Genetic modification of the bee parasite Crithidia bombi for improved visualization and protein localization.

Crithidia bombi is a trypanosomatid parasite that infects several species of bumble bees (Bombus spp.), by adhering to their intestinal tract. Crithidia bombi infection impairs learning and reduces survival of workers and the fitness of overwintering queens. Although there is extensive research on the ecology of this host-pathogen system, we understand far less about the mechanisms that mediate internal infection dynamics. Crithidia bombi infects hosts by attaching to the hindgut via the flagellum, and one previous study found that a nectar secondary compound removed the flagellum, preventing attachment. However, approaches that allow more detailed observation of parasite attachment and growth would allow us to better understand factors mediating this host-pathogen relationship. We established techniques for genetic manipulation and visualization of cultured C. bombi. Using constructs established for Crithidia fasciculata, we successfully generated C. bombi cells expressing ectopic fluorescent transgenes using two different selectable markers. To our knowledge, this is the first genetic modification of this species. We also introduced constructs that label the mitochondrion and nucleus of the parasite, showing that subcellular targeting signals can function across parasite species to highlight specific organelles. Finally, we visualized fluorescently tagged parasites in vitro in both their swimming and attached forms, and in vivo in bumble bee (Bombus impatiens) hosts. Expanding our cell and molecular toolkit for C. bombi will help us better understand how factors such as host diet, immune system, and physiology mediate outcomes of infection by these common parasites.

Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project.

BACKGROUND: A major obstacle faced by families with rare diseases is obtaining a genetic diagnosis. The average "diagnostic odyssey" lasts over five years and causal variants are identified in under 50%, even when capturing variants genome-wide. To aid in the interpretation and prioritization of the vast number of variants detected, computational methods are proliferating. Knowing which tools are most effective remains unclear. To evaluate the performance of computational methods, and to encourage innovation in method development, we designed a Critical Assessment of Genome Interpretation (CAGI) community challenge to place variant prioritization models head-to-head in a real-life clinical diagnostic setting. METHODS: We utilized genome sequencing (GS) data from families sequenced in the Rare Genomes Project (RGP), a direct-to-participant research study on the utility of GS for rare disease diagnosis and gene discovery. Challenge predictors were provided with a dataset of variant calls and phenotype terms from 175 RGP individuals (65 families), including 35 solved training set families with causal variants specified, and 30 unlabeled test set families (14 solved, 16 unsolved). We tasked teams to identify causal variants in as many families as possible. Predictors submitted variant predictions with estimated probability of causal relationship (EPCR) values. Model performance was determined by two metrics, a weighted score based on the rank position of causal variants, and the maximum F-measure, based on precision and recall of causal variants across all EPCR values. RESULTS: Sixteen teams submitted predictions from 52 models, some with manual review incorporated. Top performers recalled causal variants in up to 13 of 14 solved families within the top 5 ranked variants. Newly discovered diagnostic variants were returned to two previously unsolved families following confirmatory RNA sequencing, and two novel disease gene candidates were entered into Matchmaker Exchange. In one example, RNA sequencing demonstrated aberrant splicing due to a deep intronic indel in ASNS, identified in trans with a frameshift variant in an unsolved proband with phenotypes consistent with asparagine synthetase deficiency. CONCLUSIONS: Model methodology and performance was highly variable. Models weighing call quality, allele frequency, predicted deleteriousness, segregation, and phenotype were effective in identifying causal variants, and models open to phenotype expansion and non-coding variants were able to capture more difficult diagnoses and discover new diagnoses. Overall, computational models can significantly aid variant prioritization. For use in diagnostics, detailed review and conservative assessment of prioritized variants against established criteria is needed.

Patient-centred pathology reporting improves patient experience and understanding of disease in prostate cancer care.

