The apparent loss of PRC2 chromatin occupancy as an artifact of RNA depletion.

RNA has been implicated in the recruitment of chromatin modifiers, and previous studies have provided evidence in favor and against this idea. RNase treatment of chromatin is commonly used to study RNA-mediated regulation of chromatin modifiers, but the limitations of this approach remain unclear. RNase A treatment during chromatin immunoprecipitation (ChIP) reduces chromatin occupancy of the H3K27me3 methyltransferase Polycomb repressive complex 2 (PRC2). This led to suggestions of an "RNA bridge" between PRC2 and chromatin. Here, we show that RNase A treatment during ChIP causes the apparent loss of all facultative heterochromatin, including both PRC2 and H3K27me3 genome-wide. We track this observation to a gain of DNA from non-targeted chromatin, sequenced at the expense of DNA from facultative heterochromatin, which reduces ChIP signals. Our results emphasize substantial limitations in using RNase A treatment for mapping RNA-dependent chromatin occupancy and invalidate conclusions that were previously established for PRC2 based on this assay.

Dynamic PRC1-CBX8 stabilizes a porous structure of chromatin condensates.

The compaction of chromatin is a prevalent paradigm in gene repression. Chromatin compaction is commonly thought to repress transcription by restricting chromatin accessibility. However, the spatial organisation and dynamics of chromatin compacted by gene-repressing factors are unknown. Using cryo-electron tomography, we solved the three-dimensional structure of chromatin condensed by the Polycomb Repressive Complex 1 (PRC1) in a complex with CBX8. PRC1-condensed chromatin is porous and stabilised through multivalent dynamic interactions of PRC1 with chromatin. Mechanistically, positively charged residues on the internally disordered regions (IDRs) of CBX8 mask negative charges on the DNA to stabilize the condensed state of chromatin. Within condensates, PRC1 remains dynamic while maintaining a static chromatin structure. In differentiated mouse embryonic stem cells, CBX8-bound chromatin remains accessible. These findings challenge the idea of rigidly compacted polycomb domains and instead provides a mechanistic framework for dynamic and accessible PRC1-chromatin condensates.

Quality standards and recommendations for research in music and neuroplasticity.

Research on how music influences brain plasticity has gained momentum in recent years. Considering, however, the nonuniform methodological standards implemented, the findings end up being nonreplicable and less generalizable. To address the need for a standardized baseline of research quality, we gathered all the studies in the music and neuroplasticity field in 2019 and appraised their methodological rigor systematically and critically. The aim was to provide a preliminary and, at the minimum, acceptable quality threshold-and, ipso facto, suggested recommendations-whereupon further discussion and development may take place. Quality appraisal was performed on 89 articles by three independent raters, following a standardized scoring system. The raters' scoring was cross-referenced following an inter-rater reliability measure, and further studied by performing multiple ratings comparisons and matrix analyses. The results for methodological quality were at a quite good level (quantitative articles: mean = 0.737, SD = 0.084; qualitative articles: mean = 0.677, SD = 0.144), following a moderate but statistically significant level of agreement between the raters (W = 0.44, χ2 = 117.249, p = 0.020). We conclude that the standards for implementation and reporting are of high quality; however, certain improvements are needed to reach the stringent levels presumed for such an influential interdisciplinary scientific field.

Oral Bisphosphonate Induced Recurrent Osteonecrosis of Jaw with Atypical Femoral Fracture and Subsequent Mandible Fracture in the Same Patient: A Case Report.

INTRODUCTION: Oral bisphosphonates are commonly prescribed for osteoporosis to arrest bone loss and preserve bone density. Complications such as atypical femoral fractures (AFF) and osteonecrosis of jaw (ONJ) are rare. CASE REPORT: We describe a case of a 60-year-old patient who was on oral bisphosphonate therapy for osteoporosis and developed ONJ, AFF, recurrent ONJ, and subsequent mandible fracture with delayed AFF union - this is a very unique and extremely rare case. For the same, she underwent multiple surgeries - sequestrectomy in the mandible, proximal femoral nailing for femur fracture and plate fixation for her jaw. The delayed union needed teriparatide administration. At 1 year follow-up, the patient had a complete radiological union for AFF and on recent follow-up the patient is asymptomatic as regards the femur as well as the jaw. This unique sequence of events has not been described previously. CONCLUSION: This case report shows the possibility of extremely rare adverse effects happening sequentially in the same patient with long-term oral bisphosphonate therapy. Patients need to be informed and monitored regularly for symptoms such as jaw pain and thigh pain and if these occur, the drug must be stopped immediately, and other alternative medical treatment for the osteoporosis should be started.

