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CRISPR perturbation methods are limited in their ability to study non-coding elements and genetic interactions. In this study, we developed a system for bidirectional epigenetic editing, called CRISPRai, in which we apply activating (CRISPRa) and repressive (CRISPRi) perturbations to two loci simultaneously in the same cell. We developed CRISPRai Perturb-seq by coupling dual perturbation gRNA detection with single-cell RNA sequencing, enabling study of pooled perturbations in a mixed single-cell population. We applied this platform to study the genetic interaction between two hematopoietic lineage transcription factors, SPI1 and GATA1, and discovered novel characteristics of their co-regulation on downstream target genes, including differences in SPI1 and GATA1 occupancy at genes that are regulated through different modes. We also studied the regulatory landscape of IL2 (interleukin-2) in Jurkat T cells, primary T cells and chimeric antigen receptor (CAR) T cells and elucidated mechanisms of enhancer-mediated IL2 gene regulation. CRISPRai facilitates investigation of context-specific genetic interactions, provides new insights into gene regulation and will enable exploration of non-coding disease-associated variants., (© 2024. The Author(s).)

CRISPR-Cas9 genome editing has enabled advanced T cell therapies, but occasional loss of the targeted chromosome remains a safety concern. To investigate whether Cas9-induced chromosome loss is a universal phenomenon and evaluate its clinical significance, we conducted a systematic analysis in primary human T cells. Arrayed and pooled CRISPR screens revealed that chromosome loss was generalizable across the genome and resulted in partial and entire loss of the targeted chromosome, including in preclinical chimeric antigen receptor T cells. T cells with chromosome loss persisted for weeks in culture, implying the potential to interfere with clinical use. A modified cell manufacturing process, employed in our first-in-human clinical trial of Cas9-engineered T cells (NCT03399448), reduced chromosome loss while largely preserving genome editing efficacy. Expression of p53 correlated with protection from chromosome loss observed in this protocol, suggesting both a mechanism and strategy for T cell engineering that mitigates this genotoxicity in the clinic., Competing Interests: Declaration of interests C.A.T., J.A.D., and the Regents of the University of California have patents pending or issued related to the use of CRISPR genome editing technologies. R.B. is an employee of BioMarin Pharmaceutical Inc., J.L. is an employee of Altos Labs, and K.R.P. is a co-founder and employee of Cartography Biosciences. A.T.S. is a co-founder of Immunai and Cartography Biosciences. A.T.S. has received research support from Arsenal Biosciences, Allogene Therapeutics, and 10x Genomics. J.H.D.C. is a co-founder of Initial Therapeutics. J.E. is a co-founder of Mnemo Therapeutics, a scientific advisory board member of Cytovia Therapeutics, and a consultant for Casdin Capital, Resolution Therapeutics, IndeeLabs, and Treefrog Therapeutics. J.E. has received research support from Cytovia Therapeutics, Mnemo Therapeutics, and Takeda Pharmaceutical Company. J.A.F. has received research support from Tmunity. C.H.J. and the University of Pennsylvania have patents pending or issued related to the use of gene modification in T cells for adoptive T cell therapy. C.H.J. is a co-founder of Tmunity. H.Y.C. is a co-founder of Accent Therapeutics, Boundless Bio, Cartography Biosciences, and Orbital Therapeutics, and an advisor to 10x Genomics, Arsenal Biosciences, Chroma Medicine, Spring Discovery, and Vida Ventures. C.J.Y. is a co-founder of Survey Genomics, and a scientific advisory board member of Related Sciences and Immunai. C.J.Y. is a consultant for Maze Therapeutics, TReX Bio, ImYoo, and Santa Ana Bio. C.J.Y. has received research support from the Chan Zuckerberg Initiative, Chan Zuckerberg Biohub, Genentech, BioLegend, ScaleBio, and Illumina. J.A.D. is a co-founder of Editas Medicine, Intellia Therapeutics, Caribou Biosciences, Mammoth Biosciences, and Scribe Therapeutics, and a scientific advisory board member of Intellia Therapeutics, Caribou Biosciences, Mammoth Biosciences, Scribe Therapeutics, Vertex Pharmaceuticals, Felix Biosciences, The Column Group, Inari, and Isomorphic Labs. J.A.D. is the Chief Science Advisor at Sixth Street and a Director at Johnson & Johnson, Tempus, and Altos Labs. J.A.D. has sponsored research projects through Apple Tree Partners, Genentech, and Roche., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Background: Cisplatin (CDDP) is a mainstay treatment for advanced head and neck squamous cell carcinomas (HNSCC) despite a high frequency of innate and acquired resistance. We hypothesised that tumours acquire CDDP resistance through an enhanced reductive state dependent on metabolic rewiring., Methods: To validate this model and understand how an adaptive metabolic programme might be imprinted, we performed an integrated analysis of CDDP-resistant HNSCC clones from multiple genomic backgrounds by whole-exome sequencing, RNA-seq, mass spectrometry, steady state and flux metabolomics., Results: Inactivating KEAP1 mutations or reductions in KEAP1 RNA correlated with Nrf2 activation in CDDP-resistant cells, which functionally contributed to resistance. Proteomics identified elevation of downstream Nrf2 targets and the enrichment of enzymes involved in generation of biomass and reducing equivalents, metabolism of glucose, glutathione, NAD(P), and oxoacids. This was accompanied by biochemical and metabolic evidence of an enhanced reductive state dependent on coordinated glucose and glutamine catabolism, associated with reduced energy production and proliferation, despite normal mitochondrial structure and function., Conclusions: Our analysis identified coordinated metabolic changes associated with CDDP resistance that may provide new therapeutic avenues through targeting of these convergent pathways., (© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)

Cells communicate with each other via receptor-ligand interactions. Here, we describe lentiviral-mediated cell entry by engineered receptor-ligand interaction (ENTER) to display ligand proteins, deliver payloads, and record receptor specificity. We optimize ENTER to decode interactions between T cell receptor (TCR)-MHC peptides, antibody-antigen, and other receptor-ligand pairs. A viral presentation strategy allows ENTER to capture interactions between B cell receptor and any antigen. We engineer ENTER to deliver genetic payloads to antigen-specific T or B cells to selectively modulate cellular behavior in mixed populations. Single-cell readout of ENTER by RNA sequencing (ENTER-seq) enables multiplexed enumeration of antigen specificities, TCR clonality, cell type, and states of individual T cells. ENTER-seq of CMV-seropositive patient blood samples reveals the viral epitopes that drive effector memory T cell differentiation and inter-clonal vs. intra-clonal phenotypic diversity targeting the same epitope. ENTER technology enables systematic discovery of receptor specificity, linkage to cell fates, and antigen-specific cargo delivery., Competing Interests: Declaration of interests A patent based on this work has been filed. H.Y.C. is a co-founder of Accent Therapeutics, Boundless Bio, Cartography Biosciences, and Orbital Therapeutics; he is also an advisor of 10X Genomics, Arsenal Biosciences, and Spring Discovery. A.T.S. is a co-founder of Cartography Biosciences and Immunai. K.R.P. is a co-founder of Cartography Biosciences. K.E.Y. is a consultant for Cartography Biosciences. J.A.B. is a consultant for Foresite Capital. W.J.G. is a consultant and equity holder for 10X Genomics, Guardant Health, Quantapore, and Ultima Genomics; he is also a co-founder of Protillion Biosciences and is named on patents describing ATAC-seq., (Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.)