Introduction and Objectives: Patient-centred (PC) and holistic care improves patient satisfaction and health outcomes. We sought to investigate the benefit of utilising a PC pathology report in patients undergoing radical prostatectomy (RP) for prostate cancer (PCa). Our study aimed to evaluate and compare patient understanding of their PCa diagnosis after RP, upon receiving either a standard histopathology report or a personalised and PC report (PCR). Moreover, we evaluated knowledge retention at 4 weeks after the initial consultation. Methods: We invited patients undergoing RP at three metropolitan Urology clinics to participate in our randomised controlled study. Patients were randomised to receive either a PCR or standard pathology report. Patient satisfaction questionnaires (Perceived Efficacy in Patient-Physician Interactions [PEPPI], Consultation and Relational Empathy [CARE] and Communication Assessment Tool [CAT]) and a knowledge test were conducted within 72 h of the initial appointment and again at 4 weeks. Accurate recollection of Gleason grade group (GGG) and extracapsular extension (ECE) were classified as 'correct'. Baseline demographic data included age, education, marital and employment status, pre-op prostate specific antigen (PSA) and clinical stage. Baseline data were tested for differences between groups using the Student's t test, chi-squared test or Fisher's exact test depending on whether data were continuous, categorical or sparse. Comparison of correctly answered 'knowledge' questions was analysed using chi-squared test. A significance level of p ≤ 0.05 was used. Results: Data from 62 patients were analysed (30 standard vs. 32 PCR). No significant differences in baseline demographics were found between groups. Both groups reported high levels of satisfaction with their healthcare experiences in all domains of patient-physician rapport, empathy and communication. There were no significant differences between groups in PEPPI (p = 0.68), CAT (p = 0.39) and CARE (p = 0.66) scores, at baseline and 4 weeks. Ninety-three per cent of patients who received the PCR understood the report while 90% felt the report added to their understanding of their PCa. Regarding patient knowledge, the PCR group had significantly more correct answers on GGG and ECE as compared with the standard report group at baseline and 4 weeks (p < 0.001 and 0.001, respectively). Conclusions: Our findings demonstrate that PC pathology reports improve patient knowledge and understanding of their PCa that is retained for at least 4 weeks after initial receipt of results.

Assessment of Mammalian Target of Rapamycin Pathway Activation in Basal Cell Carcinoma as a New Therapeutic Approach.

ABSTRACT: Targeting the mammalian target of rapamycin (mTOR) pathway represents a potentially novel approach to treat basal cell carcinoma (BCC), but activation of this pathway has not been well described in human BCCs. The purpose of this study was to assess whether mTOR pathway activation occurs in BCCs (both sporadic and syndromic) and report a case of a patient with Gorlin syndrome (GS) whose clinically suspicious BCCs responded to mTOR inhibition through topical sirolimus treatment. After Stanford Institutional Review Board Approval, archived BCCs from patients with GS (n = 25), sporadic BCCs (n = 35), and control tissues were subjected to immunohistochemical analysis for the activation of mTOR pathway, and immunohistochemical staining intensity was evaluated by a dermatopathologist. BCCs (compared with normal skin) had elevated levels of eIF4EBP1 (Padjusted = 0.0336), which is downstream of mTOR. a serine/threonine kinase Phospho-(AKT), which interacts with mTOR, was also significantly elevated (perinuclear: Padjusted < 0.0001; cytoplasmic: Padjusted = 0.0021). When off-label topical 1% sirolimus was used on a pediatric patient with GS, we noted reduction of new BCC development and decreased size of existing neoplasms clinically suspicious for BCCs. This treatment was well tolerated after 2 years of continuous use, with no other treatments needed during this period. Topical sirolimus is a promising therapeutic candidate against both sporadic and GS-associated BCC. Multicenter, prospective studies are needed to understand the efficacy and safety of topical mTOR inhibitors in BCC treatment, and ascertain whether the immunohistochemical markers downstream of mTOR could have predictive value in identifying BCCs most likely to respond to topical mTOR inhibitors, such as sirolimus.

Comorbid Word Reading and Mathematics Computation Difficulty at Start of First Grade.

The purpose of this analysis was to describe cognitive processes associated with comorbid difficulty between word reading (WR) and mathematics computation (MC) at the start of first grade among children selected for WR and MC delays. A sample of 234 children (mean age 6.50 years, SD = 0.31) was assessed on WR, MC, core cognitive processes (phonological processing, rapid automatized naming, verbal counting [VC]), and domain-general cognitive processes (working memory, oral language, nonverbal reasoning, attentive behavior). Structural equation modeling was used to predict a latent Comorbidity factor, which modeled shared variance between WR and MC, and to identify processes associated with that Comorbidity factor. Results identified each of the core cognitive processes, especially VC, and each of the domain-general cognitive processes, especially working memory, as explaining shared variance between WR and MC. Implications for understanding comorbid difficulty at the start of first grade and designing coordinated first-grade interventions are discussed.

Modification of Polysulfide Surfaces with Low-Power Lasers.

