The choreography of chromatin in RNA polymerase III regulation.

Regulation of eukaryotic gene expression involves a dynamic interplay between the core transcriptional machinery, transcription factors, and chromatin organization and modification. While this applies to transcription by all RNA polymerase complexes, RNA polymerase III (RNAPIII) seems to be atypical with respect to its mechanisms of regulation. One distinctive feature of most RNAPIII transcribed genes is that they are devoid of nucleosomes, which relates to the high levels of transcription. Moreover, most of the regulatory sequences are not outside but within the transcribed open chromatin regions. Yet, several lines of evidence suggest that chromatin factors affect RNAPIII dynamics and activity and that gene sequence alone does not explain the observed regulation of RNAPIII. Here we discuss the role of chromatin modification and organization of RNAPIII transcribed genes and how they interact with the core transcriptional RNAPIII machinery and regulatory DNA elements in and around the transcribed genes.

Theory of Mind and Social Informant Discrepancy in Autism.

When autistic youth are asked to assess their own social skills, they frequently rate themselves more favorably than their parents rate them. The magnitude of this informant discrepancy has been shown to relate to key clinical outcomes such as treatment response. It has been proposed that this discrepancy arises from difficulties with Theory of Mind. Participants were 167 youth 11 to 17 years old; 72% male, and their parents. Youth completed self-report measures of social skills and social cognitive tasks, while their parents completed questionnaires regarding social skills. A repeated-measures ANOVA indicated both non-autistic and autistic youth rated themselves more favorably than their parents rated them across all measures. Zero-order correlations revealed that raw differences between parent- and participant-report were negatively correlated with scores on parent-reported Theory of Mind measures. However, polynomial analysis did not indicate interaction effects between parent- and participant-report on any of the measures used. Polynomial regression revealed that increases in parent-reported social skill predicted larger increases in parent-report Theory of Mind at low levels of parent-reported social skill compared to high levels of parent-reported social skill. Participant-report social skills predicted performance on a behavioral Theory of Mind test in a curvilinear fashion, such that the relationship was positive at low levels of participant-reported social skills, but negative at high levels. This study replicates the finding that raw difference score analyses may result in illusory effects that are not supported when using more contemporary analysis methods, and that more complex and subtle relationships between social insight and perspective-taking exist within autistic youth.

Social Anhedonia Accounts for Greater Variance in Internalizing Symptoms than Autism Symptoms in Autistic and Non-Autistic Youth.

PURPOSE: Social anhedonia is a transdiagnostic trait that reflects reduced pleasure from social interaction. It has historically been associated with autism, however, very few studies have directly examined behavioral symptoms of social anhedonia in autistic youth. We investigated rates of social anhedonia in autistic compared to non-autistic youth and the relative contributions of autism and social anhedonia symptoms to co-occurring mental health. METHODS: Participants were 290 youth (Mage=13.75, Nautistic=155) ranging in age from 8 to 18. Youth completed a cognitive assessment and a diagnostic interview. Their caregiver completed questionnaires regarding symptoms of autism and co-occurring psychiatric conditions. RESULTS: Autistic youth were more likely to meet criteria for social anhedonia than non-autistic youth. There was a significant positive relationship between age and social anhedonia symptom severity, but there was no association between sex and social anhedonia. Dominance analysis revealed that social anhedonia symptom severity had the strongest association with symptoms of depression and social anxiety, while symptoms of ADHD, generalized anxiety, and separation anxiety were most strongly associated with autism symptom severity. CONCLUSION: This was the first study to tease out the relative importance of social anhedonia and autism symptoms in understanding psychiatric symptoms in autistic youth. Findings revealed higher rates of social anhedonia in autistic youth. Our results indicate that social anhedonia is an important transdiagnostic trait that plays a unique role in understanding co-occurring depression and social anxiety in autistic youth. Future research should utilize longitudinal data to test the transactional relationships between social anhedonia and internalizing symptoms over time.