Clinico-sonographical evaluation of idiopathic clubfoot and its correction by Ponseti method - A prospective study.

BACKGROUND: Objective evaluation of infant with clubfoot is required as conventional imaging modality is of limited usefulness. Ultrasound shows to be a promising technique for assessing deformity and monitoring of clubfoot correction. AIM: Study was done to evaluate the deformity sonographically; to assess the changes in these parameters after treatment by Ponseti method and to correlate these ultrasonographic variables with clinical Pirani score. MATERIALS AND METHODS: 82 feet in 54 children were observed. Clinical assessment was done using Pirani six point system and ultrasound machine with 7.5-12MHz linear transducer was used to measure several parameters and data obtained was assessed to derive correlation between sonographic parameters and clinical system. RESULTS: Medial malleolus navicular distance (MMN) measured on medial view, calcaneo-cuboid distance (CCD) and calcaneo-cuboid angle (CCA) measured on lateral view, talar length (TAL) measured on dorsal view and tibio-calcaneal distance (TCL) measured on posterior view showed statistical significance. Sonographic parameters correlated statistically with Pirani scoring system on measuring Pearson correlation coefficient. CONCLUSION: Ultrasound is a relatively simple, non invasive and widely available procedure that can improve pathomorphological documentation of nonossified clubfoot and its correction. LEVEL OF EVIDENCE: Level II prospective study, as per guidelines for authors.

Dynamic hyper-editing underlies temperature adaptation in Drosophila.

In Drosophila, A-to-I editing is prevalent in the brain, and mutations in the editing enzyme ADAR correlate with specific behavioral defects. Here we demonstrate a role for ADAR in behavioral temperature adaptation in Drosophila. Although there is a higher level of editing at lower temperatures, at 29°C more sites are edited. These sites are less evolutionarily conserved, more disperse, less likely to be involved in secondary structures, and more likely to be located in exons. Interestingly, hypomorph mutants for ADAR display a weaker transcriptional response to temperature changes than wild-type flies and a highly abnormal behavioral response upon temperature increase. In sum, our data shows that ADAR is essential for proper temperature adaptation, a key behavior trait that is essential for survival of flies in the wild. Moreover, our results suggest a more general role of ADAR in regulating RNA secondary structures in vivo.

Variability of behavioral chronotypes of 16 mammalian species under controlled conditions.

Human chronotypes (differences in preference for early or late rising each day) have been extensively studied in recent years, but no attempt has been made to compare human chronotypes with the chronotypes of other animal species. We evaluated behavioral chronotypes in 16 mammalian species along a body size gradient of five orders of magnitude (from mice to cattle). Individuals of all species were studied under a 12L:12D photoperiod in a thermoneutral environment with food and water available at all times. Rhythms of locomotor activity were analyzed for onset time, acrophase, and robustness. Neither of these rhythmic parameters was significantly related to body size, but onset time and acrophase varied considerably from species to species, thus characterizing diurnal and nocturnal species. Chronotype spreads ranged from less than an hour in sheep to almost 24h in cats, thus extending both below and above the human chronotype spread of 6h. The variability of chronotype (as quantified by the standard deviation of group means) was much larger between species than within species and also larger between individuals of a species than within individuals on consecutive days. These results help situate the matter of human chronotypes within the broader context of variability in the phase angle of entrainment of circadian rhythms in animals.

miR-184 Regulates Pancreatic ß-Cell Function According to Glucose Metabolism.

In response to fasting or hyperglycemia, the pancreatic ß-cell alters its output of secreted insulin; however, the pathways governing this adaptive response are not entirely established. Although the precise role of microRNAs (miRNAs) is also unclear, a recurring theme emphasizes their function in cellular stress responses. We recently showed that miR-184, an abundant miRNA in the ß-cell, regulates compensatory proliferation and secretion during insulin resistance. Consistent with previous studies showing miR-184 suppresses insulin release, expression of this miRNA was increased in islets after fasting, demonstrating an active role in the ß-cell as glucose levels lower and the insulin demand ceases. Additionally, miR-184 was negatively regulated upon the administration of a sucrose-rich diet in Drosophila, demonstrating strong conservation of this pathway through evolution. Furthermore, miR-184 and its target Argonaute2 remained inversely correlated as concentrations of extracellular glucose increased, underlining a functional relationship between this miRNA and its targets. Lastly, restoration of Argonaute2 in the presence of miR-184 rescued suppression of miR-375-targeted genes, suggesting these genes act in a coordinated manner during changes in the metabolic context. Together, these results highlight the adaptive role of miR-184 according to glucose metabolism and suggest the regulatory role of this miRNA in energy homeostasis is highly conserved.