The modification of polymer surfaces using laser light is important for many applications in the nano-, bio- and chemical sciences. Such capabilities have supported advances in biomedical devices, electronics, information storage, microfluidics, and other applications. In most cases, these modifications require high power lasers that are expensive and require specialized equipment and facilities to minimize risk of hazardous radiation. Additionally, polymer systems that can be easily modified by lasers are often complex and costly to prepare. In this report, these challenges are addressed with the discovery of low-cost sulfur copolymers that can be rapidly modified with lasers emitting low-power infrared and visible light. The featured copolymers are made from elemental sulfur and either cyclopentadiene or dicyclopentadiene. Using a suite of lasers with discreet wavelengths (532, 638 and 786 nm) and powers, a variety of surface modifications could be made on the polymers such as controlled swelling or etching via ablation. The facile synthesis and laser modification of these polymer systems were exploited in applications such as direct laser lithography and erasable information storage.

A metabolic signature for NADSYN1-dependent congenital NAD deficiency disorder.

Nicotinamide adenine dinucleotide (NAD) is essential for embryonic development. To date, biallelic loss-of-function variants in 3 genes encoding nonredundant enzymes of the NAD de novo synthesis pathway - KYNU, HAAO, and NADSYN1 - have been identified in humans with congenital malformations defined as congenital NAD deficiency disorder (CNDD). Here, we identified 13 further individuals with biallelic NADSYN1 variants predicted to be damaging, and phenotypes ranging from multiple severe malformations to the complete absence of malformation. Enzymatic assessment of variant deleteriousness in vitro revealed protein domain-specific perturbation, complemented by protein structure modeling in silico. We reproduced NADSYN1-dependent CNDD in mice and assessed various maternal NAD precursor supplementation strategies to prevent adverse pregnancy outcomes. While for Nadsyn1+/- mothers, any B3 vitamer was suitable to raise NAD, preventing embryo loss and malformation, Nadsyn1-/- mothers required supplementation with amidated NAD precursors (nicotinamide or nicotinamide mononucleotide) bypassing their metabolic block. The circulatory NAD metabolome in mice and humans before and after NAD precursor supplementation revealed a consistent metabolic signature with utility for patient identification. Our data collectively improve clinical diagnostics of NADSYN1-dependent CNDD, provide guidance for the therapeutic prevention of CNDD, and suggest an ongoing need to maintain NAD levels via amidated NAD precursor supplementation after birth.

Prospects of formamide as nitrogen source in biotechnological production processes.

This review presents an analysis of formamide, focussing on its occurrence in nature, its functional roles, and its promising applications in the context of the bioeconomy. We discuss the utilization of formamide as an innovative nitrogen source achieved through metabolic engineering. These approaches underscore formamide's potential in supporting growth and production in biotechnological processes. Furthermore, our review illuminates formamide's role as a nitrogen source capable of safeguarding cultivation systems against contamination in non-sterile conditions. This attribute adds an extra layer of practicality to its application, rendering it an attractive candidate for sustainable and resilient industrial practices. Additionally, the article unveils the versatility of formamide as a potential carbon source that could be combined with formate or CO2 assimilation pathways. However, its attributes, i.e., enriched nitrogen content and comparatively limited energy content, led to conclude that formamide is more suitable as a co-substrate and that its use as a sole source of carbon for biomass and bio-production is limited. Through our exploration of formamide's properties and its applications, this review underscores the significance of formamide as valuable resource for a large spectrum of industrial applications. KEY POINTS: • Formidases enable access to formamide as source of nitrogen, carbon, and energy • The formamide/formamidase system supports non-sterile fermentation • The nitrogen source formamide supports production of nitrogenous compounds.

Pollen Diet Diversity does not Affect Gut Bacterial Communities or Melanization in a Social and Solitary Bee Species.

Pollinators face many stressors, including reduced floral diversity. A low-diversity diet can impair organisms' ability to cope with additional stressors, such as pathogens, by altering the gut microbiome and/or immune function, but these effects are understudied for most pollinators. We investigated the impact of pollen diet diversity on two ecologically and economically important generalist pollinators, the social bumble bee (Bombus impatiens) and the solitary alfalfa leafcutter bee (Megachile rotundata). We experimentally tested the effect of one-, two-, or three-species pollen diets on gut bacterial communities in both species, and the melanization immune response in B. impatiens. Pollen diets included dandelion (Taraxacum officinale), staghorn sumac (Rhus typhina), and hawthorn (Crataegus sp.) alone, each pair-wise combination, or a mix of all three species. We fed bees their diet for 7 days and then dissected out guts and sequenced 16S rRNA gene amplicons to characterize gut bacterial communities. To assess melanization in B. impatiens, we inserted microfilament implants into the bee abdomen and measured melanin deposition on the implant. We found that pollen diet did not influence gut bacterial communities in M. rotundata. In B. impatiens, pollen diet composition, but not diversity, affected gut bacterial richness in older, but not newly-emerged bees. Pollen diet did not affect the melanization response in B. impatiens. Our results suggest that even a monofloral, low-quality pollen diet such as dandelion can support diverse gut bacterial communities in captive-reared adults of these bee species. These findings shed light on the effects of reduced diet diversity on bee health.