RNA-binding proteins (RBPs), essential for skeletal muscle regeneration, cause muscle degeneration and neuromuscular disease when mutated. Why mutations in these ubiquitously expressed RBPs orchestrate complex tissue regeneration and direct cell fate decisions in skeletal muscle remains poorly understood. Single-cell RNA-sequencing of regenerating Mus musculus skeletal muscle reveals that RBP expression, including the expression of many neuromuscular disease-associated RBPs, is temporally regulated in skeletal muscle stem cells and correlates with specific stages of myogenic differentiation. By combining machine learning with RBP engagement scoring, we discovered that the neuromuscular disease-associated RBP Hnrnpa2b1 is a differentiation-specifying regulator of myogenesis that controls myogenic cell fate transitions during terminal differentiation in mice. The timing of RBP expression specifies cell fate transitions by providing post-transcriptional regulation of messenger RNAs that coordinate stem cell fate decisions during tissue regeneration., Competing Interests: JW, OW, TV, EN, BP, EL, AC, TE, ND, KP, KY, HV, TR, AJ, RP No competing interests declared, HC Reviewing editor, eLife, BO Serves on the scientific board of Satellos Biosciences

Regulatable CAR platforms could circumvent toxicities associated with CAR-T therapy, but existing systems have shortcomings including leakiness and attenuated activity. Here, we present SNIP CARs, a protease-based platform for regulating CAR activity using an FDA-approved small molecule. Design iterations yielded CAR-T cells that manifest full functional capacity with drug and no leaky activity in the absence of drug. In numerous models, SNIP CAR-T cells were more potent than constitutive CAR-T cells and showed diminished T cell exhaustion and greater stemness. In a ROR1-based CAR lethality model, drug cessation following toxicity onset reversed toxicity, thereby credentialing the platform as a safety switch. In the same model, reduced drug dosing opened a therapeutic window that resulted in tumor eradication in the absence of toxicity. SNIP CARs enable remote tuning of CAR activity, which provides solutions to safety and efficacy barriers that are currently limiting progress in using CAR-T cells to treat solid tumors., Competing Interests: Declaration of interests L.L., R.G.M., M.Z.L., and C.L.M. are coinventors on a patent related to this work. C.L.M. is a cofounder of Lyell Immunopharma, Syncopation Life Sciences, and Link Cell Therapies, which are developing CAR-based therapies, and consults for Lyell, NeoImmune Tech, Apricity, Nektar, Immatics, Ensoma, Mammoth, Glaxo Smith Kline, and Bristol Myers Squibb. L.L., R.G.M., E.S., and E.W.W. are consultants for and hold equity in Lyell Immunopharma. L.L. is a cofounder of, consults for, and holds equity in Syncopation Life Sciences. R.G.M. is a cofounder of, consults for, and holds equity in Syncopation Life Sciences and Link Cell Therapies. R.G.M. is a consultant for Illumina Radiopharmaceuticals, NKarta, ImmunAI, Arovella Therapeutics, Zai Lab, and Aptorum Group. R.G.M. serves on the Data and Safety Monitoring Board for Fate Therapeutics. J.T. is a consultant for Dorian Therapeutics. E.W.W. consults for and holds equity in VISTAN Health. A.T.S. is a founder of Immunai and Cartography Biosciences and receives research funding from Arsenal Biosciences, Allogene Therapeutics, and 10x Genomics. K.R.P. is a cofounder and employee of Cartography Biosciences. H.Y.C. is a cofounder of Accent Therapeutics, Boundless Bio, and Cartography Biosciences and is an advisor to 10x Genomics, Arsenal Biosciences, and Spring Discovery. J.R.C. is a cofounder and equity holder of Trapeze Therapeutics, Combangio, and Virsti Therapeutics; he has financial interests in Aravive, Xyence Therapeutics, and Syncopation Life Sciences; and he is a member of the Board of Directors of Ligand Pharmaceuticals and Revel Pharmaceuticals. S.A.Y.-H. is a consultant for Trapeze Therapeutics and Xyence Therapeutics., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

Pediatric cancers often mimic fetal tissues and express proteins normally silenced postnatally that could serve as immune targets. We developed T cells expressing chimeric antigen receptors (CARs) targeting glypican-2 (GPC2), a fetal antigen expressed on neuroblastoma (NB) and several other solid tumors. CARs engineered using standard designs control NBs with transgenic GPC2 overexpression, but not those expressing clinically relevant GPC2 site density (∼5,000 molecules/cell, range 1-6 × 10 3 ). Iterative engineering of transmembrane (TM) and co-stimulatory domains plus overexpression of c-Jun lowered the GPC2-CAR antigen density threshold, enabling potent and durable eradication of NBs expressing clinically relevant GPC2 antigen density, without toxicity. These studies highlight the critical interplay between CAR design and antigen density threshold, demonstrate potent efficacy and safety of a lead GPC2-CAR candidate suitable for clinical testing, and credential oncofetal antigens as a promising class of targets for CAR T cell therapy of solid tumors., Competing Interests: Declaration of interest C.L.M., S.H., J.M.M., K.R.B., R.G.M., D.S.D., and Z.Z. are co-inventors on patents related to this work. C.L.M. (and others) have multiple patents pertinent to CAR T cells. C.L.M. is a co-founder of Lyell Immunopharma and Syncopation Life Sciences, which develop CAR-based therapies, and consults for Lyell, NeoImmune Tech, Apricity, Nektar, and Immatics. K.R.B. and J.M.M. receive research funding from Tmunity for research on GPC2-directed immunotherapies. D.Z., Z.Z., D.S.D., J.M.M., and K.R.B. receive royalties from Tmunity for licensing of GPC2-related IP. R.G.M. and E.S. are consultants for and hold equity in Lyell Immunopharma. R.G.M. consults for GammaDelta Therapeutics, Aptorum Group, Zai Lab, and Illumina Radiopharmaceuticals and J.T. for Dorian Therapeutics. S.J.B. is an employee of BD Biosciences. A.T.S. is a founder of Immunai and Cartography Biosciences and receives research funding from Arsenal Biosciences and 10× Genomics. K.R.P. is a co-founder and employee of Cartography Biosciences. H.Y.C. is a co-founder of Accent Therapeutics and Boundless Bio and is an advisor to 10× Genomics, Arsenal Bio, and Spring Discovery., (Copyright © 2021. Published by Elsevier Inc.)

