MHConstructor: A high-throughput, haplotype-informed solution to the MHC assembly challenge.

The extremely high levels of genetic polymorphism within the human major histocompatibility complex (MHC) limit the usefulness of reference-based alignment methods for sequence assembly. We incorporate a short read de novo assembly algorithm into a workflow for novel application to the MHC. MHConstructor is a containerized pipeline designed for high-throughput, haplotype-informed, reproducible assembly of both whole genome sequencing and target-capture short read data in large, population cohorts. To-date, no other self-contained tool exists for the generation of de novo MHC assemblies from short read data. MHConstructor facilitates wide-spread access to high quality, alignment-free MHC sequence analysis.

Type I Interferon: Monkeypox/Mpox Viruses Achilles Heel?

Poxviruses are notorious for having acquired/evolved numerous genes to counteract host innate immunity. Chordopoxviruses have acquired/evolved at least three different inhibitors of host necroptotic death: E3, which blocks ZBP1-dependent necroptotic cell death, and vIRD and vMLKL that inhibit necroptosis downstream of initial cell death signaling. While this suggests the importance of the necroptotic cell death pathway in inhibiting chordopoxvirus replication, several chordopoxviruses have lost one or more of these inhibitory functions. Monkeypox/mpox virus (MPXV) has lost a portion of the N-terminus of its E3 homologue. The N-terminus of the vaccinia virus E3 homologue serves to inhibit activation of the interferon-inducible antiviral protein, ZBP1. This likely makes MPXV unique among the orthopoxviruses in being sensitive to interferon (IFN) treatment in many mammals, including humans, which encode a complete necroptotic cell death pathway. Thus, IFN sensitivity may be the Achille's Heel for viruses like MPXV that cannot fully inhibit IFN-inducible, ZBP1-dependent antiviral pathways.

Atypical procedural learning in children with developmental coordination disorder: A combined behavioral and neuroimaging study.

While procedural learning (PL) has been implicated in delayed motor skill observed in developmental coordination disorder (DCD), few studies have considered the impact of co-occurring attentional problems. Furthermore, the neurostructural basis of PL in children remains unclear. We investigated PL in children with DCD while controlling for inattention symptoms, and examined the role of fronto-basal ganglia-cerebellar morphology in PL. Fifty-nine children (6-14 years; nDCD = 19, ncontrol = 40) completed the serial reaction time (SRT) task to measure PL. The Attention-Deficit Hyperactivity Disorder Rating Scale-IV was administered to measure inattention symptoms. Structural T1 images were acquired for a subset of participants (nDCD = 10, ncontrol = 28), and processed using FreeSurfer. Volume was extracted for the cerebellum, basal ganglia, and frontal regions. After controlling for inattention symptoms, the reaction time profile of controls was consistent with learning on the SRT task. This was not the case for those with DCD. SRT task performance was positively correlated with cerebellar cortical volume, and children with DCD trended towards lower cerebellar volume compared to controls. Children with DCD may not engage in PL during the SRT task in the same manner as controls, with this differential performance being associated with atypical cerebellar morphology.

Investigating the impact of developmental coordination difficulties across home, school, and community settings: Findings from the Australian Impact for DCD survey.

AIM: To evaluate the participation difficulties experienced by children with developmental coordination disorder (DCD) in home, school, and community environments. METHODS: The Impact for DCD survey was completed by primary caregivers of 4-18-year-old children with DCD (or synonymous diagnosis) (n = 429). OUTCOMES AND RESULTS: The greatest participation difficulties experienced at home included dressing, eating with utensils, self-care tasks and drawing/writing reported by over 70% of families. At school, fine motor difficulties were also frequently reported, with additional difficulties keeping up or completing tasks, and not feeling supported at school. Socialisation challenges and bullying were also commonly reported (34.9%). As a result of participation difficulties at school, 5.4% were home schooled. Many children engaged in community activity, with 72.0% currently engaged in at least one organised sports-based activity. CONCLUSIONS AND IMPLICATIONS: Increased recognition of the widespread impact of DCD in a child's life is crucial at an individual and societal level. Parents reported their children experiencing significant participation restrictions and difficulties. The findings of this large-scale study have revealed that most children with DCD are not receiving the support they need to thrive, especially at school. This largely reflects a lack of understanding and recognition of the condition and its associated challenges.