Establishment of synthetic microbial consortia with Corynebacterium glutamicum and Pseudomonas putida: Design, construction, and application to production of γ-glutamylisopropylamide and l-theanine.

Microbial synthetic consortia are a promising alternative to classical monoculture for biotechnological applications and fermentative processes. Their versatile use offers advantages in the degradation of complex substrates, the allocation of the metabolic burden between individual partners, or the division of labour in energy utilisation, substrate supply or product formation. Here, stable synthetic consortia between the two industrially relevant production hosts, Pseudomonas putida KT2440 and Corynebacterium glutamicum ATCC13032, were established for the first time. By applying arginine auxotrophy/overproduction and/or formamidase-based utilisation of the rare nitrogen source formamide, different types of interaction were realised, such as commensal relationships (+/0 and 0/+) and mutualistic cross-feeding (+/+). These consortia did not only show stable growth but could also be used for fermentative production of the γ-glutamylated amines theanine and γ-glutamyl-isopropylamide (GIPA). The consortia produced up to 2.8 g L-1 of GIPA and up to 2.6 g L-1 of theanine, a taste-enhancing constituent of green tea leaves. Thus, the advantageous approach of using synthetic microbial consortia for fermentative production of value-added compounds was successfully demonstrated.

A multidimensional appraisal of early menstrual pain experience.

BACKGROUND: Symptomatic dysmenorrhea is a global problem, affecting more than 40% of menstruating persons. Cross-sectional studies have implicated psychosocial, biological, and sensory factors in dysmenorrhea but the mechanisms are not fully understood. Only a few prospective longitudinal studies have evaluated such factors in relation to the emergence and course of dysmenorrhea at menarche. OBJECTIVE: This study aimed to describe the initial menstruation experience and to evaluate the association of premenarchal psychosocial and sensory factors with the intensity of dysmenorrhea during the period in the fourth month. STUDY DESIGN: This was a prospective cohort study of adolescents who completed premenarchal assessments and postmenarchal daily menstrual diaries for their first (n=149) and fourth month periods (n=114). They were recruited shortly before menarche and completed baseline assessments, including psychosocial questionnaires and experimental pain sensitivity (pressure testing, bladder provocation), and their parents completed related pain questionnaires. The relation between the hypothesized premenarchal factors and month 4 dysmenorrhea intensity was evaluated using Kruskal-Wallis and chi-square tests for low (<3 on a 0-10 scale) vs higher (≥3) menstrual pain groups based on maximal pain ratings recorded in a daily diary. RESULTS: Low levels of dysmenorrhea characterized the first (median, 1; interquartile range, 0-2) and fourth month periods (1; 0-3). Maximal pain ratings increased from the first to the fourth period (3; 1-5 vs 4; 1-6; P=.007). The distribution of dysmenorrhea was multimodal at month 4 with 31.6% of the participants having low levels of maximal pain (1; 0-1) and 68.4% having higher levels (5; 4-6; Hartigan's dip test P<.001). The baseline demographic, psychosocial, and parental pain characteristics were not associated with the development of worse dysmenorrhea. The baseline experimental pain sensitivity, based on pressure pain thresholds, did not differ between the low (15.7 N; 12.5-22.3) and higher (15.0 N; 10.9-21.4]) level dysmenorrhea groups. Baseline bladder pain at first urge also did not differ (low, 6; 0-20 vs higher, 7; 0-19). CONCLUSION: By their fourth month period, two-thirds of adolescents fell into the higher group for maximal dysmenorrhea, half reported some related impairments in physical activity, and one-seventh reported some related school absence. Premenarchal factors (experimental pain sensitivity, psychosocial profile, parental pain experience) linked to chronic pain emergence in the adult literature did not predict dysmenorrhea intensity, suggesting the dominant factor at menarche may be peripheral afferent activation. Further research is needed to understand the evolution of psychosocial and sensory mechanisms in the development and course of dysmenorrhea.

The role of visual imagery in story reading: Evidence from aphantasia.