The remarkable specificity of antibodies has enabled precision cancer immunotherapies, including chimeric antigen receptor T cells and antibody-drug conjugates. In parallel, single-cell genomics technologies present the possibility of a comprehensive annotation of antigen expression throughout tissues of the human body and on cancer cells. We reflect on the rationale for antigen targets currently used in immunotherapies, their adverse effects revealed in the clinic, and the opportunity to utilize large genomics datasets to de-risk potential targets and nominate optimal antigens for therapy., Competing Interests: Declaration of interests C.A.L. is a consultant for Immunai and Cartography Biosciences. K.R.P. is a founder of Cartography Biosciences. A.T.S. is a founder of Immunai and Cartography Biosciences. A.T.S. receives research funding from Arsenal Biosciences, Allogene Therapeutics, and 10x Genomics., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Chimeric antigen receptor (CAR) T cells hold promise for the treatment of acute myeloid leukemia (AML), but optimal targets remain to be defined. We demonstrate that CD93 CAR T cells engineered from a novel humanized CD93-specific binder potently kill AML in vitro and in vivo but spare hematopoietic stem and progenitor cells (HSPC). No toxicity is seen in murine models, but CD93 is expressed on human endothelial cells, and CD93 CAR T cells recognize and kill endothelial cell lines. We identify other AML CAR T-cell targets with overlapping expression on endothelial cells, especially in the context of proinflammatory cytokines. To address the challenge of endothelial-specific cross-reactivity, we provide proof of concept for NOT-gated CD93 CAR T cells that circumvent endothelial cell toxicity in a relevant model system. We also identify candidates for combinatorial targeting by profiling the transcriptome of AML and endothelial cells at baseline and after exposure to proinflammatory cytokines., Significance: CD93 CAR T cells eliminate AML and spare HSPCs but exert on-target, off-tumor toxicity to endothelial cells. We show coexpression of other AML targets on endothelial cells, introduce a novel NOT-gated strategy to mitigate endothelial toxicity, and demonstrate use of high-dimensional transcriptomic profiling for rational design of combinatorial immunotherapies. See related commentary by Velasquez and Gottschalk, p. 559 . This article is highlighted in the In This Issue feature, p. 549 ., (©2021 The Authors; Published by the American Association for Cancer Research.)

Alternative strategies are needed for patients with B-cell malignancy relapsing after CD19-targeted immunotherapy. Here, cell surface proteomics revealed CD72 as an optimal target for poor-prognosis KMT2A / MLL1 -rearranged (MLLr) B-cell acute lymphoblastic leukemia (B-ALL), which we further found to be expressed in other B-cell malignancies. Using a recently described, fully in vitro system, we selected synthetic CD72-specific nanobodies, incorporated them into chimeric antigen receptors (CAR), and demonstrated robust activity against B-cell malignancy models, including CD19 loss. Taking advantage of the role of CD72 in inhibiting B-cell receptor signaling, we found that SHIP1 inhibition increased CD72 surface density. We establish that CD72-nanobody CAR-T cells are a promising therapy for MLLr B-ALL. SIGNIFICANCE: Patients with MLLr B-ALL have poor prognoses despite recent immunotherapy advances. Here, surface proteomics identifies CD72 as being enriched on MLLr B-ALL but also widely expressed across B-cell cancers. We show that a recently described, fully in vitro nanobody platform generates binders highly active in CAR-T cells and demonstrate its broad applicability for immunotherapy development. This article is highlighted in the In This Issue feature, p. 1861 ., (©2021 American Association for Cancer Research.)

SARS-CoV-2 is the cause of a pandemic with growing global mortality. Using comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS), we identified 309 host proteins that bind the SARS-CoV-2 RNA during active infection. Integration of this data with ChIRP-MS data from three other RNA viruses defined viral specificity of RNA-host protein interactions. Targeted CRISPR screens revealed that the majority of functional RNA-binding proteins protect the host from virus-induced cell death, and comparative CRISPR screens across seven RNA viruses revealed shared and SARS-specific antiviral factors. Finally, by combining the RNA-centric approach and functional CRISPR screens, we demonstrated a physical and functional connection between SARS-CoV-2 and mitochondria, highlighting this organelle as a general platform for antiviral activity. Altogether, these data provide a comprehensive catalog of functional SARS-CoV-2 RNA-host protein interactions, which may inform studies to understand the host-virus interface and nominate host pathways that could be targeted for therapeutic benefit., Competing Interests: Declaration of interests A.T.S. is a scientific co-founder of Immunai and receives research funding from Arsenal Biosciences and 10x Genomics. K.R.P., H.Y.C., and A.T.S. are co-founders of Cartography Biosciences. H.Y.C. is a co-founder of Accent Therapeutics, Boundless Bio, and an advisor for 10x Genomics, Arsenal Biosciences, and Spring Discovery. Yale University (C.B.W.) has a patent pending related to this work entitled: “Compounds and Compositions for Treating, Ameliorating, and/or Preventing SARS-CoV-2 Infection and/or Complications Thereof.” Yale University has committed to rapidly executable non-exclusive royalty-free licenses to intellectual property rights for the purpose of making and distributing products to prevent, diagnose, and treat COVID-19 infection during the pandemic and for a short period thereafter., (Copyright © 2021 The Author(s). Published by Elsevier Inc. All rights reserved.)

T cell exhaustion limits immune responses against cancer and is a major cause of resistance to chimeric antigen receptor (CAR)-T cell therapeutics. Using murine xenograft models and an in vitro model wherein tonic CAR signaling induces hallmark features of exhaustion, we tested the effect of transient cessation of receptor signaling, or rest, on the development and maintenance of exhaustion. Induction of rest through enforced down-regulation of the CAR protein using a drug-regulatable system or treatment with the multikinase inhibitor dasatinib resulted in the acquisition of a memory-like phenotype, global transcriptional and epigenetic reprogramming, and restored antitumor functionality in exhausted CAR-T cells. This work demonstrates that rest can enhance CAR-T cell efficacy by preventing or reversing exhaustion, and it challenges the notion that exhaustion is an epigenetically fixed state., (Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

