Nascent Transcript Folding Plays a Major Role in Determining RNA Polymerase Elongation Rates.

Transcription elongation rates influence RNA processing, but sequence-specific regulation is poorly understood. We addressed this in vivo, analyzing RNAPI in S. cerevisiae. Mapping RNAPI by Miller chromatin spreads or UV crosslinking revealed 5' enrichment and strikingly uneven local polymerase occupancy along the rDNA, indicating substantial variation in transcription speed. Two features of the nascent transcript correlated with RNAPI distribution: folding energy and GC content in the transcription bubble. In vitro experiments confirmed that strong RNA structures close to the polymerase promote forward translocation and limit backtracking, whereas high GC in the transcription bubble slows elongation. A mathematical model for RNAPI elongation confirmed the importance of nascent RNA folding in transcription. RNAPI from S. pombe was similarly sensitive to transcript folding, as were S. cerevisiae RNAPII and RNAPIII. For RNAPII, unstructured RNA, which favors slowed elongation, was associated with faster cotranscriptional splicing and proximal splice site use, indicating regulatory significance for transcript folding.

Mindfulness induction and executive function after high-intensity interval training with and without mindful recovery intervals.

OBJECTIVES: Determine the effect of incorporating mindfulness-based activities into the recovery intervals of high-intensity interval training (HIIT) on mindfulness induction and subsequent executive function performance. DESIGNS: A within-subject crossover trial. METHODS: Forty adults participated in two experimental conditions, including a 30-min bout of HIIT involving mindfulness recovery intervals (Mindful) and a 30-min bout of HIIT without mindfulness recovery intervals (Non-mindful), on two separate days in counterbalanced order. Before and after each condition, participants completed the flanker task, switch-flanker task, and n-back task to measure inhibitory control, cognitive flexibility, and working memory, respectively. RESULTS: A higher level of mindfulness state was observed following the Mindful condition than the Non-mindful condition. Dispositional mindfulness was positively correlated with the level of the mindful state only during the Mindful condition but not the Non-mindful condition. The switch-flanker response accuracy was improved from the pretest to posttest during the Non-mindful condition but remained unchanged over time during the Mindful condition. Time-related improvements in the flanker and n-back task outcomes were observed for both the Mindful and Non-mindful conditions and did not differ between conditions. CONCLUSION: Although incorporating mindfulness-based activities during the recovery intervals of HIIT successfully led to greater state-related mindfulness, such a heightened mindful state did not correspond with additional modulation in inhibitory control and working memory performance while attenuating HIIT-related positive changes in task performance requiring cognitive flexibility.

Rate of transcription elongation and sequence-specific pausing by RNA polymerase I directly influence rRNA processing.

One of the first steps in ribosome biogenesis is transcription of the ribosomal DNA by RNA polymerase I (Pol I). Processing of the resultant rRNA begins cotranscriptionally, and perturbation of Pol I transcription elongation results in defective rRNA processing. Mechanistic insight regarding the link between transcription elongation and ribosome assembly is lacking because of limited in vivo methods to assay Pol I transcription. Here, we use native elongating transcript sequencing (NET-Seq) with a strain of Saccharomyces cerevisiae containing a point mutation in Pol I, rpa190-F1205H, which results in impaired rRNA processing and ribosome assembly. We previously demonstrated that this mutation caused a mild reduction in the transcription elongation rate of Pol I in vitro; however, transcription elongation by the mutant has not been characterized in vivo. Here, our findings demonstrate that the mutant Pol I has an increased pause propensity during processive transcription elongation both in vitro and in vivo. NET-Seq reveals that rpa190-F1205H Pol I displays alternative pause site preferences in vivo. Specifically, the mutant is sensitized to A/G residues in the RNA:DNA hybrid and at the last incorporated nucleotide position. Furthermore, both NET-Seq and EM analysis of Miller chromatin spreads reveal pileups of rpa190-F1205H Pol I throughout the ribosomal DNA, particularly at the 5' end of the 35S gene. This combination of in vitro and in vivo analyses of a Pol I mutant provides novel insights into Pol I elongation properties and indicates how these properties are crucial for efficient cotranscriptional rRNA processing and ribosome assembly.

Total Synthesis of Atrachinenins A and B.

