A polymorphism in IRF4 affects human pigmentation through a tyrosinase-dependent MITF/TFAP2A pathway.

Sequence polymorphisms linked to human diseases and phenotypes in genome-wide association studies often affect noncoding regions. A SNP within an intron of the gene encoding Interferon Regulatory Factor 4 (IRF4), a transcription factor with no known role in melanocyte biology, is strongly associated with sensitivity of skin to sun exposure, freckles, blue eyes, and brown hair color. Here, we demonstrate that this SNP lies within an enhancer of IRF4 transcription in melanocytes. The allele associated with this pigmentation phenotype impairs binding of the TFAP2A transcription factor that, together with the melanocyte master regulator MITF, regulates activity of the enhancer. Assays in zebrafish and mice reveal that IRF4 cooperates with MITF to activate expression of Tyrosinase (TYR), an essential enzyme in melanin synthesis. Our findings provide a clear example of a noncoding polymorphism that affects a phenotype by modulating a developmental gene regulatory network.

A decline in global CFC-11 emissions during 2018-2019.

The atmospheric concentration of trichlorofluoromethane (CFC-11) has been in decline since the production of ozone-depleting substances was phased out under the Montreal Protocol1,2. Since 2013, the concentration decline of CFC-11 slowed unexpectedly owing to increasing emissions, probably from unreported production, which, if sustained, would delay the recovery of the stratospheric ozone layer1-12. Here we report an accelerated decline in the global mean CFC-11 concentration during 2019 and 2020, derived from atmospheric concentration measurements at remote sites around the world. We find that global CFC-11 emissions decreased by 18 ± 6 gigagrams per year (26 ± 9 per cent; one standard deviation) from 2018 to 2019, to a 2019 value (52 ± 10 gigagrams per year) that is similar to the 2008-2012 mean. The decline in global emissions suggests a substantial decrease in unreported CFC-11 production. If the sharp decline in unexpected global emissions and unreported production is sustained, any associated future ozone depletion is likely to be limited, despite an increase in the CFC-11 bank (the amount of CFC-11 produced, but not yet emitted) by 90 to 725 gigagrams by the beginning of 2020.

Unexpectedly rapid aerosol formation in the Hunga Tonga plume.

The Hunga Tonga-Hunga Ha'apai (HT-HH) volcanic eruptions on January 13 and 15, 2022, produced a plume with the highest signal in stratospheric aerosol optical depth observed since the eruption of Mt. Pinatubo in 1991. Suites of balloon-borne instruments on a series of launches from Réunion Island intercepted the HT-HH plume between 7 and 10 d of the eruptions, yielding observations of the aerosol number and size distribution and sulfur dioxide (SO2) and water vapor (H2O) concentrations. The measurements reveal an unexpected abundance of large particles in the plume, constrain the total sulfur injected to approximately 0.2 Tg, provide information on the altitude of the injection, and indicate that the formation of sulfuric acid aerosol was complete within 3 wk. Large H2O enhancements contributed as much as ~30% to ambient aerosol surface area and likely accelerated SO2 oxidation and aerosol formation rates in the plume to approximately three times faster than under normal stratospheric conditions.

On the stratospheric chemistry of midlatitude wildfire smoke.

SignificanceLarge wildfires have been observed to inject smoke into the stratosphere, raising questions about their potential to affect the stratospheric ozone layer that protects life on Earth from biologically damaging ultraviolet radiation. Multiple observations of aerosol and NO2 concentrations from three independent satellite instruments are used here together with model calculations to identify decreases in stratospheric NO2 concentrations following major Australian 2019 through 2020 wildfires. The data confirm that important chemistry did occur on the smoke particle surfaces. The observed behavior in NO2 with increasing particle concentrations is a marker for surface chemistry that contributes to midlatitude ozone depletion. The results indicate that increasing wildfire activity in a warming world may slow the recovery of the ozone layer.

Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours.

