Juneteenth in STEMM and the barriers to equitable science.

We are 52 Black scientists. Here, we establish the context of Juneteenth in STEMM and discuss the barriers Black scientists face, the struggles they endure, and the lack of recognition they receive. We review racism's history in science and provide institutional-level solutions to reduce the burdens on Black scientists.

Patching the Leaks: Revitalizing and Reimagining the STEM Pipeline.

We identify problematic areas throughout the Science, Technology, Engineering and Mathematics (STEM) pipeline that perpetuate racial disparities in academia. Distinct ways to curtail these disparities include early exposure and access to resources, supportive mentoring networks and comprehensive training programs specifically for racially minoritized students and trainees at each career stage. These actions will revitalize the STEM pipeline.

Recovering from the stress of the COVID-19 pandemic.

For our special issue on stress, we asked scientists about recovering from the stress of the pandemic, including some who shared insights with us in mid-2020. They discuss the importance of teamwork, reassessing priorities, and the added stresses of the cost-of-living crisis, funding cuts, and retaining scientists in academia.

Bridging lipid metabolism and mitochondrial genome maintenance.

Mitochondria are the nexus of cellular energy metabolism and major signaling hubs that integrate information from within and without the cell to implement cell function. Mitochondria harbor a distinct polyploid genome, mitochondrial DNA (mtDNA), that encodes respiratory chain components required for energy production. MtDNA mutation and depletion have been linked to obesity and metabolic syndrome in humans. At the cellular and subcellular levels, mtDNA synthesis is coordinated by membrane contact sites implicated in lipid transfer from the endoplasmic reticulum, tying genome maintenance to lipid storage and homeostasis. Here, we examine the relationship between mtDNA and lipid trafficking, the influence of lipotoxicity on mtDNA integrity, and how lipid metabolism may be disrupted in primary mtDNA disease.

GLI3 resides at the intersection of hedgehog and androgen action to promote male sex differentiation.

Urogenital tract abnormalities are among the most common congenital defects in humans. Male urogenital development requires Hedgehog-GLI signaling and testicular hormones, but how these pathways interact is unclear. We found that Gli3XtJ mutant mice exhibit cryptorchidism and hypospadias due to local effects of GLI3 loss and systemic effects of testicular hormone deficiency. Fetal Leydig cells, the sole source of these hormones in developing testis, were reduced in numbers in Gli3XtJ testes, and their functional identity diminished over time. Androgen supplementation partially rescued testicular descent but not hypospadias in Gli3XtJ mutants, decoupling local effects of GLI3 loss from systemic effects of androgen insufficiency. Reintroduction of GLI3 activator (GLI3A) into Gli3XtJ testes restored expression of Hedgehog pathway and steroidogenic genes. Together, our results show a novel function for the activated form of GLI3 that translates Hedgehog signals to reinforce fetal Leydig cell identity and stimulate timely INSL3 and testosterone synthesis in the developing testis. In turn, exquisite timing and concentrations of testosterone are required to work alongside local GLI3 activity to control development of a functionally integrated male urogenital tract.

Structured coaching as a means to improve sonographic visualization of the appendix: a quality improvement initiative.

PURPOSE: Ultrasound of the right lower quadrant for appendicitis requires specific training and practice. Improved visualization of the appendix can result in decreased utilization of computed tomography. Increasing the sensitivity of ultrasound for appendicitis thus decreases radiation exposure, reduces cost, and improves the patient healthcare experience in accordance with the three principles of the triple aim designated by the Institute for Healthcare Improvement. The purpose of this study was to examine the effect of a structured training program supplemented by technologist feedback on sonographic visualization of the appendix in a large pediatric health system. METHODS: The baseline ultrasound visualization frequency was computed for 20 ultrasound technologists in a large pediatric health system. Following this, technologists were informed of their individual and relative performance. Those with visualization frequencies less than 75% were provided structured training by a designated sonographer with an appendix visualization frequency above 75% while those with greater than 75% visualization continued to be monitored and informed of their monthly frequency. Following this structured training, appendix visualization frequencies were monitored over the next 5 months. RESULTS: There was no significant effect of sonographer career experience on the baseline appendix visualization frequency. Fourteen of 20 technologists demonstrated improved visualization frequencies post-intervention. The composite visualization frequency among these 20 technologists improved from 66.55 to 69.14%. This resulted in a potential savings of 38 CT scans during the post-intervention period. CONCLUSION: An appendix visualization rate monitoring program coupled with structured training was successful in improving the appendix visualization rate throughout a large pediatric health system. This program demonstrates the positive effect that monitoring and targeted intervention can have on a quality improvement program. The program continues to be carried out as part of a plan-study-do-act cycle.