Inspired by a new biosynthetic hypothesis, we report a biomimetic total synthesis of atrachinenins A and B that explains their racemic nature. The synthesis exploits an intermolecular Diels-Alder reaction between a quinone meroterpenoid and E-ß-ocimene, followed by intramolecular (3 + 2) cycloaddition and a late-stage aerobic oxidation. Divergent transformations of a simple model system gave several complex polycyclic scaffolds, while also suggesting a structure revision for atrachinenin C.

Peripheral blood leucocyte telomere length is associated with progression of interstitial lung disease in systemic sclerosis.

BACKGROUND: Peripheral blood leucocyte telomere length (PBL-TL) is associated with outcomes in patients with idiopathic pulmonary fibrosis. Whether PBL-TL is associated with progression of systemic sclerosis-associated interstitial lung disease (SSc-ILD) is unknown. METHODS: A retrospective observational cohort study was performed using prospectively collected data from 213 patients with SSc followed at the University of California San Francisco (UCSF) Scleroderma Center. PBL-TL was measured by quantitative PCR of DNA isolated from peripheral blood. Associations between PBL-TL and pulmonary function test trends in patients with SSc-ILD were assessed by longitudinal analysis using Generalised Linear Mixed Models. Findings were validated in a cohort of 61 patients with SSc-ILD enrolled in the Stanford University Scleroderma Center database. RESULTS: Patients with UCSF SSc with ILD were found to have shorter PBL-TL compared with those without ILD (6554±671 base pairs (bp) vs 6782±698 bp, p=0.01). Shorter PBL-TL was associated with the presence of ILD (adjusted OR 2.1 per 1000 bp TL decrease, 95% CI [1.25 to 3.70], p=0.006). PBL-TL was shorter in patients with SSc-ILD lacking SSc-specific autoantibodies compared with seropositive subjects (6237±647 bp vs 6651±653 bp, p=0.004). Shorter PBL-TL was associated with increased risk for lung function deterioration with an average of 67 mL greater loss in per year for every 1000 bp decrease in PBL-TL in the combined SSc-ILD cohorts (longitudinal analysis, adjusted model: 95% CI -104 mL to -33 mL, p<0.001). CONCLUSIONS: These findings suggest that telomere dysfunction may be associated with SSc-ILD progression and that PBL-TL measurement may be useful for stratifying risk for SSc-ILD progression.

Rrp5 binding at multiple sites coordinates pre-rRNA processing and assembly.

In vivo UV crosslinking identified numerous preribosomal RNA (pre-rRNA) binding sites for the large, highly conserved ribosome synthesis factor Rrp5. Intramolecular complementation has shown that the C-terminal domain (CTD) of Rrp5 is required for pre-rRNA cleavage at sites A0-A2 on the pathway of 18S rRNA synthesis, whereas the N-terminal domain (NTD) is required for A3 cleavage on the pathway of 5.8S/25S rRNA synthesis. The CTD was crosslinked to sequences flanking A2 and to the snoRNAs U3, U14, snR30, and snR10, which are required for cleavage at A0-A2. The NTD was crosslinked to sequences flanking A3 and to the RNA component of ribonuclease MRP, which cleaves site A3. Rrp5 could also be directly crosslinked to several large structural proteins and nucleoside triphosphatases. A key role in coordinating preribosomal assembly and processing was confirmed by chromatin spreads. Following depletion of Rrp5, cotranscriptional cleavage was lost and preribosome compaction greatly reduced.

Examining the effects of mindfulness-based yoga instruction on positive embodiment and affective responses.

Empirical evidence provides support for the inclusion of yoga as part of eating disorder prevention efforts through its positive impact on positive embodiment and experience of positive core affect. However, there is a need to identify the specific instructional strategies that will more consistently support positive embodiment and positive affect. We examined the effect of teaching a single yoga class using mindfulness-based instruction compared to appearance-based and neutral instruction alternatives on embodiment (i.e., state body surveillance, state body appreciation, pleasure during yoga) and changes in affect from before to after class. Female participants (N = 62; M age = 23.89, SD = 6.86) were randomly assigned to a yoga class that emphasized: being mindfully present in one's body, changing one's appearance, or just getting into yoga poses. ANOVAs revealed significantly higher body surveillance (ηp 2 =.10) and lower forecasted pleasure (ηp 2 =.21) in the appearance class compared to the other two classes. Participants in the mindfulness class experienced greater improvement in affect (ηp 2 =.08) from before to after class and higher remembered pleasure during the yoga class (ηp 2 =.19) compared to those in the appearance class. Emphasizing changes to appearance in yoga instruction may place participants at risk for less positive affect and less positive experiences of embodiment compared to mindfulness-based or even neutral yoga instruction.

