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Erica P Turse, Francis E Dailey, Maliha Naseer, Edward K Partyka, Jack D Bragg, Veysel Tahan Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Missouri Health Center, Columbia, MO 65212, USA Abstract: Much research has been performed over the last decade on stem cell therapy as treatment for patients with inflammatory bowel disease. Hematopoietic and mesenchymal stem cells, both allogeneic (from someone else) and autologous (from own patient), have been studied with safe and efficacious results in the majority of patients treated for luminal, perianal, and/or fistulizing disease. Here in this review, we highlight all human trials that have been conducted utilizing stem cell therapy treatment in patients with inflammatory bowel disease. Keywords: inflammatory bowel disease, Crohn’s disease, ulcerative colitis, mesenchymal, hematopoietic, autologous, allogeneic, therapy, treatment

Premise: Obligate fire ephemerals are annual plants that have germination and reproduction cued by fire occurrence, persisting between fire events in a long-lived soil seed bank. Within these species, gene flow is restricted not only geographically but also temporally because individuals are limited to reproducing with others affected by the same fire event. The patchwork-like distribution of fires may therefore promote population isolation. In contrast to past fires, the Australian fires of 2019-2020 were of unprecedented extent, providing an opportunity to investigate the landscape genetics of a fire ephemeral, Actinotus forsythii, across multiple populations and to compare it to a common congener, Actinotus helianthi., Methods: For both species, we used single nucleotide polymorphisms to infer patterns of population structure and calculate measures of genetic diversity. We also estimated a phylogeny of Actinotus forsythii to understand the differentiation of a geographically isolated population., Results: For A. forsythii, the within-population diversity (allelic richness = 1.56) was greater, and the among-population differentiation (F ST  = 0.30) was lower than that observed for A. helianthi (allelic richness = 1.33, F ST  = 0.57). Actinotus forsythii had distinct geographic groupings, and a geographically isolated population of this species was genetically highly differentiated., Conclusions: Despite the fire-dependent, asynchronous gene flow, predicted between site disconnect, and possible within-site homogeneity, our results suggest that burn mosaic could be influencing gene flow patterns and fire-triggered mass flowering may promote genetic diversity within Actinotus forsythii., (© 2024 Botanical Society of America.)

Background: Studies have linked socioeconomic factors including lower income and minority race with worse functional outcomes following total knee arthroplasty (TKA). Arthrofibrosis is a common complication following TKA, and manipulation under anesthesia (MUA) is an effective treatment option for arthrofibrosis. This study aimed to determine if neighborhood-level socioeconomic disadvantage predicts need for MUA and postoperative range of motion (ROM) among patients undergoing primary elective TKA., Methods: We performed a retrospective cohort study of primary TKAs performed at a single institution over a three-year duration. Area Deprivation Index (ADI) was used to determine each patient's level of socioeconomic disadvantage based on their home address. Patients were allocated into three groups based on ADI: least socioeconomic disadvantage (ADI 1-3), middle socioeconomic disadvantage (ADI 4-6), and most socioeconomic disadvantage (ADI 7-10). Demographic factors and comorbid conditions were recorded. Bivariate analysis was used to evaluate the relationship between degree of socioeconomic disadvantage and need for MUA and postoperative ROM., Results: In total, 600 patients were included and 26.7 % were categorized as most disadvantaged. In comparison to the middle and least disadvantaged groups, these patients were more likely to be Women (71.2 vs. 67.9 and 58.6 %; p  = 0.027), younger (60.7 vs. 62.9 and 66.3 years; p  < 0.001) and have higher BMI (34.9 vs. 33 and 31.7; p  < 0.001) (most disadvantaged vs. middle and least). Analysis revealed no difference in rate of MUA (6.3 vs. 2.5 vs. 4 %; p  = 0.179) or postoperative ROM (98 vs. 98 vs. 100°; p  = 0.753) between the three groups (most, middle, and least disadvantaged, respectively)., Conclusion: Neighborhood socioeconomic disadvantage does not predict rate of MUA or postoperative ROM following TKA. Patients residing in neighborhoods with higher ADI who underwent TKA were more likely to be younger, Women, and have higher BMI, consistent with previous literature. Our results support efforts to improve access to orthopaedic care, including TKA, to patients of all socioeconomic levels., (© 2024 Professor P K Surendran Memorial Education Foundation. Published by Elsevier B.V. All rights are reserved, including those for text and data mining, AI training, and similar technologies.)