Longitudinal Impact of the Pandemic on Social Disruption and Loneliness in Autistic and Non-Autistic Youth.

OBJECTIVE: The coronavirus pandemic drastically increased social isolation. Autistic youth already experience elevated social isolation and loneliness, making them highly vulnerable to the impact of the pandemic. We examined trajectories of social disruption and loneliness in autistic and non-autistic youth during a six-month period of the pandemic (June 2020 until November 2020). METHOD: Participants were 76 youth, ages 8 through 17, (Mage = 12.82, Nautistic = 51) with an IQ ≥ 70. Youth completed a biweekly measure of loneliness (Revised UCLA Loneliness Scale) and their parent completed a measure of pandemic-related family social disruption (Epidemic Pandemic Impacts Inventory). RESULTS: There were no time trends in loneliness across all youth, however, social disruption displayed linear, quadratic, and cubic trends. Non-autistic youth reported relatively greater declines in social disruption compared to autistic youth. Additionally, autistic youth reported relatively greater declines in loneliness relative to non-autistic youth. Greater social disruption was associated with higher loneliness, however, autistic youth demonstrated a relatively stronger relationship between social disruption and loneliness compared to non-autistic youth. CONCLUSIONS: The current study was one of the first to investigate social disruption and loneliness in autistic youth during the COVID-19 pandemic. Results indicated that autistic youth experienced relative decreases in loneliness during this time, perhaps due to reductions in social demands. Nonetheless, when autistic youth did experience social disruption, they reported relatively higher levels of loneliness. This work contributes to our understanding of risk factors for loneliness and highlights the need to understand the benefits, as well as the challenges, to remote schooling and social interactions.

Polarization, the Pandemic, and Public Trust in Health System Actors.

CONTEXT: Public opinion on the performance of health system actors is polarized today, but it remains unclear which actors enjoy the most (least) trust among Democrats and Republicans, whether the Covid-19 pandemic has influenced how people view their own physicians, and whether doctors have retained the ability to influence public beliefs about policy issues. METHODS: We conducted two national surveys in 2022 and 2023 to examine these questions. FINDINGS: Democrats rate the performance of medical research scientists and public health experts during the pandemic more highly than do Republicans and independents. About three in ten Republicans say that the pandemic decreased their trust in their personal doctors. Nonetheless, most Americans report confidence in physicians. We replicate the findings of Gerber et al. (2014) to demonstrate that respondents continue to have more positive views of doctors than other professionals, and that public opinion is responsive to cues from a doctors' group. CONCLUSIONS: What polarizes Democrats and Republicans today is not whether medical scientists and public health experts are competent, but whether the advice offered by these actors is in the public interest and should guide policymakers' decisions. Democrats strongly believe the answer to these questions is yes, while Republicans exhibit skepticism.

NORMSEQ: a tool for evaluation, selection and visualization of RNA-Seq normalization methods.

RNA-sequencing has become one of the most used high-throughput approaches to gain knowledge about the expression of all different RNA subpopulations. However, technical artifacts, either introduced during library preparation and/or data analysis, can influence the detected RNA expression levels. A critical step, especially in large and low input datasets or studies, is data normalization, which aims at eliminating the variability in data that is not related to biology. Many normalization methods have been developed, each of them relying on different assumptions, making the selection of the appropriate normalization strategy key to preserve biological information. To address this, we developed NormSeq, a free web-server tool to systematically assess the performance of normalization methods in a given dataset. A key feature of NormSeq is the implementation of information gain to guide the selection of the best normalization method, which is crucial to eliminate or at least reduce non-biological variability. Altogether, NormSeq provides an easy-to-use platform to explore different aspects of gene expression data with a special focus on data normalization to help researchers, even without bioinformatics expertise, to obtain reliable biological inference from their data. NormSeq is freely available at: https://arn.ugr.es/normSeq.