Broadband Solenoidal Haloscope for Terahertz Axion Detection.

We introduce the Broadband Reflector Experiment for Axion Detection (BREAD) conceptual design and science program. This haloscope plans to search for bosonic dark matter across the [10^{-3},1] eV ([0.24, 240] THz) mass range. BREAD proposes a cylindrical metal barrel to convert dark matter into photons, which a novel parabolic reflector design focuses onto a photosensor. This unique geometry enables enclosure in standard cryostats and high-field solenoids, overcoming limitations of current dish antennas. A pilot 0.7 m^{2} barrel experiment planned at Fermilab is projected to surpass existing dark photon coupling constraints by over a decade with one-day runtime. Axion sensitivity requires <10^{-20} W/sqrt[Hz] sensor noise equivalent power with a 10 T solenoid and 10 m^{2} barrel. We project BREAD sensitivity for various sensor technologies and discuss future prospects.

Rubrocerebellar Feedback Loop Isolates the Interposed Nucleus as an Independent Processor of Corollary Discharge Information in Mice.

Understanding cerebellar contributions to motor coordination requires deeper insight into how the output structures of the cerebellum, the cerebellar nuclei, integrate their inputs and influence downstream motor pathways. The magnocellular red nucleus (RNm), a brainstem premotor structure, is a major target of the interposed nucleus (IN), and has also been described in previous studies to send feedback collaterals to the cerebellum. Because such a pathway is in a key position to provide motor efferent information to the cerebellum, satisfying predictions about the use of corollary discharge in cerebellar computations, we studied it in mice of both sexes. Using anterograde viral tracing, we show that innervation of cerebellum by rubrospinal neuron collaterals is remarkably selective for the IN compared with the cerebellar cortex. Optogenetic activation of the pathway in acute mouse brain slices drove IN activity despite small amplitude synaptic currents, suggesting an active role in IN information processing. Monosynaptic transsynaptic rabies tracing indicated the pathway contacts multiple cell types within the IN. By contrast, IN inputs to the RNm targeted a region that lacked inhibitory neurons. Optogenetic drive of IN inputs to the RNm revealed strong, direct excitation but no inhibition of RNm neurons. Together, these data indicate that the cerebellar nuclei are under afferent control independent of the cerebellar cortex, potentially diversifying its roles in motor control.SIGNIFICANCE STATEMENT The common assumption that all cerebellar mossy fibers uniformly collateralize to the cerebellar nuclei and cortex underlies classic models of convergent Purkinje influence on cerebellar output. Specifically, mossy fibers are thought to both directly excite nuclear neurons and drive polysynaptic feedforward inhibition via Purkinje neurons, setting up a fundamental computational unit. Here we present data that challenge this rule. A dedicated cerebellar nuclear afferent comprised of feedback collaterals from premotor rubrospinal neurons can directly modulate IN output independent of Purkinje cell modulation. In contrast to the IN-RNm pathway, the RNm-IN feedback pathway targets multiple cell types, potentially influencing both motor output pathways and nucleo-olivary feedback.

A rolling circle replication mechanism produces multimeric lariats of mitochondrial DNA in Caenorhabditis elegans.

Mitochondrial DNA (mtDNA) encodes respiratory complex subunits essential to almost all eukaryotes; hence respiratory competence requires faithful duplication of this molecule. However, the mechanism(s) of its synthesis remain hotly debated. Here we have developed Caenorhabditis elegans as a convenient animal model for the study of metazoan mtDNA synthesis. We demonstrate that C. elegans mtDNA replicates exclusively by a phage-like mechanism, in which multimeric molecules are synthesized from a circular template. In contrast to previous mammalian studies, we found that mtDNA synthesis in the C. elegans gonad produces branched-circular lariat structures with multimeric DNA tails; we were able to detect multimers up to four mtDNA genome unit lengths. Further, we did not detect elongation from a displacement-loop or analogue of 7S DNA, suggesting a clear difference from human mtDNA in regard to the site(s) of replication initiation. We also identified cruciform mtDNA species that are sensitive to cleavage by the resolvase RusA; we suggest these four-way junctions may have a role in concatemer-to-monomer resolution. Overall these results indicate that mtDNA synthesis in C. elegans does not conform to any previously documented metazoan mtDNA replication mechanism, but instead are strongly suggestive of rolling circle replication, as employed by bacteriophages. As several components of the metazoan mitochondrial DNA replisome are likely phage-derived, these findings raise the possibility that the rolling circle mtDNA replication mechanism may be ancestral among metazoans.