Purpose: To compare complication rates, reoperation rates, and subjective outcomes after arthroscopic and open irrigation and debridement for treatment of native knee septic arthritis., Methods: Following The Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines, a systematic review of the Embase, Cochrane, and PubMed databases was performed. Comparative studies reporting clinical outcomes after arthroscopic versus open treatment for septic arthritis of the native knee in human adults were included. Excluded were case series with <10 patients, inclusion of patients <18 years old, studies on non-native joints, abstract-only publications, and studies without stratification of the involved joint. Two reviewers in duplicate independently performed search and data extraction. The quality of the included studies was assessed with the Methodological Index for Non-Randomized Studies instrument. The mean score among the included studies was 18.2 (range 16-23)., Results: Eleven studies were included, comprising 2,343 knees treated arthroscopically, and 1,595 treated with arthrotomy. Studies reported no differences in erythrocyte sedimentation rate, C-reactive protein, peripheral white blood cells, or symptom chronicity between groups. Nine studies (81.8%) attempted to control for potentially confounding variables in their analyses, and 4 studies (36.4%) reported significant differences in patient characteristics. Reoperation rates ranged from 0% to 50% for arthroscopy and 6% to 71% for arthrotomy. Complication rates ranged from 0% to 39.4% arthroscopically and 0% to 49% for arthrotomy. Superior patient-reported outcomes were achieved after arthroscopy in 2 studies that analyzed subjective outcomes., Conclusions: Arthroscopic management of native knee septic arthritis is a safe and effective alternative to open treatment and is associated with comparable complication rates, reoperation rates, hospitalization lengths, readmission rates, and superior patient-reported outcomes compared with open irrigation and debridement., Level of Evidence: Level IV, systematic review of Level I, III, and IV studies., (Copyright © 2023 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.)

During automotive engine operation, water may contaminate engine oil, inhibiting its role in maintaining safe engine operation. In many cases, engine oil must be capable of emulsifying any water contamination to avoid such problems. This study focuses on the impact of small molecule surfactant concentration structure and concentration in emulsions comprised of engine oil, water, and E85 fuel to understand the effects on emulsion stability and formulation optimization. Three small molecule surfacatants were tested; glycerol dioleate (GDO), glyceryl monooleate (GMO), and oleamide (OA). Three characterization methods were used to investigate their effects; the current state of the art, ASTM D7563, microscopy, and diffusing wave spectroscopy (DWS). We found that DWS could yield insights into mechanisms of emulsion stability that are otherwise inaccessible through other experimental techniques. Specifically, utilizing DWS, we are able to extract specific emulsion stability mechanisms associated directly with molecular features for the three surfactants examined., Competing Interests: Declaration of Competing Interest James K. Ferri reports financial support, equipment, drugs, or supplies, and writing assistance were provided by Afton Chemical Corporation. Benjamin M. Tansi reports a relationship with Afton Chemical Corporation that includes: employment. Joseph E. Remias reports a relationship with Afton Chemical Corporation that includes: employment., (Copyright © 2023 Elsevier Inc. All rights reserved.)

Introduction: Adverse childhood experiences (ACEs) have profound implications for adult health. Health care practitioners need effective communication tools for trauma-sensitive inquiries with patients. This study aimed to describe characteristics of effective metaphor use by health care trainees when discussing ACEs and health with adult patients, and to provide example metaphors for clinicians to use to sensitively address ACEs., Methods: Trainees engaged in a videorecorded simulation as part of a model to teach health care practitioners communication skills related to ACEs. Videos were identified in which the trainee used a metaphor to help explain ACEs during the encounter. Encounter segments that used metaphors were transcribed and metaphor type, duration, and recurrence were coded using a standardized rubric. Each metaphor was scored for effectiveness and basic statistical analysis was conducted., Results: Of the 122 videos reviewed, 24 types of metaphors were used, with the most common being the overloaded backpack (n = 24). Mean metaphor duration was 37 s (SD = 24 s). Metaphors rated as effective were shorter and less variable in duration (31.8 s, SD = 14.7 s) than those rated as ineffective (39 s, SD = 34 s). No one metaphor performed significantly better and most of the metaphors were evaluated as being adequate or effective., Conclusion: Literary devices like metaphors may be efficient and effective explanatory tools to improve clinician communication skills and patient understanding in addressing sensitive topics, such as ACEs. Minimal time investment is required to employ metaphors in ACEs discussions. The authors found no single metaphor that to be clearly superior, indicating that patient-centered metaphor use may improve communication between clinicians and patients who experienced childhood trauma., Competing Interests: Conflicts of Interest None declared