Bicyclic Engineered Sortase A Performs Transpeptidation under Denaturing Conditions.

Enzymes are of central importance to many biotechnological and biomedical applications. However, for many potential applications, the required conditions impede enzyme folding and therefore function. The enzyme Sortase A is a transpeptidase that is widely used to perform bioconjugation reactions with peptides and proteins. Thermal and chemical stress impairs Sortase A activity and prevents its application under harsh conditions, thereby limiting the scope for bioconjugation reactions. Here, we report the stabilization of a previously reported, activity-enhanced Sortase A, which suffered from particularly low thermal stability, using the in situ cyclization of proteins (INCYPRO) approach. After introduction of three spatially aligned solvent-exposed cysteines, a triselectrophilic cross-linker was attached. The resulting bicyclic INCYPRO Sortase A demonstrated activity both at elevated temperature and in the presence of chemical denaturants, conditions under which both wild-type Sortase A and the activity-enhanced version are inactive.

Trajectories of internalizing symptoms among autistic and nonautistic youth during the COVID-19 pandemic.

The COVID-19 pandemic elicited increases in anxiety and depression in youth, and youth on the autism spectrum demonstrate elevations in such symptoms pre-pandemic. However, it is unclear whether autistic youth experienced similar increases in internalizing symptoms after the COVID-19 pandemic onset or whether decreases in these symptoms were present, as speculated in qualitative work. In the current study, longitudinal changes in anxiety and depression during the COVID-19 pandemic in autistic youth were assessed in comparison to nonautistic youth. A well-characterized sample of 51 autistic and 25 nonautistic youth (ageM = 12.8, range = 8.5-17.4 years, IQ > 70) and their parents completed the Revised Children's Anxiety and Depression Scale (RCADS), a measure of internalizing symptoms, repeatedly, representing up to 7 measurement occasions from June to December 2020 (N ~ 419 occasions). Multilevel models were used to evaluate changes in internalizing symptoms over time. Internalizing symptoms did not differ between autistic and nonautistic youth in the summer of 2020. As reported by youth themselves, internalizing symptoms decreased in autistic youth, both overall and compared to nonautstic peers. This effect was driven by decreases in generalized anxiety, social anxiety, and depression symptoms in autistic youth. Reductions in generalized anxiety, social anxiety, and depression in autistic youth may be due to COVID-19 pandemic-specific differences in response to social, environmental, and contextual changes that unfolded in 2020. This highlights the importance of understanding unique protective and resilience factors that may be evident in autistic individuals in response to broad societal shifts such as those seen in response to COVID-19.

Understanding spatiotemporal coupling of gene expression using single molecule RNA imaging technologies.

Across all kingdoms of life, gene regulatory mechanisms underlie cellular adaptation to ever-changing environments. Regulation of gene expression adjusts protein synthesis and, in turn, cellular growth. Messenger RNAs are key molecules in the process of gene expression. Our ability to quantitatively measure mRNA expression in single cells has improved tremendously over the past decades. This revealed an unexpected coordination between the steps that control the life of an mRNA, from transcription to degradation. Here, we provide an overview of the state-of-the-art imaging approaches for measurement and quantitative understanding of gene expression, starting from the early visualizations of single genes by electron microscopy to current fluorescence-based approaches in single cells, including live-cell RNA-imaging approaches to FISH-based spatial transcriptomics across model organisms. We also highlight how these methods have shaped our current understanding of the spatiotemporal coupling between transcriptional and post-transcriptional events in prokaryotes. We conclude by discussing future challenges of this multidisciplinary field.Abbreviations: mRNA: messenger RNA; rRNA: ribosomal rDNA; tRNA: transfer RNA; sRNA: small RNA; FISH: fluorescence in situ hybridization; RNP: ribonucleoprotein; smFISH: single RNA molecule FISH; smiFISH: single molecule inexpensive FISH; HCR-FISH: Hybridization Chain-Reaction-FISH; RCA: Rolling Circle Amplification; seqFISH: Sequential FISH; MERFISH: Multiplexed error robust FISH; UTR: Untranslated region; RBP: RNA binding protein; FP: fluorescent protein; eGFP: enhanced GFP, MCP: MS2 coat protein; PCP: PP7 coat protein; MB: Molecular beacons; sgRNA: single guide RNA.