Mitochondrial transcription terminator family members mTTF and mTerf5 have opposing roles in coordination of mtDNA synthesis.

All genomes require a system for avoidance or handling of collisions between the machineries of DNA replication and transcription. We have investigated the roles in this process of the mTERF (mitochondrial transcription termination factor) family members mTTF and mTerf5 in Drosophila melanogaster. The two mTTF binding sites in Drosophila mtDNA, which also bind mTerf5, were found to coincide with major sites of replication pausing. RNAi-mediated knockdown of either factor resulted in mtDNA depletion and developmental arrest. mTTF knockdown decreased site-specific replication pausing, but led to an increase in replication stalling and fork regression in broad zones around each mTTF binding site. Lagging-strand DNA synthesis was impaired, with extended RNA/DNA hybrid segments seen in replication intermediates. This was accompanied by the accumulation of recombination intermediates and nicked/broken mtDNA species. Conversely, mTerf5 knockdown led to enhanced replication pausing at mTTF binding sites, a decrease in fragile replication intermediates containing single-stranded segments, and the disappearance of species containing segments of RNA/DNA hybrid. These findings indicate an essential and previously undescribed role for proteins of the mTERF family in the integration of transcription and DNA replication, preventing unregulated collisions and facilitating productive interactions between the two machineries that are inferred to be essential for completion of lagging-strand DNA synthesis.

Cellular microenvironment dictates androgen production by murine fetal Leydig cells in primary culture.

Despite the fact that fetal Leydig cells are recognized as the primary source of androgens in male embryos, the mechanisms by which steroidogenesis occurs within the developing testis remain unclear. A genetic approach was used to visualize and isolate fetal Leydig cells from remaining cells within developing mouse testes. Cyp11a1-Cre mice were bred to mT/mG dual reporter mice to target membrane-tagged enhanced green fluorescent protein (GFP) within steroidogenic cells, whereas other cells expressed membrane-tagged tandem-dimer tomato red. Fetal Leydig cell identity was validated using double-labeled immunohistochemistry against GFP and the steroidogenic enzyme 3beta-HSD, and cells were successfully isolated as indicated by qPCR results from sorted cell populations. Because fetal Leydig cells must collaborate with neighboring cells to synthesize testosterone, we hypothesized that the fetal Leydig cell microenvironment defined their capacity for androgen production. Microfluidic culture devices were used to measure androstenedione and testosterone production of fetal Leydig cells that were cultured in cell-cell contact within a mixed population, were isolated but remained in medium contact via compartmentalized co-culture with other testicular cells, or were isolated and cultured alone. Results showed that fetal Leydig cells maintained their identity and steroidogenic activity for 3-5 days in primary culture. Microenvironment dictated proficiency of testosterone production. As expected, fetal Leydig cells produced androstenedione but not testosterone when cultured in isolation. More testosterone accumulated in medium from mixed cultures than from compartmentalized co-cultures initially; however, co-cultures maintained testosterone synthesis for a longer time. These data suggest that a combination of cell-cell contact and soluble factors constitute the ideal microenvironment for fetal Leydig cell activity in primary culture.

Direct Machining of Low-Loss THz Waveguide Components With an RF Choke.

We present results for the successful fabrication of low-loss THz metallic waveguide components using direct machining with a CNC end mill. The approach uses a split-block machining process with the addition of an RF choke running parallel to the waveguide. The choke greatly reduces coupling to the parasitic mode of the parallel-plate waveguide produced by the split-block. This method has demonstrated loss as low as 0.2 dB/cm at 280 GHz for a copper WR-3 waveguide. It has also been used in the fabrication of 3 and 10 dB directional couplers in brass, demonstrating excellent agreement with design simulations from 240-260 GHz. The method may be adapted to structures with features on the order of 200 µm.

Improved temporal resolution in ultrafast electron diffraction measurements through THz compression and time-stamping.