Background and Objectives: Neurodevelopmental evaluation of toddlers with complex congenital heart disease is recommended but reported frequency is low. Data on barriers to attending neurodevelopmental follow-up are limited. This study aims to estimate the attendance rate for a toddler neurodevelopmental evaluation in a contemporary multicenter cohort and to assess patient and center level factors associated with attending this evaluation., Methods: This is a retrospective cohort study of children born between September 2017 and September 2018 who underwent cardiopulmonary bypass in their first year of life at a center contributing data to the Cardiac Neurodevelopmental Outcome Collaborative and Pediatric Cardiac Critical Care Consortium clinical registries. The primary outcome was attendance for a neurodevelopmental evaluation between 11 and 30 months of age. Sociodemographic and medical characteristics and center factors specific to neurodevelopmental program design were considered as predictors for attendance., Results: Among 2385 patients eligible from 16 cardiac centers, the attendance rate was 29.0% (692 of 2385), with a range of 7.8% to 54.3% across individual centers. In multivariable logistic regression models, hospital-initiated (versus family-initiated) scheduling for neurodevelopmental evaluation had the largest odds ratio in predicting attendance (odds ratio = 4.24, 95% confidence interval, 2.74-6.55). Other predictors of attendance included antenatal diagnosis, absence of Trisomy 21, higher Society of Thoracic Surgeons-European Association for Cardio-Thoracic Surgery mortality category, longer postoperative length of stay, private insurance, and residing a shorter distance from the hospital., Conclusions: Attendance rates reflect some improvement but remain low. Changes to program infrastructure and design and minimizing barriers affecting access to care are essential components for improving neurodevelopmental care and outcomes for children with congenital heart disease., (Copyright © 2023 by the American Academy of Pediatrics.)

Importance: Genomic testing in infancy guides medical decisions and can improve health outcomes. However, it is unclear whether genomic sequencing or a targeted neonatal gene-sequencing test provides comparable molecular diagnostic yields and times to return of results., Objective: To compare outcomes of genomic sequencing with those of a targeted neonatal gene-sequencing test., Design, Setting, and Participants: The Genomic Medicine for Ill Neonates and Infants (GEMINI) study was a prospective, comparative, multicenter study of 400 hospitalized infants younger than 1 year of age (proband) and their parents, when available, suspected of having a genetic disorder. The study was conducted at 6 US hospitals from June 2019 to November 2021., Exposure: Enrolled participants underwent simultaneous testing with genomic sequencing and a targeted neonatal gene-sequencing test. Each laboratory performed an independent interpretation of variants guided by knowledge of the patient's phenotype and returned results to the clinical care team. Change in clinical management, therapies offered, and redirection of care was provided to families based on genetic findings from either platform., Main Outcomes and Measures: Primary end points were molecular diagnostic yield (participants with ≥1 pathogenic variant or variant of unknown significance), time to return of results, and clinical utility (changes in patient care)., Results: A molecular diagnostic variant was identified in 51% of participants (n = 204; 297 variants identified with 134 being novel). Molecular diagnostic yield of genomic sequencing was 49% (95% CI, 44%-54%) vs 27% (95% CI, 23%-32%) with the targeted gene-sequencing test. Genomic sequencing did not report 19 variants found by the targeted neonatal gene-sequencing test; the targeted gene-sequencing test did not report 164 variants identified by genomic sequencing as diagnostic. Variants unidentified by the targeted genomic-sequencing test included structural variants longer than 1 kilobase (25.1%) and genes excluded from the test (24.6%) (McNemar odds ratio, 8.6 [95% CI, 5.4-14.7]). Variant interpretation by laboratories differed by 43%. Median time to return of results was 6.1 days for genomic sequencing and 4.2 days for the targeted genomic-sequencing test; for urgent cases (n = 107) the time was 3.3 days for genomic sequencing and 4.0 days for the targeted gene-sequencing test. Changes in clinical care affected 19% of participants, and 76% of clinicians viewed genomic testing as useful or very useful in clinical decision-making, irrespective of a diagnosis., Conclusions and Relevance: The molecular diagnostic yield for genomic sequencing was higher than a targeted neonatal gene-sequencing test, but the time to return of routine results was slower. Interlaboratory variant interpretation contributes to differences in molecular diagnostic yield and may have important consequences for clinical management.

