The rockefeller university

Transcription elongation by RNA polymerase II (Pol II) is an integral step in eukaryotic gene expression. The speed of Pol II is controlled by a multitude of elongation factors, but the exact regulatory mechanisms remain incompletely understood, especially for higher eukaryotes. Here we develop a single-molecule platform to visualize the dynamics of individual mammalian transcription elongation complexes (ECs) reconstituted from purified proteins. This platform allows us to follow the elongation and pausing behavior of EC in real time and unambiguously determine the role of each elongation factor in the kinetic control of Pol II. We find that the mammalian EC harbors multiple speed gears dictated by its associated factors and phosphorylation status. Moreover, the elongation factors are not functionally redundant but act hierarchically and synergistically to achieve optimal elongation activity. We propose that such elaborate kinetic regulation underlies the major speed-changing events during the transcription cycle and enables cells to adapt to a changing environment.

ObjectiveSystemic sclerosis (SSc) is a rare but severe autoimmune disease characterized by immune dysregulation, fibrosis, and vasculopathy. Although previous studies have highlighted the presence of functional autoantibodies targeting the angiotensin II receptor type 1 (AT1) and endothelin-1 type A receptor (ETAR), leading to autoantibody-mediated receptor stimulation and subsequent activation of endothelial cells (ECs), a comprehensive understanding of the direct interaction between these autoantibodies and their receptors is currently lacking. Moreover, existing data confirming the presence of these autoantibodies in SSc often rely on similar methodologies and assays. Our aim was to replicate previous findings and to investigate the functional effects of IgG derived from patients with SSc (SSc IgG) on AT1 and ETAR signaling, the downstream EC response, and the presence of AT1-binding autoantibodies in circulation.MethodsQuantitative polymerase chain reaction and cytokine enzyme-linked immunosorbent assay, alongside a real-time cell analyzer, were used to assess receptor-specific functional characteristics of purified SSc IgG (n = 18). Additionally, a novel protein capture assay using solubilized epitope-tagged AT1 was developed to detect AT1-binding autoantibodies in plasma samples from patients with SSc (n = 28) and healthy donors (n = 14).ResultsNo evidence for EC activation in an AT1- or ETAR-dependent manner was revealed. Furthermore, stimulation with SSc IgG did not induce receptor activation or alter G protein-coupled receptor signaling on agonist stimulation in a model with receptor overexpression. Lastly, no AT1-binding autoantibodies were detected in plasma samples from patients with SSc when using epitope-tagged solubilized AT1.ConclusionOverall, our study did not provide evidence to support the presence of AT1- or ETAR-activating autoantibodies in purified SSc IgG or AT1-binding autoantibodies in the circulation of patients with SSc.

In the arboviral vector Aedes aegypti, adaptation to anthropogenic environments has led to a major evolutionary shift separating the domestic Aedes aegypti aegypti (Aaa) ecotype from the wild Aedes aegypti formosus (Aaf) ecotype. Aaa mosquitoes are distributed globally and have higher vectorial capacity than Aaf, which remained in Africa. Despite the evolutionary and epidemiological relevance of this separation, inconsistent morphological data and a complex population structure have hindered the identification of genomic signals distinguishing the two ecotypes. Here we assessed the correspondence between the geographic distribution, population structure and genome-wide selection of 511 Aaf and 123 Aaa specimens and report adaptive signals in 186 genes that we call Aaa molecular signatures. Our results indicate that Aaa molecular signatures arose from standing variation associated with extensive ancestral polymorphisms in Aaf populations and have been co-opted for self-domestication through genomic and functional redundancy and local adaptation. Overall, we show that the behavioural shift of Ae. aegypti mosquitoes to live in association with humans relied on the fine regulation of chemosensory, neuronal and metabolic functions, as seen in the domestication processes of rabbits and silkworms. Our results also provide a foundation for the investigation of new genic targets for the control of Ae. aegypti populations.

