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Eukaryotic genomes are compacted into loops and topologically associating domains (TADs)1–3, which contribute to transcription, recombination and genomic stability4,5. Cohesin extrudes DNA into loops that are thought to lengthen until CTCF boundaries are encountered6–12. Little is known about whether loop extrusion is impeded by DNA-bound machines. Here we show that the minichromosome maintenance (MCM) complex is a barrier that restricts loop extrusion in G1 phase. Single-nucleus Hi-C (high-resolution chromosome conformation capture) of mouse zygotes reveals that MCM loading reduces CTCF-anchored loops and decreases TAD boundary insulation, which suggests that loop extrusion is impeded before reaching CTCF. This effect extends to HCT116 cells, in which MCMs affect the number of CTCF-anchored loops and gene expression. Simulations suggest that MCMs are abundant, randomly positioned and partially permeable barriers. Single-molecule imaging shows that MCMs are physical barriers that frequently constrain cohesin translocation in vitro. Notably, chimeric yeast MCMs that contain a cohesin-interaction motif from human MCM3 induce cohesin pausing, indicating that MCMs are ‘active’ barriers with binding sites. These findings raise the possibility that cohesin can arrive by loop extrusion at MCMs, which determine the genomic sites at which sister chromatid cohesion is established. On the basis of in vivo, in silico and in vitro data, we conclude that distinct loop extrusion barriers shape the three-dimensional genome.

The microtubule-associated protein tau plays a central role in tauopathies such as Alzheimer’s disease (AD). The exact molecular mechanisms underlying tau toxicity are unclear, but aging is irrefutably the biggest risk factor. This raises the question of how cellular senescence affects the function of tau as a microtubule regulator. Here we report that the proportion of tau that is proteolytically cleaved at the caspase-3 site (TauC3) doubles in the hippocampus of senescent mice. TauC3 is also elevated in AD patients. Through quantitative live-cell imaging, we show that TauC3 has a drastically reduced dynamics of its microtubule interaction. Single-molecule tracking of tau confirmed that TauC3 has a longer residence time on axonal microtubules. The reduced dynamics of the TauC3-microtubule interaction correlated with a decreased transport of mitochondria, a reduced processivity of APP-vesicle transport and an induction of region-specific dendritic atrophy in CA1 neurons of the hippocampus. The microtubule-targeting drug Epothilone D normalized the interaction of TauC3 with microtubules and modulated the transport of APP-vesicles dependent on the presence of overexpressed human tau. The results indicate a novel toxic gain of function, in which a post-translational modification of tau changes the dynamics of the tau-microtubule interaction and thus leads to axonal transport defects and neuronal degeneration. The data also introduce microtubule-targeting drugs as pharmacological modifiers of the tau-microtubule interaction with the potential to restore the physiological interaction of pathologically altered tau with microtubules.

Extended loop extrusion across the immunoglobulin heavy-chain (Igh) locus facilitates VH-DJH recombination following downregulation of the cohesin-release factor Wapl by Pax5, resulting in global changes in the chromosomal architecture of pro-B cells. Here, we demonstrate that chromatin looping and VK-JK recombination at the Igk locus were insensitive to Wapl upregulation in pre-B cells. Notably, the Wapl protein was expressed at a 2.2-fold higher level in pre-B cells compared with pro-B cells, which resulted in a distinct chromosomal architecture with normal loop sizes in pre-B cells. High-resolution chromosomal contact analysis of the Igk locus identified multiple internal loops, which likely juxtapose VK and JK elements to facilitate VK-JK recombination. The higher Wapl expression in Igμ-transgenic pre-B cells prevented extended loop extrusion at the Igh locus, leading to recombination of only the 6 most 3’ proximal VH genes and likely to allelic exclusion of all other VH genes in pre-B cells. These results suggest that pro-B and pre-B cells with their distinct chromosomal architectures use different chromatin folding principles for V gene recombination, thereby enabling allelic exclusion at the Igh locus, when the Igk locus is recombined.

