Synovial sarcoma (SS) is defined by the hallmark SS18-SSX fusion oncoprotein, which renders BAF complexes aberrant in two manners: gain of SSX to the SS18 subunit and concomitant loss of BAF47 ...subunit assembly. Here we demonstrate that SS18-SSX globally hijacks BAF complexes on chromatin to activate an SS transcriptional signature that we define using primary tumors and cell lines. Specifically, SS18-SSX retargets BAF complexes from enhancers to broad polycomb domains to oppose PRC2-mediated repression and activate bivalent genes. Upon suppression of SS18-SSX, reassembly of BAF47 restores enhancer activation, but is not required for proliferative arrest. These results establish a global hijacking mechanism for SS18-SSX on chromatin, and define the distinct contributions of two concurrent BAF complex perturbations.
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•SS18-SSX assembly results in concurrent gains and losses in genome-wide BAF complex targeting•Synovial sarcoma is transcriptionally distinct from other BAF complex-driven malignancies•SS18-SSX targets BAF complexes to broad polycomb domains to activate bivalent genes•BAF47 reassembly activates enhancers but is dispensable for proliferative arrest
Incorporation of the synovial sarcoma SS18-SSX fusion into BAF complexes results in concomitant eviction of BAF47. McBride et al. show that SS18-SSX retargets BAF complexes from enhancers to polycomb domains to oppose PRC2-mediated repression. Reincorporation of BAF47 upon suppression of SS18-SSX restores enhancer activation but is not required for proliferative arrest.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Solid electrolytes hold great promise for enabling the use of Li metal anodes. The main problem is that during cycling, Li can infiltrate along grain boundaries and cause short circuits, resulting in ...potentially catastrophic battery failure. At present, this phenomenon is not well understood. Here, through electron microscopy measurements on a representative system, Li7La3Zr2O12, we discover that Li infiltration in solid oxide electrolytes is strongly associated with local electronic band structure. About half of the Li7La3Zr2O12 grain boundaries were found to have a reduced bandgap, around 1–3 eV, making them potential channels for leakage current. Instead of combining with electrons at the cathode, Li+ ions are hence prematurely reduced by electrons at grain boundaries, forming local Li filaments. The eventual interconnection of these filaments results in a short circuit. Our discovery reveals that the grain-boundary electronic conductivity must be a primary concern for optimization in future solid-state battery design.Solid electrolytes are promising for enabling the use of Li metal anodes but Li infiltration along grain boundaries can lead to battery failure. Li infiltration in a model solid oxide electrolyte is now found to be strongly associated with local electronic band structure.
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GEOZS, IJS, IMTLJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK, ZAGLJ
Summary
The online resource http://www.plantrdnadatabase.com/ stores information on the number, chromosomal locations and structure of the 5S and 18S‐5.8S‐26S (35S) ribosomal DNAs (rDNA) in plants. ...This resource was exploited to study relationships between rDNA locus number, distribution, the occurrence of linked (L‐type) and separated (S‐type) 5S and 35S rDNA units, chromosome number, genome size and ploidy level. The analyses presented summarise current knowledge on rDNA locus numbers and distribution in plants. We analysed 2949 karyotypes, from 1791 species and 86 plant families, and performed ancestral character state reconstructions. The ancestral karyotype (2n = 16) has two terminal 35S sites and two interstitial 5S sites, while the median (2n = 24) presents four terminal 35S sites and three interstitial 5S sites. Whilst 86.57% of karyotypes show S‐type organisation (ancestral condition), the L‐type arrangement has arisen independently several times during plant evolution. A non‐terminal position of 35S rDNA was found in about 25% of single‐locus karyotypes, suggesting that terminal locations are not essential for functionality and expression. Single‐locus karyotypes are very common, even in polyploids. In this regard, polyploidy is followed by subsequent locus loss. This results in a decrease in locus number per monoploid genome, forming part of the diploidisation process returning polyploids to a diploid‐like state over time.
Significance Statement
Ribosomal DNAs (rDNAs) are abundant in genomes and exhibit sequence conservation. Here we analyse rDNA locus numbers, arrangements and distribution across plant phylogeny and assess their impact on general genomic processes such as polyploidisation.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
The tricarboxylic acid cycle enzyme fumarate hydratase (FH) has been identified as a tumor suppressor in a subset of human renal cell carcinomas. Human FH-deficient cancer cells display high fumarate ...concentration and ROS levels along with activation of HIF-1. The underlying mechanisms by which FH loss increases ROS and HIF-1 are not fully understood. Here, we report that glutamine-dependent oxidative citric acid cycle metabolism is required to generate fumarate and increase ROS and HIF-1 levels. Accumulated fumarate directly bonds the antioxidant glutathione in vitro and in vivo to produce the metabolite succinated glutathione (GSF). GSF acts as an alternative substrate to glutathione reductase to decrease NADPH levels and enhance mitochondrial ROS and HIF-1 activation. Increased ROS also correlates with hypermethylation of histones in these cells. Thus, fumarate serves as a proto-oncometabolite by binding to glutathione which results in the accumulation of ROS.