A Review of Numerical Models of Radiation Injury and Repair Considering Subcellular Targets and the Extracellular Microenvironment.

Astronauts in space are subject to continuous exposure to ionizing radiation. There is concern about the acute and late-occurring adverse health effects that astronauts could incur following a protracted exposure to the space radiation environment. Therefore, it is vital to consider the current tools and models used to describe and study the organic consequences of ionizing radiation exposure. It is equally important to see where these models could be improved. Historically, radiobiological models focused on how radiation damages nuclear deoxyribonucleic acid (DNA) and the role DNA repair mechanisms play in resulting biological effects, building on the hypotheses of Crowther and Lea from the 1940s and 1960s, and they neglected other subcellular targets outside of nuclear DNA. The development of these models and the current state of knowledge about radiation effects impacting astronauts in orbit, as well as how the radiation environment and cellular microenvironment are incorporated into these radiobiological models, aid our understanding of the influence space travel may have on astronaut health. It is vital to consider the current tools and models used to describe the organic consequences of ionizing radiation exposure and identify where they can be further improved.

The impact for DCD - USA study: The current state of Developmental Coordination Disorder (DCD) in the United States of America.

BACKGROUND: Developmental Coordination Disorder (DCD) is among the most under-recognized and under-supported disorders worldwide. AIMS: To present a preliminary national study that evaluated the unmet needs of children with DCD in the USA using the Impact for DCD survey. METHODS AND PROCEDURES: 232 parents of individuals aged 5-18 years provided responses from 36 items in five domains (diagnosis, activity/participation, education, therapy, and social/emotional health). OUTCOMES AND RESULTS: Most children (81.9%) had a formal diagnosis for movement difficulties, and 91.6% of parents reported that receiving a diagnosis was helpful, but most had not heard of the diagnosis before. The most common co-occurring diagnoses were childhood apraxia of speech and other speech-language disorders (24.6%), ADHD (23.1%), and anxiety (18.8%). Most parents reported that their children withdrew from or avoided movement-related activities (53%), and nearly all (94.8%) were concerned about the impact of motor difficulties on their children's social and emotional health. Only 37% of parents reported feeling that their child received sufficient therapy. CONCLUSIONS AND IMPLICATIONS: Generally, parents reported feeling frustrated with others' understanding and awareness of the condition and with therapy services. The results shown here provide timely data that can support efforts for increased awareness, improved diagnosis, and increased availability of services for DCD in the USA.

Pharmacologic Manipulation of Complement Receptor 3 Prevents Dendritic Spine Loss and Cognitive Impairment After Acute Cranial Radiation.

PURPOSE: Cranial irradiation induces healthy tissue damage that can lead to neurocognitive complications, negatively affecting patient quality of life. One damage indicator associated with cognitive impairment is loss of neuronal spine density. We previously demonstrated that irradiation-mediated spine loss is microglial complement receptor 3 (CR3) and sex dependent. We hypothesized that these changes are associated with late-delayed cognitive deficits and amenable to pharmacologic intervention. METHODS AND MATERIALS: Our model of cranial irradiation (acute, 10 Gy gamma) used male and female CR3-wild type and CR3-deficient Thy-1 YFP mice of C57BL/6 background. Forty-five days after irradiation and behavioral testing, we quantified spine density and markers of microglial reactivity in the hippocampal dentate gyrus. In a separate experiment, male Thy-1 YFP C57BL/6 mice were treated with leukadherin-1, a modulator of CR3 function. RESULTS: We found that male mice demonstrate irradiation-mediated spine loss and cognitive deficits but that female and CR3 knockout mice do not. These changes were associated with greater reactivity of microglia in male mice. Pharmacologic manipulation of CR3 with LA1 prevented spine loss and cognitive deficits in irradiated male mice. CONCLUSIONS: This work improves our understanding of irradiation-mediated mechanisms and sex dependent responses and may help identify novel therapeutics to reduce irradiation-induced cognitive decline and improve patient quality of life.