CD19-directed immunotherapies are clinically effective for treating B cell malignancies but also cause a high incidence of neurotoxicity. A subset of patients treated with chimeric antigen receptor (CAR) T cells or bispecific T cell engager (BiTE) antibodies display severe neurotoxicity, including fatal cerebral edema associated with T cell infiltration into the brain. Here, we report that mural cells, which surround the endothelium and are critical for blood-brain-barrier integrity, express CD19. We identify CD19 expression in brain mural cells using single-cell RNA sequencing data and confirm perivascular staining at the protein level. CD19 expression in the brain begins early in development alongside the emergence of mural cell lineages and persists throughout adulthood across brain regions. Mouse mural cells demonstrate lower levels of Cd19 expression, suggesting limitations in preclinical animal models of neurotoxicity. These data suggest an on-target mechanism for neurotoxicity in CD19-directed therapies and highlight the utility of human single-cell atlases for designing immunotherapies., Competing Interests: Declaration of Interests C.H.J. and A.D.P. report intellectual property licensed to Novartis and Tmunity Therapeutics related to CAR-T cells. K.R.P., A.T.S., H.Y.C., D.M., A.D.P., and C.H.J. are listed as inventors on patent applications filed by Stanford University and the University of Pennsylvania. K.R.P. is a consultant for Maze Therapeutics. A.T.S. is a scientific founder of Immunai and receives research funding from Arsenal Biosciences. H.Y.C. is a co-founder of Accent Therapeutics and Boundless Bio and an advisor to 10x Genomics, Arsenal Biosciences, and Spring Discovery., (Copyright © 2020 Elsevier Inc. All rights reserved.)

SARS-CoV-2 genomic and subgenomic RNA (sgRNA) transcripts hijack the host cell's machinery. Subcellular localization of its viral RNA could, thus, play important roles in viral replication and host antiviral immune response. We perform computational modeling of SARS-CoV-2 viral RNA subcellular residency across eight subcellular neighborhoods. We compare hundreds of SARS-CoV-2 genomes with the human transcriptome and other coronaviruses. We predict the SARS-CoV-2 RNA genome and sgRNAs to be enriched toward the host mitochondrial matrix and nucleolus, and that the 5' and 3' viral untranslated regions contain the strongest, most distinct localization signals. We interpret the mitochondrial residency signal as an indicator of intracellular RNA trafficking with respect to double-membrane vesicles, a critical stage in the coronavirus life cycle. Our computational analysis serves as a hypothesis generation tool to suggest models for SARS-CoV-2 biology and inform experimental efforts to combat the virus. A record of this paper's Transparent Peer Review process is included in the Supplemental Information., Competing Interests: Declaration of Interests K.R.P. is a consultant for Maze Therapeutics. H.Y.C. is affiliated with Accent Therapeutics, Boundless Bio, 10X Genomics, Arsenal Bio, and Spring Discovery. J.Z. is affiliated with InterVenn Biosciences., (Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.)

Subcellular localization is essential to RNA biogenesis, processing, and function across the gene expression life cycle. However, the specific nucleotide sequence motifs that direct RNA localization are incompletely understood. Fortunately, new sequencing technologies have provided transcriptome-wide atlases of RNA localization, creating an opportunity to leverage computational modeling. Here we present RNA-GPS, a new machine learning model that uses nucleotide-level features to predict RNA localization across eight different subcellular locations-the first to provide such a wide range of predictions. RNA-GPS's design enables high-throughput sequence ablation and feature importance analyses to probe the sequence motifs that drive localization prediction. We find localization informative motifs to be concentrated on 3'-UTRs and scattered along the coding sequence, and motifs related to splicing to be important drivers of predicted localization, even for cytotopic distinctions for membraneless bodies within the nucleus or for organelles within the cytoplasm. Overall, our results suggest transcript splicing is one of many elements influencing RNA subcellular localization., (© 2020 Wu et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.)

CRISPR-Cas9 gene editing provides a powerful tool to enhance the natural ability of human T cells to fight cancer. We report a first-in-human phase 1 clinical trial to test the safety and feasibility of multiplex CRISPR-Cas9 editing to engineer T cells in three patients with refractory cancer. Two genes encoding the endogenous T cell receptor (TCR) chains, TCRα ( TRAC ) and TCRβ ( TRBC ), were deleted in T cells to reduce TCR mispairing and to enhance the expression of a synthetic, cancer-specific TCR transgene (NY-ESO-1). Removal of a third gene encoding programmed cell death protein 1 (PD-1; PDCD1 ), was performed to improve antitumor immunity. Adoptive transfer of engineered T cells into patients resulted in durable engraftment with edits at all three genomic loci. Although chromosomal translocations were detected, the frequency decreased over time. Modified T cells persisted for up to 9 months, suggesting that immunogenicity is minimal under these conditions and demonstrating the feasibility of CRISPR gene editing for cancer immunotherapy., (Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

We introduce APEX-seq, a method for RNA sequencing based on direct proximity labeling of RNA using the peroxidase enzyme APEX2. APEX-seq in nine distinct subcellular locales produced a nanometer-resolution spatial map of the human transcriptome as a resource, revealing extensive patterns of localization for diverse RNA classes and transcript isoforms. We uncover a radial organization of the nuclear transcriptome, which is gated at the inner surface of the nuclear pore for cytoplasmic export of processed transcripts. We identify two distinct pathways of messenger RNA localization to mitochondria, each associated with specific sets of transcripts for building complementary macromolecular machines within the organelle. APEX-seq should be widely applicable to many systems, enabling comprehensive investigations of the spatial transcriptome., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Here, we present Perturb-ATAC, a method that combines multiplexed CRISPR interference or knockout with genome-wide chromatin accessibility profiling in single cells based on the simultaneous detection of CRISPR guide RNAs and open chromatin sites by assay of transposase-accessible chromatin with sequencing (ATAC-seq). We applied Perturb-ATAC to transcription factors (TFs), chromatin-modifying factors, and noncoding RNAs (ncRNAs) in ∼4,300 single cells, encompassing more than 63 genotype-phenotype relationships. Perturb-ATAC in human B lymphocytes uncovered regulators of chromatin accessibility, TF occupancy, and nucleosome positioning and identified a hierarchy of TFs that govern B cell state, variation, and disease-associated cis-regulatory elements. Perturb-ATAC in primary human epidermal cells revealed three sequential modules of cis-elements that specify keratinocyte fate. Combinatorial deletion of all pairs of these TFs uncovered their epistatic relationships and highlighted genomic co-localization as a basis for synergistic interactions. Thus, Perturb-ATAC is a powerful strategy to dissect gene regulatory networks in development and disease., (Copyright © 2018 Elsevier Inc. All rights reserved.)

