io Initial Resuscitation Algorithm for Children By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 Full Article
io Surviving Sepsis Campaign International Guidelines By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 Full Article
io Nickel Allergic Contact Dermatitis: Identification, Treatment, and Prevention By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 Nickel is a ubiquitous metal added to jewelry and metallic substances for its hardening properties and because it is inexpensive. Estimates suggest that at least 1.1 million children in the United States are sensitized to nickel. Nickel allergic contact dermatitis (Ni-ACD) is the most common cutaneous delayed-type hypersensitivity reaction worldwide. The incidence among children tested has almost quadrupled over the past 3 decades. The associated morbidities include itch, discomfort, school absence, and reduced quality of life. In adulthood, individuals with Ni-ACD may have severe disabling hand eczema. The increasing rate of Ni-ACD in children has been postulated to result from early and frequent exposure to metals with high amounts of nickel release (eg, as occurs with ear piercing or with products used daily in childhood such as toys, belt buckles, and electronics). To reduce exposure to metal sources with high nickel release by prolonged and direct contact with human skin, Denmark and the European Union legislated a directive several decades ago with the goal of reducing high nickel release and the incidence of Ni-ACD. Since then, there has been a global reduction in incidence of Ni-ACD in population-based studies of adults and studies of children and young adults being tested for allergic contact dermatitis. These data point to nickel exposure as a trigger for elicitation of Ni-ACD and, further, provide evidence that legislation can have a favorable effect on the economic and medical health of a population. This policy statement reviews the epidemiology, history, and appearances of Ni-ACD. Examples of sources of high nickel release are discussed to highlight how difficult it is to avoid this metal in modern daily lives. Treatments are outlined, and avoidance strategies are presented. Long-term epidemiological interventions are addressed. Advocacy for smarter nickel use is reviewed. The American Academy of Pediatrics supports US legislation that advances safety standards (as modeled by the European Union) that protect children from early and prolonged skin exposure to high–nickel-releasing items. Our final aim for this article is to aid the pediatric community in developing nickel-avoidance strategies on both individual and global levels. Full Article
io Children With Intellectual and Developmental Disabilities as Organ Transplantation Recipients By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 The demand for transplantable solid organs far exceeds the supply of deceased donor organs. Patient selection criteria are determined by individual transplant programs; given the scarcity of solid organs for transplant, allocation to those most likely to benefit takes into consideration both medical and psychosocial factors. Children with intellectual and developmental disabilities have historically been excluded as potential recipients of organ transplants. When a transplant is likely to provide significant health benefits, denying a transplant to otherwise eligible children with disabilities may constitute illegal and unjustified discrimination. Children with intellectual and developmental disabilities should not be excluded from the potential pool of recipients and should be referred for evaluation as recipients of solid organ transplants. Full Article
io Early and Often: The Need for Comprehensive Discussion of Treatment-Induced Cancer Late Effects By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 Full Article
io Ahmed A, Fend PI, Gaensbauer JT, Reves RR, Khurana R, Salcedo K, Punnoose R, Katz DJ, for the TUBERCULOSIS EPIDEMIOLOGIC STUDIES CONSORTIUM. Interferon-{gamma} Release Assays in Children <15 Years of Age. Pediatrics. 2020:145(1):e20191930 By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 Full Article
io The Time Is Now: Standardized Sedation Training for Pediatric Hospitalists By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 Full Article
io Adolescent Sexual Health Interventions: Innovation, Efficacy, Cost, and the Urgent Need to Scale By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 Full Article
io Exploring Early Childhood Factors as an Avenue to Address Chronic Peer Victimization By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 Full Article
io Optimizing Human Papillomavirus Immunization: The Role of Centralized Reminder and Recall Systems By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 Full Article
io Providing the Evidence for Managing Depression in Pregnancy By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 Full Article
io Trends in Outpatient Procedural Sedation: 2007-2018 By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 BACKGROUND: Pediatric subspecialists routinely provide procedural sedation outside the operating room. No large study has reported trends in outpatient pediatric procedural sedation. Our purpose in this study was to identify significant trends in outpatient procedural sedation using the Pediatric Sedation Research Consortium. METHODS: Prospectively collected data from 2007 to 2018 were used for trending procedural sedation. Patient characteristics, medications, type of providers, serious adverse events, and interventions were reported. The Cochran–Armitage test for trend was used to explore the association between the year and a given characteristic. RESULTS: A total of 432 842 sedation encounters were identified and divided into 3 4-year epochs (2007–2011, 2011–2014, and 2014–2018). There was a significant decrease in infants <3 months of age receiving procedural sedation (odds ratio = 0.97; 95% confidence interval, 0.96–0.98). A large increase was noticed in pediatric hospitalists providing procedural sedation (0.6%–9.5%; P < .001); there was a decreasing trend in sedation by other providers who were not in emergency medicine, critical care, or anesthesiology (13.9%–3.9%; P < .001). There was an increasing trend in the use of dexmedetomidine (6.3%–9.3%; P < .001) and a decreasing trend in the use of chloral hydrate (6.3%–0.01%; P < .001) and pentobarbital (7.3%–0.5%; P < .001). Serious adverse events showed a nonsignificant increase overall (1.35%–1.75%). CONCLUSIONS: We report an increase in pediatric hospitalists providing sedation and a significant decrease in the use of chloral hydrate and pentobarbital by providers. Further studies are required to see if sedation services decrease costs and optimize resource use. Full Article