Cross bred species such as switchgrass may benefit from advantageous breeding strategies requiring inbred lines. Doubled haploid production methods offer several ways that these lines can be produced that often involve uniparental genome elimination as the rate limiting step. We have used a centromere-mediated genome elimination strategy in which modified CENH3 is expressed to induce the process. Transgenic tetraploid switchgrass lines coexpressed Cas9, a poly-cistronic tRNA-gRNA tandem array containing eight guide RNAs that target two CENH3 genes, and different chimeric versions of CENH3 with alterations to the N-terminal tail region. Genotyping of CENH3 genes in transgenics identified edits including frameshift mutations and deletions in one or both copies of the two CENH3 genes. Flow cytometry of T 1 seedlings identified two T 0 lines that produced five haploid individuals representing an induction rate of 0.5% and 1.4%. Eight different T 0 lines produced aneuploids at rates ranging from 2.1 to 14.6%. A sample of aneuploid lines were sequenced at low coverage and aligned to the reference genome, revealing missing chromosomes and chromosome arms., (© 2022 The Authors. The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.)

Switchgrass can be used as an alternative source for bioenergy production. Many breeding programs focus on the genetic improvement of switchgrass for increasing biomass yield. Quantitative trait loci (QTL) mapping can help to discover marker-trait associations and accelerate the breeding process through marker-assisted selection. To identify significant QTL, this study mapped 7 hybrid populations and one combined of 2 hybrid populations (30-96 F1s) derived from Alamo and Kanlow genotypes. The populations were evaluated for biomass yield, plant height, and crown size in a simulated-sward plot with 2 replications at 2 locations in Tennessee from 2019 to 2021. The populations showed significant genetic variation for the evaluated traits and exhibited transgressive segregation. The 17,251 single nucleotide polymorphisms (SNPs) generated through genotyping-by-sequencing (GBS) were used to construct a linkage map using a fast algorithm for multiple outbred families. The linkage map spanned 1,941 cM with an average interval of 0.11 cM between SNPs. The QTL analysis was performed on evaluated traits for each and across environments (year and location) that identified 5 QTL for biomass yield (logarithm of the odds, LOD 3.12-4.34), 4 QTL for plant height (LOD 3.01-5.64), and 7 QTL for crown size (LOD 3.0-4.46) (P ≤ 0.05). The major QTL for biomass yield, plant height, and crown size resided on chromosomes 8N, 6N, and 8K explained phenotypic variations of 5.6, 5.1, and 6.6%, respectively. SNPs linked to QTL could be incorporated into marker-assisted breeding to maximize the selection gain in switchgrass breeding., Competing Interests: Conflicts of interest The author(s) declare no conflict of interest., (© The Author(s) 2023. Published by Oxford University Press on behalf of the Genetics Society of America.)

Increasing use of unbiased genomic sequencing in critically ill infants can expand understanding of rare diseases such as Kabuki syndrome (KS). Infants diagnosed with KS through genome-wide sequencing performed during the initial hospitalization underwent retrospective review of medical records. Human phenotype ontology terms used in genomic analysis were aggregated and analyzed. Clinicians were surveyed regarding changes in management and other care changes. Fifteen infants met inclusion criteria. KS was not suspected prior to genomic sequencing. Variants were classified as Pathogenic (n = 10) or Likely Pathogenic (n = 5) by American College of Medical Genetics and Genomics Guidelines. Fourteen variants were de novo (KMT2D, n = 12, KDM6A, n = 2). One infant inherited a likely pathogenic variant in KMT2D from an affected father. Frequent findings involved cardiovascular (14/15) and renal (7/15) systems, with palatal defects also identified (6/15). Three infants had non-immune hydrops. No minor anomalies were universally documented; ear anomalies, micrognathia, redundant nuchal skin, and hypoplastic nails were common. Changes in management were reported in 14 infants. Early use of unbiased genome-wide sequencing enabled a molecular diagnosis prior to clinical recognition including infants with atypical or rarely reported features of KS while also expanding the phenotypic spectrum of this rare disorder., (© 2023 The Authors. American Journal of Medical Genetics Part A published by Wiley Periodicals LLC.)