We present an experimental demonstration of ultrafast electron diffraction (UED) with THz-driven electron bunch compression and time-stamping that enables UED probes with improved temporal resolution. Through THz-driven longitudinal bunch compression, a compression factor of approximately four is achieved. Moreover, the time-of-arrival jitter between the compressed electron bunch and a pump laser pulse is suppressed by a factor of three. Simultaneously, the THz interaction imparts a transverse spatiotemporal correlation on the electron distribution, which we utilize to further enhance the precision of time-resolved UED measurements. We use this technique to probe single-crystal gold nanofilms and reveal transient oscillations in the THz near fields with a temporal resolution down to 50 fs. These oscillations were previously beyond reach in the absence of THz compression and time-stamping.

Peripheral auditory tuning for vowels.

In this study, 35 young, healthy adults were tested on whether speech-like stimuli evoke a unique response in the auditory efferent system. To this end, descending cortical influences on medial olivocochlear (MOC) activity were indirectly evaluated by studying the effects of contralateral suppression on distortion product otoacoustic emissions (DPOAEs) under four conditions: (a) in the absence of any contralateral noise (Baseline), (b) presence of contralateral broadband noise (Noise Baseline), (c) vowel discrimination-in-noise task (VDN) and (d) tone discrimination-in-noise (TDN) task. A statistically significant release from suppression was evident across all tested DPOAE frequencies (1, 1.5 and 2 kHz) only for the VDN task (p < 0.05), which yielded greater release from suppression than the TDN task. These findings indicate that during active listening in the presence of noise, the MOC activity may be differentially modulated depending on the type of stimulus (vowel vs. tone). Specifically, in the presence of background noise, vowels may show a greater release from suppression in the cochlea than frequency, intensity and duration matched tones.

In Situ Analysis of Mitochondrial DNA Synthesis Using Metabolic Labeling Coupled to Fluorescence Microscopy.

Metabolic labeling with the nucleoside analog 5-ethynyl-2'-deoxyuridine (EdU) enables the selective labeling of DNA synthesis in live cells. Newly synthesized EdU-containing DNA can be covalently modified after extraction or in fixed cells using copper-catalyzed azide-alkyne cycloaddition "click chemistry" reactions, enabling bioconjugation to various substrates including fluorophores for imaging studies. While often used to study nuclear DNA replication, EdU labeling can also be leveraged to detect the synthesis of organellar DNA in the cytoplasm of Eukaryotic cells. In this chapter, we outline methods for the application of EdU labeling to the study of mitochondrial genome synthesis in fixed cultured human cells, using fluorescent labeling and superresolution light microscopy.

Metatranscriptomic analysis uncovers prevalent viral ORFs compatible with mitochondrial translation.

RNA viruses are ubiquitous components of the global virosphere, yet relatively little is known about their genetic diversity or the cellular mechanisms by which they exploit the biology of their diverse eukaryotic hosts. A hallmark of (+)ssRNA (positive single-stranded RNA) viruses is the ability to remodel host endomembranes for their own replication. However, the subcellular interplay between RNA viruses and host organelles that harbor gene expression systems, such as mitochondria, is complex and poorly understood. Here we report the discovery of 763 new virus sequences belonging to the family Mitoviridae by metatranscriptomic analysis, the identification of previously uncharacterized mitovirus clades, and a putative new viral class. With this expanded understanding of the diversity of mitovirus and encoded RNA-dependent RNA polymerases (RdRps), we annotate mitovirus-specific protein motifs and identify hallmarks of mitochondrial translation, including mitochondrion-specific codons. This study expands the known diversity of mitochondrial viruses and provides additional evidence that they co-opt mitochondrial biology for their survival. IMPORTANCE Metatranscriptomic studies have rapidly expanded the cadre of known RNA viruses, yet our understanding of how these viruses navigate the cytoplasmic milieu of their hosts to survive remains poorly characterized. In this study, we identify and assemble 763 new viral sequences belonging to the Mitoviridae, a family of (+)ssRNA viruses thought to interact with and remodel host mitochondria. We exploit this genetic diversity to identify new clades of Mitoviridae, annotate clade-specific sequence motifs that distinguish the mitoviral RdRp, and reveal patterns of RdRp codon usage consistent with translation on host cell mitoribosomes. These results serve as a foundation for understanding how mitoviruses co-opt mitochondrial biology for their proliferation.

The impact of COVID-19 on sleep for autistic children: A systematic review.