io Parental Considerations Regarding Cure and Late Effects for Children With Cancer By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 BACKGROUND: More than 80% of children with cancer become long-term survivors, yet most survivors experience late effects of treatment. Little is known about how parents and physicians consider late-effects risks against a potential survival benefit when making treatment decisions. METHODS: We used a discrete choice experiment to assess the importance of late effects on treatment decision-making and acceptable trade-offs between late-effects risks and survival benefit. We surveyed 95 parents of children with cancer and 41 physicians at Dana-Farber/Boston Children’s Cancer and Blood Disorders Center to assess preferences for 5 late effects of treatment: neurocognitive impairment, infertility, cardiac toxicity, second malignancies, and impaired growth and development. RESULTS: Each late effect had a statistically significant association with treatment choice, as did survival benefit (P < .001). Avoidance of severe cognitive impairment was the most important treatment consideration to parents and physicians. Parents also valued cure and decreased risk of second malignancies; physician decision-making was driven by avoidance of second malignancies and infertility. Both parents and physicians accepted a high risk of infertility (parents, a 137% increased risk; physicians, an 80% increased risk) in exchange for a 10% greater chance of cure. CONCLUSIONS: Avoidance of severe neurocognitive impairment was the predominant driver of parent and physician treatment preferences, even over an increased chance of cure. This highlights the importance of exploring parental late-effects priorities when discussing treatment options. Full Article
io Asking for Identification and Retail Tobacco Sales to Minors By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 BACKGROUND AND OBJECTIVES: A previous single-county study found that retail stores usually asked young-looking tobacco customers to show proof-of-age identification, but a large proportion of illegal tobacco sales to minors occurred after the customers had shown identification proving they were too young to purchase tobacco. We sought to investigate these findings on a larger scale. METHODS: We obtained state reports for federal fiscal years 2017 and 2018 from a federal agency that tracks tobacco sales to supervised minors conducting compliance checks in retail stores. We used descriptive and multivariable logistic regression methods to determine (1) how often stores in 17 states requested identifications, (2) what proportion of violations occurred after identification requests, and (3) if violation rates differed when minors were required versus forbidden to carry identification. RESULTS: Stores asked minors for identification in 79.6% (95% confidence interval: 79.3%–80.8%) of compliance checks (N = 17 276). Violations after identification requests constituted 22.8% (95% confidence interval: 20.0%–25.6%; interstate range, 1.7%–66.2%) of all violations and were nearly 3 times as likely when minors were required to carry identification in compliance checks. Violations were 42% more likely when minors asked for a vaping product versus cigarettes. CONCLUSIONS: Stores that sell tobacco to underage customers are more likely to be detected and penalized when youth inspectors carry identification during undercover tobacco sales compliance checks. The new age-21 tobacco sales requirement presents an opportunity to require identifications be carried and address other long-standing weaknesses in compliance-check protocols to help combat the current adolescent vaping epidemic. Full Article
io ACA Medicaid Expansion and Insurance Coverage Among New Mothers Living in Poverty By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 BACKGROUND: Medicaid plays a critical role during the perinatal period, but pregnancy-related Medicaid eligibility only extends for 60 days post partum. In 2014, the Affordable Care Act’s (ACA’s) Medicaid expansions increased adult Medicaid eligibility to 138% of the federal poverty level in participating states, allowing eligible new mothers to remain covered after pregnancy-related coverage expires. We investigate the impact of ACA Medicaid expansions on insurance coverage among new mothers living in poverty. METHODS: We define new mothers living in poverty as women ages 19 to 44 with incomes below the federal poverty level who report giving birth in the past 12 months. We use 2010–2017 American Community Survey data and a difference-in-differences approach using parental Medicaid-eligibility thresholds to estimate the effect of ACA Medicaid expansions on insurance coverage among poor new mothers. RESULTS: A 100-percentage-point increase in parental Medicaid-eligibility is associated with an 8.8-percentage-point decrease (P < .001) in uninsurance, a 13.2-percentage-point increase (P < .001) in Medicaid coverage, and a 4.4-percentage-point decrease in private or other coverage (P = .001) among poor new mothers. The average increase in Medicaid eligibility is associated with a 28% decrease in uninsurance, a 13% increase in Medicaid coverage, and an 18% decline in private or other insurance among poor new mothers in expansion states. However, in 2017, there were ~142 000 remaining uninsured, poor new mothers. CONCLUSIONS: ACA Medicaid expansions are associated with increased Medicaid coverage and reduced uninsurance among poor new mothers. Opportunities remain for expansion and nonexpansion states to increase insurance coverage among new mothers living in poverty. Full Article
io Teenage Use of Smartphone Applications for Menstrual Cycle Tracking By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 Full Article
io Enhancing CPR During Transition From Prehospital to Emergency Department: A QI Initiative By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 BACKGROUND AND OBJECTIVES: High-quality cardiopulmonary resuscitation (CPR) increases the likelihood of survival of pediatric out-of-hospital cardiac arrest (OHCA). Maintenance of high-quality CPR during transition of care between prehospital and pediatric emergency department (PED) providers is challenging. Our objective for this initiative was to minimize pauses in compressions, in alignment with American Heart Association recommendations, for patients with OHCA during the handoffs from prehospital to PED providers. We aimed to decrease interruptions in compressions during the first 2 minutes of PED care from 17 seconds (baseline data) to 10 seconds over 12 months. Our secondary aims were to decrease the length of the longest pause in compressions to <10 seconds and eliminate encounters in which time to defibrillator pad placement was >120 seconds. METHODS: Our multidisciplinary team outlined our theory for improvement and designed interventions aimed at key drivers. Interventions included specific roles and responsibilities, CPR handoff choreography, and empowerment of frontline providers. Data were abstracted from video recordings of patients with OHCA receiving manual CPR on arrival. RESULTS: We analyzed 33 encounters between March 2018 and July 2019. We decreased total interruptions from 17 to 12 seconds during the first 2 minutes and decreased the time of the longest single pause from 14 to 7 seconds. We saw a decrease in variability of time to defibrillator pad placement. CONCLUSIONS: Implementation of a quality improvement initiative involving CPR transition choreography resulted in decreased interruptions in compressions and decreased variability of time to defibrillator pad placement. Full Article