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•FH loss increases fumarate resulting in mitochondrial ROS activation of HIF-1•Fumarate covalently bonds glutathione to produce succinated glutathione (GSF)•GSF is a substrate of glutathione reductase and consumes NADPH to enhance ROS•Increased ROS due to FH deficiency contributes to hypermethylation of histones
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
•Survey assessed perceptions of water reuse, conservation, and water shortages.•Majority of the population conserves water and supports use of reclaimed water.•Droughts were found to have some effect ...on survey responses.•Ethnicity, education, metro/non metro, and income affect survey responses.•Financial incentives influence willingness to participate in water reuse programs.
Reclaimed water programs treat wastewater to remove hazardous compounds, pathogens, and organic matter and provide reclaimed water for non-potable applications. Reusing water may significantly reduce demands on freshwater resources and provide sustainable water management strategies. Though production of reclaimed water is highly regulated, public acceptability has historically hindered the implementation of successful reclaimed water systems. The public generally opposes the use of reclaimed water due to the “yuck factor”, which is the instinctive disgust associated with the idea of recycling sewage and the fear that exposure to reclaimed water is unsafe. This paper reports the results of an extensive survey that was conducted to evaluate the potential acceptability of reclaimed water use. A total of 2800 respondents across the U.S. participated in the survey. Results demonstrate that a small percentage of the population is concerned about water shortages, the majority of the population practices some level of water conservation, and a substantial percentage of the population supports the use of reclaimed water. Climate, demographic variables, and financial incentives were tested for influence on attitudes and behaviors regarding water, including awareness, conservation, and support for water reuse. Sex, age, last monthly water bill, and location (as EPA region) showed no significant effect on the acceptance of water reuse, while ethnicity, education level, metro/non metro, and income showed significant effects. Drought conditions do not have a statistically significant effect on the number of reclaimed water supporters, but increase the number of respondents who are water concerned, the number of respondents who are the most active water conservers, and the number of respondents who limit their use of water for lawn and garden watering. Financial incentives influence the willingness of respondents to participate in water reuse programs, and a decrease in the monthly water bills increased the likelihood that respondents would participate in a reclaimed water program. Support for the use of reclaimed water for various applications ranked positively, on average, except for the application of water reuse for food crop irrigation and use of reclaimed water at respondents’ own residences. Results and conclusions of the survey can provide insight for implementing successful reclaimed water programs.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Signaling receptors dynamically exit cilia upon activation of signaling pathways such as Hedgehog. Here, we find that when activated G protein-coupled receptors (GPCRs) fail to undergo ...BBSome-mediated retrieval from cilia back into the cell, these GPCRs concentrate into membranous buds at the tips of cilia before release into extracellular vesicles named ectosomes. Unexpectedly, actin and the actin regulators drebrin and myosin 6 mediate ectosome release from the tip of cilia. Mirroring signal-dependent retrieval, signal-dependent ectocytosis is a selective and effective process that removes activated signaling molecules from cilia. Congruently, ectocytosis compensates for BBSome defects as ectocytic removal of GPR161, a negative regulator of Hedgehog signaling, permits the appropriate transduction of Hedgehog signals in Bbs mutants. Finally, ciliary receptors that lack retrieval determinants such as the anorexigenic GPCR NPY2R undergo signal-dependent ectocytosis in wild-type cells. Our data show that signal-dependent ectocytosis regulates ciliary signaling in physiological and pathological contexts.