Analysis of molecular aberrations across multiple cancer types, known as pan-cancer analysis, identifies commonalities and differences in key biological processes that are dysregulated in cancer cells from diverse lineages. Pan-cancer analyses have been performed for adult but not paediatric cancers, which commonly occur in developing mesodermic rather than adult epithelial tissues. Here we present a pan-cancer study of somatic alterations, including single nucleotide variants, small insertions or deletions, structural variations, copy number alterations, gene fusions and internal tandem duplications in 1,699 paediatric leukaemias and solid tumours across six histotypes, with whole-genome, whole-exome and transcriptome sequencing data processed under a uniform analytical framework. We report 142 driver genes in paediatric cancers, of which only 45% match those found in adult pan-cancer studies; copy number alterations and structural variants constituted the majority (62%) of events. Eleven genome-wide mutational signatures were identified, including one attributed to ultraviolet-light exposure in eight aneuploid leukaemias. Transcription of the mutant allele was detectable for 34% of protein-coding mutations, and 20% exhibited allele-specific expression. These data provide a comprehensive genomic architecture for paediatric cancers and emphasize the need for paediatric cancer-specific development of precision therapies.

Toward a gold standard for benchmarking gene set enrichment analysis.

MOTIVATION: Although gene set enrichment analysis has become an integral part of high-throughput gene expression data analysis, the assessment of enrichment methods remains rudimentary and ad hoc. In the absence of suitable gold standards, evaluations are commonly restricted to selected datasets and biological reasoning on the relevance of resulting enriched gene sets. RESULTS: We develop an extensible framework for reproducible benchmarking of enrichment methods based on defined criteria for applicability, gene set prioritization and detection of relevant processes. This framework incorporates a curated compendium of 75 expression datasets investigating 42 human diseases. The compendium features microarray and RNA-seq measurements, and each dataset is associated with a precompiled GO/KEGG relevance ranking for the corresponding disease under investigation. We perform a comprehensive assessment of 10 major enrichment methods, identifying significant differences in runtime and applicability to RNA-seq data, fraction of enriched gene sets depending on the null hypothesis tested and recovery of the predefined relevance rankings. We make practical recommendations on how methods originally developed for microarray data can efficiently be applied to RNA-seq data, how to interpret results depending on the type of gene set test conducted and which methods are best suited to effectively prioritize gene sets with high phenotype relevance. AVAILABILITY: http://bioconductor.org/packages/GSEABenchmarkeR. CONTACT: ludwig.geistlinger@sph.cuny.edu.

High-resolution mapping and characterization of open chromatin across the genome.

Mapping DNase I hypersensitive (HS) sites is an accurate method of identifying the location of genetic regulatory elements, including promoters, enhancers, silencers, insulators, and locus control regions. We employed high-throughput sequencing and whole-genome tiled array strategies to identify DNase I HS sites within human primary CD4+ T cells. Combining these two technologies, we have created a comprehensive and accurate genome-wide open chromatin map. Surprisingly, only 16%-21% of the identified 94,925 DNase I HS sites are found in promoters or first exons of known genes, but nearly half of the most open sites are in these regions. In conjunction with expression, motif, and chromatin immunoprecipitation data, we find evidence of cell-type-specific characteristics, including the ability to identify transcription start sites and locations of different chromatin marks utilized in these cells. In addition, and unexpectedly, our analyses have uncovered detailed features of nucleosome structure.

Caregiver openness in emotionally focused family therapy: A critical shift.

Through the application of a discovery-oriented task analysis, this research delineated specific therapist behaviors that resulted in a successful caregiver openness event in emotionally focused family therapy (EFFT). EFFT experts were recruited via email and asked to submit family therapy recordings where they believed a caregiver openness event occurred. Ten family therapy recordings were submitted by three experts. Within these recordings, 12 caregiver openness events were discovered and critically analyzed. Nine themes were identified and interventions therapists applied to accomplish these themes were delineated using the emotionally focused therapy-coding scheme (EFT-CS). These themes included: (1) validating and reframing the child's protected stance, (2) processing the impact of the child's unmet attachment longings, (3) validating the caregiver's blocked relational stance, (4) expanding caregiving intentions, (5) enacting the caregiver's intentions to meet the child's attachment longings, (6) processing the enactment, (7) processing and promoting caregiver accessibility to the child's response, (8) heightening the caregiver's accessible stance, and (9) enhancing shifting family dynamics. Additional findings, implications for clinical practice, training, and future research are discussed.

Direct visualization of sequence-specific DNA binding by gonococcal type IV pili.