io A Triadic Intervention for Adolescent Sexual Health: A Randomized Clinical Trial By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 OBJECTIVES: In this study, we evaluate the efficacy of Families Talking Together (FTT), a triadic intervention to reduce adolescent sexual risk behavior. METHODS: Adolescents aged 11 to 14 and their female caregivers were recruited from a pediatric clinic; 900 families were enrolled; 84 declined. Families were randomly assigned to FTT or 1 of 2 control conditions. The FTT triadic intervention consisted of a 45-minute face-to-face session for mothers, health care provider endorsement of intervention content, printed materials for families, and a booster call for mothers. The primary outcomes were ever having had vaginal intercourse, sexual debut within the past 12 months, and condom use at last sexual intercourse. Assessments occurred at baseline, 3 months post baseline, and 12 months post baseline. RESULTS: Of enrolled families, 73.4% identified as Hispanic, 20.4% as African American, and 6.2% as mixed race. Mean maternal age was 38.8 years, and mean adolescent grade was seventh grade. At the 12-month follow-up, 5.2% of adolescents in the experimental group reported having had sexual intercourse, compared with 18% of adolescents in the control groups (P < .05). In the experimental group, 4.7% of adolescents reported sexual debut within the past 12 months, compared with 14.7% of adolescents in the control group (P < .05). In the experimental group, 74.2% of sexually active adolescents indicated using a condom at last sexual intercourse, compared with 49.1% of adolescents in the control group (P < .05). CONCLUSIONS: This research suggests that the FTT triadic intervention is efficacious in delaying sexual debut and reducing sexual risk behavior among adolescents. Full Article
io Effect of State Immunization Information System Centralized Reminder and Recall on HPV Vaccination Rates By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 BACKGROUND: Although autodialer centralized reminder and recall (C-R/R) from state immunization information systems (IISs) has been shown to raise childhood vaccination rates, its impact on human papillomavirus (HPV) vaccination rates is unclear. METHODS: In a 4-arm pragmatic randomized controlled trial across 2 states, we randomly selected practices representative of the specialty (pediatrics, family medicine, and health center) where children received care. Within each practice, patients 11 to 17.9 years old who had not completed their HPV vaccine series (NY: N = 30 616 in 123 practices; CO: N = 31 502 in 80 practices) were randomly assigned to receive 0, 1, 2, or 3 IIS C-R/R autodialer messages per vaccine dose. We assessed HPV vaccine receipt via the IIS, calculated intervention costs, and compared HPV vaccine series initiation and completion rates across study arms. RESULTS: In New York, HPV vaccine initiation rates ranged from 37.0% to 37.4%, and completion rates were between 29.1% and 30.1%, with no significant differences across study arms. In Colorado, HPV vaccine initiation rates ranged from 31.2% to 33.5% and were slightly higher for 1 reminder compared with none, but vaccine completion rates, ranging from 27.0% to 27.8%, were similar. On adjusted analyses in Colorado, vaccine initiation rates were slightly higher for 1 and 3 C-R/R messages (adjusted risk ratios 1.07 and 1.04, respectively); completion rates were slightly higher for 1 and 3 C-R/R messages (adjusted risk ratios 1.02 and 1.03, respectively). CONCLUSIONS: IIS-based C-R/R for HPV vaccination did not improve HPV vaccination rates in New York and increased vaccination rates slightly in Colorado. Full Article
io Early Childhood Factors Associated With Peer Victimization Trajectories From 6 to 17 Years of Age By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 OBJECTIVES: To describe (1) the developmental trajectories of peer victimization from 6 to 17 years of age and (2) the early childhood behaviors and family characteristics associated with the trajectories. METHODS: We used data from 1760 children enrolled in the Quebec Longitudinal Study of Child Development, a population-based birth cohort. Participants self-reported peer victimization at ages 6, 7, 8, 10, 12, 13, 15, and 17 years. Participants’ behavior and family characteristics were measured repeatedly between ages 5 months and 5 years. RESULTS: We identified 4 trajectories of peer victimization from 6 to 17 years of age: low (32.9%), moderate-emerging (29.8%), childhood-limited (26.2%), and high-chronic (11.1%). Compared with children in the low peer victimization trajectory, children in the other 3 trajectories were more likely to exhibit externalizing behaviors in early childhood, and those in the high-chronic and moderate-emerging trajectories were more likely to be male. Paternal history of antisocial behavior was associated with moderate-emerging (odds ratio [OR] = 1.54; 95% confidence interval [CI] = 1.09–2.19) and high-chronic (OR = 1.93; 95% CI = 1.25–2.99) relative to low peer victimization. Living in a nonintact family in early childhood was associated with childhood-limited (OR = 1.48; 95% CI = 1.11–1.97) and high-chronic (OR = 1.59; 95% CI = 1.09–2.31) relative to low peer victimization. CONCLUSIONS: Early childhood externalizing behaviors and family vulnerabilities were associated with the development of peer victimization. Some children entered the cascade of persistent peer victimization at the beginning of primary school. Support to these children and their families early in life should be an important component of peer victimization preventive interventions. Full Article
io Systemic Sclerosis Sine Scleroderma With Pulmonary Arterial Hypertension in a 3-Year-Old Girl By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 Systemic sclerosis sine scleroderma (ssSSc) is a rare variant of systemic sclerosis, with only one pediatric case reported in the medical literature to date. Pulmonary arterial hypertension as the presenting feature of ssSSc is extremely rare, even in adults, and so far has never been reported in children. We report, for the first time, a case of pediatric ssSSc in a 3-year-old girl, who presented with interstitial lung disease and pulmonary hypertension. The patient was prescribed early aggressive pulmonary vasodilators combined with anti-inflammatory medications. The clinical response was good, and her current condition at 12 years of age is remarkable, considering the high mortality rates reported in adults. We underscore the importance of early aggressive treatment in future cases of similar presentation. Full Article