Temperature differences over time and space have been hypothesized to cause variation in the rate of molecular evolution of species, but empirical evidence is mixed. To further test this hypothesis, we utilized a large exon-capture sequence data of Australian Eugongylinae skinks, exemplifying a radiation of temperature-sensitive ectotherms spanning a large latitudinal gradient. The association between temperature (and other species traits) and long-term substitution rate was assessed based on 1268 sequenced exons of 44 species pairs from the Eugongylinae subfamily using regression analyses. Temperature is the strongest, positively correlated predictor of variation in substitution rate across the Australian Eugongylinae. It explains 45% of variation in synonymous substitution rate, and 11% after controlling for all the other factors. Synonymous substitution rate is also negatively associated with body size, with a 6% variation explained by body size after controlling for the effects of temperature. Other factors are not associated with synonymous substitution rate after controlling for temperature. Overall, this study points to temperature as a strong predictor of the molecular evolution rate in the Eugongylinae subfamily, and demonstrates the power of large-scale exonic data to identify correlates of the rate of molecular evolution., (© 2021 The Authors. Evolution © 2021 The Society for the Study of Evolution.)

We introduce the AusTraits database - a compilation of values of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across 28,640 taxa from field campaigns, published literature, taxonomic monographs, and individual taxon descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological attributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual- and species-level measurements coupled to, where available, contextual information on site properties and experimental conditions. This article provides information on version 3.0.2 of AusTraits which contains data for 997,808 trait-by-taxon combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data, which also provides a template for other national or regional initiatives globally to fill persistent gaps in trait knowledge., (© 2021. The Author(s).)

Genotype-environment association (GEA) methods have become part of the standard landscape genomics toolkit, yet, we know little about how to best filter genotype-by-sequencing data to provide robust inferences for environmental adaptation. In many cases, default filtering thresholds for minor allele frequency and missing data are applied regardless of sample size, having unknown impacts on the results, negatively affecting management strategies. Here, we investigate the effects of filtering on GEA results and the potential implications for assessment of adaptation to environment. We use empirical and simulated data sets derived from two widespread tree species to assess the effects of filtering on GEA outputs. Critically, we find that the level of filtering of missing data and minor allele frequency affect the identification of true positives. Even slight adjustments to these thresholds can change the rate of true positive detection. Using conservative thresholds for missing data and minor allele frequency substantially reduces the size of the data set, lessening the power to detect adaptive variants (i.e., simulated true positives) with strong and weak strengths of selection. Regardless, strength of selection was a good predictor for GEA detection, but even some SNPs under strong selection went undetected. False positive rates varied depending on the species and GEA method, and filtering significantly impacted the predictions of adaptive capacity in downstream analyses. We make several recommendations regarding filtering for GEA methods. Ultimately, there is no filtering panacea, but some choices are better than others, depending on the study system, availability of genomic resources, and desired objectives., (© 2021 John Wiley & Sons Ltd.)

In response to COVID-19 hygiene and physical distancing restrictions, our service rapidly shifted to delivering Circle of Security-Parenting™ (COS-P) groups via telehealth. In this article we report the perspectives and experiences of the group facilitator and the parents who received the intervention during the COVID-19 pandemic. We use semi-structured, qualitative interviews to explore the advantages, challenges, and positive impacts of the online parenting group from the perspectives of the group leader and the five group participants. Participants' narrative reflections show that they were satisfied with the convenient and engaging online delivery of the program and would recommend it to other parents. Parents reported significant improvements in their parenting and greater awareness of their strengths and struggles. The online delivery of COS-P resulted in more efficient service delivery, greater attendance rates, and adherence to the model. The stressors on the experienced facilitator, due to the abrupt transition and multiple technical and communication challenges, may have been mitigated by supervisor and collegial support, as well as careful preparation for herself and the participants. Future research should investigate the effectiveness of online versus face-to-face delivery of the intervention, including what works for whom., (© 2021 Australian Association of Family Therapy.)