Aphantasia is a condition in which people are unable to experience visual imagery. Since visual imagery is thought to be key to language processing, we hypothesized the experience of a story would differ between individuals with aphantasia and controls. Forty-seven individuals with aphantasia were compared to fifty-one matched controls on their experience of reading a short story and their general reading habits. Aphantasics were less likely to be engaged with, interested in, and absorbed in the story, and experienced reduced emotional engagement with and sympathy for the story characters, compared to controls. Yet, aphantasics and controls did not differ in how much they liked or appreciated the story, and in general, the reading habits of the two groups also did not differ. Results have implications for embodied theories of language, suggesting visual imagery may influence how a story is experienced, but it is not the only route to story enjoyment.

Transcending Limitations: A Phenomenological Exploration of How Hygge Practices Enrich the Lived Experiences of Adults with Cystic Fibrosis.

Hygge practices embody joy, peace, mindfulness, coziness, and conviviality. Cystic fibrosis (CF) is a progressive condition with complex therapies and physical limitations. Little is known about how hygge practice may impact individuals living with CF. A qualitative study explored how adults with CF use hygge practices to promote wellness and cope with their disease. A purposive network sample of 15 adults with CF who utilized hygge practices completed semistructured audio-recorded telephone interviews. Recordings were transcribed and analyzed using Colaizzi's thematic analysis approach. Results reveal that hygge practices influenced individuals' aesthetics, attitudes, and activities, deeply impacting the physical and emotional experience of living with CF. Incorporating hygge into CF care may improve psychological well-being and quality of life for members of this community.

Modeling variability in treatment effects for cluster randomized controlled trials using by-variable smooth functions in a generalized additive mixed model.

Variability in treatment effects is common in intervention studies using cluster randomized controlled trial (C-RCT) designs. Such variability is often examined in multilevel modeling (MLM) to understand how treatment effects (TRT) differ based on the level of a covariate (COV), called TRT × COV. In detecting TRT × COV effects using MLM, relationships between covariates and outcomes are assumed to vary across clusters linearly. However, this linearity assumption may not hold in all applications and an incorrect assumption may lead to biased statistical inference about TRT × COV effects. In this study, we present generalized additive mixed model (GAMM) specifications in which cluster-specific functional relationships between covariates and outcomes can be modeled using by-variable smooth functions. In addition, the implementation for GAMM specifications is explained using the mgcv R package (Wood, 2021). The usefulness of the GAMM specifications is illustrated using intervention data from a C-RCT. Results of simulation studies showed that parameters and by-variable smooth functions were recovered well in various multilevel designs and the misspecification of the relationship between covariates and outcomes led to biased estimates of TRT × COV effects. Furthermore, this study evaluated the extent to which the GAMM can be treated as an alternative model to MLM in the presence of a linear relationship.

MYSM1 attenuates DNA damage signals triggered by physiologic and genotoxic DNA breaks.

BACKGROUND: Patients with deleterious variants in MYSM1 have an immune deficiency characterized by B-cell lymphopenia, hypogammaglobulinemia, and increased radiosensitivity. MYSM1 is a histone deubiquitinase with established activity in regulating gene expression. MYSM1 also localizes to sites of DNA injury but its function in cellular responses to DNA breaks has not been elucidated. OBJECTIVES: This study sought to determine the activity of MYSM1 in regulating DNA damage responses (DDRs) to DNA double-stranded breaks (DSBs) generated during immunoglobulin receptor gene (Ig) recombination and by ionizing radiation. METHODS: MYSM1-deficient pre- and non-B cells were used to determine the role of MYSM1 in DSB generation, DSB repair, and termination of DDRs. RESULTS: Genetic testing in a newborn with abnormal screen for severe combined immune deficiency, T-cell lymphopenia, and near absence of B cells identified a novel splice variant in MYSM1 that results in nearly absent protein expression. Radiosensitivity testing in patient's peripheral blood lymphocytes showed constitutive γH2AX, a marker of DNA damage, in B cells in the absence of irradiation, suggesting a role for MYSM1 in response to DSBs generated during Ig recombination. Suppression of MYSM1 in pre-B cells did not alter generation or repair of Ig DSBs. Rather, loss of MYSM1 resulted in persistent DNA damage foci and prolonged DDR signaling. Loss of MYSM1 also led to protracted DDRs in U2OS cells with irradiation induced DSBs. CONCLUSIONS: MYSM1 regulates termination of DNA damage responses but does not function in DNA break generation and repair.