io Network Implementation of Guideline for Early Detection Decreases Age at Cerebral Palsy Diagnosis By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 BACKGROUND AND OBJECTIVES: Early diagnosis of cerebral palsy (CP) is critical in obtaining evidence-based interventions when plasticity is greatest. In 2017, international guidelines for early detection of CP were published on the basis of a systematic review of evidence. Our study aim was to reduce the age at CP diagnosis throughout a network of 5 diverse US high-risk infant follow-up programs through consistent implementation of these guidelines. METHODS: The study leveraged plan-do-study-act and Lean methodologies. The primary outcome was age at CP diagnosis. Data were acquired during the corresponding 9-month baseline and quarterly throughout study. Balancing measures were clinic no-show rates and parent perception of the diagnosis visit. Clinic teams conducted strengths, weaknesses, opportunities, and threats analyses, process flow evaluations, standardized assessments training, and parent questionnaires. Performance of a 3- to 4-month clinic visit was a critical process step because it included a Hammersmith Infant Neurologic Examination, a General Movements Assessment, and standardized assessments of motor function. RESULTS: The age at CP diagnosis decreased from a weighted average of 19.5 (95% confidence interval 16.2 to 22.8) to 9.5 months (95% confidence interval 4.5 to 14.6), with P = .008; 3- to 4-month visits per site increased from the median (interquartile range) 14 (5.2–73.7) to 54 (34.5–152.0), with P < .001; and no-show rates were not different. Parent questionnaires revealed positive provider perception with improvement opportunities for information content and understandability. CONCLUSIONS: Large-scale implementation of international guidelines for early detection of CP is feasible in diverse high-risk infant follow-up clinics. The initiative was received positively by families and without adversely affecting clinic operational flow. Additional parent support and education are necessary. Full Article
io Use of Standing Orders for Vaccination Among Pediatricians By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 OBJECTIVES: Standing orders are an effective way to increase vaccination rates, yet little is known about how pediatricians use this strategy for childhood immunizations. We assessed current use of, barriers to using, and factors associated with use of standing orders for vaccination among pediatricians. METHODS: Internet and mail survey from June 2017 to September 2017 among a nationally representative sample of pediatricians. In the principal component analysis of barrier items, we identified 2 factors: physician responsibility and concerns about office processes. A multivariable analysis that included barrier scales and physician and/or practice characteristics was used to identify factors associated with use of standing orders. RESULTS: The response rate was 79% (372 of 471); 59% of respondents reported using standing orders. The most commonly identified barriers among nonusers were concern that patients may mistakenly receive the wrong vaccine (68%), concern that patients prefer to speak with the physician about a vaccine before receiving it (62%), and belief that it is important for the physician to be the person who recommends a vaccine to patients (57%). These 3 items also made up the physician responsibility barrier factor. Respondents with higher physician responsibility scores were less likely to use standing orders (risk ratio: 0.59 [95% confidence interval: 0.53–0.66] per point increase). System-level decision-making about vaccines, suburban or rural location, and lower concerns about office processes scores were each associated with use of standing orders in the bivariate, but not the multivariable, analysis. CONCLUSIONS: Among pediatricians, use of standing orders for vaccination is far from universal. Interventions to increase use of standing orders should address physicians’ attitudinal barriers as well as organizational factors. Full Article
io Intramuscular Hematoma as a Manifestation of IgA Vasculitis By pediatrics.aappublications.org Published On :: 2020-05-01T01:00:46-07:00 We describe an atypical pediatric case of immunoglobulin A vasculitis (IgAV), also referred to as Henoch-Schönlein purpura, in which formation of spontaneous hematoma of the paraspinal muscles developed. Spontaneous or unprovoked hematomas rarely occur in IgAV. These manifestations have not been described specifically in the pediatric literature as coinciding with IgAV. These findings are alarming for nonaccidental trauma, particularly in a patient without underlying blood dyscrasia. Our objective for this report is to highlight the possible association of muscular hematoma formation with IgAV and to help providers consider this association when trauma and hemophilia has been ruled out. Full Article
io The Genetics of Mating Song Evolution Underlying Rapid Speciation: Linking Quantitative Variation to Candidate Genes for Behavioral Isolation [Corrigendum] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 Full Article
io Genetic Associations in Four Decades of Multienvironment Trials Reveal Agronomic Trait Evolution in Common Bean [Genetics of Complex Traits] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 Multienvironment trials (METs) are widely used to assess the performance of promising crop germplasm. Though seldom designed to elucidate genetic mechanisms, MET data sets are often much larger than could be duplicated for genetic research and, given proper interpretation, may offer valuable insights into the genetics of adaptation across time and space. The Cooperative Dry Bean Nursery (CDBN) is a MET for common bean (Phaseolus vulgaris) grown for > 70 years in the United States and Canada, consisting of 20–50 entries each year at 10–20 locations. The CDBN provides a rich source of phenotypic data across entries, years, and locations that is amenable to genetic analysis. To study stable genetic effects segregating in this MET, we conducted genome-wide association studies (GWAS) using best linear unbiased predictions derived across years and locations for 21 CDBN phenotypes and genotypic data (1.2 million SNPs) for 327 CDBN genotypes. The value of this approach was confirmed by the discovery of three candidate genes and genomic regions previously identified in balanced GWAS. Multivariate adaptive shrinkage (mash) analysis, which increased our power to detect significant correlated effects, found significant effects for all phenotypes. Mash found two large genomic regions with effects on multiple phenotypes, supporting a hypothesis of pleiotropic or linked effects that were likely selected on in pursuit of a crop ideotype. Overall, our results demonstrate that statistical genomics approaches can be used on MET phenotypic data to discover significant genetic effects and to define genomic regions associated with crop improvement. Full Article