Loss of Topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis.

Pre-rRNA transcription by RNA Polymerase I (Pol I) is very robust on active rDNA repeats. Loss of yeast Topoisomerase I (Top1) generated truncated pre-rRNA fragments, which were stabilized in strains lacking TRAMP (Trf4/Trf5-Air1/Air2-Mtr4 polyadenylation complexes) or exosome degradation activities. Loss of both Top1 and Top2 blocked pre-rRNA synthesis, with pre-rRNAs truncated predominately in the 18S 5' region. Positive supercoils in front of Pol I are predicted to slow elongation, while rDNA opening in its wake might cause R-loop formation. Chromatin immunoprecipitation analysis showed substantial levels of RNA/DNA hybrids in the wild type, particularly over the 18S 5' region. The absence of RNase H1 and H2 in cells depleted of Top1 increased the accumulation of RNA/DNA hybrids and reduced pre-rRNA truncation and pre-rRNA synthesis. Hybrid accumulation over the rDNA was greatly exacerbated when Top1, Top2, and RNase H were all absent. Electron microscopy (EM) analysis revealed Pol I pileups in the wild type, particularly over the 18S. Pileups were longer and more frequent in the absence of Top1, and their frequency was exacerbated when RNase H activity was also lacking. We conclude that the loss of Top1 enhances inherent R-loop formation, particularly over the 5' region of the rDNA, imposing persistent transcription blocks when RNase H is limiting.

The Transcription Factor THO Promotes Transcription Initiation and Elongation by RNA Polymerase I.

Although ribosomal RNA represents the majority of cellular RNA, and ribosome synthesis is closely connected to cell growth and proliferation rates, a complete understanding of the factors that influence transcription of ribosomal DNA is lacking. Here, we show that the THO complex positively affects transcription by RNA polymerase I (Pol I). We found that THO physically associates with the rDNA repeat and interacts genetically with Pol I transcription initiation factors. Pol I transcription in hpr1 or tho2 null mutants is dramatically reduced to less than 20% of the WT level. Pol I occupancy of the coding region of the rDNA in THO mutants is decreased to ~50% of WT level. Furthermore, although the percentage of active rDNA repeats remains unaffected in the mutant cells, the overall rDNA copy number increases ~2-fold compared with WT. Together, these data show that perturbation of THO function impairs transcription initiation and elongation by Pol I, identifying a new cellular target for the conserved THO complex.

Participant Perceptions of Character Concepts in a Physical Activity-Based Positive Youth Development Program.

Physical activity-based positive youth development (PYD) programs often aim to foster character development. This study examined youth perspectives of character development curricula and the impact these activities have on their lives within and beyond the program. This case study examined youth from low-income families in a physical activity-based summer PYD program that integrated one character concept (respect, caring, responsibility, trust) in each of 4 weeks. Participants (N = 24) included a cross section of age, gender, ethnicity, and past program experience. Semi-structured interviews were analyzed using inductive thematic analysis and constant comparative methods. Thirteen themes were grouped in four categories: building highquality reciprocal relationships; intrapersonal improvement; moral reasoning and understanding; and rejection, resistance, and compliance. The findings provide participant-centered guidance for understanding youth personal and social development through physical activity in ways that are meaningful to participants, which is particularly needed for youth in low-income communities with limited youth programming.

Sch9 regulates ribosome biogenesis via Stb3, Dot6 and Tod6 and the histone deacetylase complex RPD3L.