Psychosocial wellbeing, parental concerns, and familial impact of children with developmental coordination disorder.

BACKGROUND: Developmental Coordination Disorder (DCD) is a neurodevelopmental condition impacting motor skill acquisition and competence. While previous studies have identified adverse psychosocial outcomes in DCD, they are limited by small or population-screened, community-based samples. AIMS: To understand the psychosocial difficulties, parental concerns, and familial impacts of childhood DCD in a large population-based sample. METHODS AND PROCEDURES: Parents of 310 children aged 4 - 18 years with a diagnosis of DCD (or synonymous term) completed the Impact for DCD survey. Parent-rated measures of emotional problems, peer problems, and prosocial behaviour were compared to normative data. Parental concerns for the impact of DCD on participation, interaction, emotional well-being, and the family system were examined. OUTCOMES AND RESULTS: Compared to typically developing children, children with DCD were rated significantly higher for emotional and peer problems, and significantly lower for prosocial behaviours. Parents most commonly reported concerns for their child's future and withdrawal from physical activity. The presence of one or more co-occurring disorders did not significantly influence outcomes. CONCLUSION AND IMPLICATIONS: Findings highlight the poor psychosocial outcomes for children with DCD. Crucially, poor psychosocial outcomes were just as likely in those with a single diagnosis of DCD as those with DCD and multiple co-occurring diagnoses. Parents reported concerns for their child (i.e., non-participation and social withdrawal) that are not targeted in existing DCD intervention modalities and emphasised the impact of DCD on the whole family unit. WHAT THIS PAPER ADDS: This paper presents data from the largest parent-reported survey of children with a known diagnosis of DCD (or synonymous labels). It highlights the significant impact of DCD on psychosocial outcomes in children across age groups. The children in this study were rated by their parents to have significantly higher levels of emotional and peer problems, and lower prosocial behaviours, than similarly aged Australian children without DCD. It also challenges the misconception that poor psychosocial outcomes in DCD are the result of co-occurring disorders, with outcomes observed to be as poor in children with a sole diagnosis of DCD in this sample. Furthermore, findings highlighted the significant worry and concern that parents with DCD face, particularly around their child's participation and their emotional health. Finally, parents reported on the considerable impact that DCD had on their family unit, regularly causing worry and concern, influencing their choice of activities, and causing financial strain. These concerns and impacts are not addressed in current intervention models for DCD and highlight the need for support mechanisms moving forward.

Combined action observation and motor imagery improves learning of activities of daily living in children with Developmental Coordination Disorder.

Developmental coordination disorder (DCD) is characterised by poor motor coordination, which interferes with the ability to execute activities of daily living (ADLs). Combined action observation and motor imagery (AOMI) involves observing movement videos whilst imagining simultaneously the sensations of executing the same movement. Laboratory-based research indicates that AOMI can help improve movement coordination in children with DCD, but no previous research had investigated the efficacy of AOMI interventions for learning ADLs. This study investigated the efficacy of a home-based, parent-led, AOMI intervention for learning ADLs in children with DCD. Children with confirmed (n = 23) or suspected (n = 5) DCD (total sample n = 28), aged 7-12 years, were assigned to either an AOMI intervention or a control intervention (both n = 14). Participants attempted the following ADLs at pre-test (week 1), post-test (week 4), and retention test (week 6): shoelace tying, cutlery use, shirt buttoning, and cup stacking. Task completion times and movement techniques were recorded. The AOMI intervention produced significantly faster task completion times than the control intervention at post-test for shoelace tying, and significantly improved movement techniques for shoelace tying and cup stacking. Importantly, for children who could not tie shoelaces at pre-test (n = 9 per group), 89% of those following the AOMI intervention learnt the skill successfully by the end of the study, compared to only 44% of those following the control intervention. The findings indicate that home-based, parent-led, AOMI interventions can aid the learning of complex ADLs in children with DCD, and may be particularly effective for facilitating the learning of motor skills that do not currently exist within these children's motor repertoire.

Canonical cellular stress granules are required for arsenite-induced necroptosis mediated by Z-DNA-binding protein 1.