io Pathogen Genetic Control of Transcriptome Variation in the Arabidopsis thaliana - Botrytis cinerea Pathosystem [Genetics of Complex Traits] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 In plant–pathogen relations, disease symptoms arise from the interaction of the host and pathogen genomes. Host–pathogen functional gene interactions are well described, whereas little is known about how the pathogen genetic variation modulates both organisms’ transcriptomes. To model and generate hypotheses on a generalist pathogen control of gene expression regulation, we used the Arabidopsis thaliana–Botrytis cinerea pathosystem and the genetic diversity of a collection of 96 B. cinerea isolates. We performed expression-based genome-wide association (eGWA) for each of 23,947 measurable transcripts in Arabidopsis (host), and 9267 measurable transcripts in B. cinerea (pathogen). Unlike other eGWA studies, we detected a relative absence of locally acting expression quantitative trait loci (cis-eQTL), partly caused by structural variants and allelic heterogeneity hindering their identification. This study identified several distantly acting trans-eQTL linked to eQTL hotspots dispersed across Botrytis genome that altered only Botrytis transcripts, only Arabidopsis transcripts, or transcripts from both species. Gene membership in the trans-eQTL hotspots suggests links between gene expression regulation and both known and novel virulence mechanisms in this pathosystem. Genes annotated to these hotspots provide potential targets for blocking manipulation of the host response by this ubiquitous generalist necrotrophic pathogen. Full Article
io A Novel Variation in the FRIZZLE PANICLE (FZP) Gene Promoter Improves Grain Number and Yield in Rice [Genetics of Complex Traits] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 Secondary branch number per panicle plays a crucial role in regulating grain number and yield in rice. Here, we report the positional cloning and functional characterization for SECONDARY BRANCH NUMBER7 (qSBN7), a quantitative trait locus affecting secondary branch per panicle and grain number. Our research revealed that the causative variants of qSBN7 are located in the distal promoter region of FRIZZLE PANICLE (FZP), a gene previously associated with the repression of axillary meristem development in rice spikelets. qSBN7 is a novel allele of FZP that causes an ~56% decrease in its transcriptional level, leading to increased secondary branch and grain number, and reduced grain length. Field evaluations showed that qSBN7 increased grain yield by 10.9% in a temperate japonica variety, TN13, likely due to its positive effect on sink capacity. Our findings suggest that incorporation of qSBN7 can increase yield potential and improve the breeding of elite rice varieties. Full Article
io Deciphering Sex-Specific Genetic Architectures Using Local Bayesian Regressions [Genetics of Complex Traits] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 Many complex human traits exhibit differences between sexes. While numerous factors likely contribute to this phenomenon, growing evidence from genome-wide studies suggest a partial explanation: that males and females from the same population possess differing genetic architectures. Despite this, mapping gene-by-sex (GxS) interactions remains a challenge likely because the magnitude of such an interaction is typically and exceedingly small; traditional genome-wide association techniques may be underpowered to detect such events, due partly to the burden of multiple test correction. Here, we developed a local Bayesian regression (LBR) method to estimate sex-specific SNP marker effects after fully accounting for local linkage-disequilibrium (LD) patterns. This enabled us to infer sex-specific effects and GxS interactions either at the single SNP level, or by aggregating the effects of multiple SNPs to make inferences at the level of small LD-based regions. Using simulations in which there was imperfect LD between SNPs and causal variants, we showed that aggregating sex-specific marker effects with LBR provides improved power and resolution to detect GxS interactions over traditional single-SNP-based tests. When using LBR to analyze traits from the UK Biobank, we detected a relatively large GxS interaction impacting bone mineral density within ABO, and replicated many previously detected large-magnitude GxS interactions impacting waist-to-hip ratio. We also discovered many new GxS interactions impacting such traits as height and body mass index (BMI) within regions of the genome where both male- and female-specific effects explain a small proportion of phenotypic variance (R2 < 1 x 10–4), but are enriched in known expression quantitative trait loci. Full Article
io Dominance Effects and Functional Enrichments Improve Prediction of Agronomic Traits in Hybrid Maize [Genomic Prediction] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 Single-cross hybrids have been critical to the improvement of maize (Zea mays L.), but the characterization of their genetic architectures remains challenging. Previous studies of hybrid maize have shown the contribution of within-locus complementation effects (dominance) and their differential importance across functional classes of loci. However, they have generally considered panels of limited genetic diversity, and have shown little benefit from genomic prediction based on dominance or functional enrichments. This study investigates the relevance of dominance and functional classes of variants in genomic models for agronomic traits in diverse populations of hybrid maize. We based our analyses on a diverse panel of inbred lines crossed with two testers representative of the major heterotic groups in the U.S. (1106 hybrids), as well as a collection of 24 biparental populations crossed with a single tester (1640 hybrids). We investigated three agronomic traits: days to silking (DTS), plant height (PH), and grain yield (GY). Our results point to the presence of dominance for all traits, but also among-locus complementation (epistasis) for DTS and genotype-by-environment interactions for GY. Consistently, dominance improved genomic prediction for PH only. In addition, we assessed enrichment of genetic effects in classes defined by genic regions (gene annotation), structural features (recombination rate and chromatin openness), and evolutionary features (minor allele frequency and evolutionary constraint). We found support for enrichment in genic regions and subsequent improvement of genomic prediction for all traits. Our results suggest that dominance and gene annotations improve genomic prediction across diverse populations in hybrid maize. Full Article