TORC1 is a conserved multisubunit kinase complex that regulates many aspects of eukaryotic growth including the biosynthesis of ribosomes. The TOR protein kinase resident in TORC1 is responsive to environmental cues and is potently inhibited by the natural product rapamycin. Recent characterization of the rapamycin-sensitive phosphoproteome in yeast has yielded insights into how TORC1 regulates growth. Here, we show that Sch9, an AGC family kinase and direct substrate of TORC1, promotes ribosome biogenesis (Ribi) and ribosomal protein (RP) gene expression via direct inhibitory phosphorylation of the transcriptional repressors Stb3, Dot6 and Tod6. Deletion of STB3, DOT6 and TOD6 partially bypasses the growth and cell size defects of an sch9 strain and reveals interdependent regulation of both Ribi and RP gene expression, and other aspects of Ribi. Dephosphorylation of Stb3, Dot6 and Tod6 enables recruitment of the RPD3L histone deacetylase complex to repress Ribi/RP gene promoters. Taken together with previous studies, these results suggest that Sch9 is a master regulator of ribosome biogenesis through the control of Ribi, RP, ribosomal RNA and tRNA gene transcription.

Diels-Alder Cycloadditions of Oxacyclic Allenes and α-Pyrones.

Reactions of α-pyrones with oxacyclic allenes in Diels-Alder trappings are described. We investigate regioselectivity trends and perform competition experiments to assess the influence of structural and electronic features on relative reaction rates. We also demonstrate the stereospecific trapping of an oxacyclic allene, which proceeds in high optical yield. This study provides insight into strained cyclic allene reactivity, as well as new synthetic tools for the rapid construction of complex, heterocyclic scaffolds.

Psychological readiness for injury recovery: evaluating psychometric properties of the IPRRS and assessing group differences in injured physically active individuals.

Objectives: The primary purpose of the study was to assess the one-factor and two-factor structure of the Injury Psychological Readiness to Return to Sport Scale (IPRRS) in an injured physically active population using confirmatory factor analysis (CFA) procedures and assess group (ie, sex, age, injury type, athlete status) and longitudinal differences using structural equation modelling (eg, invariance testing). Methods: The non-experimental study included a sample of 629 physically active individuals who suffered a musculoskeletal injury who sought treatment at an outpatient integrated sport medicine and rehabilitation therapy clinic. Participants filled out a questionnaire packet at three time points. Data analysis included a CFA and multigroup and longitudinal invariance. Results: Sample mean age was 26.3 years, with females comprising 49.5%. Chronic injuries represented 29.6% of the sample and 35.0% were classified as competitive athletes. A six-item, one-factor model was confirmed in the sample with factor loadings ranging from 0.67 to 0.86. Multigroup and longitudinal invariance were established. Multigroup invariance demonstrated null differences between sex and injury type, and statistical differences between age and athlete status subgroups. Longitudinal invariance demonstrated a statistically significant increase in psychological readiness over time. Conclusions: The findings support the use of the IPRRS as a tool to measure aspects of psychological readiness. Clinicians and researchers can use the IPRRS to assess interventions in future research.

Higher prevalence of sacbrood virus in Apis mellifera (Hymenoptera: Apidae) colonies after pollinating highbush blueberries.

Highbush blueberry pollination depends on managed honey bees (Apis mellifera) L. for adequate fruit sets; however, beekeepers have raised concerns about the poor health of colonies after pollinating this crop. Postulated causes include agrochemical exposure, nutritional deficits, and interactions with parasites and pathogens, particularly Melisococcus plutonius [(ex. White) Bailey and Collins, Lactobacillales: Enterococcaceae], the causal agent of European foulbrood disease, but other pathogens could be involved. To broadly investigate common honey bee pathogens in relation to blueberry pollination, we sampled adult honey bees from colonies at time points corresponding to before (t1), during (t2), at the end (t3), and after (t4) highbush blueberry pollination in British Columbia, Canada, across 2 years (2020 and 2021). Nine viruses, as well as M. plutonius, Vairimorpha ceranae, and V. apis [Tokarev et al., Microsporidia: Nosematidae; formerly Nosema ceranae (Fries et al.) and N. apis (Zander)], were detected by PCR and compared among colonies located near and far from blueberry fields. We found a significant interactive effect of time and blueberry proximity on the multivariate pathogen community, mainly due to differences at t4 (corresponding to ~6 wk after the beginning of the pollination period). Post hoc comparisons of pathogens in near and far groups at t4 showed that detections of sacbrood virus (SBV), which was significantly higher in the near group, not M. plutonius, was the primary driver. Further research is needed to determine if the association of SBV with highbush blueberry pollination is contributing to the health decline that beekeepers observe after pollinating this crop.