T cells create vast amounts of diversity in the genes that encode their T cell receptors (TCRs), which enables individual clones to recognize specific peptide-major histocompatibility complex (MHC) ligands. Here we combined sequencing of the TCR-encoding genes with assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis at the single-cell level to provide information on the TCR specificity and epigenomic state of individual T cells. By using this approach, termed transcript-indexed ATAC-seq (T-ATAC-seq), we identified epigenomic signatures in immortalized leukemic T cells, primary human T cells from healthy volunteers and primary leukemic T cells from patient samples. In peripheral blood CD4 + T cells from healthy individuals, we identified cis and trans regulators of naive and memory T cell states and found substantial heterogeneity in surface-marker-defined T cell populations. In patients with a leukemic form of cutaneous T cell lymphoma, T-ATAC-seq enabled identification of leukemic and nonleukemic regulatory pathways in T cells from the same individual by allowing separation of the signals that arose from the malignant clone from the background T cell noise. Thus, T-ATAC-seq is a new tool that enables analysis of epigenomic landscapes in clonal T cells and should be valuable for studies of T cell malignancy, immunity and immunotherapy.

ciRS-7 is an intensely studied, highly expressed and conserved circRNA. Essentially nothing is known about its biogenesis, including the location of its promoter. A prevailing assumption has been that ciRS-7 is an exceptional circRNA because it is transcribed from a locus lacking any mature linear RNA transcripts of the same sense. To study the biogenesis of ciRS-7, we developed an algorithm to define its promoter and predicted that the human ciRS-7 promoter coincides with that of the long non-coding RNA, LINC00632. We validated this prediction using multiple orthogonal experimental assays. We also used computational approaches and experimental validation to establish that ciRS-7 exonic sequence is embedded in linear transcripts that are flanked by cryptic exons in both human and mouse. Together, this experimental and computational evidence generates a new model for regulation of this locus: (a) ciRS-7 is like other circRNAs, as it is spliced into linear transcripts; (b) expression of ciRS-7 is primarily determined by the chromatin state of LINC00632 promoters; (c) transcription and splicing factors sufficient for ciRS-7 biogenesis are expressed in cells that lack detectable ciRS-7 expression. These findings have significant implications for the study of the regulation and function of ciRS-7, and the analytic framework we developed to jointly analyze RNA-seq and ChIP-seq data reveal the potential for genome-wide discovery of important biological regulation missed in current reference annotations.

Pasteurization has long been the standard method to extend the shelf-life of dairy products, as well as a means to reduce microbial load and the risk of food-borne pathogens. However, the process has limitations, which include cost effectiveness, high energy input, and reduction of product quality/organoleptic characteristics. In an effort to reduce these limitations and extend shelf-life, this study examined a novel low temperature, short time (LTST) method in which dispersed milk in the form of droplets was treated with low heat/pressure variation over a short treatment time, in conjunction with pasteurization. Lactobacillus fermentum and Pseudomonas fluorescens Migula were exposed to conventional pasteurization treatments with and without LTST. Using these organisms, the LTST addition was able to reduce microbial load below detection limits; 1.0 × 10(1) cfu/mL, from approximately 1.2 × 10(8) and 1.0 × 10(7) cfu/mL for L. fermentum and P. fluorescens Migula, respectively. In addition, the shelf-life of the treated, raw, and uninoculated product was prolonged from 14 to 35 days, compared with standard pasteurization, to as long as 63 days with the LTST amendment. Sensory analysis of samples also demonstrated equal or greater preference for LTST + pasteurization treated milk when compared to pasteurization alone (α = 0.05). Conventional pasteurization was effective at reducing the above mentioned microorganisms by as much as 5.0 log10 cfu/mL. However, LTST was able to achieve 7.0-8.0 log10 cfu/mL reduction of the same microorganisms. In addition, BActerial Rapid Detection using Optical scattering Technology detected and identified microorganisms isolated both pre- and post-treatment, of which the only organisms surviving LTST were Bacillus spp. Increased lethality, improved shelf-life, and equal or better organoleptic characteristics without increased energy consumption demonstrate the effectiveness of the incorporation of LTST. The improved shelf-life may potentially have major impacts in the dairy industry in terms of shipping and overall sustainability.

Ecological risk assessments need to advance beyond evaluating risks to individuals that are largely based on toxicity studies conducted on a few species under laboratory conditions, to assessing population-level risks to the environment, including considerations of variability and uncertainty. Two individual-based models (IBMs), recently developed to assess current risks to sea otters and seaducks in Prince William Sound more than 2 decades after the Exxon Valdez oil spill (EVOS), are used to explore population-level risks. In each case, the models had previously shown that there were essentially no remaining risks to individuals from polycyclic aromatic hydrocarbons (PAHs) derived from the EVOS. New sensitivity analyses are reported here in which hypothetical environmental exposures to PAHs were heuristically increased until assimilated doses reached toxicity reference values (TRVs) derived at the no-observed-adverse-effects and lowest-observed-adverse-effects levels (NOAEL and LOAEL, respectively). For the sea otters, this was accomplished by artificially increasing the number of sea otter pits that would intersect remaining patches of subsurface oil residues by orders of magnitude over actual estimated rates. Similarly, in the seaduck assessment, the PAH concentrations in the constituents of diet, sediments, and seawater were increased in proportion to their relative contributions to the assimilated doses by orders of magnitude over measured environmental concentrations, to reach the NOAEL and LOAEL thresholds. The stochastic IBMs simulated millions of individuals. From these outputs, frequency distributions were derived of assimilated doses for populations of 500,000 sea otters or seaducks in each of 7 or 8 classes, respectively. Doses to several selected quantiles were analyzed, ranging from the 1-in-1000th most-exposed individuals (99.9% quantile) to the median-exposed individuals (50% quantile). The resulting families of quantile curves provide the basis for characterizing the environmental thresholds below which no population-level effects could be detected and above which population-level effects would be expected to become manifest. This approach provides risk managers an enhanced understanding of the risks to populations under various conditions and assumptions, whether under hypothetically increased exposure regimes, as demonstrated here, or in situations in which actual exposures are near toxic effects levels. This study shows that individual-based models are especially amenable and appropriate for conducting population-level risk assessments, and that they can readily be used to answer questions about the risks to individuals and populations across a variety of exposure conditions., (Copyright © 2012 SETAC.)