io Space is the Place: Effects of Continuous Spatial Structure on Analysis of Population Genetic Data [Population and Evolutionary Genetics] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 Real geography is continuous, but standard models in population genetics are based on discrete, well-mixed populations. As a result, many methods of analyzing genetic data assume that samples are a random draw from a well-mixed population, but are applied to clustered samples from populations that are structured clinally over space. Here, we use simulations of populations living in continuous geography to study the impacts of dispersal and sampling strategy on population genetic summary statistics, demographic inference, and genome-wide association studies (GWAS). We find that most common summary statistics have distributions that differ substantially from those seen in well-mixed populations, especially when Wright’s neighborhood size is < 100 and sampling is spatially clustered. "Stepping-stone" models reproduce some of these effects, but discretizing the landscape introduces artifacts that in some cases are exacerbated at higher resolutions. The combination of low dispersal and clustered sampling causes demographic inference from the site frequency spectrum to infer more turbulent demographic histories, but averaged results across multiple simulations revealed surprisingly little systematic bias. We also show that the combination of spatially autocorrelated environments and limited dispersal causes GWAS to identify spurious signals of genetic association with purely environmentally determined phenotypes, and that this bias is only partially corrected by regressing out principal components of ancestry. Last, we discuss the relevance of our simulation results for inference from genetic variation in real organisms. Full Article
io Toward an Evolutionarily Appropriate Null Model: Jointly Inferring Demography and Purifying Selection [Population and Evolutionary Genetics] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 The question of the relative evolutionary roles of adaptive and nonadaptive processes has been a central debate in population genetics for nearly a century. While advances have been made in the theoretical development of the underlying models, and statistical methods for estimating their parameters from large-scale genomic data, a framework for an appropriate null model remains elusive. A model incorporating evolutionary processes known to be in constant operation, genetic drift (as modulated by the demographic history of the population) and purifying selection, is lacking. Without such a null model, the role of adaptive processes in shaping within- and between-population variation may not be accurately assessed. Here, we investigate how population size changes and the strength of purifying selection affect patterns of variation at "neutral" sites near functional genomic components. We propose a novel statistical framework for jointly inferring the contribution of the relevant selective and demographic parameters. By means of extensive performance analyses, we quantify the utility of the approach, identify the most important statistics for parameter estimation, and compare the results with existing methods. Finally, we reanalyze genome-wide population-level data from a Zambian population of Drosophila melanogaster, and find that it has experienced a much slower rate of population growth than was inferred when the effects of purifying selection were neglected. Our approach represents an appropriate null model, against which the effects of positive selection can be assessed. Full Article
io Identifying and Classifying Shared Selective Sweeps from Multilocus Data [Population and Evolutionary Genetics] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 Positive selection causes beneficial alleles to rise to high frequency, resulting in a selective sweep of the diversity surrounding the selected sites. Accordingly, the signature of a selective sweep in an ancestral population may still remain in its descendants. Identifying signatures of selection in the ancestor that are shared among its descendants is important to contextualize the timing of a sweep, but few methods exist for this purpose. We introduce the statistic SS-H12, which can identify genomic regions under shared positive selection across populations and is based on the theory of the expected haplotype homozygosity statistic H12, which detects recent hard and soft sweeps from the presence of high-frequency haplotypes. SS-H12 is distinct from comparable statistics because it requires a minimum of only two populations, and properly identifies and differentiates between independent convergent sweeps and true ancestral sweeps, with high power and robustness to a variety of demographic models. Furthermore, we can apply SS-H12 in conjunction with the ratio of statistics we term and to further classify identified shared sweeps as hard or soft. Finally, we identified both previously reported and novel shared sweep candidates from human whole-genome sequences. Previously reported candidates include the well-characterized ancestral sweeps at LCT and SLC24A5 in Indo-Europeans, as well as GPHN worldwide. Novel candidates include an ancestral sweep at RGS18 in sub-Saharan Africans involved in regulating the platelet response and implicated in sudden cardiac death, and a convergent sweep at C2CD5 between European and East Asian populations that may explain their different insulin responses. Full Article
io Development of the Proximal-Anterior Skeletal Elements in the Mouse Hindlimb Is Regulated by a Transcriptional and Signaling Network Controlled by Sall4 [Developmental and Behavioral Genetics] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 The vertebrate limb serves as an experimental paradigm to study mechanisms that regulate development of the stereotypical skeletal elements. In this study, we simultaneously inactivated Sall4 using Hoxb6Cre and Plzf in mouse embryos, and found that their combined function regulates development of the proximal-anterior skeletal elements in hindlimbs. The Sall4; Plzf double knockout exhibits severe defects in the femur, tibia, and anterior digits, distinct defects compared to other allelic series of Sall4; Plzf. We found that Sall4 regulates Plzf expression prior to hindlimb outgrowth. Further expression analysis indicated that Hox10 genes and GLI3 are severely downregulated in the Sall4; Plzf double knockout hindlimb bud. In contrast, PLZF expression is reduced but detectable in Sall4; Gli3 double knockout limb buds, and SALL4 is expressed in the Plzf; Gli3 double knockout limb buds. These results indicate that Plzf, Gli3, and Hox10 genes downstream of Sall4, regulate femur and tibia development. In the autopod, we show that Sall4 negatively regulates Hedgehog signaling, which allows for development of the most anterior digit. Collectively, our study illustrates genetic systems that regulate development of the proximal-anterior skeletal elements in hindlimbs. Full Article