ALL-tRNAseq enables robust tRNA profiling in tissue samples.

Transfer RNAs (tRNAs) are small adaptor RNAs essential for mRNA translation. Alterations in the cellular tRNA population can directly affect mRNA decoding rates and translational efficiency during cancer development and progression. To evaluate changes in the composition of the tRNA pool, multiple sequencing approaches have been developed to overcome reverse transcription blocks caused by the stable structures of these molecules and their numerous base modifications. However, it remains unclear whether current sequencing protocols faithfully capture tRNAs existing in cells or tissues. This is specifically challenging for clinical tissue samples that often present variable RNA qualities. For this reason, we developed ALL-tRNAseq, which combines the highly processive MarathonRT and RNA demethylation for the robust assessment of tRNA expression, together with a randomized adapter ligation strategy prior to reverse transcription to assess tRNA fragmentation levels in both cell lines and tissues. Incorporation of tRNA fragments not only informed on sample integrity but also significantly improved tRNA profiling of tissue samples. Our data showed that our profiling strategy effectively improves classification of oncogenic signatures in glioblastoma and diffuse large B-cell lymphoma tissues, particularly for samples presenting higher levels of RNA fragmentation, further highlighting the utility of ALL-tRNAseq for translational research.

Predictors of Treatment Response to a Community-Delivered Group Social Skills Intervention for Youth with ASD.

Group social skills interventions (GSSIs) are among the most commonly used treatments for improving social competence in youth with ASD, however, results remain variable. The current study examined predictors of treatment response to an empirically-supported GSSI for youth with ASD delivered in the community (Ntotal=75). Participants completed a computer-based emotion recognition task and their parents completed measures of broad psychopathology, ASD symptomatology, and social skills. We utilized generalized estimating equations in an ANCOVA-of-change framework to account for nesting. Results indicate differential improvements in emotion recognition by sex as well as ADHD-specific improvements in adaptive functioning. Youth with both co-occurring anxiety and ADHD experienced iatrogenic effects, suggesting that SDARI may be most effective for youth with ASD without multiple co-occurring issues. Findings provide important directions for addressing variability in treatment outcomes for youth with ASD.

Quantifying social skill deficits and strengths profiles in autistic youth.

While social difficulties in autism are well-established, questions remain regarding whether these represent challenges in acquiring or performing such skills, reduced social strengths, or a unique distribution across these domains (i.e., social profile). This study empirically derived social profiles of 211 autistic and non-autistic youth (Mage  = 13.50; Autistic N = 150; Male N = 151; 85.3% White). Assessments occurred between 2016 and 2020. Results showed that autistic youth exhibit significantly more social acquisition and performance deficits and fewer strengths than nonautistic youth (ds = -.44 to .65). Performance deficits were most-and acquisition deficits least-prominent within autistic profiles, potentially implicating longstanding theoretical models of social difficulties in autism, and supporting new, idiographic approaches for conceptualizing, assessing, and treating social challenges.

Testing persuasive messaging to encourage COVID-19 risk reduction.

What types of public health messages are effective at changing people's beliefs and intentions to practice social distancing to slow the spread of COVID-19? We conducted two randomized experiments in summer 2020 that assigned respondents to read a public health message and then measured their beliefs and behavioral intentions across a wide variety of outcomes. Using both a convenience sample and a pre-registered replication with a nationally representative sample of Americans, we find that a message that reframes not social distancing as recklessness rather than bravery and a message that highlights the need for everyone to take action to protect one another are the most effective at increasing beliefs and intentions related to social distancing. These results provide an evidentiary basis for building effective public health campaigns to increase social distancing during flu pandemics.