Cellular stress granules arise in cells subjected to stress and promote cell survival. A cellular protein that localizes to stress granules is Z-DNA-binding protein 1 (ZBP1), which plays a major role in necroptosis, a programmed cell death pathway mediated by the kinase RIPK3. Here, we showed that the stress granule inducer arsenite activated RIPK3-dependent necroptosis. This pathway required ZBP1, which localized to arsenite-induced stress granules. RIPK3 localized to stress granules in the presence of ZBP1, leading to the formation of ZBP1-RIPK3 necrosomes, phosphorylation of the RIPK3 effector MLKL, and execution of necroptosis. Cells that did not form stress granules did not induce necroptosis in response to arsenite. Together, these results show that arsenite induces ZBP1-mediated necroptosis in a manner dependent on stress granule formation.

Modeling normal bladder injury after radiation therapy.

PURPOSE: For decades, Dr. John Moulder has been a leading radiation biologist and one of the few who consistently supported the study of normal tissue responses to radiation. His meticulous modeling and collaborations across the field have offered a prime example of how research can be taken from the bench to the bedside and back, with the ultimate goal of providing benefit to patients. Much of the focus of John's work was on mitigating damage to the kidney, whether as the result of accidental or deliberate clinical exposures. Following in his footsteps, we offer here a brief overview of work conducted in the field of radiation-induced bladder injury. We then describe our own preclinical experimental studies which originated as a response to reports from a clinical genome-wide association study (GWAS) investigating genomic biomarkers of normal tissue toxicity in prostate cancer patients treated with radiotherapy. In particular, we discuss the use of Renin-Angiotensin System (RAS) inhibitors as modulators of injury, agents championed by the Moulder group, and how RAS inhibitors are associated with a reduction in some measures of toxicity. Using a murine model, along with precise CT-image guided irradiation of the bladder using single and fractionated dosing regimens, we have been able to demonstrate radiation-induced functional injury to the bladder and mitigation of this functional damage by an inhibitor of angiotensin-converting enzyme targeting the RAS, an experimental approach akin to that used by the Moulder group. We consider our scientific trajectory as a bedside-to-bench approach because the observation was made clinically and investigated in a preclinical model; this experimental approach aligns with the exemplary career of Dr. John Moulder. CONCLUSIONS: Despite the differences in functional endpoints, recent findings indicate a commonality between bladder late effects and the work in kidney pioneered by Dr. John Moulder. We offer evidence that targeting the RAS pathway may provide a targetable pathway to reducing late bladder toxicity.

High-Energy, Whole-Body Proton Irradiation Differentially Alters Long-Term Brain Pathology and Behavior Dependent on Sex and Alzheimer's Disease Mutations.

Whole-body exposure to high-energy particle radiation remains an unmitigated hazard to human health in space. Ongoing experiments at the NASA Space Radiation Laboratory and elsewhere repeatedly show persistent changes in brain function long after exposure to simulations of this unique radiation environment, although, as is also the case with proton radiotherapy sequelae, how this occurs and especially how it interacts with common comorbidities is not well-understood. Here, we report modest differential changes in behavior and brain pathology between male and female Alzheimer's-like and wildtype littermate mice 7-8 months after exposure to 0, 0.5, or 2 Gy of 1 GeV proton radiation. The mice were examined with a battery of behavior tests and assayed for amyloid beta pathology, synaptic markers, microbleeds, microglial reactivity, and plasma cytokines. In general, the Alzheimer's model mice were more prone than their wildtype littermates to radiation-induced behavior changes, and hippocampal staining for amyloid beta pathology and microglial activation in these mice revealed a dose-dependent reduction in males but not in females. In summary, radiation-induced, long-term changes in behavior and pathology, although modest, appear specific to both sex and the underlying disease state.

Radiation and CNS effects: summary of evidence from a recent symposium of the Radiation Research Society.