io Pits and CtBP Control Tissue Growth in Drosophila melanogaster with the Hippo Pathway Transcription Repressor Tgi [Developmental and Behavioral Genetics] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 The Hippo pathway is an evolutionarily conserved signaling network that regulates organ size, cell fate, and tumorigenesis. In the context of organ size control, the pathway incorporates a large variety of cellular cues, such as cell polarity and adhesion, into an integrated transcriptional response. The central Hippo signaling effector is the transcriptional coactivator Yorkie, which controls gene expression in partnership with different transcription factors, most notably Scalloped. When it is not activated by Yorkie, Scalloped can act as a repressor of transcription, at least in part due to its interaction with the corepressor protein Tgi. The mechanism by which Tgi represses transcription is incompletely understood, and therefore we sought to identify proteins that potentially operate together with Tgi. Using an affinity purification and mass-spectrometry approach we identified Pits and CtBP as Tgi-interacting proteins, both of which have been linked to transcriptional repression. Both Pits and CtBP were required for Tgi to suppress the growth of the Drosophila melanogaster eye and CtBP loss suppressed the undergrowth of yorkie mutant eye tissue. Furthermore, as reported previously for Tgi, overexpression of Pits repressed transcription of Hippo pathway target genes. These findings suggest that Tgi might operate together with Pits and CtBP to repress transcription of genes that normally promote tissue growth. The human orthologs of Tgi, CtBP, and Pits (VGLL4, CTBP2, and IRF2BP2) have previously been shown to physically and functionally interact to control transcription, implying that the mechanism by which these proteins control transcriptional repression is conserved throughout evolution. Full Article
io Alcohol Causes Lasting Differential Transcription in Drosophila Mushroom Body Neurons [Developmental and Behavioral Genetics] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 Repeated alcohol experiences can produce long-lasting memories for sensory cues associated with intoxication. These memories can problematically trigger relapse in individuals recovering from alcohol use disorder (AUD). The molecular mechanisms by which ethanol changes memories to become long-lasting and inflexible remain unclear. New methods to analyze gene expression within precise neuronal cell types can provide further insight toward AUD prevention and treatment. Here, we used genetic tools in Drosophila melanogaster to investigate the lasting consequences of ethanol on transcription in memory-encoding neurons. Drosophila rely on mushroom body (MB) neurons to make associative memories, including memories of ethanol-associated sensory cues. Differential expression analyses revealed that distinct transcripts, but not genes, in the MB were associated with experiencing ethanol alone compared to forming a memory of an odor cue associated with ethanol. Adult MB-specific knockdown of spliceosome-associated proteins demonstrated the necessity of RNA-processing in ethanol memory formation. These findings highlight the dynamic, context-specific regulation of transcription in cue-encoding neurons, and the lasting effect of ethanol on transcript usage during memory formation. Full Article
io Promoter-Proximal Chromatin Domain Insulator Protein BEAF Mediates Local and Long-Range Communication with a Transcription Factor and Directly Activates a Housekeeping Promoter in Drosophila [Gene Expression] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 BEAF (Boundary Element-Associated Factor) was originally identified as a Drosophila melanogaster chromatin domain insulator-binding protein, suggesting a role in gene regulation through chromatin organization and dynamics. Genome-wide mapping found that BEAF usually binds near transcription start sites, often of housekeeping genes, suggesting a role in promoter function. This would be a nontraditional role for an insulator-binding protein. To gain insight into molecular mechanisms of BEAF function, we identified interacting proteins using yeast two-hybrid assays. Here, we focus on the transcription factor Serendipity (Sry-). Interactions were confirmed in pull-down experiments using bacterially expressed proteins, by bimolecular fluorescence complementation, and in a genetic assay in transgenic flies. Sry- interacted with promoter-proximal BEAF both when bound to DNA adjacent to BEAF or > 2-kb upstream to activate a reporter gene in transient transfection experiments. The interaction between BEAF and Sry- was detected using both a minimal developmental promoter (y) and a housekeeping promoter (RpS12), while BEAF alone strongly activated the housekeeping promoter. These two functions for BEAF implicate it in playing a direct role in gene regulation at hundreds of BEAF-associated promoters. Full Article
io Rif1 Functions in a Tissue-Specific Manner To Control Replication Timing Through Its PP1-Binding Motif [Genome Integrity and Transmission] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 Replication initiation in eukaryotic cells occurs asynchronously throughout S phase, yielding early- and late-replicating regions of the genome, a process known as replication timing (RT). RT changes during development to ensure accurate genome duplication and maintain genome stability. To understand the relative contributions that cell lineage, cell cycle, and replication initiation regulators have on RT, we utilized the powerful developmental systems available in Drosophila melanogaster. We generated and compared RT profiles from mitotic cells of different tissues and from mitotic and endocycling cells of the same tissue. Our results demonstrate that cell lineage has the largest effect on RT, whereas switching from a mitotic to an endoreplicative cell cycle has little to no effect on RT. Additionally, we demonstrate that the RT differences we observed in all cases are largely independent of transcriptional differences. We also employed a genetic approach in these same cell types to understand the relative contribution the eukaryotic RT control factor, Rif1, has on RT control. Our results demonstrate that Rif1 can function in a tissue-specific manner to control RT. Importantly, the Protein Phosphatase 1 (PP1) binding motif of Rif1 is essential for Rif1 to regulate RT. Together, our data support a model in which the RT program is primarily driven by cell lineage and is further refined by Rif1/PP1 to ultimately generate tissue-specific RT programs. Full Article
io Topoisomerases Modulate the Timing of Meiotic DNA Breakage and Chromosome Morphogenesis in Saccharomyces cerevisiae [Genome Integrity and Transmission] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 During meiotic prophase, concurrent transcription, recombination, and chromosome synapsis place substantial topological strain on chromosomal DNA, but the role of topoisomerases in this context remains poorly defined. Here, we analyzed the roles of topoisomerases I and II (Top1 and Top2) during meiotic prophase in Saccharomyces cerevisiae. We show that both topoisomerases accumulate primarily in promoter-containing intergenic regions of actively transcribing genes, including many meiotic double-strand break (DSB) hotspots. Despite the comparable binding patterns, top1 and top2 mutations have different effects on meiotic recombination. TOP1 disruption delays DSB induction and shortens the window of DSB accumulation by an unknown mechanism. By contrast, temperature-sensitive top2-1 mutants exhibit a marked delay in meiotic chromosome remodeling and elevated DSB signals on synapsed chromosomes. The problems in chromosome remodeling were linked to altered Top2 binding patterns rather than a loss of Top2 catalytic activity, and stemmed from a defect in recruiting the chromosome remodeler Pch2/TRIP13 to synapsed chromosomes. No chromosomal defects were observed in the absence of TOP1. Our results imply independent roles for Top1 and Top2 in modulating meiotic chromosome structure and recombination. Full Article