Key Message: Quantitation of leaf surface wax on a population of switchgrass identified three significant QTL present across six environments that contribute to leaf glaucousness and wax composition and that show complex genetic × environmental (G × E) interactions. The C4 perennial grass Panicum virgatum (switchgrass) is a native species of the North American tallgrass prairie. This adaptable plant can be grown on marginal lands and is useful for soil and water conservation, biomass production, and as a forage. Two major switchgrass ecotypes, lowland and upland, differ in a range of desirable traits, and the responsible underlying loci can be localized efficiently in a pseudotestcross design. An outbred four-way cross (4WCR) mapping population of 750 F 2 lines was used to examine the genetic basis of differences in leaf surface wax load between two lowland (AP13 and WBC) and two upland (DAC and VS16) tetraploid cultivars. The objective of our experiments was to identify wax compositional variation among the population founders and to map underlying loci responsible for surface wax variation across environments. GCMS analyses of surface wax extracted from 4WCR F 0 founders and F 1 hybrids reveal higher levels of wax in lowland genotypes and show quantitative differences of β-diketones, primary alcohols, and other wax constituents. The full mapping population was sampled over two seasons from four field sites with latitudes ranging from 30 to 42 °N, and leaf surface wax was measured. We identified three high-confidence QTL, of which two displayed significant G × E effects. Over 50 candidate genes underlying the QTL regions showed similarity to genes in either Arabidopsis or barley known to function in wax synthesis, modification, regulation, and transport.

Adverse Childhood Experiences (ACEs) are multiple sources of maltreatment and household dysfunction with tremendous impact on health. A trauma-informed (TI) approach is preferred when working with patients with ACEs. The Professional ACEs-Informed Training for Health © (PATH © ) educational program and simulation experience using standardized patients (SP) was developed to help healthcare professionals address ACEs with adults. PATH © is a 3-4 hour curriculum comprised of lecture and discussion, video-based demonstration, simulation experience, and debriefing. It was first developed for primary care (PC) residents in family medicine and internal medicine, and subsequently modified for occupational therapy (OT) and physical therapy (PT) students. This study evaluates a preliminary dataset focusing on PATH © skills of PC residents and OT and PT students during simulation. Recordings of 53 learner-SP encounters from 15 OT and PT students and 38 PC residents were coded using standardized behavioral codes. A subset of ten recordings of PC residents who participated in simulations in the first and fourth year of the training program allowed for evaluation of training outcomes over time. Results showed that medical residents and OT and PT students demonstrated skills during SP encounters congruent with TI training on addressing ACEs with adults, particularly in explaining ACEs, demonstrating empathy, collaborative treatment planning, and stigma reduction. PC residents showed both positive and negative changes in PATH © -specific skills from year 1 to 4 of the training program. This study supports the PATH © model and simulation-based training in preparing clinicians to address ACEs with adults and provides insight into further curriculum improvement.

We present a model of the growth rate and elemental stoichiometry of phytoplankton as a function of resource allocation between and within broad macromolecular pools under a variety of resource supply conditions. The model is based on four, empirically-supported, cornerstone assumptions: that there is a saturating relationship between light and photosynthesis, a linear relationship between RNA/protein and growth rate, a linear relationship between biosynthetic proteins and growth rate, and a constant macromolecular composition of the light-harvesting machinery. We combine these assumptions with statements of conservation of carbon, nitrogen, phosphorus, and energy. The model can be solved algebraically for steady state conditions and constrained with data on elemental stoichiometry from published laboratory chemostat studies. It interprets the relationships between macromolecular and elemental stoichiometry and also provides quantitative predictions of the maximum growth rate at given light intensity and nutrient supply rates. The model is compatible with data sets from several laboratory studies characterizing both prokaryotic and eukaryotic phytoplankton from marine and freshwater environments. It is conceptually simple, yet mechanistic and quantitative. Here, the model is constrained only by elemental stoichiometry, but makes predictions about allocation to measurable macromolecular pools, which could be tested in the laboratory., (Copyright © 2020 Inomura, Omta, Talmy, Bragg, Deutsch and Follows.)

Nitrogen fixation provides bioavailable nitrogen, supporting global ecosystems and influencing global cycles of other elements. It provides an additional source of nitrogen to organisms at a cost of lower growth efficiency, largely due to respiratory control of intra-cellular oxygen. Nitrogen-fixing bacteria can, however, utilize both dinitrogen gas and fixed nitrogen, decreasing energetic costs. Here we present an idealized metabolic model of the heterotrophic nitrogen fixer Azotobacter vinelandii which, constrained by laboratory data, provides quantitative predictions for conditions under which the organism uses either ammonium or nitrogen fixation, or both, as a function of the relative supply rates of carbohydrate, fixed nitrogen as well as the ambient oxygen concentration. The model reveals that the organism respires carbohydrate in excess of energetic requirements even when nitrogen fixation is inhibited and respiratory protection is not essential. The use of multiple nitrogen source expands the potential niche and range for nitrogen fixation. The model provides a quantitative framework which can be employed in ecosystem and biogeochemistry models., Competing Interests: The authors have declared that no competing interests exist.