Harlequin Ducks ( Histrionicus histrionicus) were adversely affected by the Exxon Valdez oil spill (EVOS) in Prince William Sound (PWS), Alaska, and some have suggested effects continue two decades later. We present an ecological risk assessment evaluating quantitatively whether PWS seaducks continue to be at-risk from polycyclic aromatic hydrocarbons (PAHs) in residual Exxon Valdez oil. Potential pathways for PAH exposures are identified for initially oiled and never-oiled reference sites. Some potential pathways are implausible ( e.g. , a seaduck excavating subsurface oil residues), whereas other pathways warrant quantification. We used data on PAH concentrations in PWS prey species, sediments, and seawater collected during 2001-2008 to develop a stochastic individual-based model projecting assimilated doses to seaducks. We simulated exposures to 500,000 individuals in each of eight age/gender classes, capturing the variability within a population of seaducks living in PWS. Doses to the maximum-exposed individuals are ∼400-4,000 times lower than chronic toxicity reference values established using USEPA protocols for seaducks. These exposures are so low that no individual-level effects are plausible, even within a simulated population that is orders-of-magnitude larger than exists in PWS. We conclude that toxicological risks to PWS seaducks from residual Exxon Valdez oil two decades later are essentially non-existent.

A comprehensive, quantitative risk assessment is presented of the toxicological risks from buried Exxon Valdez subsurface oil residues (SSOR) to a subpopulation of sea otters (Enhydra lutris) at Northern Knight Island (NKI) in Prince William Sound, Alaska, as it has been asserted that this subpopulation of sea otters may be experiencing adverse effects from the SSOR. The central questions in this study are: could the risk to NKI sea otters from exposure to polycyclic aromatic hydrocarbons (PAHs) in SSOR, as characterized in 2001-2003, result in individual health effects, and, if so, could that exposure cause subpopulation-level effects? We follow the U.S. Environmental Protection Agency (USEPA) risk paradigm by: (a) identifying potential routes of exposure to PAHs from SSOR; (b) developing a quantitative simulation model of exposures using the best available scientific information; (c) developing scenarios based on calculated probabilities of sea otter exposures to SSOR; (d) simulating exposures for 500,000 modeled sea otters and extracting the 99.9% quantile most highly exposed individuals; and (e) comparing projected exposures to chronic toxicity reference values. Results indicate that, even under conservative assumptions in the model, maximum-exposed sea otters would not receive a dose of PAHs sufficient to cause any health effects; consequently, no plausible toxicological risk exists from SSOR to the sea otter subpopulation at NKI.

It has been hypothesized that pink salmon eggs incubating in intertidal streams transecting Prince William Sound (PWS) beaches oiled by the Exxon Valdez oil spill were exposed to lethal doses of dissolved hydrocarbons. Since polycyclic aromatic hydrocarbon (PAH) levels in the incubation gravel were too low to cause mortality, the allegation is that dissolved high-molecular-weight hydrocarbons (HPAH) leaching from oil deposits on the beach adjacent to the streams were the source of toxicity. To evaluate this hypothesis, we placed pink salmon eggs in PWS beach sediments containing residual oil from the Exxon Valdez oil spill and in control areas without oil. We quantified the hydrocarbon concentrations in the eggs after three weeks of incubation. Tissue PAH concentrations of eggs in oiled sediments were generally < 100 ppb and similar to background levels on nonoiled beaches. Even eggs in direct contact with oil in the sediment resulted in tissue PAH loads well below the lethal threshold concentrations established in laboratory bioassays, and very low concentrations of HPAH compounds were present. These results indicate that petroleum hydrocarbons dissolved from oil deposits on intertidal beaches are not at concentrations that pose toxic risk to incubating pink salmon eggs. The evidence does not support the hypothesis that interstitial pore water in previously oiled beaches is highly toxic.

There has been much controversy regarding the origins of the natural polycyclic aromatic hydrocarbon (PAH) and chemical biomarker background in Prince William Sound (PWS), Alaska, site of the 1989 Exxon Valdez oil spill. Different authors have attributed the sources to various proportions of coal, natural seep oil, shales, and stream sediments. The different probable bioavailabilities of hydrocarbons from these various sources can affect environmental damage assessments from the spill. This study compares two different approaches to source apportionment with the same data (136 PAHs and biomarkers) and investigate whether increasing the number of coal source samples from one to six increases coal attributions. The constrained least-squares (CLS) source allocation method that fits concentrations meets geologic and chemical constraints better than partial least-squares (PLS) which predicts variance. The field data set was expanded to include coal samples reported by others, and CLS fits confirm earlier findings of low coal contributions to PWS.

Polycyclic aromatic hydrocarbon (PAH) exposure biomarkers were measured in high cockscomb prickleback (Anoplarchus purpurescens) fish collected from both previously oiled and unoiled shore in Prince William Sound (PWS), Alaska, to test the hypothesis that fish living in the nearshore environment of the sound were no longer being exposed to PAH from the Exxon Valdez oil spill. Pricklebacks spend their entire lives in the intertidal zone of rocky shores with short-term movements during feeding and breeding restricted to an area of about 15 meters in diameter. Fish were assayed for the PAH exposure biomarkers, bile fluorescent aromatic compounds (FAC), and liver ethoxyresorufin O-deethylase (EROD) activity (a measure of cytochrome P450 1A (CYP1A) monooxygenase activity). Bile FAC concentrations and EROD activities were low and not significantly different in fish from previously oiled and unoiled sites. The similar low EROD activity and bile FAC concentrations in fish from oiled and unoiled shores, supports the hypothesis that these low-level biomarker responses were not caused by exposure of the fish to residues of the spilled oil.

For sixteen years following the 1989 Exxon Valdez oil spill adult returns of pink salmon in Prince William Sound, Alaska were monitored to assess spill effects on survival. No evidence of spill effects was detected for either intertidal or whole-stream spawning fish. From 1989 through 2004 mean densities for oiled and reference streams tracked each other, illustrating similar responses of oiled and reference stream adult populations to naturally changing oceanographic and climactic conditions. Hatchery fish strayed into the study streams, but similar incursions occurred in oiled and reference streams, and their presence was compensated for to eliminate their influence on determining the success of the returning natural populations. These results, showing no detectable effects of oiling on pink salmon spawning populations, are supported by published field studies on pink salmon incubation success in oiled streams.

Seven taxa of intertidal plants and animals were sampled at 17 shoreline sites in Prince William Sound ([PWS]; AK, USA), that were heavily oiled in 1989 by the Exxon Valdez oil spill (EVOS) to determine if polycyclic aromatic hydrocarbons (PAH) from buried oil in intertidal sediments are sufficiently bioavailable to intertidal prey organisms that they might pose a health risk to populations of birds and wildlife that forage on the shore. Buried residues of EVOS oil are present in upper and middle intertidal sediments at 16 sites. Lower intertidal (0 m) sediments contain little oil. Much of the PAH in lower intertidal sediments are from combustion sources. Mean tissue total PAH (TPAH) concentrations in intertidal clams, mussels, and worms from oiled sites range from 24 to 36 ng/g (parts per billion) dry weight; sea lettuce, whelks, hermit crabs, and intertidal fish contain lower concentrations. Concentrations of TPAH are similar or slightly lower in biota from unoiled reference sites. The low EVOS PAH concentrations detected in intertidal biota at oiled shoreline sites indicate that the PAH from EVOS oil buried in intertidal sediments at these sites have a low bioavailability to intertidal plants and animals. Individual sea otters or shorebirds that consumed a diet of intertidal clams and mussels exclusively from the 17 oiled shores in 2002 were at low risk of significant health problems. The low concentrations of EVOS PAH found in some intertidal organisms at some oiled shoreline sites in PWS do not represent a health risk to populations of marine birds and mammals that forage in the intertidal zone.