io Machine Learning Techniques for Classifying the Mutagenic Origins of Point Mutations [Methods, Technology, [amp ] Resources] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 There is increasing interest in developing diagnostics that discriminate individual mutagenic mechanisms in a range of applications that include identifying population-specific mutagenesis and resolving distinct mutation signatures in cancer samples. Analyses for these applications assume that mutagenic mechanisms have a distinct relationship with neighboring bases that allows them to be distinguished. Direct support for this assumption is limited to a small number of simple cases, e.g., CpG hypermutability. We have evaluated whether the mechanistic origin of a point mutation can be resolved using only sequence context for a more complicated case. We contrasted single nucleotide variants originating from the multitude of mutagenic processes that normally operate in the mouse germline with those induced by the potent mutagen N-ethyl-N-nitrosourea (ENU). The considerable overlap in the mutation spectra of these two samples make this a challenging problem. Employing a new, robust log-linear modeling method, we demonstrate that neighboring bases contain information regarding point mutation direction that differs between the ENU-induced and spontaneous mutation variant classes. A logistic regression classifier exhibited strong performance at discriminating between the different mutation classes. Concordance between the feature set of the best classifier and information content analyses suggest our results can be generalized to other mutation classification problems. We conclude that machine learning can be used to build a practical classification tool to identify the mutation mechanism for individual genetic variants. Software implementing our approach is freely available under an open-source license. Full Article
io Fear and Foxes: An Educational Primer for Use with "Anterior Pituitary Transcriptome Suggests Differences in ACTH Release in Tame and Aggressive Foxes" [Primer] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 The way genes contribute to behavior is complicated. Although there are some single genes with large contributions, most behavioral differences are due to small effects from many interacting genes. This makes it hard to identify the genes that cause behavioral differences. Mutagenesis screens in model organisms, selective breeding experiments in animals, comparisons between related populations with different behaviors, and genome-wide association studies in humans are promising and complementary approaches to understanding the heritable aspects of complex behaviors. To connect genes to behaviors requires measuring behavioral differences, locating correlated genetic changes, determining when, where, and how these candidate genes act, and designing causative confirmatory experiments. This area of research has implications from basic discovery science to human mental health. Full Article
io Phosphoflow Protocol for Signaling Studies in Human and Murine B Cell Subpopulations [NOVEL IMMUNOLOGICAL METHODS] By www.jimmunol.org Published On :: 2020-05-04T13:00:28-07:00 Key Points Method for highly sensitive detection of phosphorylation in B cell subpopulations. B cell subpopulations show different phosphorylation levels upon BCR stimulation. Full Article
io Localized Immunomodulation with PD-L1 Results in Sustained Survival and Function of Allogeneic Islets without Chronic Immunosuppression [TRANSPLANTATION] By www.jimmunol.org Published On :: 2020-05-04T13:00:28-07:00 Key Points Islets are engineered with SA-PDL1 protein without impacting viability/function. SA-PDL1–engineered islets show indefinite survival in allogeneic hosts. Survival is associated with elevated intragraft Th2, Treg, and M2 transcripts. Full Article
io Surfactant Protein-A Protects against IL-13-Induced Inflammation in Asthma [MUCOSAL IMMUNOLOGY] By www.jimmunol.org Published On :: 2020-05-04T13:00:28-07:00 Key Points SP-A is a collectin and plays a key role in innate immunity in the lung. SP-A modulates inflammation in airway epithelial cells from patients with asthma. SP-A modulates IL-13–induced inflammation through downstream IL-6/STAT3 signaling. Full Article
io Role of V-ATPase a3-Subunit in Mouse CTL Function [MOLECULAR AND STRUCTURAL IMMUNOLOGY] By www.jimmunol.org Published On :: 2020-05-04T13:00:28-07:00 Key Points The a3-subunit of V-ATPase acidifies cytotoxic granules in mouse CD8+ T lymphocytes. Neutralization of luminal pH leads to altered morphology of cytotoxic granules. Knockdown of a3-subunit disturbs trafficking of cytotoxic granules. Full Article
io Serotonin (5-HT) Shapes the Macrophage Gene Profile through the 5-HT2B-Dependent Activation of the Aryl Hydrocarbon Receptor [INNATE IMMUNITY AND INFLAMMATION] By www.jimmunol.org Published On :: 2020-05-04T13:00:28-07:00 Key Points 5-HT2B agonists stimulate AhR transcriptional activation in human macrophages. Serotonin-induced expression of AhR target genes is 5-HT2B dependent in macrophages. Full Article
io Development of IFN-Stimulated Gene Expression from Embryogenesis through Adulthood, with and without Constitutive MDA5 Pathway Activation [INNATE IMMUNITY AND INFLAMMATION] By www.jimmunol.org Published On :: 2020-05-04T13:00:28-07:00 Key Points The augmented ISG profile of RdRP mice develops largely postnatally. Elevated ISG expression is then maintained through adulthood. The ISG signature in adults requires persistent type I IFN signaling. Full Article
io Apolipoprotein E Triggers Complement Activation in Joint Synovial Fluid of Rheumatoid Arthritis Patients by Binding C1q [INNATE IMMUNITY AND INFLAMMATION] By www.jimmunol.org Published On :: 2020-05-04T13:00:28-07:00 Key Points ApoE was found in complex with C4d in RA patient SF. Deposited ApoE activates complement whereas ApoE in solution is inhibitory. Posttranslational modifications alter ApoE's capacity to bind FH and C4BP. Full Article
io Leishmania donovani Subverts Host Immune Response by Epigenetic Reprogramming of Macrophage M(Lipopolysaccharides + IFN-{gamma})/M(IL-10) Polarization [INFECTIOUS DISEASE AND HOST RESPONSE] By www.jimmunol.org Published On :: 2020-05-04T13:00:27-07:00 Key Points L. donovani induces histone lysine methyltransferases/demethylases in the host. L. donovani–induced epigenetic enzymes induce host M(IL-10) polarization. Knockdown of epigenetic enzymes inhibited parasite multiplication in infected host. Full Article
io T Follicular Helper Cells Regulate Humoral Response for Host Protection against Intestinal Citrobacter rodentium Infection [INFECTIOUS DISEASE AND HOST RESPONSE] By www.jimmunol.org Published On :: 2020-05-04T13:00:27-07:00 Key Points Lack of Tfh cells renders the mice susceptible to C. rodentium infection. Tfh cell–dependent protective Abs are essential to control C. rodentium. Tfh cells regulate IgG1 response to C. rodentium infection. Full Article