The transcription factor Cabut coordinates energy metabolism and the circadian clock in response to sugar sensing.

Nutrient sensing pathways adjust metabolism and physiological functions in response to food intake. For example, sugar feeding promotes lipogenesis by activating glycolytic and lipogenic genes through the Mondo/ChREBP-Mlx transcription factor complex. Concomitantly, other metabolic routes are inhibited, but the mechanisms of transcriptional repression upon sugar sensing have remained elusive. Here, we characterize cabut (cbt), a transcription factor responsible for the repressive branch of the sugar sensing transcriptional network in Drosophila. We demonstrate that cbt is rapidly induced upon sugar feeding through direct regulation by Mondo-Mlx. We found that CBT represses several metabolic targets in response to sugar feeding, including both isoforms of phosphoenolpyruvate carboxykinase (pepck). Deregulation of pepck1 (CG17725) in mlx mutants underlies imbalance of glycerol and glucose metabolism as well as developmental lethality. Furthermore, we demonstrate that cbt provides a regulatory link between nutrient sensing and the circadian clock. Specifically, we show that a subset of genes regulated by the circadian clock are also targets of CBT. Moreover, perturbation of CBT levels leads to deregulation of the circadian transcriptome and circadian behavioral patterns.

A new in vivo model of pantothenate kinase-associated neurodegeneration reveals a surprising role for transcriptional regulation in pathogenesis.

Pantothenate Kinase-Associated Neurodegeneration (PKAN) is a neurodegenerative disorder with a poorly understood molecular mechanism. It is caused by mutations in Pantothenate Kinase, the first enzyme in the Coenzyme A (CoA) biosynthetic pathway. Here, we developed a Drosophila model of PKAN (tim-fbl flies) that allows us to continuously monitor the modeled disease in the brain. In tim-fbl flies, downregulation of fumble, the Drosophila PanK homologue in the cells containing a circadian clock results in characteristic features of PKAN such as developmental lethality, hypersensitivity to oxidative stress, and diminished life span. Despite quasi-normal circadian transcriptional rhythms, tim-fbl flies display brain-specific aberrant circadian locomotor rhythms, and a unique transcriptional signature. Comparison with expression data from flies exposed to paraquat demonstrates that, as previously suggested, pathways others than oxidative stress are affected by PANK downregulation. Surprisingly we found a significant decrease in the expression of key components of the photoreceptor recycling pathways, which could lead to retinal degeneration, a hallmark of PKAN. Importantly, these defects are not accompanied by changes in structural components in eye genes suggesting that changes in gene expression in the eye precede and may cause the retinal degeneration. Indeed tim-fbl flies have diminished response to light transitions, and their altered day/night patterns of activity demonstrates defects in light perception. This suggest that retinal lesions are not solely due to oxidative stress and demonstrates a role for the transcriptional response to CoA deficiency underlying the defects observed in dPanK deficient flies. Moreover, in the present study we developed a new fly model that can be applied to other diseases and that allows the assessment of neurodegeneration in the brains of living flies.

VMD: a community annotation database for oomycetes and microbial genomes.

The VBI Microbial Database (VMD) is a database system designed to host a range of microbial genome sequences. At present, the database contains genome sequence and annotation data of two plant pathogens Phytophthora sojae and Phytophthora ramorum. With the completion of the draft genome sequences of these pathogens in collaboration with the DOE Joint Genome Institute (JGI), we have created this resource to make the sequences publicly available. The genome sequences (95 MB for P.sojae and 65 MB for P.ramorum) were annotated with approximately 19,000 and approximately 16,000 gene models, respectively. We used two different statistical methods to validate these gene models, Fickett's and a log-likelihood method. Functional annotation of the gene models is based on results from BlastX and InterProScan screens. From the InterProScan results, we could assign putative functions to 17,694 genes in P.sojae and 14,700 genes in P.ramorum. We created an easy-to-use genome browser to view the genome sequence data, which opens to detailed annotation pages for each gene model. A community annotation interface is available for registered community members to add or edit annotations. There are approximately 1600 gene models for P.sojae and approximately 700 models for P.ramorum that have already been manually curated. A toolkit is provided as an additional resource for users to perform a variety of sequence analysis jobs. The database is publicly available at http://phytophthora.vbi.vt.edu/.