This article summarizes a Symposium on 'Radiation risks of the central nervous system' held virtually at the 67th Annual Meeting of the Radiation Research Society, 3-6 October 2021. Repeated low-dose radiation exposure over a certain period could lead to reduced neuronal proliferation, altered neurogenesis, neuroinflammation and various neurological complications, including psychological consequences, necessitating further research in these areas. Four speakers from radiation biology, genetics and epidemiology presented the latest data from their studies seeking insights into this important topic. This symposium highlighted new and important directions for further research on mental health disorders, neurodegenerative conditions and cognitive impairment. Future studies will examine risks of mental and behavioral disorders and neurodegenerative diseases following protracted radiation exposures to better understand risks of occupational exposures as well as provide insights into risks from exposures to galactic cosmic rays.

The impact of brain lesion characteristics and the corticospinal tract wiring on mirror movements in unilateral cerebral palsy.

Mirror movements (MM) influence bimanual performance in children with unilateral cerebral palsy (uCP). Whilst MM are related to brain lesion characteristics and the corticospinal tract (CST) wiring pattern, the combined impact of these neurological factors remains unknown. Forty-nine children with uCP (mean age 10y6mo) performed a repetitive squeezing task to quantify similarity (MM-similarity) and strength (MM-intensity) of the MM activity. We used MRI data to evaluate lesion type (periventricular white matter, N = 30; cortico-subcortical, N = 19), extent of ipsilesional damage, presence of bilateral lesions, and damage to basal ganglia, thalamus and corpus callosum. The CST wiring was assessed with Transcranial Magnetic Stimulation (17 CSTcontralateral, 16 CSTipsilateral, 16 CSTbilateral). Data was analyzed with regression analyses. In the more-affected hand, MM-similarity and intensity were higher with CSTbilateral/ipsilateral. In the less-affected hand, MM-similarity was higher in children with (1) CSTcontra with CSC lesions, (2) CSTbilat/ipsi with PVL lesions and (3) CSTbilat/ipsi with unilateralized lesions. MM-intensity was higher with larger damage to the corpus callosum and unilateral lesions. A complex combination of neurological factors influences MM characteristics, and the mechanisms differ between hands.

Fostering collaborative learning and leadership through near-peer mentorship among undergraduate nursing students.

BACKGROUND: Innovative teaching strategies in nursing education are essential with increasing enrollment. Collaborative learning and leadership (CLL) activities encourage near-peer learning through mentorship between senior-level and novice students while supporting teaching ratios in lab and clinical. In this study, senior nursing students' perceptions and performance during CLL activities were explored. METHODS: Final-semester senior students participated in CLL activities and were evaluated on their leadership and engagement. Grading rubric results were summarized using descriptive statistics. Thematic analysis of students' post-CLL reflections supported common themes. RESULTS: Students' average scores (97.53%) confirm students were prepared and engaged in CLL activities. Senior students enjoyed "building confidence" through these activities, with a consistent theme of "becoming a leader," noted in reflections. CONCLUSION: Near-peer learning activities assisted senior students in development of leadership and communication skills, preparing them for nursing practice. Recommendations include developing instructions for varied CLL activities and exploring faculty perspectives regarding this experience.

Endurance exercise attenuates juvenile irradiation-induced skeletal muscle functional decline and mitochondrial stress.

