = 9.7 x 10(-24)), and rs445925 at APOE with LDL levels (combined P = 8.7 x 10(-19)). We show that SNPs previously identified in adult cross-sectional studies tend to show age-independent effects in the BHS with effect sizes consistent with previous reports. Previously identified variants were associated with adult trait levels above and beyond those seen in childhood; however, variants with time-dependent effects were also promising predictors. This is the first GWA study to evaluate the role of common genetic variants in the development of CVD risk factors in children as they advance through adulthood and highlights the utility of using longitudinal studies to identify genetic predictors of adult traits in children.

Assessing socio-economic vulnerability to climate change impacts to support regional decision-making is conceptually and practically challenging. We report on research that tested a rapid assessment approach of socio-economic vulnerability in Australia’s natural resource management regions. The approach focuses on regionally important economic sectors, identified using existing datasets, which are likely to be sensitive to climate change impacts. Disaggregated spatial representations of factors known to be associated with vulnerability function as multiple lines of evidence for highlighting intra-regional hotspots of high potential vulnerability. Our results show that a small number of factors based upon contextually relevant empirical evidence offers a low-cost, rapid assessment process, which is readily transferable across regions and provides end-users with guidance for interpreting the results within the context of regional conditions.

The complexity of structural variation (SV) and short tandem repeats (STRs) makes it necessary to apply different calling and filtering strategies to sequencing datasets. Here, Jakubosky et al. report a comprehensive SV and STR callset from whole-genome sequencing of 477 individuals from iPSCORE and HipSci using five algorithms.

Genetic variation associated with gene expression changes has mostly been studied in the context of single nucleotide variants. Here, Jakubosky et al. report eQTL analysis of structural variants and short tandem repeats and find properties, such as length of variation, that affect the association.

Alzheimer’s disease (AD) and Parkinson’s disease (PD) are neurodegenerative disorders that affect millions of individuals worldwide. As incidence of these conditions increases with age, there will undoubtedly be an increased prevalence of cases in the near future. Neuroinflammation is a hallmark in the development and progression of neurodegenerative diseases and prevention or resolution of chronic neuroinflammation may represent a novel approach to treatment. The present review highlights the potential of the anti-inflammatory and pro-resolving effects of polyunsaturated fatty acid (PUFA)-derived mediators (Specialized Pro-resolving Mediators—SPM) in neurodegenerative disorders. PUFA-derived SPM are biosynthesized in response to chemicals produced from acute inflammatory responses. Preclinical studies from both AD and PD models suggest a dysregulation of SPM and their receptors in neurological disorders. Decreased SPM may be due to inadequate substrate, an imbalance between SPM and pro-inflammatory mediators or a disruption in SPM synthesis. SPMs hold great promise for neuroprotection in AD by altering expression of pro-inflammatory genes, modulating macrophage function, serving as a biomarker for AD status, and promoting resolution of neuroinflammation. In PD, data suggest SPM are able to cross the blood-brain barrier, inhibit microglial activation and decrease induced markers of inflammation, possibly as a result of their ability to downregulate NFκB signaling pathways. Several in vivo and in vitro studies suggest a benefit from administration of SPMs in both neurodegenerative disorders. However, extrapolation of these outcomes to humans is difficult as no models are able to replicate all features of AD or PD. Minimal data evaluating these PUFA-derived metabolites in humans with neurodegenerative disorders are available and a gap in knowledge exists regarding behavior of SPM and their receptors in patients with these conditions. There is also large gap in our knowledge regarding which lipid mediator would be most effective in which model of AD or PD and how dietary intake or supplementation can impact SPM levels. Future direction should include focused, translational efforts to investigate SPM as an add-on (in addition to standard treatment) or as standalone agents in patients with neurodegenerative disorders.

It is currently unclear how quantitative changes in chromatin loop propensity contribute to differential gene regulation. Here, the authors use phased Hi-C, RNA-seq, and ChIP-seq to show that subtle changes in loop propensity associate with differential gene regulation across cell types and haplotypes.

AbstractAt the neuromuscular junction (NMJ), postsynaptic ionotropic acetylcholine receptors (AChRs) transduce a chemical signal released from a cholinergic motor neuron into an electrical signal to induce muscle contraction. To identify regulators of postsynaptic function, we conducted a genome-wide RNAi screen for genes required for proper response to levamisole, a pharmacological agonist of ionotropic L-AChRs at the Caenorhabditis elegansepn-1Agas-1

Support for lesbian and gay (LG) civil rights has increased in recent decades, but heterosexism is still prevalent, particularly among highly religious populations. Evidence suggests, however, that it may not be affiliation, but rather conviction in one’s beliefs that relates to prejudicial attitudes. The aims of this study were to examine the relationships among religiosity, heterosexism, and level of support for LG civil rights, as well as potential moderating effects by religious fundamentalism. This study used Amazon’s Mechanical Turk (Mturk) to recruit a U.S. national sample (n = 407) to participate in an online survey. A mediation model was constructed with religiosity leading to heterosexism, which diminished support for LG civil rights. This mediation model was expanded into moderated mediations with three types of religious fundamentalism as moderators. Heterosexism fully mediated the relationship between religiosity and support for LG civil rights. A moderated mediation was observed for aspects of religious fundamentalism reflecting external authority and worldly rejection (but not fixed religion) such that the mediation was present only when participants had high levels of these types of religious fundamentalism. Despite the belief that religious people endorse higher levels of heterosexism and that this influences their support for LG civil rights, this is only true when religiosity is also coupled with fundamentalist belief systems reflecting external authority and worldly rejection.