Research was conducted at the University of Idaho (Moscow, ID, USA) on the toxicity of weathered Exxon Valdez crude oil to embryos of pink salmon from 2001 to 2003 for the purpose of comparing these data with those from the National Oceanic and Atmospheric Administration Fisheries Laboratory at Auke Bay (AK, USA). Mortality reported at Auke Bay for embryos chronically exposed to very low concentrations of aqueous solutions of weathered oil, measured as dissolved polycyclic aromatic hydrocarbons (PAHs), was inconsistent with that in other published research. Using the Auke Bay experimental design, we found that toxicity is not evident in pink salmon embryos until chronic exposure to laboratory weathered and naturally weathered oil concentrations exceeding 1,500 and 2,250 ppm, respectively, representing a total PAH tissue burden in excess of 7,100 ppb. Effluent hydrocarbons also drop well below concentrations sufficient to cause harm over the time frame of a few weeks, regardless of oiling level. Resolution of differences with Auke Bay involved the source of contributing hydrocarbons. The experimental design did not exclude dispersed oil droplets from the aqueous solution; thus, toxicity was not limited to the dissolved hydrocarbon fraction. The implications of the present results are discussed regarding the toxic risk of weathered oil to pink salmon embryos in streams of Prince William Sound (AK, USA).

Children with CHARGE syndrome frequently exhibit moderate to severe behavior difficulties, and are often diagnosed with obsessive-compulsive disorder, attention deficit disorder, Tourette syndrome, and autism. Hartshorne and Cypher (2004) surveyed parents of 100 children with CHARGE worldwide and confirmed the prevalence of behaviors that are associated with these disorders. They also found behaviors that could be described as typical of persons who are deafblind. The present study examined whether the autistic-like behaviors of children with CHARGE are more similar to those of children who are deafblind, to those of children who are autistic or are unique to CHARGE. Surveys including the Autism Behavior Checklist (ABC) were mailed to families of 204 children with CHARGE, and 160 usable surveys were returned (78%). Total scores on the ABC for children with CHARGE were significantly different from the norms for those with autism, and those who were deafblind. However, the variance for CHARGE was larger than for the normative groups, and 27.5% of those with CHARGE could be classified as autistic. The pattern of subscale scores for those with CHARGE differed from the other normative groups., (Copyright (c) 2005 Wiley-Liss, Inc.)

Seafloor sediments in Prince William Sound (PWS) and the eastern Gulf of Alaska (GOA) have a substantial regional hydrocarbon background from natural sources including oil seeps and eroding sedimentary rocks along the eastern GOA coast. Polycyclic aromatic hydrocarbons (PAH) from that background appear to be bioavailable to fish. Fish collected from PWS and the GOA in a 1999--2000 biomarker study (bile fluorescent aromatic contaminants and liver ethoxyresorufin O-deethylase) show evidence of exposure to low levels of PAH at all categories of sites sampled. Seafloor sediments at fish sampling sites in the GOA east of PWS and at three PWS site categories (nonspill path, spill path oiled, and spill path not oiled) contain hydrocarbons from four principal sources: regional background, combustion products, residues from the 1989 Exxon Valdez oil spill (EVOS), and Monterey (CA) petroleum residues. GOA sediments between PWS and Yakutat Bay, approximately 350 km to the east, are dominated by regional petrogenic background hydrocarbons (total PAH (TPAH) range approximately 60-3400 ng/g) that are the probable cause of low biomarker levels measured in halibut from this area. PWS sediments contain varying proportions of regional background, combustion products, Monterey residues, and EVOS residues at some spill path sites. Rockfish caught in PWS embayments in 1999 have liver EROD activities that correlate positively with the pyrogenic PAH indicator ratio (FI+Py)/C24Ph. Although traces (<5-100 ng/g TPAH) of EVOS residues were detected in seafloor sediments at some nearshore spill path sites, biomarker levels in fish from those sites are not elevated relative to other sites in PWS.

To test the hypothesis that biomarker levels in fish collected at Prince William Sound (PWS) sites impacted by the 1989 Exxon Valdez oil spill were higher than those collected at unimpacted sites, a 1999-2000 study collected five fish species and associated benthic sediments from 21 sites in PWS and the eastern Gulf of Alaska (GOA). PWS sites were divided in three oiling categories based upon 1989 shoreline assessments: nonspill path (NSP), spill path oiled (SPO), and spill path not oiled (SPNO). Rockfish (N = 177), rock sole (N = 30), and kelp greenling (N = 49) were collected at near-shore locations (approximately 50-500 m from shore); Pacific halibut (N = 131) and Pacific cod (N = 81) were collected further offshore (approximately 500-7000 m). Fish were assayed for bile fluorescent aromatic contaminants (FAC) and cytochrome P4501A (CYP1A) levels measured as liver ethoxyresorufin O-deethylase (EROD) activity and by immunohistochemistry (IHC) of various tissues. For all species studied at all sites, bile FAC concentrations and CYP1A levels were low and in the same range for fish collected at PWS SPO and SPNO sites relative to NSP sites in PWS and the GOA. Consequently, the hypothesis is rejected for the species studied. The bile FAC results further indicate a pervasive exposure of fish at all sites, including those in the GOA far removed from the effects of the spill, to low levels of polycyclic aromatic hydrocarbons. Analysis of the benthic sediments indicates that the probable sources of this exposure are petrogenic hydrocarbons derived from natural oil seeps and eroding sedimentary rocks in the eastern GOA.