Targeted cellular auxin distribution is required for morphogenesis and adaptive responses of plant organs. In Arabidopsis thaliana (Arabidopsis), this involves the prototypical auxin influx facilitator AUX1 and its LIKE-AUX1 (LAX) homologs, which act partially redundantly in various developmental processes. Interestingly, AUX1 and its homologs are not strictly essential for the Arabidopsis life cycle. Indeed, aux1 lax1 lax2 lax3 quadruple knock-outs are mostly viable and fertile, and strong phenotypes are only observed at low penetrance. Here we investigated the Brachypodium distachyon (Brachypodium) AUX1 homolog BdAUX1 by genetic, cell biological and physiological analyses. We report that BdAUX1 is essential for Brachypodium development. Bdaux1 loss-of-function mutants are dwarfs with aberrant flower development, and consequently infertile. Moreover, they display a counter-intuitive root phenotype. Although Bdaux1 roots are agravitropic as expected, in contrast to Arabidopsis aux1 mutants they are dramatically longer than wild type roots because of exaggerated cell elongation. Interestingly, this correlates with higher free auxin content in Bdaux1 roots. Consistently, their cell wall characteristics and transcriptome signature largely phenocopy other Brachypodium mutants with increased root auxin content. Our results imply fundamentally different wiring of auxin transport in Brachypodium roots and reveal an essential role of BdAUX1 in a broad spectrum of developmental processes, suggesting a central role for AUX1 in pooideae., (© 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.)

Detecting genetic variants under selection using F ST outlier analysis (OA) and environmental association analyses (EAAs) are popular approaches that provide insight into the genetic basis of local adaptation. Despite the frequent use of OA and EAA approaches and their increasing attractiveness for detecting signatures of selection, their application to field-based empirical data have not been synthesized. Here, we review 66 empirical studies that use Single Nucleotide Polymorphisms (SNPs) in OA and EAA. We report trends and biases across biological systems, sequencing methods, approaches, parameters, environmental variables and their influence on detecting signatures of selection. We found striking variability in both the use and reporting of environmental data and statistical parameters. For example, linkage disequilibrium among SNPs and numbers of unique SNP associations identified with EAA were rarely reported. The proportion of putatively adaptive SNPs detected varied widely among studies, and decreased with the number of SNPs analysed. We found that genomic sampling effort had a greater impact than biological sampling effort on the proportion of identified SNPs under selection. OA identified a higher proportion of outliers when more individuals were sampled, but this was not the case for EAA. To facilitate repeatability, interpretation and synthesis of studies detecting selection, we recommend that future studies consistently report geographical coordinates, environmental data, model parameters, linkage disequilibrium, and measures of genetic structure. Identifying standards for how OA and EAA studies are designed and reported will aid future transparency and comparability of SNP-based selection studies and help to progress landscape and evolutionary genomics., (© 2018 John Wiley & Sons Ltd.)

Aim: To enhance the confidence and capacity of community paediatricians and paediatric trainees to identify and respond to family violence, through a series of education sessions and evidence-based recommendations., Methods: The action research methodology included a literature search to review the data on family violence education programmes and evidence-based family violence screening tools. Six education sessions were then developed and held for physicians at the Community Paediatric and Child Health Service (CPCHS). An audit was performed on the charts of all new referrals to the CPCHS for a period of 18 months prior to the education sessions and 5 months following the education sessions. A questionnaire was distributed at the first and final education sessions to gauge physician comfort with enquiry into family violence., Results: The documented rate of enquiry into family violence at CPCHS was 24% in the retrospective chart audit. Following the series of education sessions, the documented rate of enquiry increased to 60% (P < 0.05, odds ratio 4.7, confidence interval 2.7-8.4). The documented rate of disclosure of family violence also increased from 13% of all new patients in the retrospective chart audit to 24% in the prospective arm of the study (P < 0.05, odds ratio 2.1, confidence interval 1.0-4.0). Following the education sessions, all participants agreed that they routinely enquired about family violence and were comfortable enquiring about family violence., Conclusion: This study demonstrates that clinician education about family violence supports routine enquiry about family violence in community paediatric consultations., (© 2017 Paediatrics and Child Health Division (The Royal Australasian College of Physicians).)