Ageing is associated with a decline in the number and fitness of adult stem cells1,2. Ageing-associated loss of stemness is posited to suppress tumorigenesis3,4, but this hypothesis has not been tested in vivo. Here we use physiologically aged autochthonous genetically engineered5,6 mouse models and primary cells5,6 to demonstrate that ageing suppresses lung cancer initiation and progression by degrading the stemness of the alveolar cell of origin. This phenotype is underpinned by the ageing-associated induction of the transcription factor NUPR1 and its downstream target lipocalin-2 in the cell of origin in mice and humans, which leads to functional iron insufficiency in the aged cells. Genetic inactivation of the NUPR1-lipocalin-2 axis or iron supplementation rescues stemness and promotes the tumorigenic potential of aged alveolar cells. Conversely, targeting the NUPR1-lipocalin-2 axis is detrimental to young alveolar cells through ferroptosis induction. Ageing-associated DNA hypomethylation at specific enhancer sites is associated with increased NUPR1 expression, which is recapitulated in young alveolar cells through DNA methylation inhibition. We uncover that ageing drives functional iron insufficiency that leads to loss of stemness and tumorigenesis but promotes resistance to ferroptosis. These findings have implications for the therapeutic modulation of cellular iron homeostasis in regenerative medicine and in cancer prevention. Furthermore, our findings are consistent with a model whereby most human cancers initiate at a young age, thereby highlighting the importance of directing cancer prevention efforts towards young individuals.

Background A thorough analysis of genome evolution is fundamental for biodiversity understanding. The iconic monotremes (platypus and echidna) feature extraordinary biology. However, they also exhibit rearrangements in several chromosomes, especially in the sex chromosome chain. Therefore, the lack of a chromosome-level echidna genome has limited insights into genome evolution in monotremes, in particular the multiple sex chromosomes complex.Results Here, we present a new long reads-based chromosome-level short-beaked echidna (Tachyglossus aculeatus) genome, which allowed the inference of chromosomal rearrangements in the monotreme ancestor (2n = 64) and each extant species. Analysis of the more complete sex chromosomes uncovered homology between 1 Y chromosome and multiple X chromosomes, suggesting that it is the ancestral X that has undergone reciprocal translocation with ancestral autosomes to form the complex. We also identified dozens of ampliconic genes on the sex chromosomes, with several ancestral ones expressed during male meiosis, suggesting selective constraints in pairing the multiple sex chromosomes.Conclusion The new echidna genome provides an important basis for further study of the unique biology and conservation of this species.

We studied a family with three male individuals across two generations affected by common variable immune deficiency (CVID). We identified a novel missense heterozygous variant (c.2602T>A:p.Y868N) of NFKB2 in all patients and not in healthy relatives. Functional studies of the mutant allele in an overexpression system and of the patients' cells confirmed the deleteriousness of the NFKB2 variant and genotype, respectively, on the activation of the non-canonical NF-kappa B signaling pathway. Impaired processing of p100 into p52 underlies p100 accumulation, which results in gain-of-function (GOF) of I kappa B delta inhibitory activity and loss-of-function (LOF) of p52 transcriptional activity. The three patients' plasma contained autoantibodies that neutralized IFN-alpha 2 and/or IFN-omega, accounting for the severe or recurrent viral diseases of the patients, including influenza pneumonia in one sibling, and severe COVID-19 and recurrent herpes labialis in another. Our results confirm that NFKB2 alleles that are I kappa B delta GOF and p52 LOF can underlie CVID and drive the production of autoantibodies neutralizing type I IFNs, thereby predisposing to severe viral diseases.

Germinal centres are specialized microenvironments where B cells undergo affinity maturation. B cells expressing antibodies whose affinity is improved by somatic hypermutation are selected for expansion by limiting numbers of T follicular helper cells. Cell division is accompanied by mutation of the immunoglobulin genes, at what is believed to be a fixed rate of around 1 x 10-3 per base pair per cell division1. As mutagenesis is random, the probability of acquiring deleterious mutations outweighs the probability of acquiring affinity-enhancing mutations. This effect might be heightened, and even become counterproductive, in B cells that express high-affinity antibodies and undergo the greatest number of cell divisions2. Here we experimentally examine a theoretical model that explains how affinity maturation could be optimized by varying the rate of somatic hypermutation such that cells that express higher-affinity antibodies divide more but mutate less per division. Data obtained from mice immunized with SARS-CoV-2 vaccines or a model antigen align with the theoretical model and show that cells producing high-affinity antibodies shorten the G0/G1 phases of the cell cycle and reduce their mutation rates. We propose that these mechanisms safeguard high-affinity B cell lineages and enhance the outcomes of antibody affinity maturation.