Honey bee stressor networks are complex and dependent on crop and region.

Honey bees play a major role in crop pollination but have experienced declining health throughout most of the globe. Despite decades of research on key honey bee stressors (e.g., parasitic Varroa destructor mites and viruses), researchers cannot fully explain or predict colony mortality, potentially because it is caused by exposure to multiple interacting stressors in the field. Understanding which honey bee stressors co-occur and have the potential to interact is therefore of profound importance. Here, we used the emerging field of systems theory to characterize the stressor networks found in honey bee colonies after they were placed in fields containing economically valuable crops across Canada. Honey bee stressor networks were often highly complex, with hundreds of potential interactions between stressors. Their placement in crops for the pollination season generally exposed colonies to more complex stressor networks, with an average of 23 stressors and 307 interactions. We discovered that the most influential stressors in a network-those that substantively impacted network architecture-are not currently addressed by beekeepers. Finally, the stressor networks showed substantial divergence among crop systems from different regions, which is consistent with the knowledge that some crops (e.g., highbush blueberry) are traditionally riskier to honey bees than others. Our approach sheds light on the stressor networks that honey bees encounter in the field and underscores the importance of considering interactions among stressors. Clearly, addressing and managing these issues will require solutions that are tailored to specific crops and regions and their associated stressor networks.

131I-MIBG followed by consolidation with busulfan, melphalan and autologous stem cell transplantation for refractory neuroblastoma.

BACKGROUND: (131) I-metaiodobenzylguanidine (MIBG) produces a 37% response rate in relapsed/refractory neuroblastoma, and could be used to improve remission status prior to myeloablative chemotherapy with autologous stem cell transplant (ASCT). The purpose of our report was to evaluate safety and response with MIBG therapy followed by myeloablative busulfan and melphalan (BuMel) with ASCT in patients with refractory neuroblastoma. METHODS: Retrospective chart review was done on patients treated with MIBG (18 mCi/kg) on Day 1 and ASCT on day 14. Six to eight weeks after MIBG, patients without progressive disease received IV busulfan on days -6 to -2 (target Css 700-900), melphalan (140 mg/m2 IV) on day -1, and ASCT on Day 0. Response and toxicity were evaluated after MIBG and again after myeloablative therapy. RESULTS: Eight patients completed MIBG/ASCT followed by BuMel/ASCT. MIBG was well tolerated, with grade 3 or 4 non-hematologic toxicity limited to one patient with sepsis. Grade 3 mucositis occurred in six patients after BuMel/ASCT. One patient developed sinusoidal obstructive syndrome (SOS) and died 50 days post-ASCT following myeloablative conditioning. All patients engrafted neutrophils (median 16.5 days) and platelets (median 32 days) after BuMel, excluding the patient with SOS. After all therapy, there were three complete, two partial, and one minor response in seven evaluable patients. CONCLUSIONS: MIBG at doses up to 18 mCi/kg can be safely administered 6 weeks prior to a BuMel consolidative regimen for refractory neuroblastoma. Preceding MIBG did not impair engraftment following BuMel. This regimen is being further evaluated in a Children's Oncology Group (COG) trial.

Correlates of long-term participation in a physical activity-based positive youth development program for low-income youth: sustained involvement and psychosocial outcomes.

This study examined correlates of long-term participation in a positive youth development (PYD) program. Low-income youth (N = 215) age 8-13 of diverse ethnicity participating in a summer physical activity-based PYD program completed questionnaires at the beginning and end of the program (year 1) and at the beginning of year 2. Those with lower BMI and higher attendance and leader support perceptions were more likely to return to the program the following year. Self-worth and leader support perceptions at time 2 were higher for returners compared to non-returners. Among returners, hope increased from year 1 to year 2 and increases in global self-worth across the first year were maintained over one year. Social support is linked to continued PYD participation. Returners had increased and/or sustained positive perceptions of self-worth and hope. Programs are encouraged to foster staff-participant relationships and self-worth, and minimize barriers associated with weight status.

Clinical and biological heterogeneity of multisystem inflammatory syndrome in adults following SARS-CoV-2 infection: a case series.