An 1-year study of the 1989 Exxon Valdez oil spill found that spill residues on the oiled shorelines rapidly lost toxicity through weathering. After 1990, toxicity of sediments remained at only a few heavily oiled, isolated locations in Prince William Sound (AK, USA), as measured by a standard amphipod bioassay using Rhepoxynius abronius. Data from 648 sediment samples taken during the 1990 to 1993 period were statistically analyzed to determine the relationship between the total concentration of 39 parent and methyl-substituted polycyclic aromatic hydrocarbons (defined as total polycyclic aromatic hydrocarbons [TPAH]) and amphipod mortality and the effect of oil weathering on toxicity. A logistic regression model yielded estimates of the lower threshold, LC10 (lethal concentration to 10% of the population), and LC50 (median lethal concentration) values of 2,600, 4,100, and 10,750 ng/g TPAH (dry wt), respectively. Estimates of the threshold and LC50 values in this field study relate well to corresponding sediment quality guideline (SQG) values reported in the literature. For sediment TPAH concentrations >2,600 ng/g, samples with high mortality values (>90%) had relatively high fractions of naphthalenes and those with low mortality (<20%) had relatively high fractions of chrysenes. By 1999, the median sediment TPAH concentration of 117 ng/g for the post-1989 worst-case sites studied were well below the 2,600 ng/g toxicity threshold value, confirming the lack of potential for long-term toxic effects. Analysis of biological community structure parameters for sediment samples taken concurrently found that species richness and Shannon diversity decreased with increasing TPAH above the 2,600 ng/g threshold, demonstrating a correspondence between sediment bioassay results and biological community effects in the field. The low probability of exposure to toxic concentrations of weathered spill residues at the worst-case sites sampled in this study is consistent with the rapid overall recovery of shoreline biota observed in 1990 to 1991.

The rhodopsin content of the human retina was determined spectrophotometrically. Retinas were removed completely by using an in vitro technique based on a simulation of retinal detachment. This method provides a total recovery of rod outer segments which contain the rhodopsin visual pigment or its apoprotein, opsin. Using this improved dissection method followed by a crude preparation of the retina, an opsin-rhodopsin content of 6.20 +/- 0.64 nmol/retina (n = 9) was found. This is larger than values previously reported. Regeneration with a threefold excess of 11-cis-retinal improved the recovery of rhodopsin dramatically because the corneas of these human donor eyes were removed for corneal transplant surgery under relatively bright light that bleaches the retina nearly completely. The amount of rhodopsin that can be isolated will be sufficient for studies on early events in visual transduction using laser photolysis.

Aqueous salt solutions containing NaCl, KCl, MgCl2, Na2SO4, CaCl2, NH4Cl, or sodium saccharin are mutagenic in yeast when logarithmic growth of cells is interrupted by exposure to a 0.5-2.0 M salt solution. Stationary-phase cells are not mutated by this treatment. When placed in an enriched medium with the salt, the stationary-phase cells grow after a prolonged lag period. The compounds tested (NaCl, KCl, and sodium saccharin), under conditions in which growth in medium can take place, exhibit an antimutagenic response as measured by the compartmentalization test. The antimutagenic action of salt solutions in yeast is concentration-dependent. Unlike the mutagenic action of these compounds, which approximates an osmolality-dependent response, the antimutagenic action seems to be correlated with toxicity as measured by growth rate reduction at increasing concentrations of the compounds. For example, sodium saccharin and NaCl exhibit almost identical osmolalities; however, 0.3 M sodium saccharin reduces the growth rate much more than does 0.3 M NaCl. At these same molar concentrations, the spontaneous mutation rate for histidine prototrophy is, for the control, 6.2 x 10(-8) mutations/cell/-generation, 3.5 x 10(-8) with 0.3 M NaCl, and 1.7 x 10(-8) with 0.3 M sodium saccharin.

Rabbits (Flemish giant x French lop-eared) exposed to 300 to 500 tsetses (Glossina morsitans morsitans Westw.) a day, 2 or 3 days a week, did not show significant differences from littermates receiving no exposure, with respect to weight changes, haematocrits, red and white blood cell counts or whole blood clotting times. In other rabbits, the same daily exposure, 6 days a week, resulted in sharp decreases in haematocrit levels and in some, changes in weights, but no change in citrated plasma thrombin times. Rabbit haematocrit levels correlated negatively with estimated weekly blood loss. Weights and haematocrits of most rabbits exposed to 1,200 to 1,500 flies on a single occasion were not affected. However, following heavy exposure, ears were cold and blood letting difficult, indicating the possibility of arteriolar vasoconstriction.

Rubella vaccination status and immunity to rubella were studied in 230 "active patients" aged 8 to 22 years in a teaching family practice by means of a chart review and measurement of the rubella antibody titre in a blood sample. Of the 200 patients who submitted a blood sample 161 (80%) were found to be immune, having a rubella hemagglutination-inhibiting antibody titre of 1:16 or greater. Log linear analysis showed that immunity to rubella was independent of a history of rubella, and that 94% of the vaccinated patients versus 74% of the unvaccinated patients (a significant difference; P = 0.007) were immune. In retrospect we estimated that 80% of the study group were protected at the start of the study. After surveillance and follow-up, with vaccination of 27 of the 39 patients identified as susceptible to rubella, this estimated proportion increased to 90%. The study showed that there is nothing to be gained by asking about a history of rubella but that vaccination against this disease is increasing among children aged 5 to 9 years.

A retrospective study was done to determine if specific electromyographic findings are present in spinal arachnoiditis. The electromyographic (emg) findings in 32 surgically and 35 myelographically diagnosed cases were examined. The cases were categorized into 3 groups. The 1st groups consisted of 37 cases with surgical or myelographic evidence believed to be highly diagnostic of multilevel chronic spinal arachnoiditis. The 2nd group was composed of 23 cases with surgical or myelographic evidence consistent with a localized problem. The 3rd group was a control group with normal or minimal changes on myelography or at surgery. Electromyographic findings were divided into 3 groups of changes: localized, nonlocalized or normal. Localized emg changes were considered to be present over 2 or less root levels in either or both anterior or posterior primary ramus distribution. Nonlocalized changes occurred over more than 2 such levels. A comparative analysis of the myelographic and surgical findings with the emg changes indicated that there was not diagnostic emg picture indicative of chronic spinal arachnoiditis.

Ontario students in grades 7-13 responded to open-ended and multiple-choice questions about future concerns, particularly unemployment, job/career plans, and the nuclear threat. Although worries about nuclear war were more frequent than those in other areas, their expression was associated with a sense of social efficacy rather than with feelings of helplessness.

Mg2+-ATP produces a large decrease in near-IR light scattering when added to suspensions of rod outer segments (ROS) when the plasma membranes have been disrupted by a gentle dialysis procedure. When this process is studied by light microscopy with video-enhanced image contrast, the Mg2+-ATP-dependent signal is seen to be associated with the formation of filaments which extend only from those ROS lacking plasma membranes. Both the IR light scattering signal and filament growth are inhibited by vanadate and DCCD but not by colchicine, colcemid or cytochalasins.

Diarrhea and vomiting in infancy are not common complaints in the life of a busy Canadian family practitioner, but when they do occur the person caring for the infant is usually apprehensive, frustrated and concerned, deserving one's immediate attention. Although the condition is usually acute and self-limiting, its serious consequences make it imperative that investigation be adequate and surveillance strictly followed. Most children with this complaint can be managed at home. Prevention through parental education should be stressed.