Neisseria gonorrhoeae, the causative agent of gonorrhoea, is a major burden on global healthcare systems, with an estimated ~80-90 million new global cases annually. This burden is exacerbated by increasing levels of antimicrobial resistance, which has greatly limited viable antimicrobial therapies. Decreasing gonococcal drug susceptibility has been driven largely by accumulation of chromosomal resistance determinants, which can be acquired through natural transformation, whereby DNA in the extracellular milieu is imported into cells and incorporated into the genome by homologous recombination. N. gonorrhoeae possesses a specialized system for DNA uptake, which strongly biases transformation in favour of DNA from closely related bacteria by recognizing a 10-12 bp DNA uptake sequence (DUS) motif, which is highly overrepresented in their chromosomal DNA. This process relies on numerous proteins, including the DUS-specific receptor ComP, which assemble retractile protein filaments termed type IV pili (T4P) extending from the cell surface, and one model for neisserial DNA uptake proposes that these filaments bind DNA in a DUS-dependent manner before retracting to transport DNA into the periplasm. However, conflicting evidence indicates that elongated pilus filaments may not have such a direct role in DNA binding uptake as this model suggests. Here, we quantitatively measured DNA binding to gonococcal T4P fibres by directly visualizing binding complexes with confocal fluorescence microscopy in order to confirm the sequence-specific, comP-dependent DNA binding capacity of elongated T4P fibres. This supports the idea that pilus filaments could be responsible for initially capturing DNA in the first step of sequence-specific DNA uptake.

Lineage of origin in rhabdomyosarcoma informs pharmacological response.

Lineage or cell of origin of cancers is often unknown and thus is not a consideration in therapeutic approaches. Alveolar rhabdomyosarcoma (aRMS) is an aggressive childhood cancer for which the cell of origin remains debated. We used conditional genetic mouse models of aRMS to activate the pathognomonic Pax3:Foxo1 fusion oncogene and inactivate p53 in several stages of prenatal and postnatal muscle development. We reveal that lineage of origin significantly influences tumor histomorphology and sensitivity to targeted therapeutics. Furthermore, we uncovered differential transcriptional regulation of the Pax3:Foxo1 locus by tumor lineage of origin, which led us to identify the histone deacetylase inhibitor entinostat as a pharmacological agent for the potential conversion of Pax3:Foxo1-positive aRMS to a state akin to fusion-negative RMS through direct transcriptional suppression of Pax3:Foxo1.

Super-enhancers delineate disease-associated regulatory nodes in T cells.

Enhancers regulate spatiotemporal gene expression and impart cell-specific transcriptional outputs that drive cell identity. Super-enhancers (SEs), also known as stretch-enhancers, are a subset of enhancers especially important for genes associated with cell identity and genetic risk of disease. CD4(+) T cells are critical for host defence and autoimmunity. Here we analysed maps of mouse T-cell SEs as a non-biased means of identifying key regulatory nodes involved in cell specification. We found that cytokines and cytokine receptors were the dominant class of genes exhibiting SE architecture in T cells. Nonetheless, the locus encoding Bach2, a key negative regulator of effector differentiation, emerged as the most prominent T-cell SE, revealing a network in which SE-associated genes critical for T-cell biology are repressed by BACH2. Disease-associated single-nucleotide polymorphisms for immune-mediated disorders, including rheumatoid arthritis, were highly enriched for T-cell SEs versus typical enhancers or SEs in other cell lineages. Intriguingly, treatment of T cells with the Janus kinase (JAK) inhibitor tofacitinib disproportionately altered the expression of rheumatoid arthritis risk genes with SE structures. Together, these results indicate that genes with SE architecture in T cells encompass a variety of cytokines and cytokine receptors but are controlled by a 'guardian' transcription factor, itself endowed with an SE. Thus, enumeration of SEs allows the unbiased determination of key regulatory nodes in T cells, which are preferentially modulated by pharmacological intervention.

Point Mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant.

Gastric adenocarcinoma and proximal polyposis of the stomach (GAPPS) is an autosomal-dominant cancer-predisposition syndrome with a significant risk of gastric, but not colorectal, adenocarcinoma. We mapped the gene to 5q22 and found loss of the wild-type allele on 5q in fundic gland polyps from affected individuals. Whole-exome and -genome sequencing failed to find causal mutations but, through Sanger sequencing, we identified point mutations in APC promoter 1B that co-segregated with disease in all six families. The mutations reduced binding of the YY1 transcription factor and impaired activity of the APC promoter 1B in luciferase assays. Analysis of blood and saliva from carriers showed allelic imbalance of APC, suggesting that these mutations lead to decreased allele-specific expression in vivo. Similar mutations in APC promoter 1B occur in rare families with familial adenomatous polyposis (FAP). Promoter 1A is methylated in GAPPS and sporadic FGPs and in normal stomach, which suggests that 1B transcripts are more important than 1A in gastric mucosa. This might explain why all known GAPPS-affected families carry promoter 1B point mutations but only rare FAP-affected families carry similar mutations, the colonic cells usually being protected by the expression of the 1A isoform. Gastric polyposis and cancer have been previously described in some FAP-affected individuals with large deletions around promoter 1B. Our finding that GAPPS is caused by point mutations in the same promoter suggests that families with mutations affecting the promoter 1B are at risk of gastric adenocarcinoma, regardless of whether or not colorectal polyps are present.