Nasopharyngeal carcinoma (NPC) is a squamous cell carcinoma with a proclivity for systemic dissemination, leading many patients to present with advanced stage disease and fail available treatments. There is a notable lack of targeted therapies for NPC, despite working knowledge of multiple proteins with integral roles in NPC cancer biology. These proteins include EZH2, Snail, eIF4E, and IMPDH, which are all overexpressed in NPC and correlated with poor prognosis. These proteins are known to be modulated by ribavirin, an FDA-approved hepatitis C antiviral that has recently been repurposed as a promising therapeutic in several solid and hematologic malignancies. Here, we investigated the potential of ribavirin as a targeted anticancer agent in five human NPC cell lines. Using cellular growth assays, flow cytometry, BrdU cell proliferation assays, scratch wound assays, and invasion assays, we show in vitro that ribavirin decreases NPC cellular proliferation, migration, and invasion and promotes cell-cycle arrest and cell death. Modulation of EZH2, Snail, eIF4E, IMPDH, mTOR, and cyclin D1 were observed in Western blots and enzymatic activity assays in response to ribavirin treatment. As monotherapy, ribavirin reduced flank tumor growth in multiple NPC xenograft models in vivo. Most importantly, we demonstrate that ribavirin enhanced the effects of radiotherapy, a central component of NPC treatment, both in vitro and in vivo. Our work suggests that NPC responds to ribavirin-mediated EZH2, Snail, eIF4E, IMPDH, and mTOR changes and positions ribavirin for clinical evaluation as a potential addition to our NPC treatment armamentarium.

Supplementary Figures 1-6

Michael Peters writes the text “Rationality is the activity of the most robust imagination (with apologies to Wallace Stevens): João José R. L. de Almeida, Antonio Miguel, Carolina Tamayo-Osorio, Elizabeth Gomes Souza”, in which he reveals that the review by the authors “[...] sparkles like a bright navigation star at night”. That is, Peters presents his admiration for the collective review and affirms his interest in writings of this type. He refers to the Kadiweu indigenous language of Brazil and affirms that it is a real innovation that signals the Wittgensteinian depth and one of the broad consequences of taking his thought to Really. Nevertheless, he is impressed with the writing of the article because, as he says, “[…] it is like a quartet put to music with spontaneous voices, though independent from one another, drawing out some of the consequences of my interpretation of Wittgenstein for decolonial discourse”. Peters’ admiration is revealed as he is impressed by the complexity and cultural artifact that presents itself as something more than a review, expanding the genre and focusing the content on important pedagogical issues between internal agreements and disagreements. Peters, then, dialogues with the four authors to discuss the criticisms presented.

In response to Mauro Lúcio Leitão Condé, Michael Peters writes “A Viennese Wittgenstein? A response to Mauro Lúcio Leitão Condé” in order to reveal that his process of reading Wittgenstein or any philosopher, opposing ideas through others, is part of the language game of philosophy and often brings benefits in terms of understanding.

Michael Peters writes “Wittgenstein’s Antifoundationalism: a response to Cristiane Maria Cornelia Gottschalk” to assert that one is always indebted to those who take their work seriously and engage in serious disputes over readings and arguments. For Petters, Cristiane Gottschalk advances in three aspects of disagreement: (i) the appropriation of Wittgenstein’s philosophy by analytic philosophers of education; (ii) the status of Wittgenstein’s spelling dictionary; and (iii) Wittgenstein's anti-foundationalism. Thus, he discusses and presents his arguments on the three arguments in his text.

Virtually all theories of economic growth predict a positive relationship between population size and productivity. In this paper, I study a particular historical episode to provide direct evidence for the empirical relevance of such scale effects. In the aftermath of the Second World War, 8 million ethnic Germans were expelled from their domiciles in Eastern Europe and transferred to West Germany. This inflow increased the German population by almost 20%. Using variation across counties, I show that the settlement of refugees had large and persistent effects on the size of the local population, manufacturing employment, and income per capita. These findings are quantitatively consistent with an idea‐based model of spatial growth if population mobility is subject to frictions and productivity spillovers occur locally. The estimated model implies that the refugee settlement increased aggregate income per capita by about 12% after 25 years and triggered a process of industrialization in rural areas.