Objective. The aim of this study was to uncover possible psychosocial underpinnings of pain and sleep disturbance in a safety-net primary care sample. Methods. Patients (n = 210) awaiting care in a safety-net primary care clinic waiting room completed measures of cynical hostility, social support, mental health, sleep disturbance, and pain. This study was cross-sectional and observational. Results. A structural equation model suggested that higher cynical hostility was associated with lower social support, which in turn was associated with poorer mental health, which then corresponded with higher pain and sleep disturbance. All possible indirect (mediational) effects within this model were statistically significant, suggesting a possible route through which cynical hostility may shape pain and sleep, two common presenting problems in primary care. Conclusions. These findings illustrate the interplay of psychosocial factors with chronic pain and sleep disturbance in a sample of low-income, predominantly African-American patients seeking care at a safety-net primary care clinic. The findings support integrated primary care as a way to target not only behavioral health issues but also the psychosocial factors entangled with physical health.

Only scant literature has focused on social support in Parkinson’s disease (PD) caregivers, and no studies to date have examined resilience in this population, despite both variables having been shown to be important in other caregiving populations. As a result, the purpose of the current study was to construct and validate a theoretical structural equation model whereby social support is associated with higher levels of resilience in PD caregivers and increased resilience is related to decreased mental health symptoms. Two hundred fifty three PD caregivers from two clinics in the United States and Mexico completed self-report measures of these constructs. Results suggested that the hypothesized pattern was robustly supported with the structural equation model showing generally good fit indices. Higher levels of social support were associated with increased resilience, which in turn was associated with reduced mental health symptoms. Resilience partially mediated social support’s effect on mitigating mental health symptoms. The model explained 11% of the variance in resilience and 35% in mental health symptoms. These findings have implications for future research on the development and tailoring of interventions to improve social support, resilience, and mental health in PD caregivers.

Informal caregivers are critical in the care of individuals with Parkinson’s disease (PD) and spend substantial time providing care, which may be associated with negative caregiver outcomes such as burden and mental health issues. Although research in the United States and Europe has generally supported these relations, there is very limited research on PD caregiving in Latin America. The current study examined the following connections in a sample of PD caregivers from the United States (N=105) and Mexico (N=148): (a) PD-related impairments (motor and nonmotor symptoms) and caregiver burden, (b) caregiver burden and caregiver mental health, and (c) PD-related impairments and mental health through caregiver burden. Study results uncovered significant relations among PD-related impairments, caregiver burden, and caregiver mental health. Further, caregiver burden fully mediated the relation between PD-related impairments and caregiver mental health at both study sites. Findings highlight a number of important intervention targets for caregivers and families, including caregiver burden and mental health.

Collaborative management of natural resources involves two or more parties working together to govern and/or manage a set of resources within a defined area. Although a number of collaborative management frameworks have been developed for protected area and fisheries management, few exist for freshwater resources that enable their comparative analysis. We present a framework of collaborative management for freshwater resources comprising three elements: scope, governance, and management. Application of the framework to 11 cases from Australia and New Zealand differentiates between primarily consultation/government-based arrangements through to cogovernance arrangements. Our framework differs from others because it highlights the multiscalar and nested nature of collaborative management arrangements that influence effective water resource management. Our analysis highlights the diversity of arrangements that exist for freshwater resource management. Cases involving indigenous groups, a social tradition of waterways management, and those outside the scope of national water resource management reforms generally had higher levels of power sharing and involvement. We argue for greater attention to the effectiveness of and links between governance and management processes to ensure collaborative management remains innovative and appropriate to context. We contribute a framework that contains a continua and three core elements that enables a parsimonious evaluation that could be applied to other resource management contexts and, thus avoids criticism of overly prescriptive, simplistic, and idealistic analysis.

Although a highly heritable and disabling disease, bipolar disorder's (BD) genetic variants have been challenging to identify. We present new genotype data for 1,190 cases and 401 controls and perform a genome-wide association study including additional samples for a total of 2,191 cases and 1,434 controls. We do not detect genome-wide significant associations for individual loci; however, across all SNPs, we show an association between the power to detect effects calculated from a previous genome-wide association study and evidence for replication (P = 1.5×10(-7)). To demonstrate that this result is not likely to be a false positive, we analyze replication rates in a large meta-analysis of height and show that, in a large enough study, associations replicate as a function of power, approaching a linear relationship. Within BD, SNPs near exons exhibit a greater probability of replication, supporting an enrichment of reproducible associations near functional regions of genes. These results indicate that there is likely common genetic variation associated with BD near exons (±10 kb) that could be identified in larger studies and, further, provide a framework for assessing the potential for replication when combining results from multiple studies.

The design for a simple, low-cost aerosol generation system for rodent inhalation studies is described here. This system is appropriate for low biohazard–level agents. In this study, two biosafety level 2 agents, Pasturella pneumotropica and Pseudomonas aeruginosa, were tested successfully. This system was also used to immunize mice and guinea pigs in ovalbumin-based models of pulmonary inflammation. This design is appropriate for studies with limited budgets and lower-level biosafety containment.