Background: Up to 80% of children with autism experience behavioural sleep problems, predominantly relating to bedtime resistance, sleep anxiety, sleep dysregulation, and shorter duration, which are associated with increased autistic symptom expression and emotional and behavioural difficulties. Researchers predicted the COVID-19 pandemic would worsen sleep and behavioural difficulties for autistic children, due to their need for routine and certainty. This systematic review is the first to focus on delineating the role of sleep disturbance in exacerbating autistic symptoms and internalising and externalising behaviours during the pandemic. Method: In this PROSPERO registered systematic review, we aggregated and synthesised findings from empirical studies from 2020 onwards that included children with autism and examined sleep outcomes, using narrative and framework synthesis due to the variety of methods and designs employed. We identified additional relevant themes through inductive thematic analysis. Results: Seventy-one studies met the search criteria, and we selected seventeen for review following screening and quality assessment. These studies reported mixed findings; with strongest support for worsening of sleep problems typically experienced by autistic children, including difficulties with sleep regulation and shorter sleep duration. Further, sleep problems were associated with increased expression of autistic characteristics. Conclusions: Preliminary findings of worsening sleep and increased autistic characteristics for autistic children throughout the COVID-19 pandemic highlight the need for ongoing, accessible and flexible service provision during exposure to environmental stressors. We propose that behavioural sleep interventions are well suited to telehealth adaptation and play an important role in supporting families when in-person treatment for sleep problems is not possible.

A genome-wide view of Caenorhabditis elegans base-substitution mutation processes.

Knowledge of mutation processes is central to understanding virtually all evolutionary phenomena and the underlying nature of genetic disorders and cancers. However, the limitations of standard molecular mutation detection methods have historically precluded a genome-wide understanding of mutation rates and spectra in the nuclear genomes of multicellular organisms. We applied two high-throughput DNA sequencing technologies to identify and characterize hundreds of spontaneously arising base-substitution mutations in 10 Caenorhabditis elegans mutation-accumulation (MA)-line nuclear genomes. C. elegans mutation rate estimates were similar to previous calculations based on smaller numbers of mutations. Mutations were distributed uniformly within and among chromosomes and were not associated with recombination rate variation in the MA lines, suggesting that intragenomic variation in genetic hitchhiking and/or background selection are primarily responsible for the chromosomal distribution patterns of polymorphic nucleotides in C. elegans natural populations. A strong mutational bias from G/C to A/T nucleotides was detected in the MA lines, implicating oxidative DNA damage as a major endogenous mutagenic force in C. elegans. The observed mutational bias also suggests that the C. elegans nuclear genome cannot be at equilibrium because of mutation alone. Transversions dominate the spectrum of spontaneous mutations observed here, whereas transitions dominate patterns of allegedly neutral polymorphism in natural populations of C. elegans and many other animal species; this observation challenges the assumption that natural patterns of molecular variation in noncoding regions of the nuclear genome accurately reflect underlying mutation processes.

Understanding the Benefits of Brief Classroom-Based Physical Activity Interventions on Primary School-Aged Children's Enjoyment and Subjective Wellbeing: A Systematic Review.

BACKGROUND: Engaging in classroom-based physical activity (PA) breaks may help increase children's subjective wellbeing and enjoyment of PA, important precursors for children to remain engaged in PA. We conducted a systematic review to investigate the effect of brief classroom-based PA interventions on primary school children's subjective wellbeing and enjoyment of PA. METHODS: Databases were reviewed between the earliest date of records and April 2020. Eligibility criteria included peer-reviewed empirical quantitative or mixed methods studies reporting enjoyment of PA or wellbeing outcomes of participating in a brief classroom-based PA program. Fifteen papers were included. Interventions supported 7022 child participants enrolled at baseline and 6286 children analyzed in interventions across 148 schools. RESULTS: Thirteen studies examined the effect of brief classroom-based PA interventions on subjective wellbeing. Four found a significant positive effect for children in the intervention group (specifically for children's self-efficacy in learning with video exercises, quality of life, and self-confidence). Eight studies examined the effect of brief classroom-based PA interventions on enjoyment of PA. Five studies reported a positive effect for children in the intervention group and only 1 study found a negative effect for 1 grade level of children in the intervention group. The remaining studies with wellbeing and/or enjoyment outcomes reported no significant effect. CONCLUSIONS: Findings from these studies indicate that the integration of brief PA breaks may support PA enjoyment and specific self-beliefs and quality of life perceptions that contribute to children's subjective wellbeing. However, more research is needed to confirm this effect.