What Does it Mean to be a Common Factors Informed Family Therapist?

The common factors paradigm in couple and family therapy has gained popularity over the past several decades, leading many therapists to refer to themselves as common factors family therapists. Despite this, no consensus exists on what it means to be a common factors family therapist, or if such a designation even makes sense given that the common factors paradigm is not a model. Synthesizing the existing common factors literature, a case is made for the designation "common factors informed family therapist," and the following six core principles are outlined that characterize this designation: (1) sees overlap among theories; (2) passionate about theory, not a theory; (3) client centered; (4) monitors hope and the therapeutic alliance; (5) views clients as people rather than objects; and (6) prioritizes healing over therapy. Each of the concepts is discussed in depth, and clinical implications are provided.

El paradigma de factores comunes en la terapia de parejas y familiar ha cobrado popularidad en las últimas décadas, haciendo que muchos terapeutas se refieran a sí mismos como terapeutas de factores comunes. A pesar de esto, no hay un consenso acerca de qué significa ser un terapeuta de factores comunes, o si dicha designación realmente tiene sentido, dado que el paradigma de factores comunes no es un modelo. A base de una síntesis de la literatura de factores comunes existente, se aboga por la designación "terapeuta familiar informado por factores comunes", y se esbozan seis principios fundamentales que caracterizan esta designación; 1) ve que las teorías se entrecruzan; 2) apasionado por lo teórico, no por una teoría; 3) centrado en los clientes; 4) está pendiente de la esperanza y la alianza terapéutica; 5) ve a los clientes como personas en vez de objetos; y 6) se preocupa más por la sanación que por la terapia. Se discute cada concepto a profundidad y se proporcionan las implicaciones clínicas.

High Blocking Temperature of Magnetization and Giant Coercivity in the Azafullerene Tb2 @C79 N with a Single-Electron Terbium-Terbium Bond.

The azafullerene Tb2 @C79 N is found to be a single-molecule magnet with a high 100-s blocking temperature of magnetization of 24 K and large coercivity. Tb magnetic moments with an easy-axis single-ion magnetic anisotropy are strongly coupled by the unpaired spin of the single-electron Tb-Tb bond. Relaxation of magnetization in Tb2 @C79 N below 15 K proceeds via quantum tunneling of magnetization with the characteristic time τQTM =16 462±1230 s. At higher temperature, relaxation follows the Orbach mechanism with a barrier of 757±4 K, corresponding to the excited states, in which one of the Tb spins is flipped.

Scalable Fiber-like Micelles and Block Co-micelles by Polymerization-Induced Crystallization-Driven Self-Assembly.

Self-assembled 1D block copolymer nanoparticles (micelles) are of interest for a range of applications. However, morphologically pure samples are often challenging to access, and precise dimensional control is not possible. Moreover, the development of synthetic protocols that operate on a commercially viable scale has been a major challenge. Herein, we describe the preparation 1D fiber-like micelles with crystalline cores at high concentrations by a one-pot process termed polymerization-induced crystallization-driven self-assembly (PI-CDSA). We also demonstrate the formation of uniform fibers by living PI-CDSA, a process in which block copolymer synthesis, self-assembly, and seeded growth are combined. We have demonstrated that the method is successful for block copolymers that possess the same composition as that of the seed (homoepitaxial growth) and also where the coronal chemistries differ to give segmented 1D fibers known as block co-micelles. We have also shown that heteroepitaxial growth allows the formation of scaled-up block co-micelles where the composition of both the core and corona was varied. These proof-of-concept experiments indicate that PI-CDSA is a promising, scalable route to a variety of polydisperse or uniform 1D nanoparticles based on block copolymers with different crystalline core chemistries and, therefore, functions.