BACKGROUND: Radiotherapy is commonly used to treat childhood cancers and can have adverse effects on muscle function, but the underlying mechanisms have yet to be fully elucidated. We hypothesized that endurance exercise following radiation treatment would improve skeletal muscle function. METHODS: We utilized the Small Animal Radiation Research Platform (SARRP) to irradiate juvenile male mice with a clinically relevant fractionated dose of 3× (every other day over 5 days) 8.2 Gy X-ray irradiation locally from the knee to footpad region of the right hindlimb. Mice were then singly housed for 1 month in cages equipped with either locked or free-spinning voluntary running wheels. Ex vivo muscle contractile function, RT-qPCR analyses, resting cytosolic and sarcoplasmic reticulum (SR) store Ca2+ levels, mitochondrial reactive oxygen species levels (MitoSOX), and immunohistochemical and biochemical analyses of muscle samples were conducted to assess the muscle pathology and the relative therapeutic impact of voluntary wheel running (VWR). RESULTS: Irradiation reduced fast-twitch extensor digitorum longus (EDL) muscle-specific force by 27% compared to that of non-irradiated mice, while VWR post-irradiation improved muscle-specific force by 37%. Radiation treatment similarly reduced slow-twitch soleus muscle-specific force by 14% compared to that of non-irradiated mice, while VWR post-irradiation improved specific force by 18%. We assessed intracellular Ca2+ regulation, oxidative stress, and mitochondrial homeostasis as potential mechanisms of radiation-induced pathology and exercise-mediated rescue. We found a significant reduction in resting cytosolic Ca2+ concentration following irradiation in sedentary mice. Intriguingly, however, SR Ca2+ store content was increased in myofibers from irradiated mice post-VWR compared to mice that remained sedentary. We observed a 73% elevation in the overall protein oxidization in muscle post-irradiation, while VWR reduced protein nitrosylation by 35% and mitochondrial reactive oxygen species (ROS) production by 50%. Finally, we found that VWR significantly increased the expression of PGC1α at both the transcript and protein levels, consistent with an exercise-dependent increase in mitochondrial biogenesis. CONCLUSIONS: Juvenile irradiation stunted muscle development, disrupted proper Ca2+ handling, damaged mitochondria, and increased oxidative and nitrosative stress, paralleling significant deficits in muscle force production. Exercise mitigated aberrant Ca2+ handling, mitochondrial homeostasis, and increased oxidative and nitrosative stress in a manner that correlated with improved skeletal muscle function after radiation.

Muscle-specific functional deficits and lifelong fibrosis in response to paediatric radiotherapy and tumour elimination.

BACKGROUND: As paediatric cancer survivors are living into adulthood, they suffer from the age-related, accelerated decline of functional skeletal muscle tissue, termed sarcopenia. With ionizing radiation (radiotherapy) at the core of paediatric cancer therapies, its direct and indirect effects can have lifelong negative impacts on paediatric growth and maintenance of skeletal muscle. Utilizing our recently developed preclinical rhabdomyosarcoma mouse model, we investigated the late effects of paediatric radiation treatment on skeletal muscles from late adolescent (8 weeks old) and middle-aged (16 months old) mice. METHODS: Paediatric C57BL/6J male mice (3 weeks old) were injected with rhabdomyosarcoma cells into their right hindlimbs, and then fractionated irradiation (3 × 8.2 Gy) was administered to those limbs at 4 weeks old to eliminate the tumours. Radiation-alone and tumour-irradiated mice were assessed at either 8 weeks (3 weeks post-irradiation) or 16 months (14 months post-irradiation) of age for muscle physiology, myofibre characteristics, cell loss, histopathology, fibrosis, inflammatory gene expression, and fibrotic gene expression. RESULTS: Mice that received only paediatric radiation demonstrated reduced muscle mass (-17%, P < 0.001), muscle physiological function (-25%, P < 0.01), muscle contractile kinetics (-25%, P < 0.05), satellite cell number (-45%, P < 0.05), myofibre cross-sectional area (-30%, P < 0.0001), and myonuclear number (-17%, P < 0.001). Paediatric radiation increased inflammatory gene expression, increased fibrotic gene expression, and induced extracellular matrix protein deposition (fibrosis) with tumour elimination exacerbating some phenotypes. Paediatric tumour-eliminated mice demonstrated exacerbated deficits to function (-20%, P < 0.05) and myofibre size (-17%, P < 0.001) in some muscles as well as further increases to inflammatory and fibrotic gene expression. Examining the age-related effects of paediatric radiotherapy in middle-aged mice, we found persistent myofibre atrophy (-20%, P < 0.01), myonuclear loss (-18%, P < 0.001), up-regulated inflammatory and fibrotic signalling, and lifelong fibrosis. CONCLUSIONS: The results from this paediatric radiotherapy model are consistent and recapitulate the clinical and molecular features of accelerated sarcopenia, musculoskeletal frailty, and radiation-induced fibrosis experienced by paediatric cancer survivors. We believe that this preclinical mouse model is well poised for future mechanistic insights and therapeutic interventions that improve the quality of life for paediatric cancer survivors.