Due to a large and growing collection of genomic and experimental resources, Brachypodium distachyon has emerged as a powerful experimental model for the grasses. To add to these resources we sequenced 21 165 T-DNA lines, 15 569 of which were produced in this study. This increased the number of unique insertion sites in the T-DNA collection by 21 078, bringing the overall total to 26 112. Thirty-seven per cent (9754) of these insertion sites are within genes (including untranslated regions and introns) and 28% (7217) are within 500 bp of a gene. Approximately 31% of the genes in the v.2.1 annotation have been tagged in this population. To demonstrate the utility of this collection, we phenotypically characterized six T-DNA lines with insertions in genes previously shown in other systems to be involved in cellulose biosynthesis, hemicellulose biosynthesis, secondary cell wall development, DNA damage repair, wax biosynthesis and chloroplast synthesis. In all cases, the phenotypes observed supported previous studies, demonstrating the utility of this collection for plant functional genomics. The Brachypodium T-DNA collection can be accessed at http://jgi.doe.gov/our-science/science-programs/plant-genomics/brachypodium/brachypodium-t-dna-collection/., (Published 2017. This article is a U.S. Government work and is in the public domain in the USA.)

Few genome-wide association studies (GWAS) account for environmental exposures, like smoking, potentially impacting the overall trait variance when investigating the genetic contribution to obesity-related traits. Here, we use GWAS data from 51,080 current smokers and 190,178 nonsmokers (87% European descent) to identify loci influencing BMI and central adiposity, measured as waist circumference and waist-to-hip ratio both adjusted for BMI. We identify 23 novel genetic loci, and 9 loci with convincing evidence of gene-smoking interaction (GxSMK) on obesity-related traits. We show consistent direction of effect for all identified loci and significance for 18 novel and for 5 interaction loci in an independent study sample. These loci highlight novel biological functions, including response to oxidative stress, addictive behaviour, and regulatory functions emphasizing the importance of accounting for environment in genetic analyses. Our results suggest that tobacco smoking may alter the genetic susceptibility to overall adiposity and body fat distribution.

Nitrogen fixation is advantageous in microbial competition when bioavailable nitrogen is scarce, but has substantial costs for growth rate and growth efficiency. To quantify these costs, we have developed a model of a nitrogen-fixing bacterium that constrains mass, electron and energy flow at the scale of the individual. When tested and calibrated with laboratory data for the soil bacterium Azotobacter vinelandii, the model reveals that the direct energetic cost of nitrogen fixation is small relative to the cost of managing intracellular oxygen. It quantifies the costs and benefits of several potential oxygen protection mechanisms present in nature including enhanced respiration (respiratory protection) as well as the production of extracellular polymers as a barrier to O 2 diffusion, and increasing cell size. The latter mechanisms lead to higher growth efficiencies relative to respiratory protection alone. This simple, yet mechanistic framework provides a quantitative model of nitrogen fixation, which can be applied in ecological simulations.

We describe the genomes of two mycobacteriophages, MosMoris and Gattaca, newly isolated on Mycobacterium smegmatis The two phages are very similar to each other, differing in 61 single nucleotide polymorphisms and six small insertion/deletions. Both have extensive nucleotide sequence similarity to mycobacteriophage Marvin and together form cluster S., (Copyright © 2016 Mills et al.)

The genetic transformation of monocot grasses is a resource intensive process, the quality and efficiency of which is dependent in part upon the method of DNA introduction, as well as the ability to effectively separate transformed from wildtype tissue. Agrobacterium-mediated transformation of Brachypodium has relied mainly on Agrobacterium tumefaciens strain AGL1. Currently the antibiotic hygromycin B has been the selective agent of choice for robust identification of transgenic calli in Brachypodium distachyon and Brachypodium sylvaticum but few other chemicals have been shown to work as well for selection of transgenic Brachypodium cells in tissue culture. This study demonstrates that Agrobacterium rhizogenes strain 18r12v and paromomycin selection can be successfully used for the efficient generation of transgenic B. distachyon and B. sylvaticum. Additionally we observed that the transformation rates were similar to or higher than those obtained with A. tumefaciens strain AGL1 and hygromycin selection. The A. rhizogenes strain 18r12v harboring the pARS1 binary vector and paromomycin selection is an effective means of generating transgenic Brachypodium plants. This novel approach will facilitate the transgenic complementation of T-DNA knockout mutants of B. distachyon which were created using hygromycin selection, as well as aid the implementation of more complex genome manipulation strategies which require multiple rounds of transformation.