Impact of process conditions on product quality is investigated in the recovery of high purity (NH4)3ScF6 by antisolvent crystallization.

Scandium (Sc), declared a critical raw material in the European Union (EU), could face further supply issues as the EU depends almost entirely on imports from China, Russia, and Ukraine. In this study, a tandem nanofiltration-solvent extraction procedure for Sc recovery from titania (TiO2) acid waste was piloted and then augmented by antisolvent crystallization. The new process, comprising advanced filtration (hydroxide precipitation, micro-, ultra-, and nanofiltration), solvent extraction, and antisolvent crystallization, was assessed in relation to material and energy inputs and benchmarked on ScF3 production. From ∼1 m3 of European acid waste containing traces of Sc (81 mg L-1), ∼13 g of Sc (43% yield, nine stages) was recovered as (NH4)3ScF6 with a purity of approximately 95%, demonstrating the technical feasibility of the approach. The production costs per kilogram of ScF3 were lower than reported market prices, which underscores a competitive process at scale. Although a few technical bottlenecks (e.g., S/L separation and electricity consumption) need to be overcome, combining advanced filtration with solvent extraction and antisolvent crystallization promises a future supply of this critical raw material from European secondary sources.

In eukaryotes, genomic DNA is extruded into loops by cohesin1. By restraining this process, the DNA-binding protein CCCTC-binding factor (CTCF) generates topologically associating domains (TADs)2,3 that have important roles in gene regulation and recombination during development and disease1,4–7. How CTCF establishes TAD boundaries and to what extent these are permeable to cohesin is unclear8. Here, to address these questions, we visualize interactions of single CTCF and cohesin molecules on DNA in vitro. We show that CTCF is sufficient to block diffusing cohesin, possibly reflecting how cohesive cohesin accumulates at TAD boundaries, and is also sufficient to block loop-extruding cohesin, reflecting how CTCF establishes TAD boundaries. CTCF functions asymmetrically, as predicted; however, CTCF is dependent on DNA tension. Moreover, CTCF regulates cohesin’s loop-extrusion activity by changing its direction and by inducing loop shrinkage. Our data indicate that CTCF is not, as previously assumed, simply a barrier to cohesin-mediated loop extrusion but is an active regulator of this process, whereby the permeability of TAD boundaries can be modulated by DNA tension. These results reveal mechanistic principles of how CTCF controls loop extrusion and genome architecture.

Background: The fractional exhaled nitric oxide (FENO) test is a point-of-care test that is used in the assessment of asthma.Objective: To provide evidence-based clinical guidance on whether FENO testing is indicated to optimize asthma treatment in patients with asthma in whom treatment is being considered.Methods: An international, multidisciplinary panel of experts was convened to form a consensus document regarding a single question relevant to the use of FENO. The question was selected from three potential questions based on the greatest perceived impact on clinical practice and the unmet need for evidencebased answers related to this question. The panel performed systematic reviews of published randomized controlled trials between 2004 and 2019 and followed the Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) evidence-to-decision framework to develop recommendations. All panel members evaluated and approved the recommendations.Main Results: After considering the overall low quality of the evidence, the panel made a conditional recommendation for FENO-based care. In patients with asthma in whom treatment is being considered, we suggest that FENO is beneficial and should be used in addition to usual care. This judgment is based on a balance of effects that probably favors the intervention; the moderate costs and availability of resources, which probably favors the intervention; and the perceived acceptability and feasibility of the intervention in daily practice.Conclusions: Clinicians should consider this recommendation to measure FENO in patients with asthma in whom treatment is being considered based on current best available evidence.