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•Signal-dependent exit of GPCRs from cilia proceeds through retrieval or ectocytosis•GPCRs that cannot be retrieved back into the cell are instead ectocytosed•Actin, myosin 6, and drebrin mediate the scission of ectosomes from cilia tips•Hedgehog signaling fails when both ectocytosis and retrieval are blocked
The tips of cilia are transit points where proteins can be removed by actin-mediated vesicle release rather than undergoing retrograde transport to the cell body.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Human pluripotent stem cell derived cardiomyocytes (hPSC-CMs) represent an inexhaustible cell source for in vitro disease modeling, drug discovery and toxicity screening, and potential therapeutic ...applications. However, currently available differentiation protocols yield populations of hPSC-CMs with an immature phenotype similar to cardiomyocytes in the early fetal heart. In this review, we consider the developmental processes and signaling cues involved in normal human cardiac maturation, as well as how these insights might be applied to the specific maturation of hPSC-CMs. We summarize the state-of-the-art and relative merits of reported hPSC-CM maturation strategies including prolonged duration in culture, metabolic manipulation, treatment with soluble or substrate-based cues, and tissue engineering approaches. Finally, we review the evidence that hPSC-CMs mature after implantation in injured hearts as such in vivo remodeling will likely affect the safety and efficacy of a potential hPSC-based cardiac therapy.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Older age is a strong risk factor for several diseases, including cancer. The etiology and biology of age-associated differences among cancers are poorly understood. To address this knowledge gap, we ...aim to delineate differences in tumor molecular characteristics between younger and older patients across a variety of tumor types from The Cancer Genome Atlas. We show that these groups exhibit widespread molecular differences in select tumor types. Our work shows that tumors in younger individuals exhibit a dysregulated molecular aging phenotype and are associated with hallmarks of premature senescence. Additionally, we find that these tumors are enriched for driver gene mutations, resulting in homologous recombination defects. Lastly, we observe a trend toward decreased immune infiltration and function in older patients and find that, immunologically, young tumor tissue resembles aged healthy tissue. Taken together, we find that tumors from young individuals possess unique characteristics that may be leveraged for therapy.
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•Multi-omic characterization of cancer biology in relation to aging•Identification of tumor types associated with divergent biology•Younger patients are linked to dysregulated aging and senescence•Age-group-specific targeted therapy identification
Shah et al. characterize the association between cancer biology and aging in a multi-omic study of primary tumors from The Cancer Genome Atlas. They identify features associated with aging and nominate targeted therapy based on these features.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The classical model of concerted evolution states that hundreds to thousands of ribosomal DNA (rDNA) units undergo homogenization, making the multiple copies of the individual units more uniform ...across the genome than would be expected given mutation frequencies and gene redundancy. While the universality of this over 50-year-old model has been confirmed in a range of organisms, advanced high throughput sequencing techniques have also revealed that rDNA homogenization in many organisms is partial and, in rare cases, even apparently failing. The potential underpinning processes leading to unexpected intragenomic variation have been discussed in a number of studies, but a comprehensive understanding remains to be determined. In this work, we summarize information on variation or polymorphisms in rDNAs across a wide range of taxa amongst animals, fungi, plants, and protists. We discuss the definition and description of concerted evolution and describe whether incomplete concerted evolution of rDNAs predominantly affects coding or non-coding regions of rDNA units and if it leads to the formation of pseudogenes or not. We also discuss the factors contributing to rDNA variation, such as interspecific hybridization, meiotic cycles, rDNA expression status, genome size, and the activity of effector genes involved in genetic recombination, epigenetic modifications, and DNA editing. Finally, we argue that a combination of approaches is needed to target genetic and epigenetic phenomena influencing incomplete concerted evolution, to give a comprehensive understanding of the evolution and functional consequences of intragenomic variation in rDNA.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Proximal row carpectomy (PRC) is a motion-sparing procedure with good patient-reported and clinical outcomes. Although some studies have investigated the risk of conversion to total wrist arthrodesis ...(TWA) after PRC, additional larger studies evaluating the specific risk factors that lead to failure are required. This study aimed to investigate the patient and procedure factors that are associated with increased risk for conversion to TWA in a large cohort of patients who underwent PRC.
The current procedural technology codes identified patients in a National Veteran’s Health database undergoing a PRC over a 26-year period. Risk factors of interest comprised age, posterior interosseous nerve neurectomy, wrist arthritis pattern, bilateral surgery, smoking, comorbidities, and preoperative opioid use. The primary outcome was the rate of conversion to TWA. Cox proportional hazard regression was used to create hazard ratios of selected factors for reoperation.
There were 1,070 PRCs performed, with a mean follow-up of 79.8 ± 59.6 months. A total of 5.3% (57/1,070) wrists underwent conversion to TWA. Younger age at the time of PRC (<50 years) significantly increased the risk of TWA (hazard ratio, 3.8; 95% confidence interval, 2.2–6.6). With every 1-year increase in age, there was a reduction of 4% (hazard ratio, 0.96; 95% confidence interval: 0.94–0.98) in the hazard of conversion to TWA. No other factors, including concomitant posterior interosseous nerve neurectomy or bilateral PRC, increased the risk of conversion to TWA.
Proximal row carpectomy is a motion-preserving salvage procedure with a low rate of conversion to wrist arthrodesis. Younger patient age increases the risk of conversion to arthrodesis, whereas posterior interosseous nerve neurectomy, bilateral PRCs, and comorbidity status do not appear to have an impact on the risk of arthrodesis.
Prognostic II.
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