Orchestrating high-throughput genomic analysis with Bioconductor.

Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists. Packages cover a range of bioinformatic and statistical applications. They undergo formal initial review and continuous automated testing. We present an overview for prospective users and contributors.

Public data and open source tools for multi-assay genomic investigation of disease.

Molecular interrogation of a biological sample through DNA sequencing, RNA and microRNA profiling, proteomics and other assays, has the potential to provide a systems level approach to predicting treatment response and disease progression, and to developing precision therapies. Large publicly funded projects have generated extensive and freely available multi-assay data resources; however, bioinformatic and statistical methods for the analysis of such experiments are still nascent. We review multi-assay genomic data resources in the areas of clinical oncology, pharmacogenomics and other perturbation experiments, population genomics and regulatory genomics and other areas, and tools for data acquisition. Finally, we review bioinformatic tools that are explicitly geared toward integrative genomic data visualization and analysis. This review provides starting points for accessing publicly available data and tools to support development of needed integrative methods.

Upregulation of IFN-Inducible and Damage-Response Pathways in Chronic Graft-versus-Host Disease.

Although chronic graft-versus-host disease (CGVHD) is the primary nonrelapse complication of allogeneic transplantation, understanding of its pathogenesis is limited. To identify the main operant pathways across the spectrum of CGVHD, we analyzed gene expression in circulating monocytes, chosen as in situ systemic reporter cells. Microarrays identified two interrelated pathways: 1) IFN-inducible genes, and 2) innate receptors for cellular damage. Corroborating these with multiplex RNA quantitation, we found that multiple IFN-inducible genes (affecting lymphocyte trafficking, differentiation, and Ag presentation) were concurrently upregulated in CGVHD monocytes compared with normal subjects and non-CGVHD control patients. IFN-inducible chemokines were elevated in both lichenoid and sclerotic CGHVD plasma and were linked to CXCR3+ lymphocyte trafficking. Furthermore, the levels of the IFN-inducible genes CXCL10 and TNFSF13B (BAFF) were correlated at both the gene and the plasma levels, implicating IFN induction as a factor in elevated BAFF levels in CGVHD. In the second pathway, damage-/pathogen-associated molecular pattern receptor genes capable of inducing type I IFN were upregulated. Type I IFN-inducible MxA was expressed in proportion to CGVHD activity in skin, mucosa, and glands, and expression of TLR7 and DDX58 receptor genes correlated with upregulation of type I IFN-inducible genes in monocytes. Finally, in serial analyses after transplant, IFN-inducible and damage-response genes were upregulated in monocytes at CGVHD onset and declined upon therapy and resolution in both lichenoid and sclerotic CGVHD patients. This interlocking analysis of IFN-inducible genes, plasma analytes, and tissue immunohistochemistry strongly supports a unifying hypothesis of induction of IFN by innate response to cellular damage as a mechanism for initiation and persistence of CGVHD.

Perioperative Mortality Following Oesophagectomy and Pancreaticoduodenectomy in Australia.

INTRODUCTION: Oesophagectomy (OG) and pancreaticoduodenectomy (PD) remain associated with significant perioperative mortality rates (POMR). Improved outcomes in high-volume centres have led to these procedures being centralised in some countries. This retrospective, population-based cohort study was conducted to determine the Australian national, and state and territory based POMR associated with OG and PD, and assess trends over time. METHODS: Logistic regression analysis was performed using de-identified procedural data between 1 July 2005 and 30 June 2013 from the Australian Institute of Health and Welfare. Codes relating to OG and PD contained in the Australian Classification of Health Interventions were used to extract patient data. Mortality rates were risk adjusted for age, gender and urgency of admission. Temporal trends and differences between states/territories were investigated. RESULTS: The average Australian POMR throughout the study period was 3.5 and 3.0% for OG and PD, respectively. OG POMR showed no significant change over time (P = 0.30) or variation between states (P = 0.079). The annual POMR associated with PD, however, showed a significant decrease during the study period (P = 0.01) with variation in PD POMR outcomes evident amongst different regions (P = 0.0004). CONCLUSION: This study demonstrates a comparable Australian PD and OG POMR when correlated with international studies. National PD POMR improved throughout the study with consistent improvement across the states and territories. This study does, however, show variation in PD POMR between states and territories. Potential intra-state variation merits further investigation.