Experiences of student and trainee autism researchers during the COVID-19 pandemic.

Circumstances surrounding the COVID-19 pandemic have resulted in significant personal and professional adjustments. Students and trainees, including those in autism research, face unique challenges to accomplishing their training and career goals during this unprecedented time. In this commentary, we, as members of the International Society for Autism Research Student and Trainee Committee, describe our personal experiences, which may or may not align with those of other students and trainees. Our experiences have varied both in terms of the ease (or lack thereof) with which we adapted and the degree to which we were supported in the transition to online research and clinical practice. We faced and continue to adjust to uncertainties about future training and academic positions, for which opportunities have been in decline and have subsequently negatively impacted our mental health. Students and trainees' prospects have been particularly impacted compared to more established researchers and faculty. In addition to the challenges we have faced, however, there have also been unexpected benefits in our training during the pandemic, which we describe here. We have learned new coping strategies which, we believe, have served us well. The overarching goal of this commentary is to describe these experiences and strategies in the hope that they will benefit the autism research community moving forward. Here, we provide a set of recommendations for faculty, especially mentors, to support students and trainees as well as strategies for students and trainees to bolster their self-advocacy, both of which we see as crucial for our future careers. LAY SUMMARY: The COVID-19 pandemic has affected students and trainees, including those in autism research, in different ways. Here, we describe our personal experiences. These experiences include challenges. For example, it has been difficult to move from in-person to online work. It has also been difficult to keep up with work and training goals. Moreover, working from home has made it hard to connect with our supervisors and mentors. As a result, many of us have felt unsure about how to make the best career choices. Working in clinical services and getting to know and support our patients online has also been challenging. Overall, the pandemic has made us feel more isolated and some of us have struggled to cope with that. On the other hand, our experiences have also included benefits. For example, by working online, we have been able to join meetings all over the world. Also, the pandemic has pushed us to learn new skills. Those include technical skills but also skills for well-being. Next, we describe our experiences of returning to work. Finally, we give recommendations for trainees and supervisors on how to support each other and to build a strong community.

Persuading US White evangelicals to vaccinate for COVID-19: Testing message effectiveness in fall 2020 and spring 2021.

The development of COVID-19 vaccines was an important breakthrough for ending the pandemic. However, people refusing to get vaccinated diminish the level of community protection afforded to others. In the United States, White evangelicals have proven to be a particularly difficult group to convince to get vaccinated. Here we investigate whether this group can be persuaded to get vaccinated. To do this, we leverage data from two survey experiments, one fielded prior to approval of COVID-19 vaccines (study 1) and one fielded after approval (study 2). In both experiments, respondents were randomly assigned to treatment messages to promote COVID-19 vaccination. In study 1, we find that a message that emphasizes community interest and reciprocity with an invocation of embarrassment for choosing not to vaccinate is the most effective at increasing uptake intentions, while values-consistent messaging appears to be ineffective. In contrast, in study 2 we observe that this message is no longer effective and that most messages produce little change in vaccine intent. This inconsistency may be explained by the characteristics of White evangelicals who remain unvaccinated vis à vis those who got vaccinated. These results demonstrate the importance of retesting messages over time, the apparent limitations of values-targeted messaging, and document the need to consider heterogeneity even within well-defined populations. This work also cautions against drawing broad conclusions from studies carried out at a single point in time during the COVID-19 pandemic.

Persuasive messaging to increase COVID-19 vaccine uptake intentions.