Background: Treating rheumatic musculoskeletal diseases (RMDs) during pregnancy and breastfeeding presents significant complexities, mainly due to inconsistencies between the clinical guidance documents and the reference safety information, including the summary of product characteristics (SmPC) and the patient information leaflets (PIL).Objectives: To assess healthcare professionals' (HCPs) prescribing behaviors, comfort levels, and challenges when advising patients, focusing on discrepancies between clinical guidance documents and SmPC/PIL.Design: Online survey entitled PRAISE (Perception of healthcare providers Regarding Antirheumatics in pregnancy and breastfeeding: advice, Information and patient perSpEctives) and disseminated through HCPs groups and social media.Methods: A cross-sectional survey was conducted among 414 HCPs globally. Respondents were divided into prescribers (n = 336) and non-prescribers (n = 78) based on their self-reported role in prescribing antirheumatic medications to pregnant or breastfeeding patients with RMDs. The survey covered demographics, clinical experience, confidence in prescribing, use of clinical guidelines, and experiences managing conflicting information between guidelines and SmPC/PIL.Results: Prescribers were more likely than non-prescribers to feel comfortable discussing medication safety during pregnancy. Most prescribers found clinical guidance documents useful, with 48% rating them as "very useful" and 38% as "extremely useful." In case of conflicting information between clinical guidance documents and SmPC/PIL, 58% of HCPs reported that it caused confusion and tension in patient-doctor relationships, and almost 20% of them are "likely" or "very likely" to discontinue ongoing treatment. Clear communication and shared decision-making were the most common strategies used to address patient concerns.Conclusion: HCPs often face significant challenges when advising patients with RMDs on the use of medications during pregnancy and breastfeeding. Conflicting information between clinical guidance documents and SmPC/PIL can disrupt patient-doctor relationship and lead to treatment discontinuation, with potential consequences on maternal disease control. Improved alignment between clinical guidance documents and the SmPC/PIL could enhance patient care and prevent confusion among HCPs and patients.

A search is performed for charged-lepton flavor violating processes in top quark (t) production and decay. The data were collected by the CMS experiment from proton-proton collisions at a center-of-mass energy of 13 TeV and correspond to an integrated luminosity of 138 fb(-1). The selected events are required to contain one opposite-sign electron-muon pair, a third charged lepton (electron or muon), and at least one jet of which no more than one is associated with a bottom quark. Boosted decision trees are used to distinguish signal from background, exploiting differences in the kinematics of the final states particles. The data are consistent with the standard model expectation. Upper limits at 95% confidence level are placed in the context of effective field theory on the Wilson coefficients, which range between 0.024-0.424 TeV-2 depending on the flavor of the associated light quark and the Lorentz structure of the interaction. These limits are converted to upper limits on branching fractions involving up (charm) quarks, t -> e mu u (t -> e mu c), of 0.032(0.498) x 10(-6), 0.022(0.369) x 10(-6), and 0.012(0.216) x 10(-6) for tensorlike, vectorlike, and scalarlike interactions, respectively.

Metagenomics provides access to the genetic diversity of uncultured bacteria through analysis of DNA extracted from whole microbial communities. Long-read sequencing is advancing metagenomic discovery by generating larger DNA assemblies than previously possible. However, harnessing the potential of long-read sequencing to access the vast diversity within soil microbiomes is hampered by the challenge of isolating high-quality DNA. Here we introduce a method that can liberate large, high-quality metagenomic DNA fragments from soil bacteria and pair them with optimized nanopore long-read sequencing to generate megabase-sized assemblies. Using this method, we uncover hundreds of complete circular metagenomic genomes from a single soil sample. Through a combination of bioinformatic prediction and chemical synthesis, we convert nonribosomal peptide biosynthetic gene clusters directly into bioactive molecules, identifying antibiotics with rare modes of action and activity against multidrug-resistant pathogens. Our approach advances metagenomic access to the vast genetic diversity of the uncultured bacterial majority and provides a means to convert it to bioactive molecules.