Importance: Multisystem inflammatory syndrome in adults (MIS-A) is a poorly understood complication of SARS-CoV-2 infection with significant morbidity and mortality. Objective: Identify clinical, immunological, and histopathologic features of MIS-A to improve understanding of the pathophysiology and approach to treatment. Design: Three cases of MIS-A following SARS-CoV-2 infection were clinically identified between October 2021 - March 2022 using the U.S. Centers for Disease Control and Prevention diagnostic criteria. Clinical, laboratory, imaging, and tissue data were assessed. Findings: All three patients developed acute onset cardiogenic shock and demonstrated elevated inflammatory biomarkers at the time of hospital admission that resolved over time. One case co-occurred with new onset Type 1 diabetes and sepsis. Retrospective analysis of myocardial tissue from one case identified SARS-CoV-2 RNA. All three patients fully recovered with standard of care interventions plus immunomodulatory therapy that included intravenous immunoglobulin, corticosteroids, and in two cases, anakinra. Conclusion: MIS-A is a severe post-acute sequela of COVID-19 characterized by systemic elevation of inflammatory biomarkers. In this series of three cases, we find that although clinical courses and co-existent diseases vary, even severe presentations have potential for full recovery with prompt recognition and treatment. In addition to cardiogenic shock, glucose intolerance, unmasking of autoimmune disease, and sepsis can be features of MIS-A, and SARS-CoV-2 myocarditis can lead to a similar clinical syndrome.

Acute effects of mindful interval exercise on cognitive performance in a higher education setting.

Interval exercise (IE) has been shown to have acute facilitating effects on cognition; however, the existing literature has been limited to laboratory settings and has focused on manipulating the parameters of exercise bouts during IE. This study included two classroom-based experiments to (1) investigate the effect of an acute bout of IE delivering mindfulness activity during its recovery intervals (mindful IE) on cognitive performance, and (2) compare cognitive performance following acute bouts of mindful IE with non-mindful IE. Experiment 1: Using a class-based within-subject crossover design, 59 participants completed the Stroop, d2, and trail-making tests to measure inhibitory control, attention, and cognitive flexibility, after a 30-min non-exercise or mindful IE session on separate counterbalanced days. Experiment 2: Using a similar design, 70 participants were assigned to two groups to receive a non-exercise and an IE session with (mindful) or without (non-mindful) mindfulness-based recovery intervals on separate counterbalanced days. Results from Experiment 1 showed superior d2 performance following the mindful IE than the non-exercise session. Although Experiment 2 found exercise-related decreases in commission error rate during the d2 test in both groups, the non-mindful group showed additional decreases in omission and total error rates. Further, higher scores on the nonreactivity facet of dispositional mindfulness were correlated with larger decreases in omission and total error rates during the d2 test for the mindful IE group. No exercise-related effect was found for outcomes of the Stroop and trail-making tests in both experiments. These findings in the selective improvements in d2 test performance are the first to suggest the feasibility of integrating mindfulness activity into the recovery intervals of IE for enhanced cognitive performance that may depend on individual differences in dispositional mindfulness.

The transcription elongation factor Spt5 influences transcription by RNA polymerase I positively and negatively.

Spt5p is a universally conserved transcription factor that plays multiple roles in eukaryotic transcription elongation. Spt5p forms a heterodimer with Spt4p and collaborates with other transcription factors to pause or promote RNA polymerase II transcription elongation. We have shown previously that Spt4p and Spt5p also influence synthesis of ribosomal RNA by RNA polymerase (Pol) I; however, previous studies only characterized defects in Pol I transcription induced by deletion of SPT4. Here we describe two new, partially active mutations in SPT5 and use these mutant strains to characterize the effect of Spt5p on Pol I transcription. Genetic interactions between spt5 and rpa49Δ mutations together with measurements of ribosomal RNA synthesis rates, rDNA copy number, and Pol I occupancy of the rDNA demonstrate that Spt5p plays both positive and negative roles in transcription by Pol I. Electron microscopic analysis of mutant and WT strains confirms these observations and supports the model that Spt4/5 may contribute to pausing of RNA polymerase I early during transcription elongation but promotes transcription elongation downstream of the pause(s). These findings bolster the model that Spt5p and related homologues serve diverse critical roles in the control of transcription.