Widespread vaccination remains the best option for controlling the spread of COVID-19 and ending the pandemic. Despite the considerable disruption the virus has caused to people's lives, many people are still hesitant to receive a vaccine. Without high rates of uptake, however, the pandemic is likely to be prolonged. Here we use two survey experiments to study how persuasive messaging affects COVID-19 vaccine uptake intentions. In the first experiment, we test a large number of treatment messages. One subgroup of messages draws on the idea that mass vaccination is a collective action problem and highlighting the prosocial benefit of vaccination or the reputational costs that one might incur if one chooses not to vaccinate. Another subgroup of messages built on contemporary concerns about the pandemic, like issues of restricting personal freedom or economic security. We find that persuasive messaging that invokes prosocial vaccination and social image concerns is effective at increasing intended uptake and also the willingness to persuade others and judgments of non-vaccinators. We replicate this result on a nationally representative sample of Americans and observe that prosocial messaging is robust across subgroups, including those who are most hesitant about vaccines generally. The experiments demonstrate how persuasive messaging can induce individuals to be more likely to vaccinate and also create spillover effects to persuade others to do so as well. The first experiment in this study was registered at clinicaltrials.gov and can be found under the ID number NCT04460703. This study was registered at Open Science Framework (OSF) at: https://osf.io/qu8nb/?view_only=82f06ecad77f4e54b02e8581a65047d7.

Critical roles of transcriptional coactivator MED1 in the formation and function of mouse adipose tissues.

The MED1 subunit has been shown to mediate ligand-dependent binding of the Mediator coactivator complex to multiple nuclear receptors, including the adipogenic PPARγ, and to play an essential role in ectopic PPARγ-induced adipogenesis of mouse embryonic fibroblasts. However, the precise roles of MED1, and its various domains, at various stages of adipogenesis and in adipose tissue have been unclear. Here, after establishing requirements for MED1, including specific domains, for differentiation of 3T3L1 cells and both primary white and brown preadipocytes, we used multiple genetic approaches to assess requirements for MED1 in adipocyte formation, maintenance, and function in mice. We show that MED1 is indeed essential for the differentiation and/or function of both brown and white adipocytes, as its absence in these cells leads to, respectively, defective brown fat function and lipodystrophy. This work establishes MED1 as an essential transcriptional coactivator that ensures homeostatic functions of adipocytes.

Bicyclic ß-Sheet Mimetics that Target the Transcriptional Coactivator ß-Catenin and Inhibit Wnt Signaling.

Protein complexes are defined by the three-dimensional structure of participating binding partners. Knowledge about these structures can facilitate the design of peptidomimetics which have been applied for example, as inhibitors of protein-protein interactions (PPIs). Even though ß-sheets participate widely in PPIs, they have only rarely served as the basis for peptidomimetic PPI inhibitors, in particular when addressing intracellular targets. Here, we present the structure-based design of ß-sheet mimetics targeting the intracellular protein ß-catenin, a central component of the Wnt signaling pathway. Based on a protein binding partner of ß-catenin, a macrocyclic peptide was designed and its crystal structure in complex with ß-catenin obtained. Using this structure, we designed a library of bicyclic ß-sheet mimetics employing a late-stage diversification strategy. Several mimetics were identified that compete with transcription factor binding to ß-catenin and inhibit Wnt signaling in cells. The presented design strategy can support the development of inhibitors for other ß-sheet-mediated PPIs.

Timing of COVID-19 vaccine approval and endorsement by public figures.

The global spread of COVID-19 has created an urgent need for a safe and effective vaccine. However, in the United States, the politicization of the vaccine approval process, including which public figures are endorsing it, could undermine beliefs about its safety and efficacy and willingness to receive it. Using a pair of randomized survey experiments, we show that announcing approval of a COVID-19 vaccine one week before the presidential election compared to one week after considerably reduces both beliefs about its safety and efficacy and intended uptake. However, endorsement by Dr. Anthony Fauci increases confidence and uptake among all partisan subgroups. Further, an endorsement by Dr. Fauci increased uptake and confidence in safety even if a vaccine receives pre-election approval. The results here suggest that perceptions of political influence in COVID-19 vaccine approval could significantly undermine the viability of a vaccine as a strategy to end the pandemic.