Cohesin mediates sister chromatid cohesion to enable chromosome segregation and DNA damage repair. To perform these functions, cohesin needs to be protected from WAPL, which otherwise releases cohesin from DNA. It has been proposed that cohesin is protected from WAPL by SORORIN. However,in vivoevidence for this antagonism is missing and SORORIN is only known to exist in vertebrates and insects. It is therefore unknown how important and widespread SORORIN’s functions are. Here we report the identification of SORORIN orthologs inSchizosaccharomyces pombe(Sor1) andArabidopsis thaliana(AtSORORIN).sor1Δmutants display cohesion defects, which are partially alleviated bywpl1Δ. Atsororinmutant plants display dwarfism, tissue specific cohesion defects and chromosome mis-segregation. Furthermore,Atsororinmutant plants are sterile and separate sister chromatids prematurely at anaphase I. The somatic, but not the meiotic deficiencies can be alleviated by loss of WAPL. These results providein vivoevidence for SORORIN antagonizing WAPL, reveal that SORORIN is present in organisms beyond the animal kingdom and indicate that it has acquired tissue specific functions in plants.

Eulogy for Jim Marshall (read at the funeral)Michael A. PetersBeijing Normal UniversityMy deepest condolences to Pepe, Dom and Marcus and to Jim’s grandchildren. Tina and I spent a lot of time at t...

Background Due to increasing demand for livestock products in sub-Saharan Africa, increasing livestock productivity is a priority. The core constraint is limited availability of feed of good quality. We assessed optimal harvesting time of three improved grasses, two Urochloa lines (Basilisk a selection from wild population, Cayman - a hybrid, a product of breeding) plus Mombasa, a Megathyrsus selection. All are released in Latin America and Kenya or in the registration in other regional countries. We assessed dry matter (DM) yields and quality at 4, 6, 8 and 12 weeks of age in two sites. Results DM yields (in t ha-1 ) were of the order Cayman (9.6-14.3) > Mombasa (8.0-11.3) > Basilisk (5.5-10.2) in one site, and Cayman (6.4-9.7) > Basilisk (4.9-7.6) > Mombasa (3.3-5.9) at site two. The harvesting regimes produced DM largely similar for weeks 4 and 6, 6 and 8, 8 and 12. Across the sites quality was of the order Cayman > Mombasa > Basilisk for neutral detergent fiber (NDF), metabolizable energy (ME) and crude protein (CP). With increasing harvesting interval, MJ ME ha-1 and kg CP ha-1 were inconsistent across both sites, but significant differences returned for MJ ME ha-1 unlike kg CP ha-1 . Conclusions Harvesting at either 8 or 12 weeks is not recommendable as quality drops without an increase in DM yield that can compensate despite doubling and tripling time respectively, compared to 4 weeks. We recommend harvesting at 4 through 6 weeks for any of the three grasses based on yield against time, and demand at the intensified cut-and-carry smallholder systems. © 2021 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Myocardial blood flow (MBF) is measured with 82Rb using non-linear, least-squares computerised modelling. The study aim was to explore the feasibility of Gjedde–Patlak–Rutland (GPR) graphical analysis as a simpler method for measuring MBF. Patients had myocardial perfusion imaging using adenosine (n = 45) or regadenoson (n = 33) for stressing. Blood 82Rb clearance into myocytes (K1) was measured from Cedar-Sinai QPET software using the modified Crone–Renkin equation of Lortie et al. (K1 = [1–0.77 × e−B/MBF] × MBF) to convert K1 to MBF (ml/min/100 ml), where B (63 ml/min/100 ml) is myocardial permeability-surface area product. Using aorta or left ventricular cavity (LV) to measure arterial blood 82Rb concentration, blood 82Rb clearance into myocardium (Z) was measured from GPR analysis based on data acquired between 1 and 3 min post-injection. As units of K1 and Z are, respectively, ml/min/ml intracellular space and ml/min/ml total tissue including extracellular space, myocardial extracellular fluid volume (ECV) is 1 − [Z/K1]. Using Z/K1 (see Results) to modify its index, the Lortie equation was changed to Z = (1–0.77 × $$e^{-B_Z/\text{MBF}_Z}$$ e−BZ/MBFZ)*MBFZ, following which MBFZ was calculated from Z. In GPR analysis, spillover of activity from LV to myocardium conveniently ‘drops out’ in the intercept of the plot. Both agents increased myocardial blood flow almost equally. ECV was ~ 35 ml/100 ml at rest, increasing to ~ 40 ml/100 ml after stress. Z/K1, averaged between stress, rest, stressing agents and arterial ROI, was 0.62, so BZ was taken as 39 (i.e. 0.62 × 63) ml/min/100 ml. Based on LV, MBFZ (y) correlated with MBF (x): y = 0.43x + 22 ml/min/100 ml; r = 0.84; n = 156). Their respective stress/rest ratios showed a moderate correlation (r = 0.64; n = 78). GPR analysis offers promise as a valid and analytically simpler technique for measuring myocardial blood flow, which, as with any clearance measured from GPR analysis, has units of ml/min/ml total tissue volume, and merits development as a polar map display.

Zusammenfassung Dieser Artikel zeichnet zunächst die Finanzmarkt-Turbulenzen nach, die im März 2020 durch die Corona-Krise ausgelöst wurden. Die gefährliche Schieflage von stark gehebelten Hedgefonds konnte nur durch eine massive und weltweit koordinierte Intervention der Zentralbanken entschärft werden. Damit wird deutlich, dass der Finanzmarkt in seiner aktuellen Aufstellung extrem fragil ist und regelmäßiger Interventionen von außen bedarf. In einem zweiten Teil zieht der Beitrag die Parallele zu Gefahren, die dem Finanzmarkt durch den fortschreitenden Klimawandel drohen und ihrerseits eine Quelle von Instabilität sind. Die derzeit auf europäischer Ebene verfolgte Regulierungsagenda von Sustainable Finance zielt darauf ab, diese Risiken einzudämmen und den Finanzmarkt zum Hebel für den Klimaschutz zu machen. Inwiefern diese Ziele mit den gewählten Instrumenten erreichbar sind, wird kritisch beleuchtet. Das Fazit zeigt die Grenzen von Sustainable Finance auf und verdeutlicht, welche weiteren regulatorischen Schritte nötig wären, um den Finanzmarkt nicht nur nachhaltig, sondern auch inhärent stabil zu gestalten.

The livestock sector in Ethiopia is characterized by low productivity due to inadequate supply of affordable high-quality animal feed year-round, with more acute gaps in the drought-prone regions of the country. This paper presents the economic benefits and insights into the role of cultivated forages, such as densification into pellets, in bridging gaps in feed supply. Nutrient requirement calculations for feedlot and dairy animals and meeting those requirements using cultivated forage-based diets are presented. However, forage crops need a viable forage seed supply system to assure access to quality assured seeds. This study thus explores the role of forage seed systems and presents intervention areas for Ethiopia. Results suggest diets containing greater than 85% cultivated forages can sustain daily body weight gain up to 1 kg in growing animals. The costs of nutrients from cultivated forages are up to 15-fold lower than those from conventional feed resources. The diets based on pelleted cultivated forages decrease costs of feeding animals during a 100-day drought period by 4-fold, fattening animals by 2.3-fold, and cost of feed for milk production by 4-fold. Utilization of cultivated forages could reduce methane emissions with abatement value between $165 and $240 USD per 1000 kg of body weight gain in the fattening sector. For the dairy sector, the abatement value would range from $1350 to $2400 USD per million liters of milk production. For the drought period of 120 days, the value of methane reductions would be between $5500 and $11,400 USD per 1000 animals.

SUMMARYDNA loop extrusion by structural-maintenance-of-chromosome (SMC) complexes has emerged as a primary organizing principle for chromosomes. The mechanism by which SMC motor proteins extrude DNA loops is still unresolved and much debated. The ring-like structure of SMC complexes prompted multiple models where the extruded DNA is topologically or pseudotopologically entrapped within the ring during loop extrusion. However, recent experiments showed the passage of roadblocks much bigger than the SMC ring size, suggesting a nontopological mechanism. Recently, attempts were made to reconcile the observed passage of large roadblocks with a pseudotopological mechanism. Here we examine the predictions of these pseudotopological models, and find that they are not consistent with some experimental data on SMC roadblock encounters. Particularly, these models predict the formation of two loops and that roadblocks will reside near the stem of the loop upon encounter – both in contrast to experimental observations. Overall, the experimental data reinforce the notion of a nontopological mechanism for extrusion of DNA.